diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 3fbd5eb7..893e63f6 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -34,7 +34,7 @@ jobs: with: additional-env-vars: | _R_CHECK_CRAN_INCOMING_REMOTE_=false - _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=10 + _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=5 additional-r-cmd-check-params: --as-cran enforce-note-blocklist: true note-blocklist: | diff --git a/DESCRIPTION b/DESCRIPTION index 6f0d185c..22ba0d16 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,7 +32,7 @@ Imports: lifecycle, logger (>= 0.2.0), shinyvalidate, - teal.code (>= 0.2.0), + teal.code (>= 0.3.0), teal.logger (>= 0.1.1), teal.reporter (>= 0.1.1), teal.transform (>= 0.3.0), @@ -43,15 +43,11 @@ Suggests: knitr, nestcolor (>= 0.1.0), rmarkdown, - scda (>= 0.1.5), - scda.2022 (>= 0.1.3), teal.data (>= 0.1.2), testthat (>= 2.0) Remotes: insightsengineering/osprey@*release, insightsengineering/osprey@*release, - insightsengineering/scda.2022@*release, - insightsengineering/scda@*release, insightsengineering/teal.code@*release, insightsengineering/teal.data@*release, insightsengineering/teal.logger@*release, diff --git a/NEWS.md b/NEWS.md index 034aa5e0..8477fdc5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # teal.osprey 0.1.15.9013 -* Examples now use `scda.2022` instead of `scda.2021`. +* Removed `scda` package dependency from examples. * Fixed crash in `tm_g_heat_bygrade` when not plotting `Conmed`. * Added validation to `tm_g_spiderplot.R` that checks if there are duplicates in X and Y facet variables. * Improved input validation and used the `teal::validate_inputs` mechanism to send validation messages to the output panel. @@ -10,7 +10,7 @@ ### Breaking changes * Replaced `chunks` with simpler `qenv` class. -* Replaced `datasets` argument containing `FilteredData` with the new arguments `data` (`tdata` object) and `filter_panel_api` (`FilterPanelAPI`). +* In all `tm_xyz_srv` modules `datasets` argument containing `FilteredData` have been replaced with the new argument `data` (`tdata` object) and `filter_panel_api` (`FilterPanelAPI`). * Updated `arm_var` to point to the factor column in `ANL`. It can't be a character column anymore. * Removed redundant formal arguments from `tm_g_patient_profile`. diff --git a/R/tm_g_ae_oview.R b/R/tm_g_ae_oview.R index 5106f23f..95e2a7c7 100644 --- a/R/tm_g_ae_oview.R +++ b/R/tm_g_ae_oview.R @@ -16,12 +16,10 @@ #' @export #' #' @examples -#' library(scda) #' library(nestcolor) #' -#' latest_data <- synthetic_cdisc_data("latest") -#' ADSL <- latest_data$adsl -#' ADAE <- latest_data$adae +#' ADSL <- osprey::rADSL +#' ADAE <- osprey::rADAE #' #' # Add additional dummy causality flags. #' add_event_flags <- function(dat) { @@ -47,10 +45,10 @@ #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"), +#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), #' cdisc_dataset("ADAE", ADAE, #' code = -#' "ADAE <- synthetic_cdisc_data('latest')$adae +#' "ADAE <- osprey::rADAE #' add_event_flags <- function(dat) { #' dat <- dat %>% #' dplyr::mutate( diff --git a/R/tm_g_ae_sub.R b/R/tm_g_ae_sub.R index 5a216183..bdfa82e2 100644 --- a/R/tm_g_ae_sub.R +++ b/R/tm_g_ae_sub.R @@ -18,15 +18,13 @@ #' #' @examples #' # Example using stream (ADaM) dataset -#' library(scda) -#' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADAE <- synthetic_cdisc_data("latest")$adae +#' ADSL <- osprey::rADSL +#' ADAE <- osprey::rADAE #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"), -#' cdisc_dataset("ADAE", ADAE, code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae"), +#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), +#' cdisc_dataset("ADAE", ADAE, code = "ADAE <- osprey::rADAE"), #' check = TRUE #' ), #' modules = modules( diff --git a/R/tm_g_butterfly.R b/R/tm_g_butterfly.R index 7fbefad7..eae928fe 100644 --- a/R/tm_g_butterfly.R +++ b/R/tm_g_butterfly.R @@ -43,12 +43,11 @@ #' #' # Example using stream (ADaM) dataset #' library(dplyr) -#' library(scda) #' library(nestcolor) #' #' set.seed(23) -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADAE <- synthetic_cdisc_data("latest")$adae +#' ADSL <- osprey::rADSL +#' ADAE <- osprey::rADAE #' ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), "UG")) #' ADAE <- mutate( #' ADAE, @@ -61,12 +60,12 @@ #' app <- init( #' data = cdisc_data( #' cdisc_dataset("ADSL", ADSL, -#' code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl +#' code = "ADSL <- osprey::rADSL #' set.seed(23) #' ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), 'UG'))" #' ), #' cdisc_dataset("ADAE", ADAE, -#' code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae +#' code = "ADAE <- osprey::rADAE #' ADAE <- mutate(ADAE, #' flag1 = ifelse(AETOXGR == 1, 1, 0), #' flag2 = ifelse(AETOXGR == 2, 1, 0), diff --git a/R/tm_g_events_term_id.R b/R/tm_g_events_term_id.R index 6ed7cafc..7cf77585 100644 --- a/R/tm_g_events_term_id.R +++ b/R/tm_g_events_term_id.R @@ -18,16 +18,15 @@ #' @author Molly He (hey59) \email{hey59@gene.com} #' #' @examples -#' library(scda) #' library(nestcolor) #' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADAE <- synthetic_cdisc_data("latest")$adae +#' ADSL <- osprey::rADSL +#' ADAE <- osprey::rADAE #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"), -#' cdisc_dataset("ADAE", ADAE, code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae"), +#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), +#' cdisc_dataset("ADAE", ADAE, code = "ADAE <- osprey::rADAE"), #' check = TRUE #' ), #' modules = modules( diff --git a/R/tm_g_heat_bygrade.R b/R/tm_g_heat_bygrade.R index 076707a7..a3549676 100644 --- a/R/tm_g_heat_bygrade.R +++ b/R/tm_g_heat_bygrade.R @@ -34,14 +34,12 @@ #' @export #' #' @examples -#' library(scda) #' library(dplyr) #' library(nestcolor) -#' latest_data <- synthetic_cdisc_data("latest") -#' ADSL <- latest_data$adsl %>% slice(1:30) -#' ADEX <- latest_data$adex %>% filter(USUBJID %in% ADSL$USUBJID) -#' ADAE <- latest_data$adae %>% filter(USUBJID %in% ADSL$USUBJID) -#' ADCM <- latest_data$adcm %>% filter(USUBJID %in% ADSL$USUBJID) +#' ADSL <- osprey::rADSL %>% slice(1:30) +#' ADEX <- osprey::rADEX %>% filter(USUBJID %in% ADSL$USUBJID) +#' ADAE <- osprey::rADAE %>% filter(USUBJID %in% ADSL$USUBJID) +#' ADCM <- osprey::rADCM %>% filter(USUBJID %in% ADSL$USUBJID) #' #' # This preprocess is only to force legacy standard on ADCM #' ADCM <- ADCM %>% @@ -80,11 +78,10 @@ #' cdisc_dataset("ADAE", ADAE), #' cdisc_dataset("ADCM", ADCM, keys = c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "CMDECOD")), #' code = " -#' latest_data <- synthetic_cdisc_data('latest') -#' ADSL <- latest_data$adsl %>% slice(1:30) -#' ADEX <- latest_data$adex %>% filter(USUBJID %in% ADSL$USUBJID) -#' ADAE <- latest_data$adae %>% filter(USUBJID %in% ADSL$USUBJID) -#' ADCM <- latest_data$adcm %>% filter(USUBJID %in% ADSL$USUBJID) +#' ADSL <- osprey::rADSL %>% slice(1:30) +#' ADEX <- osprey::rADEX %>% filter(USUBJID %in% ADSL$USUBJID) +#' ADAE <- osprey::rADAE %>% filter(USUBJID %in% ADSL$USUBJID) +#' ADCM <- osprey::rADCM %>% filter(USUBJID %in% ADSL$USUBJID) #' ADCM <- ADCM %>% select(-starts_with(\"ATC\")) %>% unique() #' ADEX <- ADEX %>% #' filter(PARCAT1 == 'INDIVIDUAL') %>% diff --git a/R/tm_g_patient_profile.R b/R/tm_g_patient_profile.R index 4a8a4619..77e3eccc 100644 --- a/R/tm_g_patient_profile.R +++ b/R/tm_g_patient_profile.R @@ -62,18 +62,15 @@ #' @export #' #' @examples -#' library(scda) #' library(nestcolor) #' -#' latest_data <- synthetic_cdisc_data("latest") -#' -#' ADSL <- latest_data$adsl -#' ADAE <- latest_data$adae %>% +#' ADSL <- osprey::rADSL +#' ADAE <- osprey::rADAE %>% #' mutate( #' ASTDT = as.Date(ASTDTM), #' AENDT = as.Date(AENDTM) #' ) -#' ADCM <- latest_data$adcm %>% +#' ADCM <- osprey::rADCM %>% #' mutate( #' ASTDT = as.Date(ASTDTM), #' AENDT = as.Date(AENDTM) @@ -84,14 +81,14 @@ #' select(-starts_with("ATC")) %>% #' unique() #' -#' ADRS <- latest_data$adrs %>% +#' ADRS <- osprey::rADRS %>% #' mutate(ADT = as.Date(ADTM)) -#' ADEX <- latest_data$adex %>% +#' ADEX <- osprey::rADEX %>% #' mutate( #' ASTDT = as.Date(ASTDTM), #' AENDT = as.Date(AENDTM) #' ) -#' ADLB <- latest_data$adlb %>% +#' ADLB <- osprey::rADLB %>% #' mutate( #' ADT = as.Date(ADTM), #' LBSTRESN = as.numeric(LBSTRESC) @@ -99,32 +96,27 @@ #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, -#' code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl" -#' ), -#' cdisc_dataset("ADRS", ADRS, -#' code = "ADRS <- synthetic_cdisc_data(\"latest\")$adrs %>% -#' mutate(ADT = as.Date(ADTM))" -#' ), +#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), +#' cdisc_dataset("ADRS", ADRS, code = "ADRS <- osprey::rADRS %>% mutate(ADT = as.Date(ADTM))"), #' cdisc_dataset("ADAE", ADAE, -#' code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae %>% +#' code = "ADAE <- osprey::rADAE %>% #' mutate(ASTDT = as.Date(ASTDTM), #' AENDT = as.Date(AENDTM))" #' ), #' cdisc_dataset("ADCM", ADCM, -#' code = "ADCM <- synthetic_cdisc_data(\"latest\")$adcm %>% +#' code = "ADCM <- osprey::rADCM %>% #' mutate(ASTDT = as.Date(ASTDTM), #' AENDT = as.Date(AENDTM)) #' ADCM <- ADCM %>% select(-starts_with(\"ATC\")) %>% unique()", #' keys = c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "CMDECOD") #' ), #' cdisc_dataset("ADLB", ADLB, -#' code = "ADLB <- synthetic_cdisc_data(\"latest\")$adlb %>% +#' code = "ADLB <- osprey::rADLB %>% #' mutate(ADT = as.Date(ADTM), #' LBSTRESN = as.numeric(LBSTRESC))" #' ), #' cdisc_dataset("ADEX", ADEX, -#' code = "ADEX <- synthetic_cdisc_data(\"latest\")$adex %>% +#' code = "ADEX <- osprey::rADEX %>% #' mutate(ASTDT = as.Date(ASTDTM), #' AENDT = as.Date(AENDTM))" #' ), diff --git a/R/tm_g_spiderplot.R b/R/tm_g_spiderplot.R index f9394390..933b5a45 100644 --- a/R/tm_g_spiderplot.R +++ b/R/tm_g_spiderplot.R @@ -28,17 +28,16 @@ #' #' # Example using stream (ADaM) dataset #' library(dplyr) -#' library(scda) #' library(nestcolor) #' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADTR <- synthetic_cdisc_data("latest")$adtr +#' ADSL <- osprey::rADSL +#' ADTR <- osprey::rADTR #' #' app <- teal::init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"), +#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), #' cdisc_dataset("ADTR", ADTR, -#' code = "ADTR <- synthetic_cdisc_data(\"latest\")$adtr", +#' code = "ADTR <- osprey::rADTR", #' keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT") #' ), #' check = TRUE diff --git a/README.md b/README.md index 3b4c5b84..d4640b4d 100644 --- a/README.md +++ b/README.md @@ -36,8 +36,6 @@ remotes::install_github("insightsengineering/teal.osprey@*release") A stable release of all `NEST` packages from June 2022 is also available [here](https://github.com/insightsengineering/depository#readme). -In order to run many of the examples you will also need to install the [`scda`](https://insightsengineering.github.io/scda/) package. - ## Stargazers and Forkers ### Stargazers over time diff --git a/man/tm_g_ae_oview.Rd b/man/tm_g_ae_oview.Rd index 49607ebb..f68124a4 100644 --- a/man/tm_g_ae_oview.Rd +++ b/man/tm_g_ae_oview.Rd @@ -51,12 +51,10 @@ the \code{\link[teal:module]{teal::module()}} object. Display the \code{AE} overview plot as a shiny module } \examples{ -library(scda) library(nestcolor) -latest_data <- synthetic_cdisc_data("latest") -ADSL <- latest_data$adsl -ADAE <- latest_data$adae +ADSL <- osprey::rADSL +ADAE <- osprey::rADAE # Add additional dummy causality flags. add_event_flags <- function(dat) { @@ -82,10 +80,10 @@ ADAE <- ADAE \%>\% add_event_flags() app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"), + cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), cdisc_dataset("ADAE", ADAE, code = - "ADAE <- synthetic_cdisc_data('latest')$adae + "ADAE <- osprey::rADAE add_event_flags <- function(dat) { dat <- dat \%>\% dplyr::mutate( diff --git a/man/tm_g_ae_sub.Rd b/man/tm_g_ae_sub.Rd index 10660515..2eb7a4ed 100644 --- a/man/tm_g_ae_sub.Rd +++ b/man/tm_g_ae_sub.Rd @@ -50,15 +50,13 @@ Display the \code{AE} by subgroups plot as a teal module } \examples{ # Example using stream (ADaM) dataset -library(scda) - -ADSL <- synthetic_cdisc_data("latest")$adsl -ADAE <- synthetic_cdisc_data("latest")$adae +ADSL <- osprey::rADSL +ADAE <- osprey::rADAE app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"), - cdisc_dataset("ADAE", ADAE, code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae"), + cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), + cdisc_dataset("ADAE", ADAE, code = "ADAE <- osprey::rADAE"), check = TRUE ), modules = modules( diff --git a/man/tm_g_butterfly.Rd b/man/tm_g_butterfly.Rd index cb60beb0..a1e138f8 100644 --- a/man/tm_g_butterfly.Rd +++ b/man/tm_g_butterfly.Rd @@ -89,12 +89,11 @@ used directly as filter. # Example using stream (ADaM) dataset library(dplyr) -library(scda) library(nestcolor) set.seed(23) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADAE <- synthetic_cdisc_data("latest")$adae +ADSL <- osprey::rADSL +ADAE <- osprey::rADAE ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), "UG")) ADAE <- mutate( ADAE, @@ -107,12 +106,12 @@ ADAE <- mutate( app <- init( data = cdisc_data( cdisc_dataset("ADSL", ADSL, - code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl + code = "ADSL <- osprey::rADSL set.seed(23) ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), 'UG'))" ), cdisc_dataset("ADAE", ADAE, - code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae + code = "ADAE <- osprey::rADAE ADAE <- mutate(ADAE, flag1 = ifelse(AETOXGR == 1, 1, 0), flag2 = ifelse(AETOXGR == 2, 1, 0), diff --git a/man/tm_g_events_term_id.Rd b/man/tm_g_events_term_id.Rd index c7f99a0e..6399ae81 100644 --- a/man/tm_g_events_term_id.Rd +++ b/man/tm_g_events_term_id.Rd @@ -50,16 +50,15 @@ the \code{\link[teal:module]{teal::module()}} object. Display Events by Term plot as a shiny module } \examples{ -library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADAE <- synthetic_cdisc_data("latest")$adae +ADSL <- osprey::rADSL +ADAE <- osprey::rADAE app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"), - cdisc_dataset("ADAE", ADAE, code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae"), + cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), + cdisc_dataset("ADAE", ADAE, code = "ADAE <- osprey::rADAE"), check = TRUE ), modules = modules( diff --git a/man/tm_g_heat_bygrade.Rd b/man/tm_g_heat_bygrade.Rd index 1ef896ac..7a6b452c 100644 --- a/man/tm_g_heat_bygrade.Rd +++ b/man/tm_g_heat_bygrade.Rd @@ -76,14 +76,12 @@ the \code{\link[teal:module]{teal::module()}} object. Display the heatmap by grade as a shiny module } \examples{ -library(scda) library(dplyr) library(nestcolor) -latest_data <- synthetic_cdisc_data("latest") -ADSL <- latest_data$adsl \%>\% slice(1:30) -ADEX <- latest_data$adex \%>\% filter(USUBJID \%in\% ADSL$USUBJID) -ADAE <- latest_data$adae \%>\% filter(USUBJID \%in\% ADSL$USUBJID) -ADCM <- latest_data$adcm \%>\% filter(USUBJID \%in\% ADSL$USUBJID) +ADSL <- osprey::rADSL \%>\% slice(1:30) +ADEX <- osprey::rADEX \%>\% filter(USUBJID \%in\% ADSL$USUBJID) +ADAE <- osprey::rADAE \%>\% filter(USUBJID \%in\% ADSL$USUBJID) +ADCM <- osprey::rADCM \%>\% filter(USUBJID \%in\% ADSL$USUBJID) # This preprocess is only to force legacy standard on ADCM ADCM <- ADCM \%>\% @@ -122,11 +120,10 @@ app <- init( cdisc_dataset("ADAE", ADAE), cdisc_dataset("ADCM", ADCM, keys = c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "CMDECOD")), code = " - latest_data <- synthetic_cdisc_data('latest') - ADSL <- latest_data$adsl \%>\% slice(1:30) - ADEX <- latest_data$adex \%>\% filter(USUBJID \%in\% ADSL$USUBJID) - ADAE <- latest_data$adae \%>\% filter(USUBJID \%in\% ADSL$USUBJID) - ADCM <- latest_data$adcm \%>\% filter(USUBJID \%in\% ADSL$USUBJID) + ADSL <- osprey::rADSL \%>\% slice(1:30) + ADEX <- osprey::rADEX \%>\% filter(USUBJID \%in\% ADSL$USUBJID) + ADAE <- osprey::rADAE \%>\% filter(USUBJID \%in\% ADSL$USUBJID) + ADCM <- osprey::rADCM \%>\% filter(USUBJID \%in\% ADSL$USUBJID) ADCM <- ADCM \%>\% select(-starts_with(\"ATC\")) \%>\% unique() ADEX <- ADEX \%>\% filter(PARCAT1 == 'INDIVIDUAL') \%>\% diff --git a/man/tm_g_patient_profile.Rd b/man/tm_g_patient_profile.Rd index be421c89..7d122fd6 100644 --- a/man/tm_g_patient_profile.Rd +++ b/man/tm_g_patient_profile.Rd @@ -108,18 +108,15 @@ the start date } } \examples{ -library(scda) library(nestcolor) -latest_data <- synthetic_cdisc_data("latest") - -ADSL <- latest_data$adsl -ADAE <- latest_data$adae \%>\% +ADSL <- osprey::rADSL +ADAE <- osprey::rADAE \%>\% mutate( ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM) ) -ADCM <- latest_data$adcm \%>\% +ADCM <- osprey::rADCM \%>\% mutate( ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM) @@ -130,14 +127,14 @@ ADCM <- ADCM \%>\% select(-starts_with("ATC")) \%>\% unique() -ADRS <- latest_data$adrs \%>\% +ADRS <- osprey::rADRS \%>\% mutate(ADT = as.Date(ADTM)) -ADEX <- latest_data$adex \%>\% +ADEX <- osprey::rADEX \%>\% mutate( ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM) ) -ADLB <- latest_data$adlb \%>\% +ADLB <- osprey::rADLB \%>\% mutate( ADT = as.Date(ADTM), LBSTRESN = as.numeric(LBSTRESC) @@ -145,32 +142,27 @@ ADLB <- latest_data$adlb \%>\% app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, - code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl" - ), - cdisc_dataset("ADRS", ADRS, - code = "ADRS <- synthetic_cdisc_data(\"latest\")$adrs \%>\% - mutate(ADT = as.Date(ADTM))" - ), + cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), + cdisc_dataset("ADRS", ADRS, code = "ADRS <- osprey::rADRS \%>\% mutate(ADT = as.Date(ADTM))"), cdisc_dataset("ADAE", ADAE, - code = "ADAE <- synthetic_cdisc_data(\"latest\")$adae \%>\% + code = "ADAE <- osprey::rADAE \%>\% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM))" ), cdisc_dataset("ADCM", ADCM, - code = "ADCM <- synthetic_cdisc_data(\"latest\")$adcm \%>\% + code = "ADCM <- osprey::rADCM \%>\% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM)) ADCM <- ADCM \%>\% select(-starts_with(\"ATC\")) \%>\% unique()", keys = c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "CMDECOD") ), cdisc_dataset("ADLB", ADLB, - code = "ADLB <- synthetic_cdisc_data(\"latest\")$adlb \%>\% + code = "ADLB <- osprey::rADLB \%>\% mutate(ADT = as.Date(ADTM), LBSTRESN = as.numeric(LBSTRESC))" ), cdisc_dataset("ADEX", ADEX, - code = "ADEX <- synthetic_cdisc_data(\"latest\")$adex \%>\% + code = "ADEX <- osprey::rADEX \%>\% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM))" ), diff --git a/man/tm_g_spiderplot.Rd b/man/tm_g_spiderplot.Rd index 7170b592..2d28e6eb 100644 --- a/man/tm_g_spiderplot.Rd +++ b/man/tm_g_spiderplot.Rd @@ -80,17 +80,16 @@ Display spider plot as a shiny module # Example using stream (ADaM) dataset library(dplyr) -library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADTR <- synthetic_cdisc_data("latest")$adtr +ADSL <- osprey::rADSL +ADTR <- osprey::rADTR app <- teal::init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"), + cdisc_dataset("ADSL", ADSL, code = "ADSL <- osprey::rADSL"), cdisc_dataset("ADTR", ADTR, - code = "ADTR <- synthetic_cdisc_data(\"latest\")$adtr", + code = "ADTR <- osprey::rADTR", keys = c("STUDYID", "USUBJID", "PARAMCD", "AVISIT") ), check = TRUE diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml index 3424e2f2..fb477d8a 100644 --- a/staged_dependencies.yaml +++ b/staged_dependencies.yaml @@ -27,12 +27,6 @@ upstream_repos: insightsengineering/teal: repo: insightsengineering/teal host: https://github.com - insightsengineering/scda: - repo: insightsengineering/scda - host: https://github.com - insightsengineering/scda.2022: - repo: insightsengineering/scda.2022 - host: https://github.com insightsengineering/formatters: repo: insightsengineering/formatters host: https://github.com