From bf7c287144660e2bc21af80e93b2a082a9d60781 Mon Sep 17 00:00:00 2001 From: George G Vega Yon Date: Fri, 21 May 2021 11:34:40 -0700 Subject: [PATCH] Adding citation file and DOI in README --- .github/workflows/r.yml | 2 +- DESCRIPTION | 17 ++++++++++++++--- Makefile | 27 +++++++++++++++++---------- inst/CITATION | 38 ++++++++++++++++++++++++++++++++++++++ man/cit-package.Rd | 4 ++-- 5 files changed, 72 insertions(+), 16 deletions(-) create mode 100644 inst/CITATION diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index c88ec99..804bc79 100644 --- a/.github/workflows/r.yml +++ b/.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 diff --git a/DESCRIPTION b/DESCRIPTION index 12610c7..fe5e608 100644 --- a/DESCRIPTION +++ b/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), + , 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 diff --git a/Makefile b/Makefile index aac0235..348efc7 100644 --- a/Makefile +++ b/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 $(VERSION) +.PHONY: install check clean checkv debug version diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..6371e1d --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,38 @@ +year <- sub("-.*", "", meta$Date) +note <- sprintf("R package version %s", meta$Version) + +citHeader("To cite cit in publications use:") + +citEntry( + entry = "Article", + title = "cit: hypothesis testing software for mediation analysis in genomic applications", + author = c( + person("Joshua", "Millstein", email = "joshua.millstein@usc.edu"), + person("Gary", "Chen"), + person("Carrie", "Breton") + ), + journal = "Bioinformatics", + year = 2016, + month = "aug", + volume = 32, + issue = 15, + doi = "10.1093/bioinformatics/btw135", + url = "https://doi.org/10.1093/bioinformatics/btw135", + issn = "1367-4803", + textVersion = "Joshua Millstein, Gary K. Chen, Carrie V. Breton, cit: hypothesis testing software for mediation analysis in genomic applications, Bioinformatics, Volume 32, Issue 15, 1 August 2016, Pages 2364-2365, https://doi.org/10.1093/bioinformatics/btw135" +) + +bibentry( + bibtype = "Manual", + title = "{{cit: Causal Inference Test}}", + author = person( + "Joshua", "Millstein", email = "joshua.millstein@usc.edu", + role = c("aut", "cre"), comment = c(ORCID="0000-0001-7961-8943") + ), + year = year, + note = note, + publisher="{CRAN}", + url = "https://cran.r-project.org/package=cit", + header = "Use this if you are using the CRAN version of cit:" +) + diff --git a/man/cit-package.Rd b/man/cit-package.Rd index 5f17911..bb1c917 100644 --- a/man/cit-package.Rd +++ b/man/cit-package.Rd @@ -11,8 +11,8 @@ This package implements a formal statistical hypothesis test for causal mediatio \tabular{ll}{ Package: \tab cit\cr Type: \tab Package\cr -Version: \tab 2.3.0\cr -Date: \tab 2021-05-19\cr +Version: \tab \Sexpr{packageDescription("cit")$Version}\cr +Date: \tab \Sexpr{packageDescription("cit")$Date}\cr License: \tab Artistic-2.0\cr LazyLoad: \tab yes\cr }