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Add 'rmarkdown' in suggest field + update infos

François Vieille 1 year ago
parent
commit
a7b27f51b2

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.Rbuildignore View File

@@ -3,4 +3,5 @@
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 ^data-raw$
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 ^draft$
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 ^NEWS$
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-^cran-comments.md$
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+^cran-comments.md$
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+^revdep$

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.gitignore View File

@@ -3,3 +3,4 @@
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 .RData
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 /drafts/*
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 inst/doc
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+/revdep/.cache.rds

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DESCRIPTION View File

@@ -1,7 +1,7 @@
1 1
 Package: aVirtualTwins
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 Type: Package
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 Title: Adaptation of Virtual Twins Method from Jared Foster
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-Version: 1.0.0.9000
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+Version: 1.0.1
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 Date: 2016-10-09
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 Authors@R: person("Francois", "Vieille", email = "vieille.francois@gmail.com",
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   role = c("aut", "cre"))
@@ -18,7 +18,8 @@ Imports:
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 Suggests:
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     caret,
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     knitr,
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-    rpart.plot
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+    rpart.plot,
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+    rmarkdown
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 Depends:
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     R (>= 3.2.0),
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 Collate:
@@ -42,4 +43,4 @@ Collate:
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     'tree.reg.R'
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     'tree.wrapper.R'
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 VignetteBuilder: knitr
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-RoxygenNote: 5.0.1
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+RoxygenNote: 6.0.1

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NEWS View File

@@ -1,3 +1,10 @@
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+aVirtualTwins 1.0.1 (2018-01-30)
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+----------------------------------------------------------------
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+
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+* Fix CRAN warning : CRAN packages using undeclared packages in vignettes
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+* waiting for submission approval
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+
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+
1 8
 aVirtualTwins 1.0.0.9000 (2016-10-10)
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 ----------------------------------------------------------------
3 10
 

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cran-comments.md View File

@@ -1,3 +1,32 @@
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+This is the second submission
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+
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+----------------------------------------------------------------
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+
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+## v1.0.1 : patch to cran warning:
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+
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+>CRAN packages using undeclared packages in vignettes
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+
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+`rmarkdown` seems to be the issue. Added rmarkdown to suggest field.
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+
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+## Test environments
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+
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+* Linux, Debian jessie, R 3.4.3
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+* win-builder (devel and release)
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+
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+
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+## R CMD check result
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+
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+Status: OK
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+
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+R CMD check results
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+0 errors | 0 warnings | 0 notes
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+
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+
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+
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+
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+
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+
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+
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 This is the first submission
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 ----------------------------------------------------------------

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man/VT.difft.Rd View File

@@ -33,13 +33,14 @@ So \emph{absolute} method is :
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 \item{\code{difft}}{vector of difference between twin1 and twin2}
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 }}
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+
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 \section{Methods}{
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 \describe{
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 \item{\code{computeDifft()}}{Compute difference between twin1 and twin2. See details.}
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 }}
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+
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 \seealso{
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 \code{\link{VT.forest}}, \code{\link{VT.forest.one}},
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   \code{\link{VT.forest.double}}
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 }
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-

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man/VT.forest-abstract.Rd View File

@@ -14,6 +14,7 @@ An abstract reference class to compute twin via random forests
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 \describe{
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 \item{\code{...}}{see fields of \code{\link{VT.difft}}}
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 }}
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+
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 \section{Methods}{
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 \describe{
@@ -23,7 +24,7 @@ An abstract reference class to compute twin via random forests
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 \item{\code{run()}}{Compute twin1 and twin2 estimation. Switch treatment if necessary.}
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 }}
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+
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 \seealso{
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 \code{\link{VT.difft}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
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 }
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-

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man/VT.forest.double.Rd View File

@@ -31,6 +31,7 @@ This is what \code{computeTwin2()} does.
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 \item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
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 }}
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+
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 \section{Methods}{
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 \describe{
@@ -38,8 +39,8 @@ This is what \code{computeTwin2()} does.
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 \item{\code{computeTwin2()}}{Compute twin2 by the other part of data in the other forest. See details.}
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 }}
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+
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 \seealso{
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 \code{\link{VT.difft}}, \code{\link{VT.forest}},
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   \code{\link{VT.forest.one}}
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 }
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-

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man/VT.forest.fold.Rd View File

@@ -28,13 +28,14 @@ interactions}
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 \item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
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 }}
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+
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 \section{Methods}{
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 \describe{
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 \item{\code{run()}}{Compute twin1 and twin2 estimation. Switch treatment if necessary.}
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 }}
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+
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 \seealso{
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 \code{\link{VT.difft}}, \code{\link{VT.forest}}, 
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   \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
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 }
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-

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man/VT.forest.one.Rd View File

@@ -24,6 +24,7 @@ what \code{computeTwin1()} and \code{computeTwin2()} functions do.
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 \item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
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 }}
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+
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 \section{Methods}{
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 \describe{
@@ -31,7 +32,7 @@ what \code{computeTwin1()} and \code{computeTwin2()} functions do.
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 \item{\code{computeTwin2()}}{Compute twin2 by switching treatment and applying random forest model}
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 }}
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+
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 \seealso{
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 \code{\link{VT.difft}}, \code{\link{VT.forest}}, \code{\link{VT.forest.double}}
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 }
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-

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man/VT.object.Rd View File

@@ -33,6 +33,7 @@ treatments.}
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 \item{\code{type}}{Character : binary or continous. Only binary is currently 
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 available.}
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 }}
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+
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 \section{Methods}{
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 \describe{
@@ -53,6 +54,7 @@ If trt is not NULL, return predictors for T = trt}
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 \item{\code{switchTreatment()}}{Switch treatment value.}
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 }}
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+
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 \examples{
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 \dontrun{
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 # Default use :
@@ -78,4 +80,3 @@ vt.o$getIncidences()
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 \seealso{
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 \code{\link{VT.difft}}
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 }
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-

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man/VT.predict.Rd View File

@@ -3,10 +3,10 @@
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 \docType{methods}
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 \name{VT.predict}
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 \alias{VT.predict}
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-\alias{VT.predict,RandomForest,data.frame,character-method}
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 \alias{VT.predict,RandomForest,missing,character-method}
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-\alias{VT.predict,randomForest,data.frame,character-method}
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+\alias{VT.predict,RandomForest,data.frame,character-method}
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 \alias{VT.predict,randomForest,missing,character-method}
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+\alias{VT.predict,randomForest,data.frame,character-method}
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 \alias{VT.predict,train,ANY,character-method}
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 \alias{VT.predict,train,missing,character-method}
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 \title{VT.predict generic function}

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man/VT.tree-abstract.Rd View File

@@ -52,6 +52,7 @@ screening field}
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 \item{\code{Ahat}}{vector Indicator of beglonging to Ahat}
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 }}
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+
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 \section{Methods}{
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 \describe{
@@ -74,7 +75,7 @@ screening field}
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 \item{\code{run(...)}}{Compute tree with rpart parameters}
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 }}
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+
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 \seealso{
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 \code{\link{VT.tree.reg}}, \code{\link{VT.tree.class}}
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 }
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-

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man/aVirtualTwins.Rd View File

@@ -4,6 +4,7 @@
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 \name{aVirtualTwins}
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 \alias{aVirtualTwins}
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 \alias{aVirtualTwins-package}
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+\alias{aVirtualTwins-package}
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 \title{aVirtualTwins : An adapation of VirtualTwins method created by Jared Foster.}
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 \description{
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 aVirtualTwins is written mainly with reference classes. Briefly, there is three kinds of class :

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man/formatRCTDataset.Rd View File

@@ -43,4 +43,3 @@ data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE)
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 }
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-

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man/sepsis.Rd View File

@@ -43,4 +43,3 @@ True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80}. \emph{NOTE:} This
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 subgroup is defined with the \emph{lower} event rate (survival = 1) in
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 treatement arm.
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 }
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-

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man/vt.data.Rd View File

@@ -33,4 +33,3 @@ a VT.object object.
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 }
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 }
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-

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man/vt.forest.Rd View File

@@ -69,4 +69,3 @@ parameter forest.type, any of these class can be used with its own parameter.
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 }   
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 }
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-

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man/vt.subgroups.Rd View File

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 }
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 }
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-

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man/vt.tree.Rd View File

@@ -56,4 +56,3 @@ See \code{\link{VT.tree}}, \code{\link{VT.tree.class}} and
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 }
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 }
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-

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revdep/check.R View File

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+library("devtools")
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+
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+revdep_check()
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+revdep_check_save_summary()
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+revdep_check_print_problems()

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revdep/checks.rds View File


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