diff --git a/.Rbuildignore b/.Rbuildignore index 794a039..272d789 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -3,4 +3,5 @@ ^data-raw$ ^draft$ ^NEWS$ -^cran-comments.md$ \ No newline at end of file +^cran-comments.md$ +^revdep$ diff --git a/.gitignore b/.gitignore index c4a8ce8..4b6d732 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ .RData /drafts/* inst/doc +/revdep/.cache.rds diff --git a/DESCRIPTION b/DESCRIPTION index 57e2895..30aeb58 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: aVirtualTwins Type: Package Title: Adaptation of Virtual Twins Method from Jared Foster -Version: 1.0.0.9000 +Version: 1.0.1 Date: 2016-10-09 Authors@R: person("Francois", "Vieille", email = "vieille.francois@gmail.com", role = c("aut", "cre")) @@ -18,7 +18,8 @@ Imports: Suggests: caret, knitr, - rpart.plot + rpart.plot, + rmarkdown Depends: R (>= 3.2.0), Collate: @@ -42,4 +43,4 @@ Collate: 'tree.reg.R' 'tree.wrapper.R' VignetteBuilder: knitr -RoxygenNote: 5.0.1 +RoxygenNote: 6.0.1 diff --git a/NEWS b/NEWS index 4aeffce..2d8fc05 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,10 @@ +aVirtualTwins 1.0.1 (2018-01-30) +---------------------------------------------------------------- + +* Fix CRAN warning : CRAN packages using undeclared packages in vignettes +* waiting for submission approval + + aVirtualTwins 1.0.0.9000 (2016-10-10) ---------------------------------------------------------------- diff --git a/cran-comments.md b/cran-comments.md index ee3e4f2..9ebf9bc 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,32 @@ +This is the second submission + +---------------------------------------------------------------- + +## v1.0.1 : patch to cran warning: + +>CRAN packages using undeclared packages in vignettes + +`rmarkdown` seems to be the issue. Added rmarkdown to suggest field. + +## Test environments + +* Linux, Debian jessie, R 3.4.3 +* win-builder (devel and release) + + +## R CMD check result + +Status: OK + +R CMD check results +0 errors | 0 warnings | 0 notes + + + + + + + This is the first submission ---------------------------------------------------------------- diff --git a/man/VT.difft.Rd b/man/VT.difft.Rd index 36ce963..48392e7 100644 --- a/man/VT.difft.Rd +++ b/man/VT.difft.Rd @@ -33,13 +33,14 @@ So \emph{absolute} method is : \item{\code{difft}}{vector of difference between twin1 and twin2} }} + \section{Methods}{ \describe{ \item{\code{computeDifft()}}{Compute difference between twin1 and twin2. See details.} }} + \seealso{ \code{\link{VT.forest}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}} } - diff --git a/man/VT.forest-abstract.Rd b/man/VT.forest-abstract.Rd index 0dcffce..6765e38 100644 --- a/man/VT.forest-abstract.Rd +++ b/man/VT.forest-abstract.Rd @@ -14,6 +14,7 @@ An abstract reference class to compute twin via random forests \describe{ \item{\code{...}}{see fields of \code{\link{VT.difft}}} }} + \section{Methods}{ \describe{ @@ -23,7 +24,7 @@ An abstract reference class to compute twin via random forests \item{\code{run()}}{Compute twin1 and twin2 estimation. Switch treatment if necessary.} }} + \seealso{ \code{\link{VT.difft}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}} } - diff --git a/man/VT.forest.double.Rd b/man/VT.forest.double.Rd index 8b49bc4..79d7955 100644 --- a/man/VT.forest.double.Rd +++ b/man/VT.forest.double.Rd @@ -31,6 +31,7 @@ This is what \code{computeTwin2()} does. \item{\code{...}}{field from parent class : \code{\link{VT.forest}}} }} + \section{Methods}{ \describe{ @@ -38,8 +39,8 @@ This is what \code{computeTwin2()} does. \item{\code{computeTwin2()}}{Compute twin2 by the other part of data in the other forest. See details.} }} + \seealso{ \code{\link{VT.difft}}, \code{\link{VT.forest}}, \code{\link{VT.forest.one}} } - diff --git a/man/VT.forest.fold.Rd b/man/VT.forest.fold.Rd index 32c4fa3..f00c339 100644 --- a/man/VT.forest.fold.Rd +++ b/man/VT.forest.fold.Rd @@ -28,13 +28,14 @@ interactions} \item{\code{...}}{field from parent class : \code{\link{VT.forest}}} }} + \section{Methods}{ \describe{ \item{\code{run()}}{Compute twin1 and twin2 estimation. Switch treatment if necessary.} }} + \seealso{ \code{\link{VT.difft}}, \code{\link{VT.forest}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}} } - diff --git a/man/VT.forest.one.Rd b/man/VT.forest.one.Rd index e9e4005..0227c31 100644 --- a/man/VT.forest.one.Rd +++ b/man/VT.forest.one.Rd @@ -24,6 +24,7 @@ what \code{computeTwin1()} and \code{computeTwin2()} functions do. \item{\code{...}}{field from parent class : \code{\link{VT.forest}}} }} + \section{Methods}{ \describe{ @@ -31,7 +32,7 @@ what \code{computeTwin1()} and \code{computeTwin2()} functions do. \item{\code{computeTwin2()}}{Compute twin2 by switching treatment and applying random forest model} }} + \seealso{ \code{\link{VT.difft}}, \code{\link{VT.forest}}, \code{\link{VT.forest.double}} } - diff --git a/man/VT.object.Rd b/man/VT.object.Rd index a4c1f76..c211f69 100644 --- a/man/VT.object.Rd +++ b/man/VT.object.Rd @@ -33,6 +33,7 @@ treatments.} \item{\code{type}}{Character : binary or continous. Only binary is currently available.} }} + \section{Methods}{ \describe{ @@ -53,6 +54,7 @@ If trt is not NULL, return predictors for T = trt} \item{\code{switchTreatment()}}{Switch treatment value.} }} + \examples{ \dontrun{ # Default use : @@ -78,4 +80,3 @@ vt.o$getIncidences() \seealso{ \code{\link{VT.difft}} } - diff --git a/man/VT.predict.Rd b/man/VT.predict.Rd index 1c7a49b..e157a41 100644 --- a/man/VT.predict.Rd +++ b/man/VT.predict.Rd @@ -3,10 +3,10 @@ \docType{methods} \name{VT.predict} \alias{VT.predict} -\alias{VT.predict,RandomForest,data.frame,character-method} \alias{VT.predict,RandomForest,missing,character-method} -\alias{VT.predict,randomForest,data.frame,character-method} +\alias{VT.predict,RandomForest,data.frame,character-method} \alias{VT.predict,randomForest,missing,character-method} +\alias{VT.predict,randomForest,data.frame,character-method} \alias{VT.predict,train,ANY,character-method} \alias{VT.predict,train,missing,character-method} \title{VT.predict generic function} diff --git a/man/VT.tree-abstract.Rd b/man/VT.tree-abstract.Rd index ac7121b..d6bedb7 100644 --- a/man/VT.tree-abstract.Rd +++ b/man/VT.tree-abstract.Rd @@ -52,6 +52,7 @@ screening field} \item{\code{Ahat}}{vector Indicator of beglonging to Ahat} }} + \section{Methods}{ \describe{ @@ -74,7 +75,7 @@ screening field} \item{\code{run(...)}}{Compute tree with rpart parameters} }} + \seealso{ \code{\link{VT.tree.reg}}, \code{\link{VT.tree.class}} } - diff --git a/man/aVirtualTwins.Rd b/man/aVirtualTwins.Rd index da56540..8f91663 100644 --- a/man/aVirtualTwins.Rd +++ b/man/aVirtualTwins.Rd @@ -4,6 +4,7 @@ \name{aVirtualTwins} \alias{aVirtualTwins} \alias{aVirtualTwins-package} +\alias{aVirtualTwins-package} \title{aVirtualTwins : An adapation of VirtualTwins method created by Jared Foster.} \description{ aVirtualTwins is written mainly with reference classes. Briefly, there is three kinds of class : diff --git a/man/formatRCTDataset.Rd b/man/formatRCTDataset.Rd index 6501c09..0844031 100644 --- a/man/formatRCTDataset.Rd +++ b/man/formatRCTDataset.Rd @@ -43,4 +43,3 @@ data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE) } - diff --git a/man/sepsis.Rd b/man/sepsis.Rd index e902206..7579398 100644 --- a/man/sepsis.Rd +++ b/man/sepsis.Rd @@ -43,4 +43,3 @@ True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80}. \emph{NOTE:} This subgroup is defined with the \emph{lower} event rate (survival = 1) in treatement arm. } - diff --git a/man/vt.data.Rd b/man/vt.data.Rd index 2f5d78d..1b4ddb2 100644 --- a/man/vt.data.Rd +++ b/man/vt.data.Rd @@ -33,4 +33,3 @@ a VT.object object. } } - diff --git a/man/vt.forest.Rd b/man/vt.forest.Rd index e47bbc8..ffbf0e1 100644 --- a/man/vt.forest.Rd +++ b/man/vt.forest.Rd @@ -69,4 +69,3 @@ parameter forest.type, any of these class can be used with its own parameter. } } - diff --git a/man/vt.subgroups.Rd b/man/vt.subgroups.Rd index c4a072d..5eb2f65 100644 --- a/man/vt.subgroups.Rd +++ b/man/vt.subgroups.Rd @@ -46,4 +46,3 @@ rpart.plot must be loaded. See \code{\link{VT.tree}} for details. } } - diff --git a/man/vt.tree.Rd b/man/vt.tree.Rd index a5c252d..f2e6241 100644 --- a/man/vt.tree.Rd +++ b/man/vt.tree.Rd @@ -56,4 +56,3 @@ See \code{\link{VT.tree}}, \code{\link{VT.tree.class}} and } } - diff --git a/revdep/check.R b/revdep/check.R new file mode 100644 index 0000000..e262948 --- /dev/null +++ b/revdep/check.R @@ -0,0 +1,5 @@ +library("devtools") + +revdep_check() +revdep_check_save_summary() +revdep_check_print_problems() diff --git a/revdep/checks.rds b/revdep/checks.rds new file mode 100644 index 0000000..82941ab Binary files /dev/null and b/revdep/checks.rds differ