From cf51a80cf39da477d114dc02e8c6cb8e283f1f10 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 02:50:01 -0500
Subject: [PATCH 01/51] Updated location of LIBCIM10MULTI.TXT

issue #189
---
 R/cim-10-fr.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cim-10-fr.R b/R/cim-10-fr.R
index ec8419ae..5cf4eefa 100644
--- a/R/cim-10-fr.R
+++ b/R/cim-10-fr.R
@@ -8,7 +8,7 @@
       "https://www.atih.sante.fr",
       "plateformes-de-transmission-et-logiciels",
       "logiciels-espace-de-telechargement",
-      "telecharger/gratuit/11616/456"
+      "telecharger/gratuit/12713/456"
     ),
     file_name = "LIBCIM10MULTI.TXT",
     dl_msg = "Working on ICD-10-FR (CIM-10-FR)",

From f7a19058be6a110872dcc958a9ccdd76677c9b5b Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 03:16:17 -0500
Subject: [PATCH 02/51] Fix error on memoising JsonGetRootConcepts

On Windows, the following errors are reported due to trying to save the file "WHO.2016.en.JsonGetRootConcepts?useHtml=false.json".  The ? is not a valid character on Windows.

````
Getting WHO data with JSON: https://icd.who.int/browse10/2016/en/JsonGetRootConcepts?useHtml=false
Saving memoised data for  2016 en JsonGetRootConcepts?useHtml=false in C:\Users\user\AppData\Local\icd\icd/memoise/WHO.2016.en.JsonGetRootConcepts?useHtml=false.json
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
  cannot open compressed file 'C:\Users\user\AppData\Local\icd\icd/memoise/WHO.2016.en.JsonGetRootConcepts?useHtml=false.json', probable reason 'Invalid argument'
````
---
 R/who.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/who.R b/R/who.R
index b1c8cdfd..34117cb9 100644
--- a/R/who.R
+++ b/R/who.R
@@ -19,7 +19,7 @@
   # memoise package has given me problems and crashes. DIY
   mem_file_name <- paste(
     "WHO", year, lang,
-    gsub("JsonGetChildrenConcepts\\?ConceptId=|&useHtml=false", "", resource),
+    gsub("JsonGetChildrenConcepts\\?ConceptId=|(&|\\?)useHtml=false", "", resource),
     "json",
     sep = "."
   )

From 8cd9fe50a8cd97c4c3f09273381a7309af42bf53 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 03:59:40 -0500
Subject: [PATCH 03/51] change system.file to fail fast if directory cannot be
 located

On Windows at least (and maybe other OSes) the `data-raw` directory is not included in the package unless it is moved into the `inst` directory.
---
 R/util.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/util.R b/R/util.R
index b6f6ddde..12b1e359 100644
--- a/R/util.R
+++ b/R/util.R
@@ -398,7 +398,8 @@ capitalize_first <- function(x) {
 #' @noRd
 #' @keywords internal
 get_raw_data_dir <- function() {
-  system.file("data-raw", package = "icd")
+  # use mustWork = TRUE to throw an error if the directory is not found
+  system.file("data-raw", package = "icd", mustWork = TRUE)
 }
 
 .stopifnot_year <- function(year) {

From 39d9ccad15a17db9405af807939bb64ccb125484 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 04:00:24 -0500
Subject: [PATCH 04/51] change raw to cache for icd10be

icd10be files are not included in data-raw so they should be pulled from the cache directory
---
 R/icd10be.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/icd10be.R b/R/icd10be.R
index f2972741..30006c42 100644
--- a/R/icd10be.R
+++ b/R/icd10be.R
@@ -6,7 +6,7 @@
                             ...) {
   site_file_2017 <-
     "fy2017_reflist_icd-10-be.xlsx_last_updatet_28-07-2017_1.xlsx"
-  fnp <- .download_to_data_raw(
+  fnp <- .download_to_data_cache(
     paste(.icd10be_site,
       .icd10be_url_path,
       site_file_2017,
@@ -28,7 +28,7 @@
   }
   site_file <- "fy2014_reflist_icd-10-be.xlsx"
   .msg("Downloading or getting cached icd10be2014 data")
-  .download_to_data_raw(
+  .download_to_data_cache(
     paste(.icd10be_site,
       .icd10be_url_path,
       site_file,
@@ -58,7 +58,7 @@
 #' \url{https://www.health.belgium.be/sites/default/files/uploads/fields/fpshealth_theme_file/fy2017_reflist_icd-10-be.xlsx_last_updatet_28-07-2017_1.xlsx}
 # nolint end
 #' \url{https://www.health.belgium.be/fr/fy2014reflisticd-10-bexlsx}
-#' @param ... passed to \code{.download_to_data_raw}, e.g., \code{offline =
+#' @param ... passed to \code{.download_to_data_cache}, e.g., \code{offline =
 #'   FALSE}.
 #' @seealso \code{link{parse_icd10be2014_be}}
 #' @keywords internal
@@ -133,7 +133,7 @@
 #'   \url{https://www.health.belgium.be/fr/sante/organisation-des-soins-de-sante/hopitaux/systemes-denregistrement/icd-10-be}
 # nolint end
 #'    \url{https://www.health.belgium.be/fr/fy2014reflisticd-10-bexlsx}
-#' @param ... passed to \code{.download_to_data_raw}, e.g., \code{offline =
+#' @param ... passed to \code{.download_to_data_cache}, e.g., \code{offline =
 #'   FALSE}.
 #' @seealso \code{link{parse_icd10be2014_be}}
 #' @keywords internal

From a8b4a737c99313c380356c09181b96912882dc3c Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:44:33 -0500
Subject: [PATCH 05/51] use httr::content to properly handle UTF-8
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The call `.dl_icd10who_json(2008, "fr", "JsonGetRootConcepts?useHtml=false")` was returning malformed text that had not been reencoded properly.  For example "Autres infections intestinales bactériennes".
---
 R/who.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/who.R b/R/who.R
index 34117cb9..68d39476 100644
--- a/R/who.R
+++ b/R/who.R
@@ -70,8 +70,7 @@
       )
     }
   } # end 400+
-  json_data <- rawToChar(http_response$content)
-  jsonlite::fromJSON(json_data)
+  httr::content(http_response, simplifyDataFrame=TRUE)
 }
 
 #' Use WHO API to discover chapters
@@ -91,7 +90,7 @@
 }
 
 #' Get the children of a concept (ICD-10 chapter, code or range)
-#' @param concept_id NULl for root, concept string for any leaf or intermediate.
+#' @param concept_id NULL for root, concept string for any leaf or intermediate.
 #' @examples
 #' .dl_icd10who_children("XXII")
 #' .dl_icd10who_children("U84")

From 3a3347bdbed76bf0940ccba719ad3d6b63eaeed1 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:12 -0500
Subject: [PATCH 06/51] remove stringsAsFactors argument

stringsAsFactors is being deprecated generally.  The code here is causing test-score.R#333 to fail on R-devel because the id column is not a factor.  See https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/
---
 R/score.R                   | 22 ++---------
 tests/testthat/test-score.R | 77 +------------------------------------
 2 files changed, 6 insertions(+), 93 deletions(-)

diff --git a/R/score.R b/R/score.R
index a4c1cc7e..9fbf2ab1 100644
--- a/R/score.R
+++ b/R/score.R
@@ -24,11 +24,6 @@
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
-#' @param stringsAsFactors single logical, passed on when constructing
-#'   data.frame if \code{return_df} is \code{TRUE}. If the input data frame
-#'   \code{x} has a factor for the \code{visit_name}, this is not changed, but a
-#'   non-factor \code{visit_name} may be converted or not converted according to
-#'   your system default or this setting.
 #' @param ... further arguments to pass on to \code{icd9_comorbid_quan_deyo},
 #'   e.g. \code{name}
 #' @examples
@@ -46,7 +41,6 @@
 charlson <- function(x, visit_name = NULL,
                      scoring_system = c("original", "charlson", "quan"),
                      return_df = FALSE,
-                     stringsAsFactors = getOption("stringsAsFactors"), # nolint
                      ...) {
   UseMethod("charlson")
 }
@@ -60,7 +54,6 @@ charlson.data.frame <- function(x,
                                 visit_name = NULL,
                                 scoring_system = c("original", "charlson", "quan"),
                                 return_df = FALSE,
-                                stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                 ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
@@ -68,7 +61,6 @@ charlson.data.frame <- function(x,
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
-  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   res <- charlson_from_comorbid(
     comorbid_quan_deyo(x,
@@ -84,9 +76,8 @@ charlson.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("Charlson" = unname(res)),
-    stringsAsFactors = stringsAsFactors
-  ) # nolint
+    data.frame("Charlson" = unname(res))
+  )
   names(out)[1] <- visit_name
   out
 }
@@ -301,7 +292,6 @@ count_codes_wide <- function(x,
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
-#' @template stringsAsFactors
 #' @template dotdotdot
 #' @examples
 #' mydf <- data.frame(
@@ -325,7 +315,6 @@ count_codes_wide <- function(x,
 van_walraven <- function(x,
                          visit_name = NULL,
                          return_df = FALSE,
-                         stringsAsFactors = getOption("stringsAsFactors"), # nolint
                          ...) {
   UseMethod("van_walraven")
 }
@@ -336,13 +325,11 @@ van_walraven <- function(x,
 van_walraven.data.frame <- function(x,
                                     visit_name = NULL,
                                     return_df = FALSE,
-                                    stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                     ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
-  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   tmp <- icd9_comorbid_quan_elix(x,
     visit_name,
@@ -357,9 +344,8 @@ van_walraven.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("vanWalraven" = unname(res)),
-    stringsAsFactors = stringsAsFactors
-  ) # nolint
+    data.frame("vanWalraven" = unname(res))
+  )
   names(out)[1] <- visit_name
   out
 }
diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index 2c30c69b..731b145c 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -48,8 +48,7 @@ test_that("only matrix or data.frame accepted", {
 test_that("Charlson score", {
   mydf <- data.frame(
     visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042"),
-    stringsAsFactors = TRUE
+    icd9 = c("441", "412.93", "042")
   )
   expect_equal(
     charlson_from_comorbid(
@@ -64,7 +63,6 @@ test_that("Charlson score", {
   expect_equivalent(
     charlson(mydf,
       return_df = TRUE,
-      stringsAsFactors = TRUE,
       short_code = FALSE
     ),
     structure(list(
@@ -79,77 +77,6 @@ test_that("Charlson score", {
     class = "data.frame"
     )
   )
-  mydff <- data.frame(
-    visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042"),
-    stringsAsFactors = FALSE
-  )
-  expect_identical(
-    charlson(mydff,
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      visit_id = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("visit_id", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  expect_identical(
-    charlson(mydff,
-      return_df = TRUE,
-      stringsAsFactors = TRUE,
-      short_code = FALSE
-    ),
-    structure(list(
-      visit_id = factor(c("a", "b", "c")),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("visit_id", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  mydfff <- mydff
-  names(mydfff)[1] <- "v"
-  expect_equivalent(
-    charlson(mydfff,
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      v = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("v", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  mydffff <- cbind(mydfff, data.frame(v2 = mydfff$v, stringsAsFactors = FALSE))
-  mydffff$v <- NULL
-  expect_identical(get_icd_name(mydffff, NULL), "icd9")
-  expect_equivalent(
-    charlson(mydffff,
-      visit_name = "v2",
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      v2 = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("v2", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
 })
 
 test_that("Charlson - errors?", {
@@ -308,7 +235,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comodbidity index and score", {
+test_that("van_walraven comorbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =

From 5badf21e25c0bd6d1c63ae1178b6dd34ad0b5537 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:44 -0500
Subject: [PATCH 07/51] export categorize_simple

On r-devel the check for this example is failing with "could not find function "categorize_simple""
---
 R/categorize.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/categorize.R b/R/categorize.R
index 08f4d76e..1ea0c0a6 100644
--- a/R/categorize.R
+++ b/R/categorize.R
@@ -31,6 +31,7 @@
 #' u$icd10 <- decimal_to_short(u$icd10)
 #' j <- categorize_simple(u, m, id_name = "case", code_name = "icd10")
 #' @keywords internal
+#' @export
 categorize_simple <- function(x,
                               map,
                               id_name,

From ddd1fac0584e76a3002179b6c75a60e9d4d18e36 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:51 -0500
Subject: [PATCH 08/51] Update NAMESPACE

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index f8062774..9db92ca6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -161,6 +161,7 @@ export(as.icd_long_data)
 export(as.icd_short_diag)
 export(as.icd_wide_data)
 export(as.short_diag)
+export(categorize_simple)
 export(chapters_to_map)
 export(charlson)
 export(charlson_from_comorbid)

From 6bf2f840091fba3205021fa028a51710a3104611 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 22:17:30 -0500
Subject: [PATCH 09/51] add R_REMOTES_STANDALONE=true to fix appveyor curl
 error

See https://github.com/r-lib/remotes#standalone-mode and https://github.com/krlmlr/r-appveyor/issues/135
---
 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appveyor.yml b/appveyor.yml
index 1349c12e..d9e2e1e2 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -36,6 +36,7 @@ build_script:
 
 environment:
   # APPVEYOR_CACHE_SKIP_RESTORE: true
+  R_REMOTES_STANDALONE: true
   WARNINGS_ARE_ERRORS: 1
   _R_CHECK_EXIT_ON_FIRST_ERROR_: true
   USE_RTOOLS: true

From aefd69687e16c5d2b298e3abd9ed0679697b7316 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 22:44:15 -0500
Subject: [PATCH 10/51] revert stringsToFactor change

---
 R/score.R                   | 22 +++++++++--
 tests/testthat/test-score.R | 77 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 93 insertions(+), 6 deletions(-)

diff --git a/R/score.R b/R/score.R
index 9fbf2ab1..a4c1cc7e 100644
--- a/R/score.R
+++ b/R/score.R
@@ -24,6 +24,11 @@
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
+#' @param stringsAsFactors single logical, passed on when constructing
+#'   data.frame if \code{return_df} is \code{TRUE}. If the input data frame
+#'   \code{x} has a factor for the \code{visit_name}, this is not changed, but a
+#'   non-factor \code{visit_name} may be converted or not converted according to
+#'   your system default or this setting.
 #' @param ... further arguments to pass on to \code{icd9_comorbid_quan_deyo},
 #'   e.g. \code{name}
 #' @examples
@@ -41,6 +46,7 @@
 charlson <- function(x, visit_name = NULL,
                      scoring_system = c("original", "charlson", "quan"),
                      return_df = FALSE,
+                     stringsAsFactors = getOption("stringsAsFactors"), # nolint
                      ...) {
   UseMethod("charlson")
 }
@@ -54,6 +60,7 @@ charlson.data.frame <- function(x,
                                 visit_name = NULL,
                                 scoring_system = c("original", "charlson", "quan"),
                                 return_df = FALSE,
+                                stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                 ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
@@ -61,6 +68,7 @@ charlson.data.frame <- function(x,
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
+  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   res <- charlson_from_comorbid(
     comorbid_quan_deyo(x,
@@ -76,8 +84,9 @@ charlson.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("Charlson" = unname(res))
-  )
+    data.frame("Charlson" = unname(res)),
+    stringsAsFactors = stringsAsFactors
+  ) # nolint
   names(out)[1] <- visit_name
   out
 }
@@ -292,6 +301,7 @@ count_codes_wide <- function(x,
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
+#' @template stringsAsFactors
 #' @template dotdotdot
 #' @examples
 #' mydf <- data.frame(
@@ -315,6 +325,7 @@ count_codes_wide <- function(x,
 van_walraven <- function(x,
                          visit_name = NULL,
                          return_df = FALSE,
+                         stringsAsFactors = getOption("stringsAsFactors"), # nolint
                          ...) {
   UseMethod("van_walraven")
 }
@@ -325,11 +336,13 @@ van_walraven <- function(x,
 van_walraven.data.frame <- function(x,
                                     visit_name = NULL,
                                     return_df = FALSE,
+                                    stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                     ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
+  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   tmp <- icd9_comorbid_quan_elix(x,
     visit_name,
@@ -344,8 +357,9 @@ van_walraven.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("vanWalraven" = unname(res))
-  )
+    data.frame("vanWalraven" = unname(res)),
+    stringsAsFactors = stringsAsFactors
+  ) # nolint
   names(out)[1] <- visit_name
   out
 }
diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index 731b145c..2c30c69b 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -48,7 +48,8 @@ test_that("only matrix or data.frame accepted", {
 test_that("Charlson score", {
   mydf <- data.frame(
     visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042")
+    icd9 = c("441", "412.93", "042"),
+    stringsAsFactors = TRUE
   )
   expect_equal(
     charlson_from_comorbid(
@@ -63,6 +64,7 @@ test_that("Charlson score", {
   expect_equivalent(
     charlson(mydf,
       return_df = TRUE,
+      stringsAsFactors = TRUE,
       short_code = FALSE
     ),
     structure(list(
@@ -77,6 +79,77 @@ test_that("Charlson score", {
     class = "data.frame"
     )
   )
+  mydff <- data.frame(
+    visit_id = c("a", "b", "c"),
+    icd9 = c("441", "412.93", "042"),
+    stringsAsFactors = FALSE
+  )
+  expect_identical(
+    charlson(mydff,
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      visit_id = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("visit_id", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  expect_identical(
+    charlson(mydff,
+      return_df = TRUE,
+      stringsAsFactors = TRUE,
+      short_code = FALSE
+    ),
+    structure(list(
+      visit_id = factor(c("a", "b", "c")),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("visit_id", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  mydfff <- mydff
+  names(mydfff)[1] <- "v"
+  expect_equivalent(
+    charlson(mydfff,
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      v = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("v", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  mydffff <- cbind(mydfff, data.frame(v2 = mydfff$v, stringsAsFactors = FALSE))
+  mydffff$v <- NULL
+  expect_identical(get_icd_name(mydffff, NULL), "icd9")
+  expect_equivalent(
+    charlson(mydffff,
+      visit_name = "v2",
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      v2 = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("v2", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
 })
 
 test_that("Charlson - errors?", {
@@ -235,7 +308,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comorbidity index and score", {
+test_that("van_walraven comodbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =

From 7eab1a52f59b2918f352286cd5570f27912e2efa Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 22:45:21 -0500
Subject: [PATCH 11/51] update test to succeed in a stringsAsFactors=FALSE
 environment

---
 tests/testthat/test-score.R | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index 2c30c69b..6899308f 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -332,10 +332,17 @@ test_that("van_walraven comodbidity index and score", {
   )
   expect_equivalent(
     van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE),
-    data.frame(
-      id = factor(c(1, 2, 3)),
-      vanWalraven = c(10, 12, -2)
-    )
+    if(getOption("stringsAsFactors")) {
+      data.frame(
+        id = factor(c("1", "2", "3")),
+        vanWalraven = c(10, 12, -2)
+      )
+    } else {
+      data.frame(
+        id = c("1", "2", "3"),
+        vanWalraven = c(10, 12, -2)
+      )
+    }
   )
   expect_equal(
     van_walraven(mydf, icd_name = "value"),

From 37f7e4688d1e9972cef9ffb6d22ded34d088f67d Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:13:51 -0500
Subject: [PATCH 12/51] fix typos

---
 tests/testthat/test-score.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index 6899308f..b1cbd0df 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -308,7 +308,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comodbidity index and score", {
+test_that("van_walraven comorbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =
@@ -350,7 +350,7 @@ test_that("van_walraven comodbidity index and score", {
   )
 })
 
-test_that("github issue #64 - quan revised charleson scores", {
+test_that("github issue #64 - quan revised charlson scores", {
   mydf <- data.frame(visit_id = "a", icd9 = "250.0")
   comorbids <- comorbid_quan_deyo(mydf, short_code = FALSE, return_df = TRUE)
 

From 6b8c7a5ff5cd23e4e27a43d9268de4efcb275f21 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:15:41 -0500
Subject: [PATCH 13/51] move data-raw to inst directory

---
 {data-raw => inst/data-raw}/.gitignore                            | 0
 {data-raw => inst/data-raw}/ICD10_Charlson.sas                    | 0
 {data-raw => inst/data-raw}/ICD10_Elixhauser.sas                  | 0
 {data-raw => inst/data-raw}/ICD9_E_Charlson.sas                   | 0
 {data-raw => inst/data-raw}/ICD9_E_Elixhauser.sas                 | 0
 {data-raw => inst/data-raw}/X.dxref.2015.csv                      | 0
 {data-raw => inst/data-raw}/ccs_multi_dx_tool_2013.csv            | 0
 {data-raw => inst/data-raw}/ccs_multi_dx_tool_2015.csv            | 0
 {data-raw => inst/data-raw}/ccs_multi_pr_tool_2014.csv            | 0
 {data-raw => inst/data-raw}/comformat2012-2013.txt                | 0
 {data-raw => inst/data-raw}/comoanaly2012-2013.txt                | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2016_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2017_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2018_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2019_icd10hcc.txt             | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2007_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2008_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2009_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2010_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2011_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2012_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2013_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2014_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2015_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2016_icd9hcc.txt | 0
 .../data-raw}/icd_hcc_rawdata/labels/2007_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2008_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2009_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2010_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2011_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2012_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2013_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2014_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2015_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2016_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2017_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2018_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2019_labels.txt              | 0
 .../data-raw}/ver2016_ahrq-comformat_icd10cm_2016.txt             | 0
 51 files changed, 0 insertions(+), 0 deletions(-)
 rename {data-raw => inst/data-raw}/.gitignore (100%)
 rename {data-raw => inst/data-raw}/ICD10_Charlson.sas (100%)
 rename {data-raw => inst/data-raw}/ICD10_Elixhauser.sas (100%)
 rename {data-raw => inst/data-raw}/ICD9_E_Charlson.sas (100%)
 rename {data-raw => inst/data-raw}/ICD9_E_Elixhauser.sas (100%)
 rename {data-raw => inst/data-raw}/X.dxref.2015.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_dx_tool_2013.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_dx_tool_2015.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_pr_tool_2014.csv (100%)
 rename {data-raw => inst/data-raw}/comformat2012-2013.txt (100%)
 rename {data-raw => inst/data-raw}/comoanaly2012-2013.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd10/2016_icd10hcc.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd10/2017_icd10hcc.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd10/2018_icd10hcc.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd10/2019_icd10hcc.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2007_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2008_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2009_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2010_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2011_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2012_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2013_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2014_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2015_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2016_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2007_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2008_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2009_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2010_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2011_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2012_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2013_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2014_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2015_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2016_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2017_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2018_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2019_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/ver2016_ahrq-comformat_icd10cm_2016.txt (100%)

diff --git a/data-raw/.gitignore b/inst/data-raw/.gitignore
similarity index 100%
rename from data-raw/.gitignore
rename to inst/data-raw/.gitignore
diff --git a/data-raw/ICD10_Charlson.sas b/inst/data-raw/ICD10_Charlson.sas
similarity index 100%
rename from data-raw/ICD10_Charlson.sas
rename to inst/data-raw/ICD10_Charlson.sas
diff --git a/data-raw/ICD10_Elixhauser.sas b/inst/data-raw/ICD10_Elixhauser.sas
similarity index 100%
rename from data-raw/ICD10_Elixhauser.sas
rename to inst/data-raw/ICD10_Elixhauser.sas
diff --git a/data-raw/ICD9_E_Charlson.sas b/inst/data-raw/ICD9_E_Charlson.sas
similarity index 100%
rename from data-raw/ICD9_E_Charlson.sas
rename to inst/data-raw/ICD9_E_Charlson.sas
diff --git a/data-raw/ICD9_E_Elixhauser.sas b/inst/data-raw/ICD9_E_Elixhauser.sas
similarity index 100%
rename from data-raw/ICD9_E_Elixhauser.sas
rename to inst/data-raw/ICD9_E_Elixhauser.sas
diff --git a/data-raw/X.dxref.2015.csv b/inst/data-raw/X.dxref.2015.csv
similarity index 100%
rename from data-raw/X.dxref.2015.csv
rename to inst/data-raw/X.dxref.2015.csv
diff --git a/data-raw/ccs_multi_dx_tool_2013.csv b/inst/data-raw/ccs_multi_dx_tool_2013.csv
similarity index 100%
rename from data-raw/ccs_multi_dx_tool_2013.csv
rename to inst/data-raw/ccs_multi_dx_tool_2013.csv
diff --git a/data-raw/ccs_multi_dx_tool_2015.csv b/inst/data-raw/ccs_multi_dx_tool_2015.csv
similarity index 100%
rename from data-raw/ccs_multi_dx_tool_2015.csv
rename to inst/data-raw/ccs_multi_dx_tool_2015.csv
diff --git a/data-raw/ccs_multi_pr_tool_2014.csv b/inst/data-raw/ccs_multi_pr_tool_2014.csv
similarity index 100%
rename from data-raw/ccs_multi_pr_tool_2014.csv
rename to inst/data-raw/ccs_multi_pr_tool_2014.csv
diff --git a/data-raw/comformat2012-2013.txt b/inst/data-raw/comformat2012-2013.txt
similarity index 100%
rename from data-raw/comformat2012-2013.txt
rename to inst/data-raw/comformat2012-2013.txt
diff --git a/data-raw/comoanaly2012-2013.txt b/inst/data-raw/comoanaly2012-2013.txt
similarity index 100%
rename from data-raw/comoanaly2012-2013.txt
rename to inst/data-raw/comoanaly2012-2013.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt b/inst/data-raw/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt
rename to inst/data-raw/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt
diff --git a/data-raw/icd_hcc_rawdata/icd10/2016_icd10hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd10/2016_icd10hcc.txt
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd10/2016_icd10hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd10/2016_icd10hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd10/2017_icd10hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd10/2017_icd10hcc.txt
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd10/2017_icd10hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd10/2017_icd10hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd10/2018_icd10hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd10/2018_icd10hcc.txt
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd10/2018_icd10hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd10/2018_icd10hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd10/2019_icd10hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd10/2019_icd10hcc.txt
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd10/2019_icd10hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd10/2019_icd10hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2007_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2007_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2007_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2007_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2008_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2008_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2008_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2008_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2009_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2009_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2009_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2009_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2010_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2010_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2010_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2010_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2011_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2011_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2011_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2011_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2012_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2012_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2012_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2012_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2013_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2013_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2013_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2013_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2014_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2014_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2014_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2014_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2015_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2015_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2015_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2015_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/icd9/2016_icd9hcc.txt b/inst/data-raw/icd_hcc_rawdata/icd9/2016_icd9hcc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/icd9/2016_icd9hcc.txt
rename to inst/data-raw/icd_hcc_rawdata/icd9/2016_icd9hcc.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2007_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2007_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2007_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2007_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2008_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2008_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2008_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2008_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2009_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2009_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2009_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2009_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2010_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2010_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2010_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2010_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2011_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2011_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2011_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2011_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2012_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2012_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2012_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2012_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2013_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2013_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2013_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2013_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2014_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2014_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2014_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2014_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2015_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2015_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2015_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2015_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2016_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2016_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2016_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2016_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2017_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2017_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2017_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2017_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2018_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2018_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2018_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2018_labels.txt
diff --git a/data-raw/icd_hcc_rawdata/labels/2019_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2019_labels.txt
old mode 100755
new mode 100644
similarity index 100%
rename from data-raw/icd_hcc_rawdata/labels/2019_labels.txt
rename to inst/data-raw/icd_hcc_rawdata/labels/2019_labels.txt
diff --git a/data-raw/ver2016_ahrq-comformat_icd10cm_2016.txt b/inst/data-raw/ver2016_ahrq-comformat_icd10cm_2016.txt
similarity index 100%
rename from data-raw/ver2016_ahrq-comformat_icd10cm_2016.txt
rename to inst/data-raw/ver2016_ahrq-comformat_icd10cm_2016.txt

From 192a0e5a77b964dc902b923219a5a155f569d955 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:48:14 -0500
Subject: [PATCH 14/51] attempt to fix "non-portable flag(s)" error on 3.6.2
 travis build

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 81cbabd5..f4a4253b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -85,7 +85,8 @@ env:
     - _R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
     - _R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
     # some of the following are ignored if --as-cran is set
-    - _R_CHECK_COMPILATION_FLAGS_=FALSE
+    - _R_CHECK_COMPILATION_FLAGS_=TRUE
+    - _R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option"
     # the following are to simulate cran, and
     # help debugging if we didn't use --as-cran
     - _R_CHECK_ALL_NON_ISO_C_=TRUE

From df80a4011571b015d5b45704b1355deff74f1a0e Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Fri, 13 Mar 2020 01:49:17 -0400
Subject: [PATCH 15/51] updated URL
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

CIM-10-FR adds U071: Maladie à coronavirus 2019 [COVID-19]
---
 R/cim-10-fr.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cim-10-fr.R b/R/cim-10-fr.R
index 5cf4eefa..559ee340 100644
--- a/R/cim-10-fr.R
+++ b/R/cim-10-fr.R
@@ -8,7 +8,7 @@
       "https://www.atih.sante.fr",
       "plateformes-de-transmission-et-logiciels",
       "logiciels-espace-de-telechargement",
-      "telecharger/gratuit/12713/456"
+      "telecharger/gratuit/13332/456"
     ),
     file_name = "LIBCIM10MULTI.TXT",
     dl_msg = "Working on ICD-10-FR (CIM-10-FR)",

From 4b420cf2c4594bba82f89879f349ea5cb9683bc3 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:44:33 -0500
Subject: [PATCH 16/51] use httr::content to properly handle UTF-8
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The call `.dl_icd10who_json(2008, "fr", "JsonGetRootConcepts?useHtml=false")` was returning malformed text that had not been reencoded properly.  For example "Autres infections intestinales bactériennes".
---
 R/who.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/who.R b/R/who.R
index 34117cb9..68d39476 100644
--- a/R/who.R
+++ b/R/who.R
@@ -70,8 +70,7 @@
       )
     }
   } # end 400+
-  json_data <- rawToChar(http_response$content)
-  jsonlite::fromJSON(json_data)
+  httr::content(http_response, simplifyDataFrame=TRUE)
 }
 
 #' Use WHO API to discover chapters
@@ -91,7 +90,7 @@
 }
 
 #' Get the children of a concept (ICD-10 chapter, code or range)
-#' @param concept_id NULl for root, concept string for any leaf or intermediate.
+#' @param concept_id NULL for root, concept string for any leaf or intermediate.
 #' @examples
 #' .dl_icd10who_children("XXII")
 #' .dl_icd10who_children("U84")

From 214c62576ddae14422017d28506d701b82b9f11d Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:12 -0500
Subject: [PATCH 17/51] remove stringsAsFactors argument

stringsAsFactors is being deprecated generally.  The code here is causing test-score.R#333 to fail on R-devel because the id column is not a factor.  See https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/
---
 R/score.R                   | 22 ++---------
 tests/testthat/test-score.R | 77 +------------------------------------
 2 files changed, 6 insertions(+), 93 deletions(-)

diff --git a/R/score.R b/R/score.R
index a4c1cc7e..9fbf2ab1 100644
--- a/R/score.R
+++ b/R/score.R
@@ -24,11 +24,6 @@
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
-#' @param stringsAsFactors single logical, passed on when constructing
-#'   data.frame if \code{return_df} is \code{TRUE}. If the input data frame
-#'   \code{x} has a factor for the \code{visit_name}, this is not changed, but a
-#'   non-factor \code{visit_name} may be converted or not converted according to
-#'   your system default or this setting.
 #' @param ... further arguments to pass on to \code{icd9_comorbid_quan_deyo},
 #'   e.g. \code{name}
 #' @examples
@@ -46,7 +41,6 @@
 charlson <- function(x, visit_name = NULL,
                      scoring_system = c("original", "charlson", "quan"),
                      return_df = FALSE,
-                     stringsAsFactors = getOption("stringsAsFactors"), # nolint
                      ...) {
   UseMethod("charlson")
 }
@@ -60,7 +54,6 @@ charlson.data.frame <- function(x,
                                 visit_name = NULL,
                                 scoring_system = c("original", "charlson", "quan"),
                                 return_df = FALSE,
-                                stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                 ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
@@ -68,7 +61,6 @@ charlson.data.frame <- function(x,
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
-  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   res <- charlson_from_comorbid(
     comorbid_quan_deyo(x,
@@ -84,9 +76,8 @@ charlson.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("Charlson" = unname(res)),
-    stringsAsFactors = stringsAsFactors
-  ) # nolint
+    data.frame("Charlson" = unname(res))
+  )
   names(out)[1] <- visit_name
   out
 }
@@ -301,7 +292,6 @@ count_codes_wide <- function(x,
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
-#' @template stringsAsFactors
 #' @template dotdotdot
 #' @examples
 #' mydf <- data.frame(
@@ -325,7 +315,6 @@ count_codes_wide <- function(x,
 van_walraven <- function(x,
                          visit_name = NULL,
                          return_df = FALSE,
-                         stringsAsFactors = getOption("stringsAsFactors"), # nolint
                          ...) {
   UseMethod("van_walraven")
 }
@@ -336,13 +325,11 @@ van_walraven <- function(x,
 van_walraven.data.frame <- function(x,
                                     visit_name = NULL,
                                     return_df = FALSE,
-                                    stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                     ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
-  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   tmp <- icd9_comorbid_quan_elix(x,
     visit_name,
@@ -357,9 +344,8 @@ van_walraven.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("vanWalraven" = unname(res)),
-    stringsAsFactors = stringsAsFactors
-  ) # nolint
+    data.frame("vanWalraven" = unname(res))
+  )
   names(out)[1] <- visit_name
   out
 }
diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index c00e093a..645c8113 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -48,8 +48,7 @@ test_that("only matrix or data.frame accepted", {
 test_that("Charlson score", {
   mydf <- data.frame(
     visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042"),
-    stringsAsFactors = TRUE
+    icd9 = c("441", "412.93", "042")
   )
   expect_equal(
     charlson_from_comorbid(
@@ -64,7 +63,6 @@ test_that("Charlson score", {
   expect_equivalent(
     charlson(mydf,
       return_df = TRUE,
-      stringsAsFactors = TRUE,
       short_code = FALSE
     ),
     structure(list(
@@ -79,77 +77,6 @@ test_that("Charlson score", {
     class = "data.frame"
     )
   )
-  mydff <- data.frame(
-    visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042"),
-    stringsAsFactors = FALSE
-  )
-  expect_identical(
-    charlson(mydff,
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      visit_id = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("visit_id", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  expect_identical(
-    charlson(mydff,
-      return_df = TRUE,
-      stringsAsFactors = TRUE,
-      short_code = FALSE
-    ),
-    structure(list(
-      visit_id = factor(c("a", "b", "c")),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("visit_id", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  mydfff <- mydff
-  names(mydfff)[1] <- "v"
-  expect_equivalent(
-    charlson(mydfff,
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      v = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("v", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  mydffff <- cbind(mydfff, data.frame(v2 = mydfff$v, stringsAsFactors = FALSE))
-  mydffff$v <- NULL
-  expect_identical(get_icd_name(mydffff, NULL), "icd9")
-  expect_equivalent(
-    charlson(mydffff,
-      visit_name = "v2",
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      v2 = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("v2", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
 })
 
 test_that("Charlson - errors?", {
@@ -308,7 +235,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comodbidity index and score", {
+test_that("van_walraven comorbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =

From 18c601760a404a69085a9e31bae25b998e0d67fc Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:44 -0500
Subject: [PATCH 18/51] export categorize_simple

On r-devel the check for this example is failing with "could not find function "categorize_simple""
---
 R/categorize.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/categorize.R b/R/categorize.R
index 4df9f6da..08f4eb59 100644
--- a/R/categorize.R
+++ b/R/categorize.R
@@ -35,6 +35,7 @@
 #' u$icd10 <- decimal_to_short(u$icd10)
 #' j <- icd:::categorize_simple(u, m, id_name = "case", code_name = "icd10")
 #' @keywords internal
+#' @export
 categorize_simple <- function(x,
                               map,
                               id_name,

From 3465a2a8b054160fb77112428cfc6652d2d367e7 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:51 -0500
Subject: [PATCH 19/51] Update NAMESPACE

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index f8062774..9db92ca6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -161,6 +161,7 @@ export(as.icd_long_data)
 export(as.icd_short_diag)
 export(as.icd_wide_data)
 export(as.short_diag)
+export(categorize_simple)
 export(chapters_to_map)
 export(charlson)
 export(charlson_from_comorbid)

From 28b155559628220d8bd43311330f439fc7863358 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 22:17:30 -0500
Subject: [PATCH 20/51] add R_REMOTES_STANDALONE=true to fix appveyor curl
 error

See https://github.com/r-lib/remotes#standalone-mode and https://github.com/krlmlr/r-appveyor/issues/135
---
 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appveyor.yml b/appveyor.yml
index 1349c12e..d9e2e1e2 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -36,6 +36,7 @@ build_script:
 
 environment:
   # APPVEYOR_CACHE_SKIP_RESTORE: true
+  R_REMOTES_STANDALONE: true
   WARNINGS_ARE_ERRORS: 1
   _R_CHECK_EXIT_ON_FIRST_ERROR_: true
   USE_RTOOLS: true

From 5d0a4b09998673f280c7b1144af9a3dbbe88c51c Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 22:44:15 -0500
Subject: [PATCH 21/51] revert stringsToFactor change

---
 R/score.R                   | 22 +++++++++--
 tests/testthat/test-score.R | 77 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 93 insertions(+), 6 deletions(-)

diff --git a/R/score.R b/R/score.R
index 9fbf2ab1..a4c1cc7e 100644
--- a/R/score.R
+++ b/R/score.R
@@ -24,6 +24,11 @@
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
+#' @param stringsAsFactors single logical, passed on when constructing
+#'   data.frame if \code{return_df} is \code{TRUE}. If the input data frame
+#'   \code{x} has a factor for the \code{visit_name}, this is not changed, but a
+#'   non-factor \code{visit_name} may be converted or not converted according to
+#'   your system default or this setting.
 #' @param ... further arguments to pass on to \code{icd9_comorbid_quan_deyo},
 #'   e.g. \code{name}
 #' @examples
@@ -41,6 +46,7 @@
 charlson <- function(x, visit_name = NULL,
                      scoring_system = c("original", "charlson", "quan"),
                      return_df = FALSE,
+                     stringsAsFactors = getOption("stringsAsFactors"), # nolint
                      ...) {
   UseMethod("charlson")
 }
@@ -54,6 +60,7 @@ charlson.data.frame <- function(x,
                                 visit_name = NULL,
                                 scoring_system = c("original", "charlson", "quan"),
                                 return_df = FALSE,
+                                stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                 ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
@@ -61,6 +68,7 @@ charlson.data.frame <- function(x,
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
+  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   res <- charlson_from_comorbid(
     comorbid_quan_deyo(x,
@@ -76,8 +84,9 @@ charlson.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("Charlson" = unname(res))
-  )
+    data.frame("Charlson" = unname(res)),
+    stringsAsFactors = stringsAsFactors
+  ) # nolint
   names(out)[1] <- visit_name
   out
 }
@@ -292,6 +301,7 @@ count_codes_wide <- function(x,
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
+#' @template stringsAsFactors
 #' @template dotdotdot
 #' @examples
 #' mydf <- data.frame(
@@ -315,6 +325,7 @@ count_codes_wide <- function(x,
 van_walraven <- function(x,
                          visit_name = NULL,
                          return_df = FALSE,
+                         stringsAsFactors = getOption("stringsAsFactors"), # nolint
                          ...) {
   UseMethod("van_walraven")
 }
@@ -325,11 +336,13 @@ van_walraven <- function(x,
 van_walraven.data.frame <- function(x,
                                     visit_name = NULL,
                                     return_df = FALSE,
+                                    stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                     ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
+  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   tmp <- icd9_comorbid_quan_elix(x,
     visit_name,
@@ -344,8 +357,9 @@ van_walraven.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("vanWalraven" = unname(res))
-  )
+    data.frame("vanWalraven" = unname(res)),
+    stringsAsFactors = stringsAsFactors
+  ) # nolint
   names(out)[1] <- visit_name
   out
 }
diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index 645c8113..c00e093a 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -48,7 +48,8 @@ test_that("only matrix or data.frame accepted", {
 test_that("Charlson score", {
   mydf <- data.frame(
     visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042")
+    icd9 = c("441", "412.93", "042"),
+    stringsAsFactors = TRUE
   )
   expect_equal(
     charlson_from_comorbid(
@@ -63,6 +64,7 @@ test_that("Charlson score", {
   expect_equivalent(
     charlson(mydf,
       return_df = TRUE,
+      stringsAsFactors = TRUE,
       short_code = FALSE
     ),
     structure(list(
@@ -77,6 +79,77 @@ test_that("Charlson score", {
     class = "data.frame"
     )
   )
+  mydff <- data.frame(
+    visit_id = c("a", "b", "c"),
+    icd9 = c("441", "412.93", "042"),
+    stringsAsFactors = FALSE
+  )
+  expect_identical(
+    charlson(mydff,
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      visit_id = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("visit_id", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  expect_identical(
+    charlson(mydff,
+      return_df = TRUE,
+      stringsAsFactors = TRUE,
+      short_code = FALSE
+    ),
+    structure(list(
+      visit_id = factor(c("a", "b", "c")),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("visit_id", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  mydfff <- mydff
+  names(mydfff)[1] <- "v"
+  expect_equivalent(
+    charlson(mydfff,
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      v = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("v", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  mydffff <- cbind(mydfff, data.frame(v2 = mydfff$v, stringsAsFactors = FALSE))
+  mydffff$v <- NULL
+  expect_identical(get_icd_name(mydffff, NULL), "icd9")
+  expect_equivalent(
+    charlson(mydffff,
+      visit_name = "v2",
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      v2 = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("v2", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
 })
 
 test_that("Charlson - errors?", {
@@ -235,7 +308,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comorbidity index and score", {
+test_that("van_walraven comodbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =

From fc6c099ee2a41b4c9dd4c2c194316e72c40f6b41 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:13:51 -0500
Subject: [PATCH 22/51] fix typos

---
 tests/testthat/test-score.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index c00e093a..cd9d32a7 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -308,7 +308,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comodbidity index and score", {
+test_that("van_walraven comorbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =
@@ -350,7 +350,7 @@ test_that("van_walraven comodbidity index and score", {
   )
 })
 
-test_that("github issue #64 - quan revised charleson scores", {
+test_that("github issue #64 - quan revised charlson scores", {
   mydf <- data.frame(visit_id = "a", icd9 = "250.0")
   comorbids <- comorbid_quan_deyo(mydf, short_code = FALSE, return_df = TRUE)
 

From 1d533d2e2a096bc5d5e2cdace7066b824956c959 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:15:41 -0500
Subject: [PATCH 23/51] move data-raw to inst directory

---
 {data-raw => inst/data-raw}/.gitignore                            | 0
 {data-raw => inst/data-raw}/ICD10_Charlson.sas                    | 0
 {data-raw => inst/data-raw}/ICD10_Elixhauser.sas                  | 0
 {data-raw => inst/data-raw}/ICD9_E_Charlson.sas                   | 0
 {data-raw => inst/data-raw}/ICD9_E_Elixhauser.sas                 | 0
 {data-raw => inst/data-raw}/X.dxref.2015.csv                      | 0
 {data-raw => inst/data-raw}/ccs_multi_dx_tool_2013.csv            | 0
 {data-raw => inst/data-raw}/ccs_multi_dx_tool_2015.csv            | 0
 {data-raw => inst/data-raw}/ccs_multi_pr_tool_2014.csv            | 0
 {data-raw => inst/data-raw}/comformat2012-2013.txt                | 0
 {data-raw => inst/data-raw}/comoanaly2012-2013.txt                | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2016_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2017_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2018_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2019_icd10hcc.txt             | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2007_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2008_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2009_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2010_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2011_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2012_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2013_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2014_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2015_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2016_icd9hcc.txt | 0
 .../data-raw}/icd_hcc_rawdata/labels/2007_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2008_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2009_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2010_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2011_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2012_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2013_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2014_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2015_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2016_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2017_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2018_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2019_labels.txt              | 0
 .../data-raw}/ver2016_ahrq-comformat_icd10cm_2016.txt             | 0
 51 files changed, 0 insertions(+), 0 deletions(-)
 rename {data-raw => inst/data-raw}/.gitignore (100%)
 rename {data-raw => inst/data-raw}/ICD10_Charlson.sas (100%)
 rename {data-raw => inst/data-raw}/ICD10_Elixhauser.sas (100%)
 rename {data-raw => inst/data-raw}/ICD9_E_Charlson.sas (100%)
 rename {data-raw => inst/data-raw}/ICD9_E_Elixhauser.sas (100%)
 rename {data-raw => inst/data-raw}/X.dxref.2015.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_dx_tool_2013.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_dx_tool_2015.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_pr_tool_2014.csv (100%)
 rename {data-raw => inst/data-raw}/comformat2012-2013.txt (100%)
 rename {data-raw => inst/data-raw}/comoanaly2012-2013.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd10/2016_icd10hcc.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd10/2017_icd10hcc.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd10/2018_icd10hcc.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd10/2019_icd10hcc.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2007_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2008_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2009_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2010_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2011_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2012_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2013_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2014_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2015_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2016_icd9hcc.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2007_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2008_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2009_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2010_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2011_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2012_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2013_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2014_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2015_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2016_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2017_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2018_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/labels/2019_labels.txt (100%)
 mode change 100755 => 100644
 rename {data-raw => inst/data-raw}/ver2016_ahrq-comformat_icd10cm_2016.txt (100%)

diff --git a/data-raw/.gitignore b/inst/data-raw/.gitignore
similarity index 100%
rename from data-raw/.gitignore
rename to inst/data-raw/.gitignore
diff --git a/data-raw/ICD10_Charlson.sas b/inst/data-raw/ICD10_Charlson.sas
similarity index 100%
rename from data-raw/ICD10_Charlson.sas
rename to inst/data-raw/ICD10_Charlson.sas
diff --git a/data-raw/ICD10_Elixhauser.sas b/inst/data-raw/ICD10_Elixhauser.sas
similarity index 100%
rename from data-raw/ICD10_Elixhauser.sas
rename to inst/data-raw/ICD10_Elixhauser.sas
diff --git a/data-raw/ICD9_E_Charlson.sas b/inst/data-raw/ICD9_E_Charlson.sas
similarity index 100%
rename from data-raw/ICD9_E_Charlson.sas
rename to inst/data-raw/ICD9_E_Charlson.sas
diff --git a/data-raw/ICD9_E_Elixhauser.sas b/inst/data-raw/ICD9_E_Elixhauser.sas
similarity index 100%
rename from data-raw/ICD9_E_Elixhauser.sas
rename to inst/data-raw/ICD9_E_Elixhauser.sas
diff --git a/data-raw/X.dxref.2015.csv b/inst/data-raw/X.dxref.2015.csv
similarity index 100%
rename from data-raw/X.dxref.2015.csv
rename to inst/data-raw/X.dxref.2015.csv
diff --git a/data-raw/ccs_multi_dx_tool_2013.csv b/inst/data-raw/ccs_multi_dx_tool_2013.csv
similarity index 100%
rename from data-raw/ccs_multi_dx_tool_2013.csv
rename to inst/data-raw/ccs_multi_dx_tool_2013.csv
diff --git a/data-raw/ccs_multi_dx_tool_2015.csv b/inst/data-raw/ccs_multi_dx_tool_2015.csv
similarity index 100%
rename from data-raw/ccs_multi_dx_tool_2015.csv
rename to inst/data-raw/ccs_multi_dx_tool_2015.csv
diff --git a/data-raw/ccs_multi_pr_tool_2014.csv b/inst/data-raw/ccs_multi_pr_tool_2014.csv
similarity index 100%
rename from data-raw/ccs_multi_pr_tool_2014.csv
rename to inst/data-raw/ccs_multi_pr_tool_2014.csv
diff --git a/data-raw/comformat2012-2013.txt b/inst/data-raw/comformat2012-2013.txt
similarity index 100%
rename from data-raw/comformat2012-2013.txt
rename to inst/data-raw/comformat2012-2013.txt
diff --git a/data-raw/comoanaly2012-2013.txt b/inst/data-raw/comoanaly2012-2013.txt
similarity index 100%
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diff --git a/data-raw/icd_hcc_rawdata/labels/2007_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2007_labels.txt
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diff --git a/data-raw/icd_hcc_rawdata/labels/2016_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2016_labels.txt
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diff --git a/data-raw/icd_hcc_rawdata/labels/2017_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2017_labels.txt
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diff --git a/data-raw/icd_hcc_rawdata/labels/2018_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2018_labels.txt
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diff --git a/data-raw/icd_hcc_rawdata/labels/2019_labels.txt b/inst/data-raw/icd_hcc_rawdata/labels/2019_labels.txt
old mode 100755
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rename to inst/data-raw/icd_hcc_rawdata/labels/2019_labels.txt
diff --git a/data-raw/ver2016_ahrq-comformat_icd10cm_2016.txt b/inst/data-raw/ver2016_ahrq-comformat_icd10cm_2016.txt
similarity index 100%
rename from data-raw/ver2016_ahrq-comformat_icd10cm_2016.txt
rename to inst/data-raw/ver2016_ahrq-comformat_icd10cm_2016.txt

From bc6fdcd8c842cf309cf33bfa5eae7796e70b29bc Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:48:14 -0500
Subject: [PATCH 24/51] attempt to fix "non-portable flag(s)" error on 3.6.2
 travis build

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 87e34ffb..4ffd72a4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -85,7 +85,7 @@ env:
     - _R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
     - _R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
     # some of the following are ignored if --as-cran is set
-    - _R_CHECK_COMPILATION_FLAGS_=FALSE
+    - _R_CHECK_COMPILATION_FLAGS_=TRUE
     - _R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option"
     # the following are to simulate cran, and
     # help debugging if we didn't use --as-cran

From 6a243e85f5387da831fc83799754180c466ba540 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Fri, 13 Mar 2020 01:49:17 -0400
Subject: [PATCH 25/51] updated URL
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

CIM-10-FR adds U071: Maladie à coronavirus 2019 [COVID-19]
---
 R/cim-10-fr.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cim-10-fr.R b/R/cim-10-fr.R
index 5cf4eefa..559ee340 100644
--- a/R/cim-10-fr.R
+++ b/R/cim-10-fr.R
@@ -8,7 +8,7 @@
       "https://www.atih.sante.fr",
       "plateformes-de-transmission-et-logiciels",
       "logiciels-espace-de-telechargement",
-      "telecharger/gratuit/12713/456"
+      "telecharger/gratuit/13332/456"
     ),
     file_name = "LIBCIM10MULTI.TXT",
     dl_msg = "Working on ICD-10-FR (CIM-10-FR)",

From ccd8d055b5702841fa0c8eedb40f5d11162243d6 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Fri, 13 Mar 2020 02:36:45 -0400
Subject: [PATCH 26/51] fix typo

---
 R/util-file.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/util-file.R b/R/util-file.R
index 8d327e8c..979513ed 100644
--- a/R/util-file.R
+++ b/R/util-file.R
@@ -121,7 +121,7 @@
 #' @param url URL of a zip file
 #' @param file_name file name of the resource within the zip file
 #' @param save_path file path to save the first file from the zip
-#' @param insecure Logical value, wil disable certificate check which fails on
+#' @param insecure Logical value, will disable certificate check which fails on
 #'   some platforms for some ICD data from CDC and CMS, probably because of TLS
 #'   version or certificate key length issues. Default is \code{TRUE}.
 #' @param ... additional arguments passed to \code{utils::download.file}

From b77f5a32e4f6dcf8bc342ca7ddef719183ad8e23 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Fri, 13 Mar 2020 02:41:23 -0400
Subject: [PATCH 27/51] revert _R_CHECK_COMPILATION_FLAGS_=TRUE change

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 4ffd72a4..87e34ffb 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -85,7 +85,7 @@ env:
     - _R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
     - _R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
     # some of the following are ignored if --as-cran is set
-    - _R_CHECK_COMPILATION_FLAGS_=TRUE
+    - _R_CHECK_COMPILATION_FLAGS_=FALSE
     - _R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option"
     # the following are to simulate cran, and
     # help debugging if we didn't use --as-cran

From 5be56320deb6fae83341b59f96e5885ca95fedd8 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:44:33 -0500
Subject: [PATCH 28/51] use httr::content to properly handle UTF-8
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The call `.dl_icd10who_json(2008, "fr", "JsonGetRootConcepts?useHtml=false")` was returning malformed text that had not been reencoded properly.  For example "Autres infections intestinales bactériennes".
---
 R/who.R | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/R/who.R b/R/who.R
index 34117cb9..68d39476 100644
--- a/R/who.R
+++ b/R/who.R
@@ -70,8 +70,7 @@
       )
     }
   } # end 400+
-  json_data <- rawToChar(http_response$content)
-  jsonlite::fromJSON(json_data)
+  httr::content(http_response, simplifyDataFrame=TRUE)
 }
 
 #' Use WHO API to discover chapters
@@ -91,7 +90,7 @@
 }
 
 #' Get the children of a concept (ICD-10 chapter, code or range)
-#' @param concept_id NULl for root, concept string for any leaf or intermediate.
+#' @param concept_id NULL for root, concept string for any leaf or intermediate.
 #' @examples
 #' .dl_icd10who_children("XXII")
 #' .dl_icd10who_children("U84")

From eadddc2403653d9fd5e02608755c399f8a4ab2e6 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:12 -0500
Subject: [PATCH 29/51] remove stringsAsFactors argument

stringsAsFactors is being deprecated generally.  The code here is causing test-score.R#333 to fail on R-devel because the id column is not a factor.  See https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/
---
 R/score.R                   | 22 ++---------
 tests/testthat/test-score.R | 77 +------------------------------------
 2 files changed, 6 insertions(+), 93 deletions(-)

diff --git a/R/score.R b/R/score.R
index a4c1cc7e..9fbf2ab1 100644
--- a/R/score.R
+++ b/R/score.R
@@ -24,11 +24,6 @@
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
-#' @param stringsAsFactors single logical, passed on when constructing
-#'   data.frame if \code{return_df} is \code{TRUE}. If the input data frame
-#'   \code{x} has a factor for the \code{visit_name}, this is not changed, but a
-#'   non-factor \code{visit_name} may be converted or not converted according to
-#'   your system default or this setting.
 #' @param ... further arguments to pass on to \code{icd9_comorbid_quan_deyo},
 #'   e.g. \code{name}
 #' @examples
@@ -46,7 +41,6 @@
 charlson <- function(x, visit_name = NULL,
                      scoring_system = c("original", "charlson", "quan"),
                      return_df = FALSE,
-                     stringsAsFactors = getOption("stringsAsFactors"), # nolint
                      ...) {
   UseMethod("charlson")
 }
@@ -60,7 +54,6 @@ charlson.data.frame <- function(x,
                                 visit_name = NULL,
                                 scoring_system = c("original", "charlson", "quan"),
                                 return_df = FALSE,
-                                stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                 ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
@@ -68,7 +61,6 @@ charlson.data.frame <- function(x,
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
-  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   res <- charlson_from_comorbid(
     comorbid_quan_deyo(x,
@@ -84,9 +76,8 @@ charlson.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("Charlson" = unname(res)),
-    stringsAsFactors = stringsAsFactors
-  ) # nolint
+    data.frame("Charlson" = unname(res))
+  )
   names(out)[1] <- visit_name
   out
 }
@@ -301,7 +292,6 @@ count_codes_wide <- function(x,
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
-#' @template stringsAsFactors
 #' @template dotdotdot
 #' @examples
 #' mydf <- data.frame(
@@ -325,7 +315,6 @@ count_codes_wide <- function(x,
 van_walraven <- function(x,
                          visit_name = NULL,
                          return_df = FALSE,
-                         stringsAsFactors = getOption("stringsAsFactors"), # nolint
                          ...) {
   UseMethod("van_walraven")
 }
@@ -336,13 +325,11 @@ van_walraven <- function(x,
 van_walraven.data.frame <- function(x,
                                     visit_name = NULL,
                                     return_df = FALSE,
-                                    stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                     ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
-  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   tmp <- icd9_comorbid_quan_elix(x,
     visit_name,
@@ -357,9 +344,8 @@ van_walraven.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("vanWalraven" = unname(res)),
-    stringsAsFactors = stringsAsFactors
-  ) # nolint
+    data.frame("vanWalraven" = unname(res))
+  )
   names(out)[1] <- visit_name
   out
 }
diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index c00e093a..645c8113 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -48,8 +48,7 @@ test_that("only matrix or data.frame accepted", {
 test_that("Charlson score", {
   mydf <- data.frame(
     visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042"),
-    stringsAsFactors = TRUE
+    icd9 = c("441", "412.93", "042")
   )
   expect_equal(
     charlson_from_comorbid(
@@ -64,7 +63,6 @@ test_that("Charlson score", {
   expect_equivalent(
     charlson(mydf,
       return_df = TRUE,
-      stringsAsFactors = TRUE,
       short_code = FALSE
     ),
     structure(list(
@@ -79,77 +77,6 @@ test_that("Charlson score", {
     class = "data.frame"
     )
   )
-  mydff <- data.frame(
-    visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042"),
-    stringsAsFactors = FALSE
-  )
-  expect_identical(
-    charlson(mydff,
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      visit_id = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("visit_id", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  expect_identical(
-    charlson(mydff,
-      return_df = TRUE,
-      stringsAsFactors = TRUE,
-      short_code = FALSE
-    ),
-    structure(list(
-      visit_id = factor(c("a", "b", "c")),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("visit_id", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  mydfff <- mydff
-  names(mydfff)[1] <- "v"
-  expect_equivalent(
-    charlson(mydfff,
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      v = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("v", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  mydffff <- cbind(mydfff, data.frame(v2 = mydfff$v, stringsAsFactors = FALSE))
-  mydffff$v <- NULL
-  expect_identical(get_icd_name(mydffff, NULL), "icd9")
-  expect_equivalent(
-    charlson(mydffff,
-      visit_name = "v2",
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      v2 = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("v2", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
 })
 
 test_that("Charlson - errors?", {
@@ -308,7 +235,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comodbidity index and score", {
+test_that("van_walraven comorbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =

From 03dbbf415bfd9410a69b2bfdd0632136d0d3d84b Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:44 -0500
Subject: [PATCH 30/51] export categorize_simple

On r-devel the check for this example is failing with "could not find function "categorize_simple""
---
 R/categorize.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/categorize.R b/R/categorize.R
index 4df9f6da..08f4eb59 100644
--- a/R/categorize.R
+++ b/R/categorize.R
@@ -35,6 +35,7 @@
 #' u$icd10 <- decimal_to_short(u$icd10)
 #' j <- icd:::categorize_simple(u, m, id_name = "case", code_name = "icd10")
 #' @keywords internal
+#' @export
 categorize_simple <- function(x,
                               map,
                               id_name,

From a11f8cd67bea32da450e67129aa87f7c6210f8bf Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:51 -0500
Subject: [PATCH 31/51] Update NAMESPACE

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index f8062774..9db92ca6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -161,6 +161,7 @@ export(as.icd_long_data)
 export(as.icd_short_diag)
 export(as.icd_wide_data)
 export(as.short_diag)
+export(categorize_simple)
 export(chapters_to_map)
 export(charlson)
 export(charlson_from_comorbid)

From 7ac94512fbc176ad1971d2b1158713e6929f6edd Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 22:17:30 -0500
Subject: [PATCH 32/51] add R_REMOTES_STANDALONE=true to fix appveyor curl
 error

See https://github.com/r-lib/remotes#standalone-mode and https://github.com/krlmlr/r-appveyor/issues/135
---
 appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/appveyor.yml b/appveyor.yml
index 1349c12e..d9e2e1e2 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -36,6 +36,7 @@ build_script:
 
 environment:
   # APPVEYOR_CACHE_SKIP_RESTORE: true
+  R_REMOTES_STANDALONE: true
   WARNINGS_ARE_ERRORS: 1
   _R_CHECK_EXIT_ON_FIRST_ERROR_: true
   USE_RTOOLS: true

From 2bbdf54c48ba11440c524b79561bed156b7299f5 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 22:44:15 -0500
Subject: [PATCH 33/51] revert stringsToFactor change

---
 R/score.R                   | 22 +++++++++--
 tests/testthat/test-score.R | 77 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 93 insertions(+), 6 deletions(-)

diff --git a/R/score.R b/R/score.R
index 9fbf2ab1..a4c1cc7e 100644
--- a/R/score.R
+++ b/R/score.R
@@ -24,6 +24,11 @@
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
+#' @param stringsAsFactors single logical, passed on when constructing
+#'   data.frame if \code{return_df} is \code{TRUE}. If the input data frame
+#'   \code{x} has a factor for the \code{visit_name}, this is not changed, but a
+#'   non-factor \code{visit_name} may be converted or not converted according to
+#'   your system default or this setting.
 #' @param ... further arguments to pass on to \code{icd9_comorbid_quan_deyo},
 #'   e.g. \code{name}
 #' @examples
@@ -41,6 +46,7 @@
 charlson <- function(x, visit_name = NULL,
                      scoring_system = c("original", "charlson", "quan"),
                      return_df = FALSE,
+                     stringsAsFactors = getOption("stringsAsFactors"), # nolint
                      ...) {
   UseMethod("charlson")
 }
@@ -54,6 +60,7 @@ charlson.data.frame <- function(x,
                                 visit_name = NULL,
                                 scoring_system = c("original", "charlson", "quan"),
                                 return_df = FALSE,
+                                stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                 ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
@@ -61,6 +68,7 @@ charlson.data.frame <- function(x,
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
+  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   res <- charlson_from_comorbid(
     comorbid_quan_deyo(x,
@@ -76,8 +84,9 @@ charlson.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("Charlson" = unname(res))
-  )
+    data.frame("Charlson" = unname(res)),
+    stringsAsFactors = stringsAsFactors
+  ) # nolint
   names(out)[1] <- visit_name
   out
 }
@@ -292,6 +301,7 @@ count_codes_wide <- function(x,
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
+#' @template stringsAsFactors
 #' @template dotdotdot
 #' @examples
 #' mydf <- data.frame(
@@ -315,6 +325,7 @@ count_codes_wide <- function(x,
 van_walraven <- function(x,
                          visit_name = NULL,
                          return_df = FALSE,
+                         stringsAsFactors = getOption("stringsAsFactors"), # nolint
                          ...) {
   UseMethod("van_walraven")
 }
@@ -325,11 +336,13 @@ van_walraven <- function(x,
 van_walraven.data.frame <- function(x,
                                     visit_name = NULL,
                                     return_df = FALSE,
+                                    stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                     ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
+  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   tmp <- icd9_comorbid_quan_elix(x,
     visit_name,
@@ -344,8 +357,9 @@ van_walraven.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("vanWalraven" = unname(res))
-  )
+    data.frame("vanWalraven" = unname(res)),
+    stringsAsFactors = stringsAsFactors
+  ) # nolint
   names(out)[1] <- visit_name
   out
 }
diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index 645c8113..c00e093a 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -48,7 +48,8 @@ test_that("only matrix or data.frame accepted", {
 test_that("Charlson score", {
   mydf <- data.frame(
     visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042")
+    icd9 = c("441", "412.93", "042"),
+    stringsAsFactors = TRUE
   )
   expect_equal(
     charlson_from_comorbid(
@@ -63,6 +64,7 @@ test_that("Charlson score", {
   expect_equivalent(
     charlson(mydf,
       return_df = TRUE,
+      stringsAsFactors = TRUE,
       short_code = FALSE
     ),
     structure(list(
@@ -77,6 +79,77 @@ test_that("Charlson score", {
     class = "data.frame"
     )
   )
+  mydff <- data.frame(
+    visit_id = c("a", "b", "c"),
+    icd9 = c("441", "412.93", "042"),
+    stringsAsFactors = FALSE
+  )
+  expect_identical(
+    charlson(mydff,
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      visit_id = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("visit_id", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  expect_identical(
+    charlson(mydff,
+      return_df = TRUE,
+      stringsAsFactors = TRUE,
+      short_code = FALSE
+    ),
+    structure(list(
+      visit_id = factor(c("a", "b", "c")),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("visit_id", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  mydfff <- mydff
+  names(mydfff)[1] <- "v"
+  expect_equivalent(
+    charlson(mydfff,
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      v = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("v", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  mydffff <- cbind(mydfff, data.frame(v2 = mydfff$v, stringsAsFactors = FALSE))
+  mydffff$v <- NULL
+  expect_identical(get_icd_name(mydffff, NULL), "icd9")
+  expect_equivalent(
+    charlson(mydffff,
+      visit_name = "v2",
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      v2 = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("v2", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
 })
 
 test_that("Charlson - errors?", {
@@ -235,7 +308,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comorbidity index and score", {
+test_that("van_walraven comodbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =

From cb3b34854e1799e133e4b452bbf179895ec9f8e2 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:13:51 -0500
Subject: [PATCH 34/51] fix typos

---
 tests/testthat/test-score.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index c00e093a..cd9d32a7 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -308,7 +308,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comodbidity index and score", {
+test_that("van_walraven comorbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =
@@ -350,7 +350,7 @@ test_that("van_walraven comodbidity index and score", {
   )
 })
 
-test_that("github issue #64 - quan revised charleson scores", {
+test_that("github issue #64 - quan revised charlson scores", {
   mydf <- data.frame(visit_id = "a", icd9 = "250.0")
   comorbids <- comorbid_quan_deyo(mydf, short_code = FALSE, return_df = TRUE)
 

From 24afec4317a2530263f7c9ab8dbf3c5cd65ca285 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:15:41 -0500
Subject: [PATCH 35/51] move data-raw to inst directory

---
 {data-raw => inst/data-raw}/.gitignore                            | 0
 {data-raw => inst/data-raw}/ICD10_Charlson.sas                    | 0
 {data-raw => inst/data-raw}/ICD10_Elixhauser.sas                  | 0
 {data-raw => inst/data-raw}/ICD9_E_Charlson.sas                   | 0
 {data-raw => inst/data-raw}/ICD9_E_Elixhauser.sas                 | 0
 {data-raw => inst/data-raw}/X.dxref.2015.csv                      | 0
 {data-raw => inst/data-raw}/ccs_multi_dx_tool_2013.csv            | 0
 {data-raw => inst/data-raw}/ccs_multi_dx_tool_2015.csv            | 0
 {data-raw => inst/data-raw}/ccs_multi_pr_tool_2014.csv            | 0
 {data-raw => inst/data-raw}/comformat2012-2013.txt                | 0
 {data-raw => inst/data-raw}/comoanaly2012-2013.txt                | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2008_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2009_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2010_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2011_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2012_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2013_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2014_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2015_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2016_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2017_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/hierarchy/2018_hierarchy.txt        | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2016_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2017_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2018_icd10hcc.txt             | 0
 .../data-raw}/icd_hcc_rawdata/icd10/2019_icd10hcc.txt             | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2007_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2008_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2009_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2010_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2011_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2012_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2013_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2014_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2015_icd9hcc.txt | 0
 {data-raw => inst/data-raw}/icd_hcc_rawdata/icd9/2016_icd9hcc.txt | 0
 .../data-raw}/icd_hcc_rawdata/labels/2007_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2008_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2009_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2010_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2011_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2012_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2013_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2014_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2015_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2016_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2017_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2018_labels.txt              | 0
 .../data-raw}/icd_hcc_rawdata/labels/2019_labels.txt              | 0
 .../data-raw}/ver2016_ahrq-comformat_icd10cm_2016.txt             | 0
 51 files changed, 0 insertions(+), 0 deletions(-)
 rename {data-raw => inst/data-raw}/.gitignore (100%)
 rename {data-raw => inst/data-raw}/ICD10_Charlson.sas (100%)
 rename {data-raw => inst/data-raw}/ICD10_Elixhauser.sas (100%)
 rename {data-raw => inst/data-raw}/ICD9_E_Charlson.sas (100%)
 rename {data-raw => inst/data-raw}/ICD9_E_Elixhauser.sas (100%)
 rename {data-raw => inst/data-raw}/X.dxref.2015.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_dx_tool_2013.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_dx_tool_2015.csv (100%)
 rename {data-raw => inst/data-raw}/ccs_multi_pr_tool_2014.csv (100%)
 rename {data-raw => inst/data-raw}/comformat2012-2013.txt (100%)
 rename {data-raw => inst/data-raw}/comoanaly2012-2013.txt (100%)
 rename {data-raw => inst/data-raw}/icd_hcc_rawdata/hierarchy/2007_hierarchy.txt (100%)
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From dd851699e13a34d90a5081c407d93aefa8083274 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:48:14 -0500
Subject: [PATCH 36/51] attempt to fix "non-portable flag(s)" error on 3.6.2
 travis build

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 87e34ffb..4ffd72a4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -85,7 +85,7 @@ env:
     - _R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
     - _R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
     # some of the following are ignored if --as-cran is set
-    - _R_CHECK_COMPILATION_FLAGS_=FALSE
+    - _R_CHECK_COMPILATION_FLAGS_=TRUE
     - _R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option"
     # the following are to simulate cran, and
     # help debugging if we didn't use --as-cran

From 8461d8dc182a3517233779bad3c036cef24d333e Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Fri, 13 Mar 2020 01:49:17 -0400
Subject: [PATCH 37/51] updated URL
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

CIM-10-FR adds U071: Maladie à coronavirus 2019 [COVID-19]
---
 R/cim-10-fr.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/cim-10-fr.R b/R/cim-10-fr.R
index 5cf4eefa..559ee340 100644
--- a/R/cim-10-fr.R
+++ b/R/cim-10-fr.R
@@ -8,7 +8,7 @@
       "https://www.atih.sante.fr",
       "plateformes-de-transmission-et-logiciels",
       "logiciels-espace-de-telechargement",
-      "telecharger/gratuit/12713/456"
+      "telecharger/gratuit/13332/456"
     ),
     file_name = "LIBCIM10MULTI.TXT",
     dl_msg = "Working on ICD-10-FR (CIM-10-FR)",

From 44dbc61eb26b33cb06735e9324c09b0d0ea4ff8b Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 15:47:12 -0500
Subject: [PATCH 38/51] remove stringsAsFactors argument

stringsAsFactors is being deprecated generally.  The code here is causing test-score.R#333 to fail on R-devel because the id column is not a factor.  See https://developer.r-project.org/Blog/public/2020/02/16/stringsasfactors/
---
 R/score.R                   | 22 ++---------
 tests/testthat/test-score.R | 75 +------------------------------------
 2 files changed, 5 insertions(+), 92 deletions(-)

diff --git a/R/score.R b/R/score.R
index a4c1cc7e..9fbf2ab1 100644
--- a/R/score.R
+++ b/R/score.R
@@ -24,11 +24,6 @@
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
-#' @param stringsAsFactors single logical, passed on when constructing
-#'   data.frame if \code{return_df} is \code{TRUE}. If the input data frame
-#'   \code{x} has a factor for the \code{visit_name}, this is not changed, but a
-#'   non-factor \code{visit_name} may be converted or not converted according to
-#'   your system default or this setting.
 #' @param ... further arguments to pass on to \code{icd9_comorbid_quan_deyo},
 #'   e.g. \code{name}
 #' @examples
@@ -46,7 +41,6 @@
 charlson <- function(x, visit_name = NULL,
                      scoring_system = c("original", "charlson", "quan"),
                      return_df = FALSE,
-                     stringsAsFactors = getOption("stringsAsFactors"), # nolint
                      ...) {
   UseMethod("charlson")
 }
@@ -60,7 +54,6 @@ charlson.data.frame <- function(x,
                                 visit_name = NULL,
                                 scoring_system = c("original", "charlson", "quan"),
                                 return_df = FALSE,
-                                stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                 ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
@@ -68,7 +61,6 @@ charlson.data.frame <- function(x,
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
-  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   res <- charlson_from_comorbid(
     comorbid_quan_deyo(x,
@@ -84,9 +76,8 @@ charlson.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("Charlson" = unname(res)),
-    stringsAsFactors = stringsAsFactors
-  ) # nolint
+    data.frame("Charlson" = unname(res))
+  )
   names(out)[1] <- visit_name
   out
 }
@@ -301,7 +292,6 @@ count_codes_wide <- function(x,
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
-#' @template stringsAsFactors
 #' @template dotdotdot
 #' @examples
 #' mydf <- data.frame(
@@ -325,7 +315,6 @@ count_codes_wide <- function(x,
 van_walraven <- function(x,
                          visit_name = NULL,
                          return_df = FALSE,
-                         stringsAsFactors = getOption("stringsAsFactors"), # nolint
                          ...) {
   UseMethod("van_walraven")
 }
@@ -336,13 +325,11 @@ van_walraven <- function(x,
 van_walraven.data.frame <- function(x,
                                     visit_name = NULL,
                                     return_df = FALSE,
-                                    stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                     ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
-  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   tmp <- icd9_comorbid_quan_elix(x,
     visit_name,
@@ -357,9 +344,8 @@ van_walraven.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("vanWalraven" = unname(res)),
-    stringsAsFactors = stringsAsFactors
-  ) # nolint
+    data.frame("vanWalraven" = unname(res))
+  )
   names(out)[1] <- visit_name
   out
 }
diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index cd9d32a7..6ec50555 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -48,8 +48,7 @@ test_that("only matrix or data.frame accepted", {
 test_that("Charlson score", {
   mydf <- data.frame(
     visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042"),
-    stringsAsFactors = TRUE
+    icd9 = c("441", "412.93", "042")
   )
   expect_equal(
     charlson_from_comorbid(
@@ -64,7 +63,6 @@ test_that("Charlson score", {
   expect_equivalent(
     charlson(mydf,
       return_df = TRUE,
-      stringsAsFactors = TRUE,
       short_code = FALSE
     ),
     structure(list(
@@ -79,77 +77,6 @@ test_that("Charlson score", {
     class = "data.frame"
     )
   )
-  mydff <- data.frame(
-    visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042"),
-    stringsAsFactors = FALSE
-  )
-  expect_identical(
-    charlson(mydff,
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      visit_id = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("visit_id", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  expect_identical(
-    charlson(mydff,
-      return_df = TRUE,
-      stringsAsFactors = TRUE,
-      short_code = FALSE
-    ),
-    structure(list(
-      visit_id = factor(c("a", "b", "c")),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("visit_id", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  mydfff <- mydff
-  names(mydfff)[1] <- "v"
-  expect_equivalent(
-    charlson(mydfff,
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      v = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("v", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
-  mydffff <- cbind(mydfff, data.frame(v2 = mydfff$v, stringsAsFactors = FALSE))
-  mydffff$v <- NULL
-  expect_identical(get_icd_name(mydffff, NULL), "icd9")
-  expect_equivalent(
-    charlson(mydffff,
-      visit_name = "v2",
-      return_df = TRUE,
-      stringsAsFactors = FALSE,
-      short_code = FALSE
-    ),
-    structure(list(
-      v2 = c("a", "b", "c"),
-      Charlson = c(1, 1, 6)
-    ),
-    .Names = c("v2", "Charlson"),
-    row.names = c(NA, -3L),
-    class = "data.frame"
-    )
-  )
 })
 
 test_that("Charlson - errors?", {

From 494810e19181b9ca6c7e0ba9dd69311629b086ea Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 22:44:15 -0500
Subject: [PATCH 39/51] revert stringsToFactor change

---
 R/score.R                   | 22 +++++++++--
 tests/testthat/test-score.R | 77 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 93 insertions(+), 6 deletions(-)

diff --git a/R/score.R b/R/score.R
index 9fbf2ab1..a4c1cc7e 100644
--- a/R/score.R
+++ b/R/score.R
@@ -24,6 +24,11 @@
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
+#' @param stringsAsFactors single logical, passed on when constructing
+#'   data.frame if \code{return_df} is \code{TRUE}. If the input data frame
+#'   \code{x} has a factor for the \code{visit_name}, this is not changed, but a
+#'   non-factor \code{visit_name} may be converted or not converted according to
+#'   your system default or this setting.
 #' @param ... further arguments to pass on to \code{icd9_comorbid_quan_deyo},
 #'   e.g. \code{name}
 #' @examples
@@ -41,6 +46,7 @@
 charlson <- function(x, visit_name = NULL,
                      scoring_system = c("original", "charlson", "quan"),
                      return_df = FALSE,
+                     stringsAsFactors = getOption("stringsAsFactors"), # nolint
                      ...) {
   UseMethod("charlson")
 }
@@ -54,6 +60,7 @@ charlson.data.frame <- function(x,
                                 visit_name = NULL,
                                 scoring_system = c("original", "charlson", "quan"),
                                 return_df = FALSE,
+                                stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                 ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
@@ -61,6 +68,7 @@ charlson.data.frame <- function(x,
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
+  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   res <- charlson_from_comorbid(
     comorbid_quan_deyo(x,
@@ -76,8 +84,9 @@ charlson.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("Charlson" = unname(res))
-  )
+    data.frame("Charlson" = unname(res)),
+    stringsAsFactors = stringsAsFactors
+  ) # nolint
   names(out)[1] <- visit_name
   out
 }
@@ -292,6 +301,7 @@ count_codes_wide <- function(x,
 #'   frame will be returned, with the first column named as in input data frame
 #'   (i.e., \code{visit_name}), containing all the visits, and the second column
 #'   containing the Charlson Comorbidity Index.
+#' @template stringsAsFactors
 #' @template dotdotdot
 #' @examples
 #' mydf <- data.frame(
@@ -315,6 +325,7 @@ count_codes_wide <- function(x,
 van_walraven <- function(x,
                          visit_name = NULL,
                          return_df = FALSE,
+                         stringsAsFactors = getOption("stringsAsFactors"), # nolint
                          ...) {
   UseMethod("van_walraven")
 }
@@ -325,11 +336,13 @@ van_walraven <- function(x,
 van_walraven.data.frame <- function(x,
                                     visit_name = NULL,
                                     return_df = FALSE,
+                                    stringsAsFactors = getOption("stringsAsFactors"), # nolint
                                     ...) {
   stopifnot(is.data.frame(x), ncol(x) >= 2, !is.null(colnames(x)))
   stopifnot(is.null(visit_name) ||
     (is.character(visit_name) && length(visit_name) == 1L))
   assert_flag(return_df)
+  assert_flag(stringsAsFactors) # nolint
   visit_name <- get_visit_name(x, visit_name)
   tmp <- icd9_comorbid_quan_elix(x,
     visit_name,
@@ -344,8 +357,9 @@ van_walraven.data.frame <- function(x,
     return(res)
   }
   out <- cbind(names(res),
-    data.frame("vanWalraven" = unname(res))
-  )
+    data.frame("vanWalraven" = unname(res)),
+    stringsAsFactors = stringsAsFactors
+  ) # nolint
   names(out)[1] <- visit_name
   out
 }
diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index 6ec50555..fa3cbdd3 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -48,7 +48,8 @@ test_that("only matrix or data.frame accepted", {
 test_that("Charlson score", {
   mydf <- data.frame(
     visit_id = c("a", "b", "c"),
-    icd9 = c("441", "412.93", "042")
+    icd9 = c("441", "412.93", "042"),
+    stringsAsFactors = TRUE
   )
   expect_equal(
     charlson_from_comorbid(
@@ -63,6 +64,7 @@ test_that("Charlson score", {
   expect_equivalent(
     charlson(mydf,
       return_df = TRUE,
+      stringsAsFactors = TRUE,
       short_code = FALSE
     ),
     structure(list(
@@ -77,6 +79,77 @@ test_that("Charlson score", {
     class = "data.frame"
     )
   )
+  mydff <- data.frame(
+    visit_id = c("a", "b", "c"),
+    icd9 = c("441", "412.93", "042"),
+    stringsAsFactors = FALSE
+  )
+  expect_identical(
+    charlson(mydff,
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      visit_id = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("visit_id", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  expect_identical(
+    charlson(mydff,
+      return_df = TRUE,
+      stringsAsFactors = TRUE,
+      short_code = FALSE
+    ),
+    structure(list(
+      visit_id = factor(c("a", "b", "c")),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("visit_id", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  mydfff <- mydff
+  names(mydfff)[1] <- "v"
+  expect_equivalent(
+    charlson(mydfff,
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      v = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("v", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
+  mydffff <- cbind(mydfff, data.frame(v2 = mydfff$v, stringsAsFactors = FALSE))
+  mydffff$v <- NULL
+  expect_identical(get_icd_name(mydffff, NULL), "icd9")
+  expect_equivalent(
+    charlson(mydffff,
+      visit_name = "v2",
+      return_df = TRUE,
+      stringsAsFactors = FALSE,
+      short_code = FALSE
+    ),
+    structure(list(
+      v2 = c("a", "b", "c"),
+      Charlson = c(1, 1, 6)
+    ),
+    .Names = c("v2", "Charlson"),
+    row.names = c(NA, -3L),
+    class = "data.frame"
+    )
+  )
 })
 
 test_that("Charlson - errors?", {
@@ -235,7 +308,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comorbidity index and score", {
+test_that("van_walraven comodbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =

From 192bfbc923c8b781b615c1516e3600c81018bfff Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 1 Mar 2020 23:13:51 -0500
Subject: [PATCH 40/51] fix typos

---
 tests/testthat/test-score.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-score.R b/tests/testthat/test-score.R
index fa3cbdd3..cd9d32a7 100644
--- a/tests/testthat/test-score.R
+++ b/tests/testthat/test-score.R
@@ -308,7 +308,7 @@ test_that("van_walraven_from_comorbid score calculation", {
   )
 })
 
-test_that("van_walraven comodbidity index and score", {
+test_that("van_walraven comorbidity index and score", {
   mydf <- data.frame(
     id = factor(c(rep(1, 20), rep(2, 20), rep(3, 18))),
     value =

From b33b1a178de21bd6843ef37b2cb7100862ef4192 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Fri, 13 Mar 2020 02:36:45 -0400
Subject: [PATCH 41/51] fix typo

---
 R/util-file.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/util-file.R b/R/util-file.R
index 8d327e8c..979513ed 100644
--- a/R/util-file.R
+++ b/R/util-file.R
@@ -121,7 +121,7 @@
 #' @param url URL of a zip file
 #' @param file_name file name of the resource within the zip file
 #' @param save_path file path to save the first file from the zip
-#' @param insecure Logical value, wil disable certificate check which fails on
+#' @param insecure Logical value, will disable certificate check which fails on
 #'   some platforms for some ICD data from CDC and CMS, probably because of TLS
 #'   version or certificate key length issues. Default is \code{TRUE}.
 #' @param ... additional arguments passed to \code{utils::download.file}

From 12a77bef1bfd3e1d43a215be06bbfa9a82ac6ba0 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Fri, 13 Mar 2020 02:41:23 -0400
Subject: [PATCH 42/51] revert _R_CHECK_COMPILATION_FLAGS_=TRUE change

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 4ffd72a4..87e34ffb 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -85,7 +85,7 @@ env:
     - _R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
     - _R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
     # some of the following are ignored if --as-cran is set
-    - _R_CHECK_COMPILATION_FLAGS_=TRUE
+    - _R_CHECK_COMPILATION_FLAGS_=FALSE
     - _R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option"
     # the following are to simulate cran, and
     # help debugging if we didn't use --as-cran

From 17e6f9b4001b38846072089f39455c96f9e718a5 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sat, 28 Mar 2020 17:25:28 -0400
Subject: [PATCH 43/51] add qpdf

avoid "WARNING 'qpdf' is needed for checks on size reduction of PDFs"
---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 87e34ffb..2b317094 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,6 +25,8 @@ addons:
   apt:
     packages:
       - valgrind
+      # avoid "WARNING 'qpdf' is needed for checks on size reduction of PDFs"
+      - qpdf
       #- r-cran-tinytex
 
 #r_packages:

From c7045eda2a7b22f6983537b576bb8f7dcf74ab2e Mon Sep 17 00:00:00 2001
From: Jack Wasey <jack@jackwasey.com>
Date: Wed, 18 Mar 2020 10:52:59 -0400
Subject: [PATCH 44/51] try biarch true for remote builds/tests, e.g. rhub;
 redocumented with new roxyen

travis and build tweaks

add sets of environment variable definitions for bash and makevars, and enable in travis

add R_REMOTES_STANDALONE=true to fix appveyor curl error

See https://github.com/r-lib/remotes#standalone-mode and https://github.com/krlmlr/r-appveyor/issues/135

add qpdf

avoid "WARNING 'qpdf' is needed for checks on size reduction of PDFs"
---
 .Rbuildignore              |   1 +
 .travis.yml                | 153 +++++++++++++++++--------------------
 DESCRIPTION                |   3 +-
 codemeta.json              |   9 ++-
 configure                  | 148 +++++++++++++++++++++++++++--------
 configure.ac               |  74 ++++++++++++------
 man/get_icd10cm2019_pc.Rd  |   6 +-
 man/get_icd9cm2014_leaf.Rd |   6 +-
 man/icd9_map_ahrq.Rd       |   4 +-
 man/icd9_map_elix.Rd       |   4 +-
 man/icd9_map_hcc.Rd        |   6 +-
 man/icd9_map_quan_deyo.Rd  |   4 +-
 man/icd9_map_quan_elix.Rd  |   4 +-
 man/icd9_map_single_ccs.Rd |   4 +-
 man/names_elix.Rd          |   6 +-
 man/poa_choices.Rd         |   4 +-
 src/Makevars.in            |  16 +---
 tools/env/cran             |  13 ++++
 tools/env/full             |  23 ++++++
 tools/env/jit              |  46 +++++++++++
 tools/env/plus             |  44 +++++++++++
 tools/env/quick            |  33 ++++++++
 tools/env/rhub             |   3 +
 tools/env/rhub-san         |  21 +++++
 tools/env/travis-global    |  37 +++++++++
 tools/mk/strip.mk          |  12 +++
 tools/mk/travis-debug.mk   |   8 ++
 tools/mk/travis-macos.mk   |   9 +++
 tools/mk/travis-nowarn.mk  |   8 ++
 29 files changed, 535 insertions(+), 174 deletions(-)
 create mode 100755 tools/env/cran
 create mode 100755 tools/env/full
 create mode 100755 tools/env/jit
 create mode 100755 tools/env/plus
 create mode 100755 tools/env/quick
 create mode 100644 tools/env/rhub
 create mode 100644 tools/env/rhub-san
 create mode 100644 tools/env/travis-global
 create mode 100644 tools/mk/strip.mk
 create mode 100644 tools/mk/travis-debug.mk
 create mode 100644 tools/mk/travis-macos.mk
 create mode 100644 tools/mk/travis-nowarn.mk

diff --git a/.Rbuildignore b/.Rbuildignore
index 2c84616e..fd557918 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -32,6 +32,7 @@
 ^data-raw$
 ^doc$
 ^docs$
+^Dockerfile$
 ^icd.*\.out$
 ^icd\.Rcheck$
 ^icd_.*tar\.gz
diff --git a/.travis.yml b/.travis.yml
index 2b317094..bf26bee5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,7 +4,7 @@ language: r
 # https://docs.travis-ci.com/user/ci-environment/
 
 # for RcppEigen to compile, (but disable if brew gcc on mac to avoid conflict)
-# fortran: true # set explicitly in each stanza
+# fortran: true # set explicitly in each stanza? but not recognized by an "include" group.
 
 # may need this for clang:
 # export LD_LIBRARY_PATH=/usr/local/clang/lib:$LD_LIBRARY_PATH
@@ -16,7 +16,10 @@ language: r
 #
 # https://docs.travis-ci.com/user/languages/cpp/
 
-sudo: false
+# assert the defaults for os and dist - will add macos and bionic etc. later
+os: linux
+dist: xenial
+
 cache:
   - packages
   - ccache
@@ -24,9 +27,8 @@ cache:
 addons:
   apt:
     packages:
-      - valgrind
-      # avoid "WARNING 'qpdf' is needed for checks on size reduction of PDFs"
       - qpdf
+#      - valgrind # when I do do this (probably too slow for travis anyway, then just put the apt addon in the specific build)
       #- r-cran-tinytex
 
 #r_packages:
@@ -38,103 +40,60 @@ cran: https://cloud.r-project.org
 r_check_args: ""
 warnings_are_errors: true
 
-# try to speed up compilation time
 before_install:
+  # - set -o allexport; source tools/env/travis-global; set +o allexport;
   # May need to set the R library directory so R CMD check finds packages
   # installed by travis (automatically, and in my scripts) and by R itself
   # https://stackoverflow.com/questions/31879011/r-cant-find-packages-installed-by-travis
   # - mkdir -p "$HOME/R.icd.lib"
   # - echo R_LIBS=$HOME/R.icd.lib:/usr/lib/R/site-library/" > ~/.Renviron
   # - sudo chmod 2777 "$HOME/R.icd.lib"
-  #
-  # Work-around r-lib/remotes bug which prevents travis building.
-  # https://github.com/r-lib/devtools/issues/2020#issuecomment-481219296
-  - Rscript -e 'source("https://install-github.me/r-lib/remotes")'
-  # ready for Makevars
   - mkdir -p ~/.R ;
-  - echo 'CXXFLAGS=-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option' >> ~/.R/Makevars ;
-  - echo 'CXX11FLAGS=-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option' >> ~/.R/Makevars ;
-  - if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then
-      echo 'CFLAGS=-O0' >> ~/.R/Makevars ;
-      echo 'CXXFLAGS=-O0' >> ~/.R/Makevars ;
-      echo 'CXX11FLAGS=-O0' >> ~/.R/Makevars ;
-      fi
-  # ignore the stubs for the pre-built vignettes, as the latex environments on
-  # travis are heterogeneous!
+  - if [[ $TRAVIS_R_VERSION_STRING == devel ]]; then cat tools/mk/travis-debug.mk >> ~/.R/Makevars; fi;
+  # this is one of oldrel, release or devel per https://docs.travis-ci.com/user/languages/r#configuration-options
+  - cat tools/mk/travis-nowarn.mk >> ~/.R/Makevars
+  # ignore the stubs for the pre-built vignettes, as the latex environments on travis are heterogeneous!
   - echo '^vignettes\/.*-vignette\.Rnw$' >> .Rbuildignore
-  # Homebrew GCC currently version 8.3 from
+
   # https://github.com/Homebrew/homebrew-core/blob/master/Formula/gcc.rb
-  - if [[ "$(uname -s)" = 'Darwin' && x"$ICD_USE_XCODE_CLANG" != 'xtrue' ]]; then
-      brew upgrade gcc;
-      command -v g++-9 >/dev/null 2>&1 || brew install gcc && echo 'CC=gcc-9' >> ~/.R/Makevars && echo 'CXX=g++-9' >> ~/.R/Makevars && echo 'CXX11=g++-9' >> ~/.R/Makevars && Rscript -e 'install.packages("Rcpp", type = "source")';
+  # I think PKG_CXX etc only needed if Makevars in the package itself, not ~/.R/Makevars
+  # openblas may need brew linking. may be best NOT to overwrite gfortran?
+  - export HOMEBREW_NO_INSTALL_CLEANUP=1 && if [[ "$(uname -s)" = 'Darwin' ]] && [[ $ICD_USE_XCODE_CLANG != 'true' ]]; then
+      brew upgrade ;
+      brew install gcc ;
+      brew link --overwrite gcc ;
+      cat tools/mk/travis-macos.mk  >> ~/.R/Makevars ;
+      Rscript -e 'install.packages("Rcpp", type = "source")' ;
     fi
   - cat ~/.R/Makevars
   - cat .Rbuildignore
-  - Rscript -e '.libPaths()'
+  - Rscript -e '.libPaths(); getOption("repos")'
   - pwd
-  - ls -R
   # for the pre-built static vignette stubs to include the actual vignettes.
-  # Make sure travis latex option is not false for relevant builds.
-  # - Rscript -e 'if (!require("tinytex")) {quit(status=1)} else {tinytex::install_tinytex(); tinytex::tlmgr_install("pdfpages", "ae")}' || hash tlmgr 2>/dev/null && { tlmgr --usermode install pdfpages ae; }
+  # Make sure travis latex: true is set just for relevant builds. Official way to add latex packages is:
+  # before_install:
+  #   - tlmgr install index
+  # and/or? something like:
+  # - Rscript -e 'if (!require("tinytex", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)) {quit(status=1)} else {tinytex::install_tinytex(); tinytex::tlmgr_install("pdfpages", "ae")}' || hash tlmgr 2>/dev/null && { tlmgr --usermode install pdfpages ae; }
 
-env:
-  global:
-    - _R_CHECK_CRAN_INCOMING_=FALSE
-    - _R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
-    - _R_CHECK_FORCE_SUGGESTS_=FALSE
-    - _R_CHECK_USE_INSTALL_LOG_=TRUE
-    - _R_CHECK_LENGTH_1_CONDITION_="verbose,abort"
-    - _R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
-    - _R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
-    # some of the following are ignored if --as-cran is set
-    - _R_CHECK_COMPILATION_FLAGS_=FALSE
-    - _R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option"
-    # the following are to simulate cran, and
-    # help debugging if we didn't use --as-cran
-    - _R_CHECK_ALL_NON_ISO_C_=TRUE
-    - _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=TRUE
-    - _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
-    - _R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
-    - _R_CHECK_EXIT_ON_FIRST_ERROR_=FALSE
-    - _R_CHECK_NATIVE_ROUTINE_REGISTRATION_=TRUE
-    - _R_CHECK_NO_STOP_ON_TEST_ERROR_=TRUE
-    - _R_CHECK_RD_EXAMPLES_T_AND_F_=TRUE
-    - _R_CHECK_RD_LINE_WIDTHS_=true
-    - _R_CHECK_TESTS_NLINES_=0
-    - _R_CHECK_USE_INSTALL_LOG_=TRUE
-    - _R_CHECK_VIGNETTES_NLINES_=0
-    - _R_CHECK_PKG_SIZES_THRESHOLD_=50
-    - ICD_COVERAGE=false
-    - ICD_MINI_BENCH=false
-    - ICD_DATA_VERBOSE=true
-    - ICD_DATA_OFFLINE=true
-    - ICD_DATA_INTERACT=false
-    # 4 is the official travis suggestion, but the docker images only seem to
-    # have access to two cores/threads.
-    - OMP_NUM_THREADS=2
+#env: #  global: instead of defining here, source tools/env/travis-global
 
-matrix:
+jobs:
   fast_finish: true
   include:
   - r: devel
-    os: linux
-    dist: xenial
-    compiler:
-      - gcc
-      - clang
+    dist: bionic
+    # note that the default compilers are quite far behind, e.g. bionic is only gcc 7 by default. See:
+    # https://docs.travis-ci.com/user/languages/c/#choosing-compilers-to-test-against
+    compiler: gcc
     env:
       - ICD_MINI_BENCH=true
   - r: release
-    os: linux
-    compiler:
-      - gcc
-      - clang
-    dist: xenial
+    compiler: clang
+    dist: bionic
     env:
       - ICD_MINI_BENCH=true
-  # https://docs.travis-ci.com/user/languages/c/#gcc-on-macos
   - r: release
-    os: linux
     compiler: gcc
     latex: false
     r_build_args: --no-build-vignettes --no-manual --resave-data=no
@@ -144,48 +103,68 @@ matrix:
     - ICD_MINI_BENCH=false
     - ICD_TEST_SLOW=true
   - r: oldrel
-    os: linux
-    dist: trusty
+    compiler: gcc
     latex: false
     r_build_args: --no-build-vignettes --no-manual --resave-data=no
     r_check_args: --no-build-vignettes --no-vignettes --ignore-vignettes --no-codoc --no-manual
-  # MacOS:
+  # MacOS: https://docs.travis-ci.com/user/languages/c/#gcc-on-macos
   - r: release
     os: osx
     # xcode image is needed so things like _stdio.h are available to GCC.
-    osx_image: xcode10.1
+    osx_image: xcode10.3
 #    compiler: gcc # redundant: done by logic in before_intall
-    fortran: false
+    addons:
+      homebrew:
+        packages:
+          - checkbashisms
     env:
       - ICD_MINI_BENCH=true
   - r: devel
     os: osx
-    osx_image: xcode10.2
+    osx_image: xcode10.3
+    addons:
+      homebrew:
+        packages:
+          - checkbashisms
 #    compiler: gcc # redundant: done by logic in before_intall
-    fortran: false
   - r: devel
     os: osx
+    addons:
+      homebrew:
+        packages:
+          - checkbashisms
     # as of May 2019, default osx image is 9.4.1
     # https://docs.travis-ci.com/user/reference/osx#xcode-version
     # compiler: clang # redundant
-    fortran: true
     env: ICD_USE_XCODE_CLANG=true
   - r: release
     os: osx
+    addons:
+      homebrew:
+        packages:
+          - checkbashisms
     # compiler: clang # redundant
-    fortran: true
     latex: false
     r_build_args: --no-build-vignettes --no-manual --resave-data=no
     r_check_args: --no-build-vignettes --no-vignettes --ignore-vignettes --no-codoc --no-manual
     env:
     - ICD_USE_XCODE_CLANG=true
     - ICD_MINI_BENCH=true
+  - r: release
+    arch: arm64
+    r_build_args: --no-build-vignettes --no-manual --resave-data=no
+    r_check_args: --no-build-vignettes --no-vignettes --ignore-vignettes --no-codoc --no-manual
+    env:
+    - ICD_MINI_BENCH=true
+    - ICD_TEST_SLOW=true
   allow_failures:
   # allow any osx to fail for now: error prone tool chain
   - os: osx
+  - arch: arm64
+  - arch: ppc64le
+  - arch: s390x
   - r: oldrel
   - r: release
-    os: linux
     latex: false
     r_build_args: --no-build-vignettes --no-manual --resave-data=no
     r_check_args: --no-build-vignettes --no-vignettes --ignore-vignettes --no-codoc --no-manual
@@ -195,6 +174,10 @@ matrix:
     - ICD_TEST_SLOW=true
 
 before_script:
+# n.b., before_install bash exports are not preserved beyond each shell invocation.
+ - set -o allexport; source tools/env/travis-global; set +o allexport;
+ - set
+ - echo "$LD_LIBRARY_PATH"
  - if [ x"$ICD_TEST_SLOW" = x"true" ]; then
      Rscript -e 'source("tools/split-tests.R"); testthat_split();';
    fi
diff --git a/DESCRIPTION b/DESCRIPTION
index 2210a901..d77d9f06 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -71,6 +71,7 @@ LinkingTo:
     RcppEigen
 VignetteBuilder: 
     knitr
+Biarch: true
 Classification/ACM-2012: Social and professional topics~Medical
     records, Applied computing~Health care information systems, Applied
     computing~Health informatics, Applied computing~Bioinformatics
@@ -79,4 +80,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 LazyDataCompression: xz
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
diff --git a/codemeta.json b/codemeta.json
index 633c621c..baa2c8c8 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -14,10 +14,10 @@
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
-    "version": "3.6.0",
+    "version": "3.6.3",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 3.6.0 (2019-04-26)",
+  "runtimePlatform": "R version 3.6.3 (2020-02-29)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -275,7 +275,7 @@
       "sameAs": "https://CRAN.R-project.org/package=Rcpp"
     }
   ],
-  "releaseNotes": "https://github.com/jackwasey/icd/blob/master/NEWS.md",
+  "releaseNotes": "ssh://git@github.com/jackwasey/icd/blob/master/NEWS.md",
   "contIntegration": [
     "https://travis-ci.org/jackwasey/icd",
     "https://ci.appveyor.com/project/jackwasey/icd/branch/master",
@@ -285,5 +285,6 @@
     "https://www.tidyverse.org/lifecycle/#stable",
     "https://www.repostatus.org/#active"
   ],
-  "relatedLink": "https://CRAN.R-project.org/package=icd"
+  "relatedLink": "https://CRAN.R-project.org/package=icd",
+  "readme": "https://github.com/jackwasey/icd/blob/master/README.md"
 }
diff --git a/configure b/configure
index 8ae1309a..955943aa 100755
--- a/configure
+++ b/configure
@@ -9,7 +9,7 @@
 # This configure script is free software; the Free Software Foundation
 # gives unlimited permission to copy, distribute and modify it.
 #
-# Copyright (C) 2014 - 2019  Jack O. Wasey
+# Copyright (C) 2014 - 2020  Jack O. Wasey
 ## -------------------- ##
 ## M4sh Initialization. ##
 ## -------------------- ##
@@ -596,6 +596,7 @@ CPPFLAGS
 LDFLAGS
 CXXFLAGS
 CXX
+ICD_SHUTUP
 target_alias
 host_alias
 build_alias
@@ -635,15 +636,18 @@ PACKAGE_TARNAME
 PACKAGE_NAME
 PATH_SEPARATOR
 SHELL'
-ac_subst_files=''
+ac_subst_files='ICD_STRIP'
 ac_user_opts='
 enable_option_checking
+enable_icd_shutup
 enable_openmp
-enable_makevars
+enable_icd_makevars
+enable_icd_strip
 '
       ac_precious_vars='build_alias
 host_alias
 target_alias
+ICD_SHUTUP
 CXX
 CXXFLAGS
 LDFLAGS
@@ -1268,11 +1272,14 @@ Optional Features:
   --disable-option-checking  ignore unrecognized --enable/--with options
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
+  --enable-icd-shutup     Enable peaceful compilation on travis with yes or no
   --disable-openmp        do not use OpenMP
-  --enable-makevars       keep ~/.R/Makevars contents in binary for debugging
+  --enable-icd-makevars   keep ~/.R/Makevars contents in binary for debugging
                           (default is no)
+  --enable-icd-strip      Enable stripping of binary on Linux and MacOS
 
 Some influential environment variables:
+  ICD_SHUTUP  "If ICD_SHUTUP is defined
   CXX         C++ compiler command
   CXXFLAGS    C++ compiler flags
   LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
@@ -1354,7 +1361,7 @@ Copyright (C) 2012 Free Software Foundation, Inc.
 This configure script is free software; the Free Software Foundation
 gives unlimited permission to copy, distribute and modify it.
 
-Copyright (C) 2014 - 2019  Jack O. Wasey
+Copyright (C) 2014 - 2020  Jack O. Wasey
 _ACEOF
   exit
 fi
@@ -1805,6 +1812,7 @@ ac_config_files="$ac_config_files src/Makevars"
 
 
 
+
 : ${R_HOME=$(R RHOME)}
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking R_HOME already set" >&5
 $as_echo_n "checking R_HOME already set... " >&6; }
@@ -1863,6 +1871,25 @@ CFLAGS=`"${R_BIN}" CMD config CFLAGS`
 CPPFLAGS=`"${R_BIN}" CMD config CPPFLAGS`
 LIBS="${PKG_LIBS}"
 
+# try to shut up travis/r-hub builds with huge warning burden with default compiler settings (Eigen). Can't seem to do with MAKEFLAGS, or string of R CMD check --install-opts=.....
+
+
+# Check whether --enable-icd_shutup was given.
+if test "${enable_icd_shutup+set}" = set; then :
+  enableval=$enable_icd_shutup; { $as_echo "$as_me:${as_lineno-$LINENO}: icd shutup enabled, without arguments." >&5
+$as_echo "$as_me: icd shutup enabled, without arguments." >&6;}
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: icd shutup enabled, with arguments..." >&5
+$as_echo "$as_me: icd shutup enabled, with arguments..." >&6;}
+fi
+
+
+if test "x$enable_icd-shutup" = "xyes"; then :
+
+       CXX11FLAGS="${CXX11FLAGS} -w"
+
+fi
+
 # changes what R_OPENMP and rest of script does:
 ac_ext=cpp
 ac_cpp='$CXXCPP $CPPFLAGS'
@@ -1873,7 +1900,7 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 # https://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Generic-Compiler-Characteristics.html
 
-# this macro is borrowed from R-devel source, and included in the icd/tools/m4 directory
+# this macro is borrowed from R-devel source, and included in the icd /inst/m4 directory
 ac_ext=cpp
 ac_cpp='$CXXCPP $CPPFLAGS'
 ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -2458,9 +2485,9 @@ ac_pkg_openmp=no
 #  AC_MSG_RESULT([Do have OPENMP_CFLAGS from R_OPENMP])
 #fi
 if test -n "${OPENMP_CXXFLAGS}"; then
-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking OpenMP available, but does it work in a package" >&5
+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking OpenMP available, but does it work in a package" >&5
 $as_echo_n "checking OpenMP available, but does it work in a package... " >&6; }
-  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 #include <omp.h>
 int
@@ -2471,30 +2498,31 @@ main ()
   return 0;
 }
 _ACEOF
-  PKG_CFLAGS="${OPENMP_CFLAGS}" PKG_LIBS="${OPENMP_CFLAGS}" "$R_BIN" CMD SHLIB conftest.c 1>&5 2>&5 && "$R_BIN" --vanilla -q -e "dyn.load(paste('conftest',.Platform\$dynlib.ext,sep=''))" 1>&5 2>&5 && ac_pkg_openmp=yes
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: OpenMP available and working: ${ac_pkg_openmp}" >&5
+    PKG_CFLAGS="${OPENMP_CFLAGS}" PKG_LIBS="${OPENMP_CFLAGS}" "$R_BIN" CMD SHLIB conftest.c 1>&5 2>&5 && "$R_BIN" --vanilla -q -e "dyn.load(paste('conftest',.Platform\$dynlib.ext,sep=''))" 1>&5 2>&5 && ac_pkg_openmp=yes
+    { $as_echo "$as_me:${as_lineno-$LINENO}: result: OpenMP available and working: ${ac_pkg_openmp}" >&5
 $as_echo "OpenMP available and working: ${ac_pkg_openmp}" >&6; }
-else
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: R did not think OpenMP is available" >&5
+    else
+        { $as_echo "$as_me:${as_lineno-$LINENO}: result: R did not think OpenMP is available" >&5
 $as_echo "R did not think OpenMP is available" >&6; }
-fi
+        fi
 
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: icd thinks openmp compilation possible: ${ac_pkg_openmp}" >&5
+        { $as_echo "$as_me:${as_lineno-$LINENO}: result: icd thinks openmp compilation possible: ${ac_pkg_openmp}" >&5
 $as_echo "icd thinks openmp compilation possible: ${ac_pkg_openmp}" >&6; }
 
-# if ${ac_pkg_openmp} = "yes" then we have OMP, otherwise it will be "no"
-if test "${ac_pkg_openmp}" = no; then
-  ICD_OPENMP_FLAG=''
-else
-  ICD_OPENMP_FLAG='$(SHLIB_OPENMP_CXXFLAGS)'
-fi
+        # if ${ac_pkg_openmp} = "yes" then we have OMP, otherwise it will be "no"
+        if test "${ac_pkg_openmp}" = no; then
+            ICD_OPENMP_FLAG=''
+        else
+            ICD_OPENMP_FLAG='$(SHLIB_OPENMP_CXXFLAGS)'
+        fi
+
 
 echo "unsigned char Makevars[] = { 0x00 };" > src/makevars.h
 
-# Check whether --enable-makevars was given.
-if test "${enable_makevars+set}" = set; then :
-  enableval=$enable_makevars;
-        if test "x$enable_makevars" = "xyes"; then :
+# Check whether --enable-icd_makevars was given.
+if test "${enable_icd_makevars+set}" = set; then :
+  enableval=$enable_icd_makevars;
+        if test "x$enable_icd_makevars" = "xyes"; then :
 
       { $as_echo "$as_me:${as_lineno-$LINENO}: Enabling Makevars inclusion for debugging" >&5
 $as_echo "$as_me: Enabling Makevars inclusion for debugging" >&6;}
@@ -2523,8 +2551,8 @@ $as_echo "no" >&6; }
 
 else
 
-      { $as_echo "$as_me:${as_lineno-$LINENO}: Not enabling Makevars inclusion due to --enable-makevars=!yes" >&5
-$as_echo "$as_me: Not enabling Makevars inclusion due to --enable-makevars=!yes" >&6;}
+      { $as_echo "$as_me:${as_lineno-$LINENO}: Not enabling Makevars inclusion due to --enable-icd-makevars=!yes" >&5
+$as_echo "$as_me: Not enabling Makevars inclusion due to --enable-icd-makevars=!yes" >&6;}
 
 fi
 
@@ -2536,7 +2564,24 @@ $as_echo "$as_me: Not enabling Makevars inclusion" >&6;}
 
 fi
 
-# put the flag in Makevars
+
+# Check whether --enable-icd_strip was given.
+if test "${enable_icd_strip+set}" = set; then :
+  enableval=$enable_icd_strip; { $as_echo "$as_me:${as_lineno-$LINENO}: icd strip enable, without arguments." >&5
+$as_echo "$as_me: icd strip enable, without arguments." >&6;}
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: icd strip enabled, with arguments..." >&5
+$as_echo "$as_me: icd strip enabled, with arguments..." >&6;}
+fi
+
+
+if test "x$enable_icd_strip" != "xno"; then :
+  ICD_STRIP=tools/mk/strip.mk
+else
+  ICD_STRIP=''
+fi
+
+
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -3290,7 +3335,24 @@ ac_tmp=$tmp
 # This happens for instance with `./config.status config.h'.
 if test -n "$CONFIG_FILES"; then
 
-
+if $AWK 'BEGIN { getline <"/dev/null" }' </dev/null 2>/dev/null; then
+  ac_cs_awk_getline=:
+  ac_cs_awk_pipe_init=
+  ac_cs_awk_read_file='
+      while ((getline aline < (F[key])) > 0)
+	print(aline)
+      close(F[key])'
+  ac_cs_awk_pipe_fini=
+else
+  ac_cs_awk_getline=false
+  ac_cs_awk_pipe_init="print \"cat <<'|#_!!_#|' &&\""
+  ac_cs_awk_read_file='
+      print "|#_!!_#|"
+      print "cat " F[key] " &&"
+      '$ac_cs_awk_pipe_init
+  # The final `:' finishes the AND list.
+  ac_cs_awk_pipe_fini='END { print "|#_!!_#|"; print ":" }'
+fi
 ac_cr=`echo X | tr X '\015'`
 # On cygwin, bash can eat \r inside `` if the user requested igncr.
 # But we know of no other shell where ac_cr would be empty at this
@@ -3308,6 +3370,17 @@ fi
 echo 'BEGIN {' >"$ac_tmp/subs1.awk" &&
 _ACEOF
 
+# Create commands to substitute file output variables.
+{
+  echo "cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1" &&
+  echo 'cat >>"\$ac_tmp/subs1.awk" <<\\_ACAWK &&' &&
+  echo "$ac_subst_files" | sed 's/.*/F["&"]="$&"/' &&
+  echo "_ACAWK" &&
+  echo "_ACEOF"
+} >conf$$files.sh &&
+. ./conf$$files.sh ||
+  as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
+rm -f conf$$files.sh
 
 {
   echo "cat >conf$$subs.awk <<_ACEOF" &&
@@ -3384,7 +3457,7 @@ _ACAWK
 cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
   for (key in S) S_is_set[key] = 1
   FS = ""
-
+  \$ac_cs_awk_pipe_init
 }
 {
   line = $ 0
@@ -3402,10 +3475,16 @@ cat >>"\$ac_tmp/subs1.awk" <<_ACAWK &&
     } else
       len += 1 + keylen
   }
-
+  if (nfields == 3 && !substed) {
+    key = field[2]
+    if (F[key] != "" && line ~ /^[	 ]*@.*@[	 ]*$/) {
+      \$ac_cs_awk_read_file
+      next
+    }
+  }
   print line
 }
-
+\$ac_cs_awk_pipe_fini
 _ACAWK
 _ACEOF
 cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
@@ -3633,7 +3712,12 @@ s&@abs_builddir@&$ac_abs_builddir&;t t
 s&@abs_top_builddir@&$ac_abs_top_builddir&;t t
 $ac_datarootdir_hack
 "
-eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$ac_tmp/subs.awk" \
+eval sed \"\$ac_sed_extra\" "$ac_file_inputs" |
+if $ac_cs_awk_getline; then
+  $AWK -f "$ac_tmp/subs.awk"
+else
+  $AWK -f "$ac_tmp/subs.awk" | $SHELL
+fi \
   >$ac_tmp/out || as_fn_error $? "could not create $ac_file" "$LINENO" 5
 
 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
diff --git a/configure.ac b/configure.ac
index 85ed70ce..11d55af5 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-# Copyright (C) 2014 - 2018  Jack O. Wasey
+# Copyright (C) 2014 - 2020  Jack O. Wasey
 #
 # This file is part of icd.
 #
@@ -15,14 +15,19 @@
 # You should have received a copy of the GNU General Public License
 # along with icd. If not, see <http:#www.gnu.org/licenses/>.
 
+# to regenerate quickly and test:
+# # e..g. export ICD_HOME=~/icd
+# autoreconf -fv && "${ICD_HOME:-.}/configure" --enable-icd-strip --enable-icd-shutup && cat "${ICD_HOME:-.}/src/Makevars" && grep -v -q '@' "${ICD_HOME:-.}/src/Makevars" || echo "MISSING REPLACEMENT"
+
 AC_PREREQ([2.62])
 AC_INIT(icd)
-AC_COPYRIGHT(Copyright (C) 2014 - 2019  Jack O. Wasey)
+AC_COPYRIGHT(Copyright (C) 2014 - 2020  Jack O. Wasey)
 AC_CONFIG_SRCDIR([src])
 AC_CONFIG_FILES([src/Makevars])
 AC_CONFIG_MACRO_DIR([m4])
 AC_CONFIG_MACRO_DIR([inst/m4])
 
+
 : ${R_HOME=$(R RHOME)}
 AC_MSG_CHECKING([R_HOME already set])
 if test -z "${R_HOME}"; then
@@ -69,12 +74,24 @@ CFLAGS=`"${R_BIN}" CMD config CFLAGS`
 CPPFLAGS=`"${R_BIN}" CMD config CPPFLAGS`
 LIBS="${PKG_LIBS}"
 
+# try to shut up travis/r-hub builds with huge warning burden with default compiler settings (Eigen). Can't seem to do with MAKEFLAGS, or string of R CMD check --install-opts=.....
+AC_ARG_VAR(ICD_SHUTUP, "If ICD_SHUTUP is defined, it tells configure to silence all compiler warnings. Alternatively, use --enable-icd-shutup in configure")
+
+AC_ARG_ENABLE([icd_shutup], 
+              [AS_HELP_STRING([--enable-icd-shutup], [Enable peaceful compilation on travis with yes or no])],
+              [AC_MSG_NOTICE([icd shutup enabled, without arguments.])],
+              [AC_MSG_NOTICE([icd shutup enabled, with arguments...])])
+
+AS_IF([test "x$enable_icd-shutup" = "xyes"], [
+       CXX11FLAGS="${CXX11FLAGS} -w"
+       ])
+
 # changes what R_OPENMP and rest of script does:
 AC_LANG(C++)
 
 # https://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Generic-Compiler-Characteristics.html
 
-# this macro is borrowed from R-devel source, and included in the icd/tools/m4 directory
+# this macro is borrowed from R-devel source, and included in the icd /inst/m4 directory
 R_OPENMP
 
 # since some systems have broken OMP libraries
@@ -84,33 +101,34 @@ ac_pkg_openmp=no
 #  AC_MSG_RESULT([Do have OPENMP_CFLAGS from R_OPENMP])
 #fi
 if test -n "${OPENMP_CXXFLAGS}"; then
-  AC_MSG_CHECKING([OpenMP available, but does it work in a package])
-  AC_LANG_CONFTEST(
-  [AC_LANG_PROGRAM([[#include <omp.h>]], [[ omp_get_num_threads (); return 0; ]])])
-  PKG_CFLAGS="${OPENMP_CFLAGS}" PKG_LIBS="${OPENMP_CFLAGS}" "$R_BIN" CMD SHLIB conftest.c 1>&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD && "$R_BIN" --vanilla -q -e "dyn.load(paste('conftest',.Platform\$dynlib.ext,sep=''))" 1>&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD && ac_pkg_openmp=yes
-  AC_MSG_RESULT([OpenMP available and working: ${ac_pkg_openmp}])
-else
-  AC_MSG_RESULT([R did not think OpenMP is available])
-fi
+    AC_MSG_CHECKING([OpenMP available, but does it work in a package])
+    AC_LANG_CONFTEST(
+                     [AC_LANG_PROGRAM([[#include <omp.h>]], [[ omp_get_num_threads (); return 0; ]])])
+    PKG_CFLAGS="${OPENMP_CFLAGS}" PKG_LIBS="${OPENMP_CFLAGS}" "$R_BIN" CMD SHLIB conftest.c 1>&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD && "$R_BIN" --vanilla -q -e "dyn.load(paste('conftest',.Platform\$dynlib.ext,sep=''))" 1>&AS_MESSAGE_LOG_FD 2>&AS_MESSAGE_LOG_FD && ac_pkg_openmp=yes
+    AC_MSG_RESULT([OpenMP available and working: ${ac_pkg_openmp}])
+    else
+        AC_MSG_RESULT([R did not think OpenMP is available])
+        fi
 
-AC_MSG_RESULT([icd thinks openmp compilation possible: ${ac_pkg_openmp}])
+        AC_MSG_RESULT([icd thinks openmp compilation possible: ${ac_pkg_openmp}])
 
-# if ${ac_pkg_openmp} = "yes" then we have OMP, otherwise it will be "no"
-if test "${ac_pkg_openmp}" = no; then
-  ICD_OPENMP_FLAG=''
-else
-  ICD_OPENMP_FLAG='$(SHLIB_OPENMP_CXXFLAGS)'
-fi
+        # if ${ac_pkg_openmp} = "yes" then we have OMP, otherwise it will be "no"
+        if test "${ac_pkg_openmp}" = no; then
+            ICD_OPENMP_FLAG=''
+        else
+            ICD_OPENMP_FLAG='$(SHLIB_OPENMP_CXXFLAGS)'
+        fi
+AC_SUBST(ICD_OPENMP_FLAG)
 
 dnl Always write the stub as default to not include Makevars content:
 echo "unsigned char Makevars[[]] = { 0x00 };" > src/makevars.h
 
-AC_ARG_ENABLE([makevars],
-    AS_HELP_STRING([--enable-makevars],
+AC_ARG_ENABLE([icd_makevars],
+    AS_HELP_STRING([--enable-icd-makevars],
       [keep ~/.R/Makevars contents in binary for debugging (default is no)]),
     [
     dnl also check that user didn't write --enable-makevars=no
-    AS_IF([test "x$enable_makevars" = "xyes"],
+    AS_IF([test "x$enable_icd_makevars" = "xyes"],
     [
       AC_MSG_NOTICE([Enabling Makevars inclusion for debugging])
       AC_MSG_CHECKING([$HOME/.R exists])
@@ -130,13 +148,21 @@ AC_ARG_ENABLE([makevars],
         AC_MSG_RESULT([no])
       fi
     ], [
-      AC_MSG_NOTICE([Not enabling Makevars inclusion due to --enable-makevars=!yes])
+      AC_MSG_NOTICE([Not enabling Makevars inclusion due to --enable-icd-makevars=!yes])
     ])
   ],
   [
     AC_MSG_NOTICE([Not enabling Makevars inclusion])
   ]
 )
-# put the flag in Makevars
-AC_SUBST(ICD_OPENMP_FLAG)
+	
+AC_ARG_ENABLE([icd_strip], 
+              [AS_HELP_STRING([--enable-icd-strip], [Enable stripping of binary on Linux and MacOS])],
+              [AC_MSG_NOTICE([icd strip enable, without arguments.])],
+              [AC_MSG_NOTICE([icd strip enabled, with arguments...])])
+
+AS_IF([test "x$enable_icd_strip" != "xno"], [ICD_STRIP=[tools/mk/strip.mk]], [ICD_STRIP=''])
+AC_SUBST_FILE([ICD_STRIP])
+
+AC_SUBST(ICD_SHUTUP)
 AC_OUTPUT
diff --git a/man/get_icd10cm2019_pc.Rd b/man/get_icd10cm2019_pc.Rd
index 018cb7cc..75c16c3c 100644
--- a/man/get_icd10cm2019_pc.Rd
+++ b/man/get_icd10cm2019_pc.Rd
@@ -4,10 +4,12 @@
 \name{get_icd10cm2019_pc}
 \alias{get_icd10cm2019_pc}
 \title{ICD-10-CM Procedure Codes}
-\format{A named list of data frames. The elements of the list are named by
+\format{
+A named list of data frames. The elements of the list are named by
   the year, e.g., \code{"2018"}. Each data frame contains two character
   columns, the first, named \code{code} is the procedure code; the second,
-  named \code{desc}, has the description.}
+  named \code{desc}, has the description.
+}
 \description{
 ICD-10-PCS is the annually-updated set of procedure codes designed by 3M for
 the US CMS. There is no directory of WHO ICD procedure codes.
diff --git a/man/get_icd9cm2014_leaf.Rd b/man/get_icd9cm2014_leaf.Rd
index c7481151..6fe00999 100644
--- a/man/get_icd9cm2014_leaf.Rd
+++ b/man/get_icd9cm2014_leaf.Rd
@@ -14,8 +14,10 @@
 \alias{get_icd9cm2013_leaf}
 \alias{get_icd9cm2005_leaf}
 \title{ICD-9-CM, just billable/leaf codes}
-\format{data frames with columns \code{code}, \code{short_desc}, and
-  \code{long_desc}.}
+\format{
+data frames with columns \code{code}, \code{short_desc}, and
+  \code{long_desc}.
+}
 \source{
 \url{http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html}
 }
diff --git a/man/icd9_map_ahrq.Rd b/man/icd9_map_ahrq.Rd
index 374ff1b7..ae1cf2e4 100644
--- a/man/icd9_map_ahrq.Rd
+++ b/man/icd9_map_ahrq.Rd
@@ -6,7 +6,9 @@
 \alias{ahrq}
 \alias{icd10_map_ahrq}
 \title{AHRQ comorbidities}
-\format{list of character vectors}
+\format{
+list of character vectors
+}
 \source{
 \url{http://www.hcup-us.ahrq.gov/toolssoftware/comorbidity/comorbidity.jsp}
 \url{http://www.hcup-us.ahrq.gov/toolssoftware/comorbidityicd10/comorbidity_icd10.jsp}
diff --git a/man/icd9_map_elix.Rd b/man/icd9_map_elix.Rd
index 50371051..546a52fd 100644
--- a/man/icd9_map_elix.Rd
+++ b/man/icd9_map_elix.Rd
@@ -5,7 +5,9 @@
 \alias{icd9_map_elix}
 \alias{icd10_map_elix}
 \title{Elixhauser comorbidities}
-\format{list of character vectors, each named by co-morbidity}
+\format{
+list of character vectors, each named by co-morbidity
+}
 \description{
 This data comprises the original mapping of Elixhauser's ICD-9-CM to
 30 comorbidities. According to Sharabiani, this mapping provides the
diff --git a/man/icd9_map_hcc.Rd b/man/icd9_map_hcc.Rd
index 148b4820..a532edc2 100644
--- a/man/icd9_map_hcc.Rd
+++ b/man/icd9_map_hcc.Rd
@@ -7,8 +7,10 @@
 \alias{icd10_map_cc}
 \alias{icd_map_cc_hcc}
 \title{Medicare Hierarchical Condition Categories}
-\format{\code{dataframe} with 3 columns (\code{icd_code}, \code{cc},
-  and \code{year})}
+\format{
+\code{dataframe} with 3 columns (\code{icd_code}, \code{cc},
+  and \code{year})
+}
 \description{
 Medicare HCC model was developed to use current year diagnoses and
 demographics predict current year healthcare expenditure. This
diff --git a/man/icd9_map_quan_deyo.Rd b/man/icd9_map_quan_deyo.Rd
index 65d461fe..3bf0337a 100644
--- a/man/icd9_map_quan_deyo.Rd
+++ b/man/icd9_map_quan_deyo.Rd
@@ -7,7 +7,9 @@
 \alias{icd9_map_charlson}
 \alias{icd10_map_charlson}
 \title{Quan adaptation of Deyo/Charlson comorbidities}
-\format{list of character vectors, each named by co-morbidity}
+\format{
+list of character vectors, each named by co-morbidity
+}
 \description{
 Derived automatically from the SAS code used in the original
 publication. According to the referenced study, this provides the
diff --git a/man/icd9_map_quan_elix.Rd b/man/icd9_map_quan_elix.Rd
index 80a7db15..d3450aad 100644
--- a/man/icd9_map_quan_elix.Rd
+++ b/man/icd9_map_quan_elix.Rd
@@ -5,7 +5,9 @@
 \alias{icd9_map_quan_elix}
 \alias{icd10_map_quan_elix}
 \title{Quan adaptation of Elixhauser comorbidities}
-\format{list of character vectors, each named by co-morbidity}
+\format{
+list of character vectors, each named by co-morbidity
+}
 \description{
 These were transcribed directly from the Quan paper referenced.
 }
diff --git a/man/icd9_map_single_ccs.Rd b/man/icd9_map_single_ccs.Rd
index 94716fdd..43a1b900 100644
--- a/man/icd9_map_single_ccs.Rd
+++ b/man/icd9_map_single_ccs.Rd
@@ -6,7 +6,9 @@
 \alias{icd9_map_multi_ccs}
 \alias{icd10_map_ccs}
 \title{Clinical Classifications Software (CCS) for ICD9/10-CM}
-\format{list of character vectors, each numbered by co-morbidity}
+\format{
+list of character vectors, each numbered by co-morbidity
+}
 \description{
 The Clinical Classifications Software (CCS) for ICD-9/10-CM is one in
 a family of databases and software tools developed as part of the
diff --git a/man/names_elix.Rd b/man/names_elix.Rd
index 5f475cfb..40d27b9b 100644
--- a/man/names_elix.Rd
+++ b/man/names_elix.Rd
@@ -38,11 +38,13 @@
 \alias{names_pccc}
 \alias{names_pccc_abbrev}
 \title{Comorbidity names}
-\format{list, with character/numeric code. 'Hypertension,
+\format{
+list, with character/numeric code. 'Hypertension,
   uncomplicated' and 'Hypertension, complicated' are labelled '6a'
   and '6b'. Diabetes, cancer, and metastasis are counted
   independently, as in the original paper, giving the original 30
-  groups. "01" to "30"}
+  groups. "01" to "30"
+}
 \description{
 These lists provide correctly sorted names of the comorbidities and
 their particular permutations in both full and abbreviated forms.
diff --git a/man/poa_choices.Rd b/man/poa_choices.Rd
index 05f2ae25..b1f26b2d 100644
--- a/man/poa_choices.Rd
+++ b/man/poa_choices.Rd
@@ -4,7 +4,9 @@
 \name{poa_choices}
 \alias{poa_choices}
 \title{Present-on-admission flags}
-\format{An object of class \code{character} of length 4.}
+\format{
+An object of class \code{character} of length 4.
+}
 \usage{
 poa_choices
 }
diff --git a/src/Makevars.in b/src/Makevars.in
index ca5fa8e4..4a9404b0 100644
--- a/src/Makevars.in
+++ b/src/Makevars.in
@@ -1,16 +1,4 @@
 CXX_STD=CXX11
-
-#PKG_CXXFLAGS=-DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS $(SHLIB_OPENMP_CXXFLAGS)
-#PKG_LIBS=$(SHLIB_OPENMP_CXXFLAGS)
-
-PKG_CXXFLAGS=@ICD_OPENMP_FLAG@ -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
+PKG_CXXFLAGS=@ICD_OPENMP_FLAG@ -DEIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS @ICD_SHUTUP@
 PKG_LIBS=@ICD_OPENMP_FLAG@
-
-# size is about 10% of unstripped on Linux, about 90% on Mac. CRAN Windows DLL is already small.
-#
-# Don't forget to comment out for debugging... and CRAN?
-#
-#strippedLib: $(SHLIB)
-#	if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" || `uname` == "Darwin" ]] ; \
-#		then /usr/bin/strip -S $(SHLIB); fi
-#.phony: strippedLib
+@ICD_STRIP@
diff --git a/tools/env/cran b/tools/env/cran
new file mode 100755
index 00000000..7a1c4a18
--- /dev/null
+++ b/tools/env/cran
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+#the goal here is to just go with the defaults from --as-cran for the active R release
+#shellcheck disable=SC2034
+ICD_TEST_SLOW=FALSE
+MAKEFLAGS=-j$(getconf _NPROCESSORS_ONLN)
+_R_CHECK_COMPILATION_FLAGS_=FALSE
+_R_CHECK_CRAN_INCOMING_=FALSE
+_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
+_R_CHECK_LENGTH_1_CONDITION_="verbose,abort"
+_R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
+_R_CHECK_PKG_SIZES_=FALSE
+_R_CHECK_USE_INSTALL_LOG_=TRUE
diff --git a/tools/env/full b/tools/env/full
new file mode 100755
index 00000000..ac99d9db
--- /dev/null
+++ b/tools/env/full
@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+#shellcheck disable=SC2034
+ICD_TEST_SLOW=TRUE
+MAKEFLAGS=-j$(getconf _NPROCESSORS_ONLN)
+_R_CHECK_ALL_NON_ISO_C_=TRUE
+_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=TRUE
+_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
+_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
+_R_CHECK_COMPILATION_FLAGS_=FALSE
+_R_CHECK_CRAN_INCOMING_=FALSE
+_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
+_R_CHECK_EXIT_ON_FIRST_ERROR_=TRUE
+_R_CHECK_LENGTH_1_CONDITION_="verbose,abort"
+_R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
+_R_CHECK_NATIVE_ROUTINE_REGISTRATION_=TRUE
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=TRUE
+_R_CHECK_PKG_SIZES_=FALSE
+_R_CHECK_PKG_SIZES_=FALSE
+_R_CHECK_RD_EXAMPLES_T_AND_F_=TRUE
+_R_CHECK_RD_LINE_WIDTHS_=TRUE
+_R_CHECK_TESTS_NLINES_=0
+_R_CHECK_USE_INSTALL_LOG_=TRUE
+_R_CHECK_VIGNETTES_NLINES_=0
diff --git a/tools/env/jit b/tools/env/jit
new file mode 100755
index 00000000..c2b9f91b
--- /dev/null
+++ b/tools/env/jit
@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+#shellcheck disable=SC2034
+ICD_TEST_SLOW=TRUE
+MAKEFLAGS=-j$(getconf _NPROCESSORS_ONLN)
+R_CHECK_CONSTANTS=5
+R_JIT_STRATEGY=3
+_R_CHECK_ALL_NON_ISO_C_=TRUE
+_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=TRUE
+_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
+_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
+_R_CHECK_CODE_ATTACH_=TRUE
+_R_CHECK_CODE_DATA_INTO_GLOBALENV_=TRUE
+_R_CHECK_CODE_USAGE_VIA_NAMESPACES_=TRUE
+_R_CHECK_COMPACT_DATA_=TRUE
+_R_CHECK_COMPILATION_FLAGS_=FALSE
+_R_CHECK_CRAN_INCOMING_=FALSE
+_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
+_R_CHECK_DEPRECATED_DEFUNCT_=TRUE
+_R_CHECK_DOC_SIZES2_=TRUE
+_R_CHECK_DOT_FIRSTLIB_=TRUE
+_R_CHECK_EXECUTABLES_EXCLUSIONS_=FALSE
+_R_CHECK_EXIT_ON_FIRST_ERROR_=FALSE
+_R_CHECK_INSTALL_DEPENDS_=TRUE
+_R_CHECK_LENGTH_1_CONDITION_="verbose,abort"
+_R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
+_R_CHECK_NATIVE_ROUTINE_REGISTRATION_=TRUE
+_R_CHECK_NO_RECOMMENDED_=TRUE
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=TRUE
+_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=TRUE
+_R_CHECK_PKG_SIZES_=FALSE
+_R_CHECK_PRAGMAS_=TRUE
+_R_CHECK_RD_EXAMPLES_T_AND_F_=TRUE
+_R_CHECK_RD_LINE_WIDTHS_=TRUE
+_R_CHECK_REPLACING_IMPORTS_=TRUE
+_R_CHECK_R_DEPENDS_=warn
+_R_CHECK_R_ON_PATH_=TRUE
+_R_CHECK_S3_METHODS_NOT_REGISTERED_=TRUE
+_R_CHECK_SCREEN_DEVICE_=stop
+_R_CHECK_SERIALIZATION_=TRUE
+_R_CHECK_SUGGESTS_ONLY_=TRUE
+_R_CHECK_TESTS_NLINES_=0
+_R_CHECK_TIMINGS_=0
+_R_CHECK_TOPLEVEL_FILES_=TRUE
+_R_CHECK_USE_INSTALL_LOG_=FALSE
+_R_CHECK_VC_DIRS_=TRUE
+_R_CHECK_VIGNETTES_NLINES_=0
diff --git a/tools/env/plus b/tools/env/plus
new file mode 100755
index 00000000..2b0fb58b
--- /dev/null
+++ b/tools/env/plus
@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+#shellcheck disable=SC2034
+ICD_TEST_SLOW=TRUE
+MAKEFLAGS=-j$(getconf _NPROCESSORS_ONLN)
+_R_CHECK_ALL_NON_ISO_C_=TRUE
+_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=TRUE
+_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
+_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
+_R_CHECK_CODE_ATTACH_=TRUE
+_R_CHECK_CODE_DATA_INTO_GLOBALENV_=TRUE
+_R_CHECK_CODE_USAGE_VIA_NAMESPACES_=TRUE
+_R_CHECK_COMPACT_DATA_=TRUE
+_R_CHECK_COMPILATION_FLAGS_=FALSE
+_R_CHECK_CRAN_INCOMING_=FALSE
+_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
+_R_CHECK_DEPRECATED_DEFUNCT_=TRUE
+_R_CHECK_DOC_SIZES2_=TRUE
+_R_CHECK_DOT_FIRSTLIB_=TRUE
+_R_CHECK_EXECUTABLES_EXCLUSIONS_=TRUE
+_R_CHECK_EXIT_ON_FIRST_ERROR_=FALSE
+_R_CHECK_INSTALL_DEPENDS_=TRUE
+_R_CHECK_LENGTH_1_CONDITION_="verbose,abort"
+_R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
+_R_CHECK_NATIVE_ROUTINE_REGISTRATION_=TRUE
+_R_CHECK_NO_RECOMMENDED_=TRUE
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=TRUE
+_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=TRUE
+_R_CHECK_PKG_SIZES_=FALSE
+_R_CHECK_PRAGMAS_=TRUE
+_R_CHECK_RD_EXAMPLES_T_AND_F_=TRUE
+_R_CHECK_RD_LINE_WIDTHS_=TRUE
+_R_CHECK_REPLACING_IMPORTS_=TRUE
+_R_CHECK_R_DEPENDS_=warn
+_R_CHECK_R_ON_PATH_=TRUE
+_R_CHECK_S3_METHODS_NOT_REGISTERED_=TRUE
+_R_CHECK_SCREEN_DEVICE_=stop
+_R_CHECK_SERIALIZATION_=TRUE
+_R_CHECK_SUGGESTS_ONLY_=TRUE
+_R_CHECK_TESTS_NLINES_=0
+_R_CHECK_TIMINGS_=0
+_R_CHECK_TOPLEVEL_FILES_=TRUE
+_R_CHECK_USE_INSTALL_LOG_=FALSE
+_R_CHECK_VC_DIRS_=TRUE
+_R_CHECK_VIGNETTES_NLINES_=0
diff --git a/tools/env/quick b/tools/env/quick
new file mode 100755
index 00000000..a12024f1
--- /dev/null
+++ b/tools/env/quick
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+#R_MAKEVARS_USER=${ICD_HOME}/tools/Makevars.quick
+#shellcheck disable=SC2034
+ICD_TEST_SLOW=FALSE
+MAKEFLAGS=-j$(getconf _NPROCESSORS_ONLN)
+_R_CHECK_ALL_NON_ISO_C_=TRUE
+_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
+_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
+_R_CHECK_CODE_ATTACH_=FALSE
+_R_CHECK_CODE_DATA_INTO_GLOBALENV_=TRUE
+_R_CHECK_CODE_USAGE_VIA_NAMESPACES_=TRUE
+_R_CHECK_COMPACT_DATA_=FALSE
+_R_CHECK_COMPILATION_FLAGS_=FALSE
+_R_CHECK_CRAN_INCOMING_=FALSE
+_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
+_R_CHECK_DEPRECATED_DEFUNCT_=FALSE
+_R_CHECK_DOC_SIZES2_=FALSE
+_R_CHECK_DOT_FIRSTLIB_=FALSE
+_R_CHECK_EXECUTABLES_EXCLUSIONS_=FALSE
+_R_CHECK_EXIT_ON_FIRST_ERROR_=TRUE
+_R_CHECK_INSTALL_DEPENDS_=FALSE
+_R_CHECK_LENGTH_1_CONDITION_="verbose,abort"
+_R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
+_R_CHECK_NATIVE_ROUTINE_REGISTRATION_=TRUE
+_R_CHECK_NO_RECOMMENDED_=FALSE
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
+_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=FALSE
+_R_CHECK_PKG_SIZES_=FALSE
+_R_CHECK_RD_EXAMPLES_T_AND_F_=TRUE
+_R_CHECK_RD_LINE_WIDTHS_=TRUE
+_R_CHECK_TESTS_NLINES_=0
+_R_CHECK_USE_INSTALL_LOG_=FALSE
+_R_CHECK_VIGNETTES_NLINES_=0
diff --git a/tools/env/rhub b/tools/env/rhub
new file mode 100644
index 00000000..dc477586
--- /dev/null
+++ b/tools/env/rhub
@@ -0,0 +1,3 @@
+_R_CHECK_DOC_SIZES_=FALSE
+_R_CHECK_DOC_SIZES2_=FALSE
+MAKEFLAGS="CXXFLAGS=-Wno-unused-parameter\\ -Wno-unused-variable\\ -Wno-ignored-attributes\\ -Wno-cast-function-type\\ -Wno-unknown-warning-option\\ -Wno-unknown-pragma"
diff --git a/tools/env/rhub-san b/tools/env/rhub-san
new file mode 100644
index 00000000..96dd1e23
--- /dev/null
+++ b/tools/env/rhub-san
@@ -0,0 +1,21 @@
+CXX=g++ -std=c++11
+CXX11=g++ -std=c++11
+MAKEFLAGS = "CXX11FLAGS+=-std=c++11\\ -Wno-ignored-attributes CXXFLAGS+=-std=c++11\\ -Wno-ignored-attributes")
+GNUMAKEFLAGS = "CXX11FLAGS+=-std=c++11\\ -Wno-ignored-attributes CXXFLAGS+=-std=c++11\\ -Wno-ignored-attributes")
+ICD_TEST_SLOW=TRUE
+_R_CHECK_COMPACT_DATA_=FALSE
+_R_CHECK_COMPILATION_FLAGS_=FALSE
+_R_CHECK_CRAN_INCOMING_=FALSE
+_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
+_R_CHECK_DEPRECATED_DEFUNCT_=FALSE
+_R_CHECK_DOC_SIZES2_=FALSE
+_R_CHECK_DOC_SIZES_=FALSE
+_R_CHECK_DOT_FIRSTLIB_=FALSE
+_R_CHECK_EXECUTABLES_EXCLUSIONS_=FALSE
+_R_CHECK_EXIT_ON_FIRST_ERROR_=FALSE
+_R_CHECK_INSTALL_DEPENDS_=FALSE
+_R_CHECK_NO_RECOMMENDED_=FALSE
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
+_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=FALSE
+_R_CHECK_PKG_SIZES_=FALSE
+_R_CHECK_S3_METHODS_NOT_REGISTERED_=TRUE
diff --git a/tools/env/travis-global b/tools/env/travis-global
new file mode 100644
index 00000000..cb126bae
--- /dev/null
+++ b/tools/env/travis-global
@@ -0,0 +1,37 @@
+_R_CHECK_CRAN_INCOMING_=FALSE
+_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE
+_R_CHECK_FORCE_SUGGESTS_=FALSE
+_R_CHECK_USE_INSTALL_LOG_=TRUE
+_R_CHECK_LENGTH_1_CONDITION_="verbose,abort"
+_R_CHECK_LENGTH_1_LOGIC2_="verbose,abort"
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=FALSE
+
+# some/all of the following are ignored if --as-cran is set, so not using --as-cran, and setting env directly.
+_R_CHECK_COMPILATION_FLAGS_=FALSE
+_R_CHECK_COMPILATION_FLAGS_KNOWN_="-Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option -Wno-unknown-pragmas -Qunused-arguments"
+
+# the following are to simulate cran, and
+# help debugging if we didn't use --as-cran
+_R_CHECK_ALL_NON_ISO_C_=TRUE
+_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=TRUE
+_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
+_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
+_R_CHECK_DOC_SIZES_=FALSE
+_R_CHECK_DOC_SIZES2_=FALSE
+_R_CHECK_EXIT_ON_FIRST_ERROR_=FALSE
+_R_CHECK_NATIVE_ROUTINE_REGISTRATION_=TRUE
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=TRUE
+_R_CHECK_RD_EXAMPLES_T_AND_F_=TRUE
+_R_CHECK_RD_LINE_WIDTHS_=true
+_R_CHECK_TESTS_NLINES_=0
+_R_CHECK_USE_INSTALL_LOG_=TRUE
+_R_CHECK_VIGNETTES_NLINES_=0
+_R_CHECK_PKG_SIZES_THRESHOLD_=50
+ICD_COVERAGE=false
+ICD_MINI_BENCH=false
+ICD_DATA_VERBOSE=true
+ICD_DATA_OFFLINE=true
+ICD_DATA_INTERACT=false
+
+# 4 is the official travis suggestion, the docker images have two cores, presumably four threads.
+OMP_NUM_THREADS=4
diff --git a/tools/mk/strip.mk b/tools/mk/strip.mk
new file mode 100644
index 00000000..d15e17db
--- /dev/null
+++ b/tools/mk/strip.mk
@@ -0,0 +1,12 @@
+#!/usr/bin/env make
+#Enable using configure --enable-icd-strip
+#With binary stripping, size is about 10% on Linux, 90% on Mac. CRAN Windows DLL is already small.
+strippedLib: $(SHLIB)
+	# so clumsy, but unambiguous, avoids weird multi level make vs bash escaping
+	command -v strip >/dev/null && \
+		command -v uname >/dev/null && \
+		[ x$(uname -s) = xLinux ] && strip -S $(SHLIB) || true
+	command -v strip >/dev/null && \
+		command -v uname >/dev/null && \
+		[ x$(uname -s) = xDarwin ] && strip -S $(SHLIB) || true
+.phony: strippedLib
diff --git a/tools/mk/travis-debug.mk b/tools/mk/travis-debug.mk
new file mode 100644
index 00000000..23931e9d
--- /dev/null
+++ b/tools/mk/travis-debug.mk
@@ -0,0 +1,8 @@
+#!/usr/bin/env make
+
+CFLAGS+=-O0
+CXXFLAGS+=-O0
+CXX11FLAGS+=-O0
+CXX14FLAGS+=-O0
+CXX17FLAGS+=-O0
+CXX20FLAGS+=-O0
diff --git a/tools/mk/travis-macos.mk b/tools/mk/travis-macos.mk
new file mode 100644
index 00000000..f2fa7078
--- /dev/null
+++ b/tools/mk/travis-macos.mk
@@ -0,0 +1,9 @@
+#!/usr/bin/env make
+
+# belt and braces
+CC+=/usr/local/bin/gcc-9
+CXX+=/usr/local/bin/g++-9
+CXX11+=/usr/local/bin/g++-9
+CXX14+=/usr/local/bin/g++-9
+CXX17+=/usr/local/bin/g++-9
+CXX20+=/usr/local/bin/g++-9
diff --git a/tools/mk/travis-nowarn.mk b/tools/mk/travis-nowarn.mk
new file mode 100644
index 00000000..9a7a962e
--- /dev/null
+++ b/tools/mk/travis-nowarn.mk
@@ -0,0 +1,8 @@
+#!/usr/bin/env make
+
+# belt and braces - should just need CXXFLAGS
+CXXFLAGS+=-Wno-unknown-warning-option -Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-pragmas
+CXX11FLAGS+=-Wno-unknown-warning-option -Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option -Wno-unknown-pragmas
+CXX14FLAGS+=-Wno-unknown-warning-option -Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option -Wno-unknown-pragmas
+CXX17FLAGS+=-Wno-unknown-warning-option -Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option -Wno-unknown-pragmas
+CXX20FLAGS+=-Wno-unknown-warning-option -Wno-unused-parameter -Wno-unused-variable -Wno-ignored-attributes -Wno-cast-function-type -Wno-unknown-warning-option -Wno-unknown-pragmas

From 00e04b891c15c3777ae676ba503a3308befbda63 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sat, 28 Mar 2020 18:41:39 -0400
Subject: [PATCH 45/51] fix conflict

---
 .travis.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index bf26bee5..ab6816d6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,10 +24,9 @@ cache:
   - packages
   - ccache
 
-addons:
-  apt:
-    packages:
-      - qpdf
+#addons:
+#  apt:
+#   packages:
 #      - valgrind # when I do do this (probably too slow for travis anyway, then just put the apt addon in the specific build)
       #- r-cran-tinytex
 

From 71c1cd7a133b91b8de721c8324900f2a275da2b1 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sat, 28 Mar 2020 18:43:02 -0400
Subject: [PATCH 46/51] resolve conflict

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index ab6816d6..338c5f37 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -26,7 +26,7 @@ cache:
 
 #addons:
 #  apt:
-#   packages:
+#    packages:
 #      - valgrind # when I do do this (probably too slow for travis anyway, then just put the apt addon in the specific build)
       #- r-cran-tinytex
 

From 70167219abc39cc1d5ff120b10386feb1f3f4da8 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sat, 28 Mar 2020 18:55:25 -0400
Subject: [PATCH 47/51] add qpdf to packages

---
 .travis.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 338c5f37..bf26bee5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,9 +24,10 @@ cache:
   - packages
   - ccache
 
-#addons:
-#  apt:
-#    packages:
+addons:
+  apt:
+    packages:
+      - qpdf
 #      - valgrind # when I do do this (probably too slow for travis anyway, then just put the apt addon in the specific build)
       #- r-cran-tinytex
 

From 24cb44d9cb75d17c6e22248c8b9156c94aac8c57 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sat, 28 Mar 2020 18:56:35 -0400
Subject: [PATCH 48/51] fix conflict

---
 .travis.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index bf26bee5..8630abe0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -28,6 +28,9 @@ addons:
   apt:
     packages:
       - qpdf
+#addons:
+#  apt:
+#    packages:
 #      - valgrind # when I do do this (probably too slow for travis anyway, then just put the apt addon in the specific build)
       #- r-cran-tinytex
 

From 1df316c69573f97e4cc5cd2ac2faa0d05273c563 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sat, 28 Mar 2020 18:57:23 -0400
Subject: [PATCH 49/51] fix conflict

---
 .travis.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 8630abe0..338c5f37 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,10 +24,6 @@ cache:
   - packages
   - ccache
 
-addons:
-  apt:
-    packages:
-      - qpdf
 #addons:
 #  apt:
 #    packages:

From 570acbde94737e2b1670954678cd0f2add05a027 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sat, 28 Mar 2020 18:58:34 -0400
Subject: [PATCH 50/51] add qpdf

---
 .travis.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 338c5f37..19a2c82c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -33,6 +33,12 @@ cache:
 #r_packages:
 #  - tinytex
 
+# git conflict if I modify above lines
+addons:
+  apt:
+    packages:
+      - qpdf
+
 cran: https://cloud.r-project.org
 # by default, DON'T do --as-cran, as it stops us using environment variables
 # that conflict. Instead, state approximate CRAN check environment variables explicitly.

From eb82ba543e9bf377d2b8b05fb45407c9413f82d5 Mon Sep 17 00:00:00 2001
From: Patrick <patrick@patrickmd.net>
Date: Sun, 29 Mar 2020 17:46:13 -0400
Subject: [PATCH 51/51] set R_QPDF

---
 .travis.yml             | 10 ++++------
 tools/env/travis-global |  1 +
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 19a2c82c..a13ce8c2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -33,12 +33,6 @@ cache:
 #r_packages:
 #  - tinytex
 
-# git conflict if I modify above lines
-addons:
-  apt:
-    packages:
-      - qpdf
-
 cran: https://cloud.r-project.org
 # by default, DON'T do --as-cran, as it stops us using environment variables
 # that conflict. Instead, state approximate CRAN check environment variables explicitly.
@@ -183,6 +177,10 @@ before_script:
  - set -o allexport; source tools/env/travis-global; set +o allexport;
  - set
  - echo "$LD_LIBRARY_PATH"
+# qpdf debugging start
+ - which qpdf || true
+ - which gs || true
+# qpdf debugging end
  - if [ x"$ICD_TEST_SLOW" = x"true" ]; then
      Rscript -e 'source("tools/split-tests.R"); testthat_split();';
    fi
diff --git a/tools/env/travis-global b/tools/env/travis-global
index cb126bae..4beb8a94 100644
--- a/tools/env/travis-global
+++ b/tools/env/travis-global
@@ -27,6 +27,7 @@ _R_CHECK_TESTS_NLINES_=0
 _R_CHECK_USE_INSTALL_LOG_=TRUE
 _R_CHECK_VIGNETTES_NLINES_=0
 _R_CHECK_PKG_SIZES_THRESHOLD_=50
+R_QPDF=
 ICD_COVERAGE=false
 ICD_MINI_BENCH=false
 ICD_DATA_VERBOSE=true