Adding citation file and DOI in README

.github/workflows/r.yml

@@ -19,7 +19,7 @@ jobs:
     runs-on: Ubuntu-latest
     strategy:
       matrix:
-        r-version: [3.5, 3.6, 4.0.4]
+        r-version: [3.5, 3.6, 4.1.0]
 
     steps:
       - uses: actions/checkout@v2

DESCRIPTION

@@ -1,11 +1,22 @@
 Package: cit
 Type: Package
 Title: Causal Inference Test
-Version: 2.3.0
-Date: 2021-05-19
+Version: 2.3.1
+Date: 2021-05-21
 Authors@R: person("Joshua", "Millstein", email = "joshua.millstein@usc.edu", role =
 	c("aut", "cre"), comment = c(ORCID="0000-0001-7961-8943"))
-Description: A likelihood-based hypothesis testing approach is implemented for assessing causal mediation. For example, it could be used to test for mediation of a known causal association between a DNA variant, the 'instrumental variable', and a clinical outcome or phenotype by gene expression or DNA methylation, the potential mediator. Another example would be testing mediation of the effect of a drug on a clinical outcome by the molecular target. The hypothesis test generates a p-value or permutation-based FDR value with confidence intervals to quantify uncertainty in the causal inference. The outcome can be represented by either a continuous or binary variable, the potential mediator is continuous, and the instrumental variable can be continuous or binary and is not limited to a single variable but may be a design matrix representing multiple variables.
+Description: A likelihood-based hypothesis testing approach is implemented for
+  assessing causal mediation. Described in Millstein, Chen, and Breton (2016),
+  <DOI:10.1093/bioinformatics/btw135>, it could be used to test for mediation
+  of a known causal association between a DNA variant, the 'instrumental variable',
+  and a clinical outcome or phenotype by gene expression or DNA methylation, the
+  potential mediator. Another example would be testing mediation of the effect
+  of a drug on a clinical outcome by the molecular target. The hypothesis test
+  generates a p-value or permutation-based FDR value with confidence intervals
+  to quantify uncertainty in the causal inference. The outcome can be represented
+  by either a continuous or binary variable, the potential mediator is continuous,
+  and the instrumental variable can be continuous or binary and is not limited to
+  a single variable but may be a design matrix representing multiple variables.
 SystemRequirements: gsl (with development libraries libgsl-dev)
 License: Artistic-2.0
 LazyLoad: yes

Makefile

@@ -1,17 +1,24 @@
-cit.tar.gz: inst/NEWS 
-	R CMD build . && mv cit_*.tar.gz cit.tar.gz
-install: cit.tar.gz
-	cd .. && R CMD INSTALL cit_.tar.gz
-checkv: cit.tar.gz
-	R CMD check --use-valgrind cit.tar.gz
-check: cit.tar.gz
-	R CMD check cit.tar.gz
+VERSION:=$(shell Rscript -e 'x<-readLines("DESCRIPTION");cat(gsub(".+[:]\\s*", "", x[grepl("^Vers", x)]))')
+
+cit_$(VERSION).tar.gz: inst/NEWS R/*.R src/*.cpp
+	R CMD build . 
+
+install: cit_$(VERSION).tar.gz
+	R CMD INSTALL cit_$(VERSION).tar.gz
+
+checkv: cit_$(VERSION).tar.gz
+	R CMD check --use-valgrind cit_$(VERSION).tar.gz
+
+check: cit_$(VERSION).tar.gz
+	R CMD check --as-cran cit_$(VERSION).tar.gz
 clean:
-	rm -rf cit.tar.gz; rm -rf cit.Rcheck
+	rm -rf cit*.tar.gz; rm -rf cit*.Rcheck
 debug:
 	R -d valgrind --debugger-args='--leak-check=full'
 inst/NEWS: NEWS.md
 	Rscript -e "rmarkdown::pandoc_convert('NEWS.md', 'plain', output='inst/NEWS')"&& \
 		head -n 80 inst/NEWS
-.PHONY: install check clean checkv debug
+version:
+	echo $(VERSION)
+.PHONY: install check clean checkv debug version
 

inst/CITATION

@@ -0,0 +1,38 @@
+year <- sub("-.*", "", meta$Date)
+note <- sprintf("R package version %s", meta$Version)
+
+citHeader("To cite cit in publications use:")
+
+citEntry(
+  entry  = "Article",
+  title = "cit: hypothesis testing software for mediation analysis in genomic applications",
+  author = c(
+    person("Joshua", "Millstein", email = "joshua.millstein@usc.edu"),
+    person("Gary", "Chen"),
+    person("Carrie", "Breton")
+    ),
+  journal = "Bioinformatics",
+  year    = 2016,
+  month   = "aug",
+  volume  = 32,
+  issue  = 15,
+  doi     = "10.1093/bioinformatics/btw135",
+  url     = "https://doi.org/10.1093/bioinformatics/btw135",
+  issn = "1367-4803",
+ textVersion = "Joshua Millstein, Gary K. Chen, Carrie V. Breton, cit: hypothesis testing software for mediation analysis in genomic applications, Bioinformatics, Volume 32, Issue 15, 1 August 2016, Pages 2364-2365, https://doi.org/10.1093/bioinformatics/btw135"
+)
+
+bibentry(
+  bibtype = "Manual",
+  title = "{{cit: Causal Inference Test}}",
+  author = person(
+    "Joshua", "Millstein", email = "joshua.millstein@usc.edu",
+    role = c("aut", "cre"), comment = c(ORCID="0000-0001-7961-8943")
+    ),
+  year = year,
+  note = note,
+  publisher="{CRAN}",
+  url = "https://cran.r-project.org/package=cit",
+  header = "Use this if you are using the CRAN version of cit:"
+)
+

man/cit-package.Rd

@@ -11,8 +11,8 @@ This package implements a formal statistical hypothesis test for causal mediatio
 \tabular{ll}{
 Package: \tab cit\cr
 Type: \tab Package\cr
-Version: \tab 2.3.0\cr
-Date: \tab 2021-05-19\cr
+Version: \tab \Sexpr{packageDescription("cit")$Version}\cr
+Date: \tab \Sexpr{packageDescription("cit")$Date}\cr
 License: \tab Artistic-2.0\cr
 LazyLoad: \tab yes\cr
 }