Add 'rmarkdown' in suggest field + update infos

This commit is contained in:
François Vieille 2018-01-30 23:43:25 +01:00
vecāks ea072ba3fc
revīzija a7b27f51b2
22 mainīti faili ar 65 papildinājumiem un 19 dzēšanām

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

1
.gitignore ārējs
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@ -3,3 +3,4 @@
.RData
/drafts/*
inst/doc
/revdep/.cache.rds

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@ -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

7
NEWS
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@ -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)
----------------------------------------------------------------

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@ -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
----------------------------------------------------------------

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@ -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}}
}

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@ -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}}
}

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@ -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}}
}

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@ -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}}
}

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@ -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}}
}

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@ -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}}
}

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@ -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}

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@ -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}}
}

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@ -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 :

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

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@ -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.
}

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

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

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@ -46,4 +46,3 @@ rpart.plot must be loaded. See \code{\link{VT.tree}} for details.
}
}

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

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revdep/check.R Normal file
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@ -0,0 +1,5 @@
library("devtools")
revdep_check()
revdep_check_save_summary()
revdep_check_print_problems()

Binārs
revdep/checks.rds Normal file

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