diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..466e8a8 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,3 @@ +^.*\.Rproj$ +^.*\.Rproj$ +materials/* diff --git a/package/DESCRIPTION b/DESCRIPTION similarity index 100% rename from package/DESCRIPTION rename to DESCRIPTION diff --git a/package/NAMESPACE b/NAMESPACE similarity index 100% rename from package/NAMESPACE rename to NAMESPACE diff --git a/package/R/LUAD.R b/R/LUAD.R similarity index 100% rename from package/R/LUAD.R rename to R/LUAD.R diff --git a/package/R/crSummary.R b/R/crSummary.R similarity index 100% rename from package/R/crSummary.R rename to R/crSummary.R diff --git a/package/R/eventsTab.R b/R/eventsTab.R similarity index 100% rename from package/R/eventsTab.R rename to R/eventsTab.R diff --git a/package/R/fitAndTestCompRiskReg.R b/R/fitAndTestCompRiskReg.R similarity index 100% rename from package/R/fitAndTestCompRiskReg.R rename to R/fitAndTestCompRiskReg.R diff --git a/package/R/fitAndTestCox.R b/R/fitAndTestCox.R similarity index 100% rename from package/R/fitAndTestCox.R rename to R/fitAndTestCox.R diff --git a/package/R/fitAndTestCuminc.R b/R/fitAndTestCuminc.R similarity index 100% rename from package/R/fitAndTestCuminc.R rename to R/fitAndTestCuminc.R diff --git a/package/R/fitAndTestSurvival.R b/R/fitAndTestSurvival.R similarity index 100% rename from package/R/fitAndTestSurvival.R rename to R/fitAndTestSurvival.R diff --git a/package/R/plotCuminc.R b/R/plotCuminc.R similarity index 100% rename from package/R/plotCuminc.R rename to R/plotCuminc.R diff --git a/package/R/plotSurvival.R b/R/plotSurvival.R similarity index 100% rename from package/R/plotSurvival.R rename to R/plotSurvival.R diff --git a/package/R/riskTab.R b/R/riskTab.R similarity index 100% rename from package/R/riskTab.R rename to R/riskTab.R diff --git a/README.md b/README.md index f72724c..ca18a16 100644 --- a/README.md +++ b/README.md @@ -3,9 +3,9 @@ ## Installation ``` -devtools::install_github("geneticsMiNIng/cr17/package") +devtools::install_github("geneticsMiNIng/cr17") ``` ## Competing Risks with R and ggplot2 -* example data from RTCGA package [LUAD cancer](https://github.com/geneticsMiNIng/cr07/blob/master/getLUADdata.R) +* example data from RTCGA package [LUAD cancer](https://github.com/geneticsMiNIng/cr07/blob/master/materials/getLUADdata.R) diff --git a/package/cr17.Rproj b/cr17.Rproj similarity index 100% rename from package/cr17.Rproj rename to cr17.Rproj diff --git a/cr17_0.1.0.tar.gz b/cr17_0.1.0.tar.gz deleted file mode 100644 index 7810470..0000000 Binary files a/cr17_0.1.0.tar.gz and /dev/null differ diff --git a/package/data/LUAD.rda b/data/LUAD.rda similarity index 100% rename from package/data/LUAD.rda rename to data/LUAD.rda diff --git a/package/man/LUAD.Rd b/man/LUAD.Rd similarity index 100% rename from package/man/LUAD.Rd rename to man/LUAD.Rd diff --git a/package/man/eventTab.Rd b/man/eventTab.Rd similarity index 100% rename from package/man/eventTab.Rd rename to man/eventTab.Rd diff --git a/package/man/fitCuminc.Rd b/man/fitCuminc.Rd similarity index 100% rename from package/man/fitCuminc.Rd rename to man/fitCuminc.Rd diff --git a/package/man/fitReg.Rd b/man/fitReg.Rd similarity index 100% rename from package/man/fitReg.Rd rename to man/fitReg.Rd diff --git a/package/man/fitSurvival.Rd b/man/fitSurvival.Rd similarity index 100% rename from package/man/fitSurvival.Rd rename to man/fitSurvival.Rd diff --git a/package/man/plotCuminc.Rd b/man/plotCuminc.Rd similarity index 100% rename from package/man/plotCuminc.Rd rename to man/plotCuminc.Rd diff --git a/package/man/plotSurvival.Rd b/man/plotSurvival.Rd similarity index 100% rename from package/man/plotSurvival.Rd rename to man/plotSurvival.Rd diff --git a/package/man/riskTab.Rd b/man/riskTab.Rd similarity index 100% rename from package/man/riskTab.Rd rename to man/riskTab.Rd diff --git a/package/man/simpleCox.Rd b/man/simpleCox.Rd similarity index 100% rename from package/man/simpleCox.Rd rename to man/simpleCox.Rd diff --git a/package/man/summarizeCR.Rd b/man/summarizeCR.Rd similarity index 100% rename from package/man/summarizeCR.Rd rename to man/summarizeCR.Rd diff --git a/package/man/testCox.Rd b/man/testCox.Rd similarity index 100% rename from package/man/testCox.Rd rename to man/testCox.Rd diff --git a/package/man/testCuminc.Rd b/man/testCuminc.Rd similarity index 100% rename from package/man/testCuminc.Rd rename to man/testCuminc.Rd diff --git a/package/man/testReg.Rd b/man/testReg.Rd similarity index 100% rename from package/man/testReg.Rd rename to man/testReg.Rd diff --git a/package/man/testSurvival.Rd b/man/testSurvival.Rd similarity index 100% rename from package/man/testSurvival.Rd rename to man/testSurvival.Rd diff --git a/getLUADdata.R b/materials/getLUADdata.R similarity index 100% rename from getLUADdata.R rename to materials/getLUADdata.R diff --git a/package/.Rbuildignore b/package/.Rbuildignore deleted file mode 100644 index 91114bf..0000000 --- a/package/.Rbuildignore +++ /dev/null @@ -1,2 +0,0 @@ -^.*\.Rproj$ -^\.Rproj\.user$