From 98b28e9c941d947b0fef60789f7dcbb8af53b344 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 26 Sep 2024 13:35:56 +1100 Subject: [PATCH 01/10] Sort TAF exports to facilitate diffs between releases --- TAF-exports/create-TAF-exports.R | 1 + 1 file changed, 1 insertion(+) diff --git a/TAF-exports/create-TAF-exports.R b/TAF-exports/create-TAF-exports.R index 0682719..7c3b757 100644 --- a/TAF-exports/create-TAF-exports.R +++ b/TAF-exports/create-TAF-exports.R @@ -7,6 +7,7 @@ ns <- loadNamespace("TAF") TAF_functions <- unlist(eapply(ns, inherits, "function")) TAF_functions <- names(TAF_functions)[which(TAF_functions)] TAF_functions <- setdiff(TAF_functions, "taf.skeleton") +TAF_functions <- sort(TAF_functions) import_block <- function(fun_name, first = FALSE) { From 218e24b854a71deee40f7a7943881caae95c8497 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 26 Sep 2024 13:39:58 +1100 Subject: [PATCH 02/10] Create TAF exports for version 4.2.0 --- R/TAF.R | 338 ++++++++++++++++++++++++++++---------------------------- 1 file changed, 169 insertions(+), 169 deletions(-) diff --git a/R/TAF.R b/R/TAF.R index 514462c..8482fc5 100644 --- a/R/TAF.R +++ b/R/TAF.R @@ -4,433 +4,433 @@ #' These functions are re-exported from the TAF package. #' #' Follow the links below to see the documentation. -#' \code{\link[TAF]{makeAll}}, \code{\link[TAF]{taf.install}}, \code{\link[TAF]{parse.repo}}, \code{\link[TAF]{taf2long}}, \code{\link[TAF]{write.taf}}, \code{\link[TAF]{utf8.to.latin1}}, \code{\link[TAF]{download}}, \code{\link[TAF]{clean.boot}}, \code{\link[TAF]{flr2taf}}, \code{\link[TAF]{get.remote.sha}}, \code{\link[TAF]{taf.bootstrap}}, \code{\link[TAF]{xtab2taf}}, \code{\link[TAF]{long2taf}}, \code{\link[TAF]{source.taf}}, \code{\link[TAF]{ds.file}}, \code{\link[TAF]{div}}, \code{\link[TAF]{detach.packages}}, \code{\link[TAF]{rnd}}, \code{\link[TAF]{taf2xtab}}, \code{\link[TAF]{ds.package}}, \code{\link[TAF]{long2xtab}}, \code{\link[TAF]{os.linux}}, \code{\link[TAF]{taf.png}}, \code{\link[TAF]{os.macos}}, \code{\link[TAF]{os}}, \code{\link[TAF]{period}}, \code{\link[TAF]{tt}}, \code{\link[TAF]{clean.data}}, \code{\link[TAF]{zoom.trellis}}, \code{\link[TAF]{zoom}}, \code{\link[TAF]{unix2dos}}, \code{\link[TAF]{dos2unix}}, \code{\link[TAF]{mkdir}}, \code{\link[TAF]{convert.spaces}}, \code{\link[TAF]{lim}}, \code{\link[TAF]{is.r.package}}, \code{\link[TAF]{clean.software}}, \code{\link[TAF]{taf.boot.path}}, \code{\link[TAF]{sourceAll}}, \code{\link[TAF]{plus}}, \code{\link[TAF]{taf.sources}}, \code{\link[TAF]{msg}}, \code{\link[TAF]{process.entry}}, \code{\link[TAF]{taf.data.path}}, \code{\link[TAF]{download.github}}, \code{\link[TAF]{deps}}, \code{\link[TAF]{taf.session}}, \code{\link[TAF]{os.unix}}, \code{\link[TAF]{xtab2long}}, \code{\link[TAF]{os.windows}}, \code{\link[TAF]{draft.data}}, \code{\link[TAF]{read.taf}}, \code{\link[TAF]{clean}}, \code{\link[TAF]{model.script}}, \code{\link[TAF]{taf.libPaths}}, \code{\link[TAF]{draft.software}}, \code{\link[TAF]{sourceDir}}, \code{\link[TAF]{taf.boot}}, \code{\link[TAF]{file.encoding}}, \code{\link[TAF]{latin1.to.utf8}}, \code{\link[TAF]{clean.library}}, \code{\link[TAF]{tafpng}}, \code{\link[TAF]{sourceTAF}}, \code{\link[TAF]{taf2html}}, \code{\link[TAF]{source.all}}, \code{\link[TAF]{extract.subdir}}, \code{\link[TAF]{taf.library}}, \code{\link[TAF]{read.bib}}, \code{\link[TAF]{boot.exists}}, \code{\link[TAF]{boot.dir}}, \code{\link[TAF]{stamp.description}}, \code{\link[TAF]{make.all}}, \code{\link[TAF]{make.taf}}, \code{\link[TAF]{make}}, \code{\link[TAF]{boot.dir.inside}}, \code{\link[TAF]{model.dir}}, \code{\link[TAF]{line.endings}}, \code{\link[TAF]{already.in.taf.library}}, \code{\link[TAF]{taf.unzip}}, \code{\link[TAF]{process.bibfile}}, \code{\link[TAF]{cp}}, \code{\link[TAF]{makeTAF}}, \code{\link[TAF]{rmdir}}, \code{\link[TAF]{source.dir}}, \code{\link[TAF]{sam2taf}} +#' \code{\link[TAF]{already.in.taf.library}}, \code{\link[TAF]{boot.dir}}, \code{\link[TAF]{boot.dir.inside}}, \code{\link[TAF]{boot.exists}}, \code{\link[TAF]{clean}}, \code{\link[TAF]{clean.boot}}, \code{\link[TAF]{clean.data}}, \code{\link[TAF]{clean.library}}, \code{\link[TAF]{clean.software}}, \code{\link[TAF]{convert.spaces}}, \code{\link[TAF]{cp}}, \code{\link[TAF]{deps}}, \code{\link[TAF]{detach.packages}}, \code{\link[TAF]{div}}, \code{\link[TAF]{dos2unix}}, \code{\link[TAF]{download}}, \code{\link[TAF]{download.github}}, \code{\link[TAF]{draft.data}}, \code{\link[TAF]{draft.software}}, \code{\link[TAF]{ds.file}}, \code{\link[TAF]{ds.package}}, \code{\link[TAF]{extract.subdir}}, \code{\link[TAF]{file.encoding}}, \code{\link[TAF]{flr2taf}}, \code{\link[TAF]{get.remote.sha}}, \code{\link[TAF]{is.r.package}}, \code{\link[TAF]{latin1.to.utf8}}, \code{\link[TAF]{lim}}, \code{\link[TAF]{line.endings}}, \code{\link[TAF]{long2taf}}, \code{\link[TAF]{long2xtab}}, \code{\link[TAF]{make}}, \code{\link[TAF]{make.all}}, \code{\link[TAF]{make.taf}}, \code{\link[TAF]{makeAll}}, \code{\link[TAF]{makeTAF}}, \code{\link[TAF]{mkdir}}, \code{\link[TAF]{model.dir}}, \code{\link[TAF]{model.script}}, \code{\link[TAF]{msg}}, \code{\link[TAF]{os}}, \code{\link[TAF]{os.linux}}, \code{\link[TAF]{os.macos}}, \code{\link[TAF]{os.unix}}, \code{\link[TAF]{os.windows}}, \code{\link[TAF]{parse.repo}}, \code{\link[TAF]{period}}, \code{\link[TAF]{plus}}, \code{\link[TAF]{process.bibfile}}, \code{\link[TAF]{process.entry}}, \code{\link[TAF]{read.bib}}, \code{\link[TAF]{read.taf}}, \code{\link[TAF]{rmdir}}, \code{\link[TAF]{rnd}}, \code{\link[TAF]{sam2taf}}, \code{\link[TAF]{source.all}}, \code{\link[TAF]{source.dir}}, \code{\link[TAF]{source.taf}}, \code{\link[TAF]{sourceAll}}, \code{\link[TAF]{sourceDir}}, \code{\link[TAF]{sourceTAF}}, \code{\link[TAF]{stamp.description}}, \code{\link[TAF]{taf.boot}}, \code{\link[TAF]{taf.boot.path}}, \code{\link[TAF]{taf.bootstrap}}, \code{\link[TAF]{taf.data.path}}, \code{\link[TAF]{taf.install}}, \code{\link[TAF]{taf.libPaths}}, \code{\link[TAF]{taf.library}}, \code{\link[TAF]{taf.png}}, \code{\link[TAF]{taf.session}}, \code{\link[TAF]{taf.sources}}, \code{\link[TAF]{taf.unzip}}, \code{\link[TAF]{taf2html}}, \code{\link[TAF]{taf2long}}, \code{\link[TAF]{taf2xtab}}, \code{\link[TAF]{tafpng}}, \code{\link[TAF]{tt}}, \code{\link[TAF]{unix2dos}}, \code{\link[TAF]{utf8.to.latin1}}, \code{\link[TAF]{write.taf}}, \code{\link[TAF]{xtab2long}}, \code{\link[TAF]{xtab2taf}}, \code{\link[TAF]{zoom}}, \code{\link[TAF]{zoom.trellis}} #' -#' @importFrom TAF makeAll +#' @importFrom TAF already.in.taf.library #' @name taf-reexports #' @keywords internal #' @export -makeAll <- TAF::makeAll - -#' @importFrom TAF taf.install -#' @rdname taf-reexports -#' @export -taf.install <- TAF::taf.install - -#' @importFrom TAF parse.repo -#' @rdname taf-reexports -#' @export -parse.repo <- TAF::parse.repo +already.in.taf.library <- TAF::already.in.taf.library -#' @importFrom TAF taf2long +#' @importFrom TAF boot.dir #' @rdname taf-reexports #' @export -taf2long <- TAF::taf2long +boot.dir <- TAF::boot.dir -#' @importFrom TAF write.taf +#' @importFrom TAF boot.dir.inside #' @rdname taf-reexports #' @export -write.taf <- TAF::write.taf +boot.dir.inside <- TAF::boot.dir.inside -#' @importFrom TAF utf8.to.latin1 +#' @importFrom TAF boot.exists #' @rdname taf-reexports #' @export -utf8.to.latin1 <- TAF::utf8.to.latin1 +boot.exists <- TAF::boot.exists -#' @importFrom TAF download +#' @importFrom TAF clean #' @rdname taf-reexports #' @export -download <- TAF::download +clean <- TAF::clean #' @importFrom TAF clean.boot #' @rdname taf-reexports #' @export clean.boot <- TAF::clean.boot -#' @importFrom TAF flr2taf +#' @importFrom TAF clean.data #' @rdname taf-reexports #' @export -flr2taf <- TAF::flr2taf +clean.data <- TAF::clean.data -#' @importFrom TAF get.remote.sha +#' @importFrom TAF clean.library #' @rdname taf-reexports #' @export -get.remote.sha <- TAF::get.remote.sha +clean.library <- TAF::clean.library -#' @importFrom TAF taf.bootstrap +#' @importFrom TAF clean.software #' @rdname taf-reexports #' @export -taf.bootstrap <- TAF::taf.bootstrap +clean.software <- TAF::clean.software -#' @importFrom TAF xtab2taf +#' @importFrom TAF convert.spaces #' @rdname taf-reexports #' @export -xtab2taf <- TAF::xtab2taf +convert.spaces <- TAF::convert.spaces -#' @importFrom TAF long2taf +#' @importFrom TAF cp #' @rdname taf-reexports #' @export -long2taf <- TAF::long2taf +cp <- TAF::cp -#' @importFrom TAF source.taf +#' @importFrom TAF deps #' @rdname taf-reexports #' @export -source.taf <- TAF::source.taf +deps <- TAF::deps -#' @importFrom TAF ds.file +#' @importFrom TAF detach.packages #' @rdname taf-reexports #' @export -ds.file <- TAF::ds.file +detach.packages <- TAF::detach.packages #' @importFrom TAF div #' @rdname taf-reexports #' @export div <- TAF::div -#' @importFrom TAF detach.packages +#' @importFrom TAF dos2unix #' @rdname taf-reexports #' @export -detach.packages <- TAF::detach.packages +dos2unix <- TAF::dos2unix -#' @importFrom TAF rnd +#' @importFrom TAF download #' @rdname taf-reexports #' @export -rnd <- TAF::rnd +download <- TAF::download -#' @importFrom TAF taf2xtab +#' @importFrom TAF download.github #' @rdname taf-reexports #' @export -taf2xtab <- TAF::taf2xtab +download.github <- TAF::download.github -#' @importFrom TAF ds.package +#' @importFrom TAF draft.data #' @rdname taf-reexports #' @export -ds.package <- TAF::ds.package +draft.data <- TAF::draft.data -#' @importFrom TAF long2xtab +#' @importFrom TAF draft.software #' @rdname taf-reexports #' @export -long2xtab <- TAF::long2xtab +draft.software <- TAF::draft.software -#' @importFrom TAF os.linux +#' @importFrom TAF ds.file #' @rdname taf-reexports #' @export -os.linux <- TAF::os.linux +ds.file <- TAF::ds.file -#' @importFrom TAF taf.png +#' @importFrom TAF ds.package #' @rdname taf-reexports #' @export -taf.png <- TAF::taf.png +ds.package <- TAF::ds.package -#' @importFrom TAF os.macos +#' @importFrom TAF extract.subdir #' @rdname taf-reexports #' @export -os.macos <- TAF::os.macos +extract.subdir <- TAF::extract.subdir -#' @importFrom TAF os +#' @importFrom TAF file.encoding #' @rdname taf-reexports #' @export -os <- TAF::os +file.encoding <- TAF::file.encoding -#' @importFrom TAF period +#' @importFrom TAF flr2taf #' @rdname taf-reexports #' @export -period <- TAF::period +flr2taf <- TAF::flr2taf -#' @importFrom TAF tt +#' @importFrom TAF get.remote.sha #' @rdname taf-reexports #' @export -tt <- TAF::tt +get.remote.sha <- TAF::get.remote.sha -#' @importFrom TAF clean.data +#' @importFrom TAF is.r.package #' @rdname taf-reexports #' @export -clean.data <- TAF::clean.data +is.r.package <- TAF::is.r.package -#' @importFrom TAF zoom.trellis +#' @importFrom TAF latin1.to.utf8 #' @rdname taf-reexports #' @export -zoom.trellis <- TAF::zoom.trellis +latin1.to.utf8 <- TAF::latin1.to.utf8 -#' @importFrom TAF zoom +#' @importFrom TAF lim #' @rdname taf-reexports #' @export -zoom <- TAF::zoom +lim <- TAF::lim -#' @importFrom TAF unix2dos +#' @importFrom TAF line.endings #' @rdname taf-reexports #' @export -unix2dos <- TAF::unix2dos +line.endings <- TAF::line.endings -#' @importFrom TAF dos2unix +#' @importFrom TAF long2taf #' @rdname taf-reexports #' @export -dos2unix <- TAF::dos2unix +long2taf <- TAF::long2taf -#' @importFrom TAF mkdir +#' @importFrom TAF long2xtab #' @rdname taf-reexports #' @export -mkdir <- TAF::mkdir +long2xtab <- TAF::long2xtab -#' @importFrom TAF convert.spaces +#' @importFrom TAF make #' @rdname taf-reexports #' @export -convert.spaces <- TAF::convert.spaces +make <- TAF::make -#' @importFrom TAF lim +#' @importFrom TAF make.all #' @rdname taf-reexports #' @export -lim <- TAF::lim +make.all <- TAF::make.all -#' @importFrom TAF is.r.package +#' @importFrom TAF make.taf #' @rdname taf-reexports #' @export -is.r.package <- TAF::is.r.package +make.taf <- TAF::make.taf -#' @importFrom TAF clean.software +#' @importFrom TAF makeAll #' @rdname taf-reexports #' @export -clean.software <- TAF::clean.software +makeAll <- TAF::makeAll -#' @importFrom TAF taf.boot.path +#' @importFrom TAF makeTAF #' @rdname taf-reexports #' @export -taf.boot.path <- TAF::taf.boot.path +makeTAF <- TAF::makeTAF -#' @importFrom TAF sourceAll +#' @importFrom TAF mkdir #' @rdname taf-reexports #' @export -sourceAll <- TAF::sourceAll +mkdir <- TAF::mkdir -#' @importFrom TAF plus +#' @importFrom TAF model.dir #' @rdname taf-reexports #' @export -plus <- TAF::plus +model.dir <- TAF::model.dir -#' @importFrom TAF taf.sources +#' @importFrom TAF model.script #' @rdname taf-reexports #' @export -taf.sources <- TAF::taf.sources +model.script <- TAF::model.script #' @importFrom TAF msg #' @rdname taf-reexports #' @export msg <- TAF::msg -#' @importFrom TAF process.entry +#' @importFrom TAF os #' @rdname taf-reexports #' @export -process.entry <- TAF::process.entry +os <- TAF::os -#' @importFrom TAF taf.data.path +#' @importFrom TAF os.linux #' @rdname taf-reexports #' @export -taf.data.path <- TAF::taf.data.path +os.linux <- TAF::os.linux -#' @importFrom TAF download.github +#' @importFrom TAF os.macos #' @rdname taf-reexports #' @export -download.github <- TAF::download.github +os.macos <- TAF::os.macos -#' @importFrom TAF deps +#' @importFrom TAF os.unix #' @rdname taf-reexports #' @export -deps <- TAF::deps +os.unix <- TAF::os.unix -#' @importFrom TAF taf.session +#' @importFrom TAF os.windows #' @rdname taf-reexports #' @export -taf.session <- TAF::taf.session +os.windows <- TAF::os.windows -#' @importFrom TAF os.unix +#' @importFrom TAF parse.repo #' @rdname taf-reexports #' @export -os.unix <- TAF::os.unix +parse.repo <- TAF::parse.repo -#' @importFrom TAF xtab2long +#' @importFrom TAF period #' @rdname taf-reexports #' @export -xtab2long <- TAF::xtab2long +period <- TAF::period -#' @importFrom TAF os.windows +#' @importFrom TAF plus #' @rdname taf-reexports #' @export -os.windows <- TAF::os.windows +plus <- TAF::plus -#' @importFrom TAF draft.data +#' @importFrom TAF process.bibfile #' @rdname taf-reexports #' @export -draft.data <- TAF::draft.data +process.bibfile <- TAF::process.bibfile -#' @importFrom TAF read.taf +#' @importFrom TAF process.entry #' @rdname taf-reexports #' @export -read.taf <- TAF::read.taf +process.entry <- TAF::process.entry -#' @importFrom TAF clean +#' @importFrom TAF read.bib #' @rdname taf-reexports #' @export -clean <- TAF::clean +read.bib <- TAF::read.bib -#' @importFrom TAF model.script +#' @importFrom TAF read.taf #' @rdname taf-reexports #' @export -model.script <- TAF::model.script +read.taf <- TAF::read.taf -#' @importFrom TAF taf.libPaths +#' @importFrom TAF rmdir #' @rdname taf-reexports #' @export -taf.libPaths <- TAF::taf.libPaths +rmdir <- TAF::rmdir -#' @importFrom TAF draft.software +#' @importFrom TAF rnd #' @rdname taf-reexports #' @export -draft.software <- TAF::draft.software +rnd <- TAF::rnd -#' @importFrom TAF sourceDir +#' @importFrom TAF sam2taf #' @rdname taf-reexports #' @export -sourceDir <- TAF::sourceDir +sam2taf <- TAF::sam2taf -#' @importFrom TAF taf.boot +#' @importFrom TAF source.all #' @rdname taf-reexports #' @export -taf.boot <- TAF::taf.boot +source.all <- TAF::source.all -#' @importFrom TAF file.encoding +#' @importFrom TAF source.dir #' @rdname taf-reexports #' @export -file.encoding <- TAF::file.encoding +source.dir <- TAF::source.dir -#' @importFrom TAF latin1.to.utf8 +#' @importFrom TAF source.taf #' @rdname taf-reexports #' @export -latin1.to.utf8 <- TAF::latin1.to.utf8 +source.taf <- TAF::source.taf -#' @importFrom TAF clean.library +#' @importFrom TAF sourceAll #' @rdname taf-reexports #' @export -clean.library <- TAF::clean.library +sourceAll <- TAF::sourceAll -#' @importFrom TAF tafpng +#' @importFrom TAF sourceDir #' @rdname taf-reexports #' @export -tafpng <- TAF::tafpng +sourceDir <- TAF::sourceDir #' @importFrom TAF sourceTAF #' @rdname taf-reexports #' @export sourceTAF <- TAF::sourceTAF -#' @importFrom TAF taf2html +#' @importFrom TAF stamp.description #' @rdname taf-reexports #' @export -taf2html <- TAF::taf2html +stamp.description <- TAF::stamp.description -#' @importFrom TAF source.all +#' @importFrom TAF taf.boot #' @rdname taf-reexports #' @export -source.all <- TAF::source.all +taf.boot <- TAF::taf.boot -#' @importFrom TAF extract.subdir +#' @importFrom TAF taf.boot.path #' @rdname taf-reexports #' @export -extract.subdir <- TAF::extract.subdir +taf.boot.path <- TAF::taf.boot.path -#' @importFrom TAF taf.library +#' @importFrom TAF taf.bootstrap #' @rdname taf-reexports #' @export -taf.library <- TAF::taf.library +taf.bootstrap <- TAF::taf.bootstrap -#' @importFrom TAF read.bib +#' @importFrom TAF taf.data.path #' @rdname taf-reexports #' @export -read.bib <- TAF::read.bib +taf.data.path <- TAF::taf.data.path -#' @importFrom TAF boot.exists +#' @importFrom TAF taf.install #' @rdname taf-reexports #' @export -boot.exists <- TAF::boot.exists +taf.install <- TAF::taf.install -#' @importFrom TAF boot.dir +#' @importFrom TAF taf.libPaths #' @rdname taf-reexports #' @export -boot.dir <- TAF::boot.dir +taf.libPaths <- TAF::taf.libPaths -#' @importFrom TAF stamp.description +#' @importFrom TAF taf.library #' @rdname taf-reexports #' @export -stamp.description <- TAF::stamp.description +taf.library <- TAF::taf.library -#' @importFrom TAF make.all +#' @importFrom TAF taf.png #' @rdname taf-reexports #' @export -make.all <- TAF::make.all +taf.png <- TAF::taf.png -#' @importFrom TAF make.taf +#' @importFrom TAF taf.session #' @rdname taf-reexports #' @export -make.taf <- TAF::make.taf +taf.session <- TAF::taf.session -#' @importFrom TAF make +#' @importFrom TAF taf.sources #' @rdname taf-reexports #' @export -make <- TAF::make +taf.sources <- TAF::taf.sources -#' @importFrom TAF boot.dir.inside +#' @importFrom TAF taf.unzip #' @rdname taf-reexports #' @export -boot.dir.inside <- TAF::boot.dir.inside +taf.unzip <- TAF::taf.unzip -#' @importFrom TAF model.dir +#' @importFrom TAF taf2html #' @rdname taf-reexports #' @export -model.dir <- TAF::model.dir +taf2html <- TAF::taf2html -#' @importFrom TAF line.endings +#' @importFrom TAF taf2long #' @rdname taf-reexports #' @export -line.endings <- TAF::line.endings +taf2long <- TAF::taf2long -#' @importFrom TAF already.in.taf.library +#' @importFrom TAF taf2xtab #' @rdname taf-reexports #' @export -already.in.taf.library <- TAF::already.in.taf.library +taf2xtab <- TAF::taf2xtab -#' @importFrom TAF taf.unzip +#' @importFrom TAF tafpng #' @rdname taf-reexports #' @export -taf.unzip <- TAF::taf.unzip +tafpng <- TAF::tafpng -#' @importFrom TAF process.bibfile +#' @importFrom TAF tt #' @rdname taf-reexports #' @export -process.bibfile <- TAF::process.bibfile +tt <- TAF::tt -#' @importFrom TAF cp +#' @importFrom TAF unix2dos #' @rdname taf-reexports #' @export -cp <- TAF::cp +unix2dos <- TAF::unix2dos -#' @importFrom TAF makeTAF +#' @importFrom TAF utf8.to.latin1 #' @rdname taf-reexports #' @export -makeTAF <- TAF::makeTAF +utf8.to.latin1 <- TAF::utf8.to.latin1 -#' @importFrom TAF rmdir +#' @importFrom TAF write.taf #' @rdname taf-reexports #' @export -rmdir <- TAF::rmdir +write.taf <- TAF::write.taf -#' @importFrom TAF source.dir +#' @importFrom TAF xtab2long #' @rdname taf-reexports #' @export -source.dir <- TAF::source.dir +xtab2long <- TAF::xtab2long -#' @importFrom TAF sam2taf +#' @importFrom TAF xtab2taf #' @rdname taf-reexports #' @export -sam2taf <- TAF::sam2taf +xtab2taf <- TAF::xtab2taf + +#' @importFrom TAF zoom +#' @rdname taf-reexports +#' @export +zoom <- TAF::zoom + +#' @importFrom TAF zoom.trellis +#' @rdname taf-reexports +#' @export +zoom.trellis <- TAF::zoom.trellis #' @importFrom TAF taf.skeleton #' @rdname taf-reexports From ac9e4767a45617e5fa50d3e2a00c69db34178ef4 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 26 Sep 2024 13:43:10 +1100 Subject: [PATCH 03/10] Create TAF exports for version 4.3.0 --- R/TAF.R | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/R/TAF.R b/R/TAF.R index 8482fc5..4abe2e7 100644 --- a/R/TAF.R +++ b/R/TAF.R @@ -4,7 +4,7 @@ #' These functions are re-exported from the TAF package. #' #' Follow the links below to see the documentation. -#' \code{\link[TAF]{already.in.taf.library}}, \code{\link[TAF]{boot.dir}}, \code{\link[TAF]{boot.dir.inside}}, \code{\link[TAF]{boot.exists}}, \code{\link[TAF]{clean}}, \code{\link[TAF]{clean.boot}}, \code{\link[TAF]{clean.data}}, \code{\link[TAF]{clean.library}}, \code{\link[TAF]{clean.software}}, \code{\link[TAF]{convert.spaces}}, \code{\link[TAF]{cp}}, \code{\link[TAF]{deps}}, \code{\link[TAF]{detach.packages}}, \code{\link[TAF]{div}}, \code{\link[TAF]{dos2unix}}, \code{\link[TAF]{download}}, \code{\link[TAF]{download.github}}, \code{\link[TAF]{draft.data}}, \code{\link[TAF]{draft.software}}, \code{\link[TAF]{ds.file}}, \code{\link[TAF]{ds.package}}, \code{\link[TAF]{extract.subdir}}, \code{\link[TAF]{file.encoding}}, \code{\link[TAF]{flr2taf}}, \code{\link[TAF]{get.remote.sha}}, \code{\link[TAF]{is.r.package}}, \code{\link[TAF]{latin1.to.utf8}}, \code{\link[TAF]{lim}}, \code{\link[TAF]{line.endings}}, \code{\link[TAF]{long2taf}}, \code{\link[TAF]{long2xtab}}, \code{\link[TAF]{make}}, \code{\link[TAF]{make.all}}, \code{\link[TAF]{make.taf}}, \code{\link[TAF]{makeAll}}, \code{\link[TAF]{makeTAF}}, \code{\link[TAF]{mkdir}}, \code{\link[TAF]{model.dir}}, \code{\link[TAF]{model.script}}, \code{\link[TAF]{msg}}, \code{\link[TAF]{os}}, \code{\link[TAF]{os.linux}}, \code{\link[TAF]{os.macos}}, \code{\link[TAF]{os.unix}}, \code{\link[TAF]{os.windows}}, \code{\link[TAF]{parse.repo}}, \code{\link[TAF]{period}}, \code{\link[TAF]{plus}}, \code{\link[TAF]{process.bibfile}}, \code{\link[TAF]{process.entry}}, \code{\link[TAF]{read.bib}}, \code{\link[TAF]{read.taf}}, \code{\link[TAF]{rmdir}}, \code{\link[TAF]{rnd}}, \code{\link[TAF]{sam2taf}}, \code{\link[TAF]{source.all}}, \code{\link[TAF]{source.dir}}, \code{\link[TAF]{source.taf}}, \code{\link[TAF]{sourceAll}}, \code{\link[TAF]{sourceDir}}, \code{\link[TAF]{sourceTAF}}, \code{\link[TAF]{stamp.description}}, \code{\link[TAF]{taf.boot}}, \code{\link[TAF]{taf.boot.path}}, \code{\link[TAF]{taf.bootstrap}}, \code{\link[TAF]{taf.data.path}}, \code{\link[TAF]{taf.install}}, \code{\link[TAF]{taf.libPaths}}, \code{\link[TAF]{taf.library}}, \code{\link[TAF]{taf.png}}, \code{\link[TAF]{taf.session}}, \code{\link[TAF]{taf.sources}}, \code{\link[TAF]{taf.unzip}}, \code{\link[TAF]{taf2html}}, \code{\link[TAF]{taf2long}}, \code{\link[TAF]{taf2xtab}}, \code{\link[TAF]{tafpng}}, \code{\link[TAF]{tt}}, \code{\link[TAF]{unix2dos}}, \code{\link[TAF]{utf8.to.latin1}}, \code{\link[TAF]{write.taf}}, \code{\link[TAF]{xtab2long}}, \code{\link[TAF]{xtab2taf}}, \code{\link[TAF]{zoom}}, \code{\link[TAF]{zoom.trellis}} +#' \code{\link[TAF]{already.in.taf.library}}, \code{\link[TAF]{boot.dir}}, \code{\link[TAF]{boot.dir.inside}}, \code{\link[TAF]{boot.exists}}, \code{\link[TAF]{check.software}}, \code{\link[TAF]{clean}}, \code{\link[TAF]{clean.boot}}, \code{\link[TAF]{clean.data}}, \code{\link[TAF]{clean.library}}, \code{\link[TAF]{clean.software}}, \code{\link[TAF]{convert.spaces}}, \code{\link[TAF]{cp}}, \code{\link[TAF]{ddim}}, \code{\link[TAF]{deps}}, \code{\link[TAF]{detach.packages}}, \code{\link[TAF]{div}}, \code{\link[TAF]{dos2unix}}, \code{\link[TAF]{download}}, \code{\link[TAF]{download.github}}, \code{\link[TAF]{draft.data}}, \code{\link[TAF]{draft.software}}, \code{\link[TAF]{ds.file}}, \code{\link[TAF]{ds.package}}, \code{\link[TAF]{extract.subdir}}, \code{\link[TAF]{file.encoding}}, \code{\link[TAF]{flr2taf}}, \code{\link[TAF]{get.remote.sha}}, \code{\link[TAF]{is.r.package}}, \code{\link[TAF]{latin1.to.utf8}}, \code{\link[TAF]{lim}}, \code{\link[TAF]{line.endings}}, \code{\link[TAF]{long2taf}}, \code{\link[TAF]{long2xtab}}, \code{\link[TAF]{make}}, \code{\link[TAF]{make.all}}, \code{\link[TAF]{make.taf}}, \code{\link[TAF]{makeAll}}, \code{\link[TAF]{makeTAF}}, \code{\link[TAF]{mkdir}}, \code{\link[TAF]{model.dir}}, \code{\link[TAF]{model.script}}, \code{\link[TAF]{msg}}, \code{\link[TAF]{os}}, \code{\link[TAF]{os.linux}}, \code{\link[TAF]{os.macos}}, \code{\link[TAF]{os.unix}}, \code{\link[TAF]{os.windows}}, \code{\link[TAF]{parse.repo}}, \code{\link[TAF]{period}}, \code{\link[TAF]{plus}}, \code{\link[TAF]{process.bibfile}}, \code{\link[TAF]{process.entry}}, \code{\link[TAF]{read.bib}}, \code{\link[TAF]{read.taf}}, \code{\link[TAF]{rmdir}}, \code{\link[TAF]{rnd}}, \code{\link[TAF]{sam2taf}}, \code{\link[TAF]{source.all}}, \code{\link[TAF]{source.dir}}, \code{\link[TAF]{source.taf}}, \code{\link[TAF]{sourceAll}}, \code{\link[TAF]{sourceDir}}, \code{\link[TAF]{sourceTAF}}, \code{\link[TAF]{stamp.description}}, \code{\link[TAF]{taf.boot}}, \code{\link[TAF]{taf.boot.path}}, \code{\link[TAF]{taf.bootstrap}}, \code{\link[TAF]{taf.data.path}}, \code{\link[TAF]{taf.install}}, \code{\link[TAF]{taf.libPaths}}, \code{\link[TAF]{taf.libraries}}, \code{\link[TAF]{taf.library}}, \code{\link[TAF]{taf.png}}, \code{\link[TAF]{taf.session}}, \code{\link[TAF]{taf.sources}}, \code{\link[TAF]{taf.unzip}}, \code{\link[TAF]{taf2html}}, \code{\link[TAF]{taf2long}}, \code{\link[TAF]{taf2xtab}}, \code{\link[TAF]{tafpng}}, \code{\link[TAF]{tt}}, \code{\link[TAF]{unix2dos}}, \code{\link[TAF]{utf8.to.latin1}}, \code{\link[TAF]{write.taf}}, \code{\link[TAF]{xtab2long}}, \code{\link[TAF]{xtab2taf}}, \code{\link[TAF]{zoom}}, \code{\link[TAF]{zoom.trellis}} #' #' @importFrom TAF already.in.taf.library #' @name taf-reexports @@ -27,6 +27,11 @@ boot.dir.inside <- TAF::boot.dir.inside #' @export boot.exists <- TAF::boot.exists +#' @importFrom TAF check.software +#' @rdname taf-reexports +#' @export +check.software <- TAF::check.software + #' @importFrom TAF clean #' @rdname taf-reexports #' @export @@ -62,6 +67,11 @@ convert.spaces <- TAF::convert.spaces #' @export cp <- TAF::cp +#' @importFrom TAF ddim +#' @rdname taf-reexports +#' @export +ddim <- TAF::ddim + #' @importFrom TAF deps #' @rdname taf-reexports #' @export @@ -347,6 +357,11 @@ taf.install <- TAF::taf.install #' @export taf.libPaths <- TAF::taf.libPaths +#' @importFrom TAF taf.libraries +#' @rdname taf-reexports +#' @export +taf.libraries <- TAF::taf.libraries + #' @importFrom TAF taf.library #' @rdname taf-reexports #' @export From aebf2f1286af74688465428a4d78e60c20fb609d Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 26 Sep 2024 14:03:42 +1100 Subject: [PATCH 04/10] Update DESCRIPTION and NEWS.md to version 4.3.0 --- DESCRIPTION | 2 +- NEWS.md | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 50b3241..422eb82 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: icesTAF -Version: 4.2.0 +Version: 4.3.0 Title: Functions to Support the ICES Transparent Assessment Framework Authors@R: c( diff --git a/NEWS.md b/NEWS.md index d7cedb6..e5f7318 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# icesTAF 4.3.0 (2024-06-11) + +* See: news(package="TAF", Version=="4.3.0"). + + # icesTAF 4.2.0 (2023-03-14) * The term 'boot' is now preferred for what used to be called 'bootstrap', From 326652a5c9f77b975965e83be1e72cc0d661e872 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 26 Sep 2024 14:12:37 +1100 Subject: [PATCH 05/10] Adapt package help page to Roxygen 7.3.0 --- R/icesTAF-package.R | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/R/icesTAF-package.R b/R/icesTAF-package.R index 358d90a..48ea184 100644 --- a/R/icesTAF-package.R +++ b/R/icesTAF-package.R @@ -1,5 +1,3 @@ -#' @docType package -#' #' @name icesTAF-package #' #' @aliases icesTAF @@ -29,4 +27,4 @@ #' The \href{https://github.com/ices-taf/doc/wiki}{TAF Wiki} provides additional #' help resources. -NA +"_PACKAGE" From be989c2a2eed8d6883277e2a2cca3eee14e07d7e Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 26 Sep 2024 14:13:03 +1100 Subject: [PATCH 06/10] Roxygenize --- DESCRIPTION | 2 +- NAMESPACE | 6 + man/icesTAF-package.Rd | 8 + man/taf-reexports.Rd | 350 +++++++++++++++++++++-------------------- 4 files changed, 195 insertions(+), 171 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 422eb82..56fc21e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,5 +20,5 @@ Description: Functions to support the ICES Transparent Assessment Framework License: GPL-3 URL: https://taf.ices.dk, https://github.com/ices-tools-prod/icesTAF Encoding: UTF-8 -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 Roxygen: list(old_usage=TRUE) diff --git a/NAMESPACE b/NAMESPACE index 1837941..f5fe41d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -12,6 +12,7 @@ export(already.in.taf.library) export(boot.dir) export(boot.dir.inside) export(boot.exists) +export(check.software) export(clean) export(clean.boot) export(clean.data) @@ -19,6 +20,7 @@ export(clean.library) export(clean.software) export(convert.spaces) export(cp) +export(ddim) export(deps) export(detach.packages) export(dir.tree) @@ -81,6 +83,7 @@ export(taf.bootstrap) export(taf.data.path) export(taf.install) export(taf.libPaths) +export(taf.libraries) export(taf.library) export(taf.png) export(taf.roxygenise) @@ -104,6 +107,7 @@ importFrom(TAF,already.in.taf.library) importFrom(TAF,boot.dir) importFrom(TAF,boot.dir.inside) importFrom(TAF,boot.exists) +importFrom(TAF,check.software) importFrom(TAF,clean) importFrom(TAF,clean.boot) importFrom(TAF,clean.data) @@ -111,6 +115,7 @@ importFrom(TAF,clean.library) importFrom(TAF,clean.software) importFrom(TAF,convert.spaces) importFrom(TAF,cp) +importFrom(TAF,ddim) importFrom(TAF,deps) importFrom(TAF,detach.packages) importFrom(TAF,div) @@ -168,6 +173,7 @@ importFrom(TAF,taf.bootstrap) importFrom(TAF,taf.data.path) importFrom(TAF,taf.install) importFrom(TAF,taf.libPaths) +importFrom(TAF,taf.libraries) importFrom(TAF,taf.library) importFrom(TAF,taf.png) importFrom(TAF,taf.session) diff --git a/man/icesTAF-package.Rd b/man/icesTAF-package.Rd index 63880b0..76279f0 100644 --- a/man/icesTAF-package.Rd +++ b/man/icesTAF-package.Rd @@ -25,6 +25,14 @@ To explore example TAF stock assessments, see the introductory The \href{https://github.com/ices-taf/doc/wiki}{TAF Wiki} provides additional help resources. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://taf.ices.dk} + \item \url{https://github.com/ices-tools-prod/icesTAF} +} + } \author{ Colin Millar and Arni Magnusson. diff --git a/man/taf-reexports.Rd b/man/taf-reexports.Rd index 0e5c7ea..6439941 100644 --- a/man/taf-reexports.Rd +++ b/man/taf-reexports.Rd @@ -2,282 +2,292 @@ % Please edit documentation in R/TAF.R \name{taf-reexports} \alias{taf-reexports} -\alias{makeAll} -\alias{taf.install} -\alias{parse.repo} -\alias{taf2long} -\alias{write.taf} -\alias{utf8.to.latin1} -\alias{download} +\alias{already.in.taf.library} +\alias{boot.dir} +\alias{boot.dir.inside} +\alias{boot.exists} +\alias{check.software} +\alias{clean} \alias{clean.boot} +\alias{clean.data} +\alias{clean.library} +\alias{clean.software} +\alias{convert.spaces} +\alias{cp} +\alias{ddim} +\alias{deps} +\alias{detach.packages} +\alias{div} +\alias{dos2unix} +\alias{download} +\alias{download.github} +\alias{draft.data} +\alias{draft.software} +\alias{ds.file} +\alias{ds.package} +\alias{extract.subdir} +\alias{file.encoding} \alias{flr2taf} \alias{get.remote.sha} -\alias{taf.bootstrap} -\alias{xtab2taf} +\alias{is.r.package} +\alias{latin1.to.utf8} +\alias{lim} +\alias{line.endings} \alias{long2taf} -\alias{source.taf} -\alias{ds.file} -\alias{div} -\alias{detach.packages} -\alias{rnd} -\alias{taf2xtab} -\alias{ds.package} \alias{long2xtab} +\alias{make} +\alias{make.all} +\alias{make.taf} +\alias{makeAll} +\alias{makeTAF} +\alias{mkdir} +\alias{model.dir} +\alias{model.script} +\alias{msg} +\alias{os} \alias{os.linux} -\alias{taf.png} \alias{os.macos} -\alias{os} +\alias{os.unix} +\alias{os.windows} +\alias{parse.repo} \alias{period} -\alias{tt} -\alias{clean.data} -\alias{zoom.trellis} -\alias{zoom} -\alias{unix2dos} -\alias{dos2unix} -\alias{mkdir} -\alias{convert.spaces} -\alias{lim} -\alias{is.r.package} -\alias{clean.software} -\alias{taf.boot.path} -\alias{sourceAll} \alias{plus} -\alias{taf.sources} -\alias{msg} +\alias{process.bibfile} \alias{process.entry} -\alias{taf.data.path} -\alias{download.github} -\alias{deps} -\alias{taf.session} -\alias{os.unix} -\alias{xtab2long} -\alias{os.windows} -\alias{draft.data} +\alias{read.bib} \alias{read.taf} -\alias{clean} -\alias{model.script} -\alias{taf.libPaths} -\alias{draft.software} +\alias{rmdir} +\alias{rnd} +\alias{sam2taf} +\alias{source.all} +\alias{source.dir} +\alias{source.taf} +\alias{sourceAll} \alias{sourceDir} -\alias{taf.boot} -\alias{file.encoding} -\alias{latin1.to.utf8} -\alias{clean.library} -\alias{tafpng} \alias{sourceTAF} -\alias{taf2html} -\alias{source.all} -\alias{extract.subdir} -\alias{taf.library} -\alias{read.bib} -\alias{boot.exists} -\alias{boot.dir} \alias{stamp.description} -\alias{make.all} -\alias{make.taf} -\alias{make} -\alias{boot.dir.inside} -\alias{model.dir} -\alias{line.endings} -\alias{already.in.taf.library} +\alias{taf.boot} +\alias{taf.boot.path} +\alias{taf.bootstrap} +\alias{taf.data.path} +\alias{taf.install} +\alias{taf.libPaths} +\alias{taf.libraries} +\alias{taf.library} +\alias{taf.png} +\alias{taf.session} +\alias{taf.sources} \alias{taf.unzip} -\alias{process.bibfile} -\alias{cp} -\alias{makeTAF} -\alias{rmdir} -\alias{source.dir} -\alias{sam2taf} +\alias{taf2html} +\alias{taf2long} +\alias{taf2xtab} +\alias{tafpng} +\alias{tt} +\alias{unix2dos} +\alias{utf8.to.latin1} +\alias{write.taf} +\alias{xtab2long} +\alias{xtab2taf} +\alias{zoom} +\alias{zoom.trellis} \alias{taf.skeleton} \title{Functions re-exported from the TAF package} \usage{ -makeAll(...) - -taf.install(targz = NULL, lib = "boot/library", quiet = FALSE) +already.in.taf.library(targz, lib) -parse.repo(repo) +boot.dir() -taf2long(x, names = c("Year", "Age", "Value")) +boot.dir.inside(inside = ".") -write.taf(x, file = NULL, dir = NULL, quote = FALSE, row.names = FALSE, - fileEncoding = "UTF-8", underscore = TRUE, ...) +boot.exists() -utf8.to.latin1(file, force = FALSE) +check.software(full = FALSE) -download(url, dir = ".", mode = "wb", chmod = file_ext(url) == "", - destfile = file.path(dir, basename(url)), quiet = TRUE, ...) +clean(dirs = c("data", model.dir(), "output", "report"), force = FALSE) clean.boot(force = FALSE) -flr2taf(x, colname = "Value") +clean.data(folder = "boot/data", quiet = FALSE, force = FALSE) -get.remote.sha(owner, repo, ref, seven = TRUE) +clean.library(folder = "boot/library", quiet = FALSE, force = FALSE) -taf.bootstrap(...) +clean.software(folder = "boot/software", quiet = FALSE, force = FALSE) -xtab2taf(x, colname = "Year") +convert.spaces(file, sep = "_") -long2taf(x) +cp(from, to, move = FALSE, ignore = FALSE, overwrite = TRUE, + quiet = TRUE) -source.taf(script, rm = FALSE, clean = TRUE, detach = FALSE, - taf = NULL, quiet = FALSE) +ddim(x, reduce = FALSE) -ds.file(package, author, year, title, version, source) +deps(path = ".", base = FALSE, installed = TRUE, available = TRUE, + list = FALSE) + +detach.packages(quiet = FALSE) div(x, cols, by = 1000, grep = FALSE, ...) -detach.packages(quiet = FALSE) +dos2unix(file) -rnd(x, cols, digits = 0, grep = FALSE, ...) +download(url, dir = ".", mode = "wb", chmod = file_ext(url) == "", + destfile = file.path(dir, basename(url)), quiet = TRUE, ...) -taf2xtab(x) +download.github(repo, dir = ".", quiet = FALSE) -ds.package(package, author, year, title, version, source) +draft.data(originator = NULL, year = format(Sys.time(), "\%Y"), + title = NULL, period = NULL, access = "Public", source = NULL, + file = "", append = FALSE, + data.files = dir(taf.boot.path("initial/data")), + data.scripts = dir(boot.dir(), pattern = "\\\\.R$")) -long2xtab(x) +draft.software(package, author = NULL, year = NULL, title = NULL, + version = NULL, source = NULL, file = "", append = FALSE) -os.linux() +ds.file(package, author, year, title, version, source) -taf.png(filename, width = 1600, height = 1200, res = 200, ...) +ds.package(package, author, year, title, version, source) -os.macos() +extract.subdir(targz, subtargz, subdir) -os() +file.encoding(file) -period(x, y = NULL) +flr2taf(x, colname = "Value") -tt(x, column = FALSE) +get.remote.sha(owner, repo, ref, seven = TRUE) -clean.data(folder = "boot/data", quiet = FALSE, force = FALSE) +is.r.package(targz, spec = NULL, warn = TRUE) -\method{zoom}{trellis}(x, size = 1, main = 1.2 * size, lab = size, - axis = size, strip = size, sub = 0.9 * size, legend = 0.9 * size, - splom = 0.9 * size, ...) +latin1.to.utf8(file, force = FALSE) -zoom(x, ...) +lim(x, mult = 1.1) -unix2dos(file) +line.endings(file) -dos2unix(file) +long2taf(x) -mkdir(path) +long2xtab(x) -convert.spaces(file, sep = "_") +make(recipe, prereq, target, include = TRUE, engine = source, + details = FALSE, force = FALSE, recon = FALSE, quiet = TRUE, ...) -lim(x, mult = 1.1) +make.all(...) -is.r.package(targz, spec = NULL, warn = TRUE) +make.taf(script, ...) -clean.software(folder = "boot/software", quiet = FALSE, force = FALSE) +makeAll(...) -taf.boot.path(..., fsep = .Platform$file.sep) +makeTAF(...) -sourceAll(...) +mkdir(path) -plus(x) +model.dir() -taf.sources(type) +model.script() msg(...) -process.entry(bib, quiet = FALSE, force = FALSE, clean = FALSE) +os() -taf.data.path(..., fsep = .Platform$file.sep) +os.linux() -download.github(repo, dir = ".", quiet = FALSE) +os.macos() -deps(path = ".", base = FALSE, installed = TRUE, available = TRUE, - list = FALSE) +os.unix() -taf.session(sort = FALSE, imports = TRUE, details = FALSE) +os.windows() -os.unix() +parse.repo(repo) -xtab2long(x, names = c("Year", "Age", "Value")) +period(x, y = NULL) -os.windows() +plus(x) -draft.data(originator = NULL, year = format(Sys.time(), "\%Y"), - title = NULL, period = NULL, access = "Public", source = NULL, - file = "", append = FALSE, - data.files = dir(taf.boot.path("initial/data")), - data.scripts = dir(boot.dir(), pattern = "\\\\.R$")) +process.bibfile(type, clean = TRUE, quiet = FALSE, ...) + +process.entry(bib, clean = FALSE, comma.split = TRUE, force = FALSE, + quiet = FALSE) + +read.bib(file) read.taf(file, check.names = FALSE, stringsAsFactors = FALSE, fileEncoding = "UTF-8", ...) -clean(dirs = c("data", model.dir(), "output", "report"), force = FALSE) +rmdir(path, recursive = FALSE) -model.script() +rnd(x, cols, digits = 0, grep = FALSE, ...) -taf.libPaths(remove = FALSE) +sam2taf(x, colname = NULL, year = TRUE) -draft.software(package, author = NULL, year = NULL, title = NULL, - version = NULL, source = NULL, file = "", append = FALSE) +source.all(...) -sourceDir(...) +source.dir(dir, pattern = "\\\\.[r|R]$", all.files = FALSE, + recursive = FALSE, quiet = TRUE, ...) -taf.boot(software = TRUE, data = TRUE, clean = TRUE, force = FALSE, +source.taf(script, rm = FALSE, clean = TRUE, detach = FALSE, taf = NULL, quiet = FALSE) -file.encoding(file) +sourceAll(...) -latin1.to.utf8(file, force = FALSE) +sourceDir(...) -clean.library(folder = "boot/library", quiet = FALSE, force = FALSE) +sourceTAF(...) -tafpng(...) +stamp.description(targz, spec, sha.full) -sourceTAF(...) +taf.boot(software = TRUE, data = TRUE, clean = TRUE, force = FALSE, + taf = NULL, quiet = FALSE, ...) -taf2html(x, file = "", align = "", header = align, - digits = getOption("digits"), center = "style=\\"text-align:center\\"", - left = "style=\\"text-align:left\\"", - right = "style=\\"text-align:right\\"", append = FALSE) +taf.boot.path(..., fsep = .Platform$file.sep) -source.all(...) +taf.bootstrap(...) -extract.subdir(targz, subtargz, subdir) +taf.data.path(..., fsep = .Platform$file.sep) -taf.library(package, messages = FALSE, warnings = FALSE) +taf.install(targz = NULL, lib = taf.boot.path("library"), quiet = FALSE) -read.bib(file) +taf.libPaths(remove = FALSE) -boot.exists() +taf.libraries(messages = FALSE, warnings = FALSE) -boot.dir() +taf.library(package, messages = FALSE, warnings = FALSE) -stamp.description(targz, spec, sha.full) +taf.png(filename, width = 1600, height = 1200, res = 200, ...) -make.all(...) +taf.session(sort = FALSE, imports = TRUE, details = FALSE) -make.taf(script, ...) +taf.sources(type) -make(recipe, prereq, target, include = TRUE, engine = source, - debug = FALSE, force = FALSE, recon = FALSE, ...) +taf.unzip(zipfile, files = NULL, exdir = ".", unzip = NULL, ...) -boot.dir.inside(inside = ".") +taf2html(x, file = "", align = "", header = align, + digits = getOption("digits"), center = "style=\\"text-align:center\\"", + left = "style=\\"text-align:left\\"", + right = "style=\\"text-align:right\\"", append = FALSE) -model.dir() +taf2long(x, names = c("Year", "Age", "Value")) -line.endings(file) +taf2xtab(x) -already.in.taf.library(targz, lib) +tafpng(...) -taf.unzip(zipfile, files = NULL, exdir = ".", unzip = NULL, ...) +tt(x, column = FALSE) -process.bibfile(type, clean = TRUE, quiet = FALSE) +unix2dos(file) -cp(from, to, move = FALSE, ignore = FALSE, overwrite = TRUE, - quiet = TRUE) +utf8.to.latin1(file, force = FALSE) -makeTAF(...) +write.taf(x, file = NULL, dir = NULL, quote = FALSE, row.names = FALSE, + fileEncoding = "UTF-8", underscore = TRUE, ...) -rmdir(path, recursive = FALSE) +xtab2long(x, names = c("Year", "Age", "Value")) -source.dir(dir, pattern = "\\\\.[r|R]$", all.files = FALSE, - recursive = FALSE, quiet = TRUE, ...) +xtab2taf(x, colname = "Year") -sam2taf(x, colname = NULL, year = TRUE) +zoom(x, ...) + +\method{zoom}{trellis}(x, size = 1, main = 1.2 * size, lab = size, + axis = size, strip = size, sub = 0.9 * size, legend = 0.9 * size, + splom = 0.9 * size, ...) taf.skeleton(path = ".", force = FALSE, pkgs = "icesTAF") } @@ -286,6 +296,6 @@ These functions are re-exported from the TAF package. } \details{ Follow the links below to see the documentation. -\code{\link[TAF]{makeAll}}, \code{\link[TAF]{taf.install}}, \code{\link[TAF]{parse.repo}}, \code{\link[TAF]{taf2long}}, \code{\link[TAF]{write.taf}}, \code{\link[TAF]{utf8.to.latin1}}, \code{\link[TAF]{download}}, \code{\link[TAF]{clean.boot}}, \code{\link[TAF]{flr2taf}}, \code{\link[TAF]{get.remote.sha}}, \code{\link[TAF]{taf.bootstrap}}, \code{\link[TAF]{xtab2taf}}, \code{\link[TAF]{long2taf}}, \code{\link[TAF]{source.taf}}, \code{\link[TAF]{ds.file}}, \code{\link[TAF]{div}}, \code{\link[TAF]{detach.packages}}, \code{\link[TAF]{rnd}}, \code{\link[TAF]{taf2xtab}}, \code{\link[TAF]{ds.package}}, \code{\link[TAF]{long2xtab}}, \code{\link[TAF]{os.linux}}, \code{\link[TAF]{taf.png}}, \code{\link[TAF]{os.macos}}, \code{\link[TAF]{os}}, \code{\link[TAF]{period}}, \code{\link[TAF]{tt}}, \code{\link[TAF]{clean.data}}, \code{\link[TAF]{zoom.trellis}}, \code{\link[TAF]{zoom}}, \code{\link[TAF]{unix2dos}}, \code{\link[TAF]{dos2unix}}, \code{\link[TAF]{mkdir}}, \code{\link[TAF]{convert.spaces}}, \code{\link[TAF]{lim}}, \code{\link[TAF]{is.r.package}}, \code{\link[TAF]{clean.software}}, \code{\link[TAF]{taf.boot.path}}, \code{\link[TAF]{sourceAll}}, \code{\link[TAF]{plus}}, \code{\link[TAF]{taf.sources}}, \code{\link[TAF]{msg}}, \code{\link[TAF]{process.entry}}, \code{\link[TAF]{taf.data.path}}, \code{\link[TAF]{download.github}}, \code{\link[TAF]{deps}}, \code{\link[TAF]{taf.session}}, \code{\link[TAF]{os.unix}}, \code{\link[TAF]{xtab2long}}, \code{\link[TAF]{os.windows}}, \code{\link[TAF]{draft.data}}, \code{\link[TAF]{read.taf}}, \code{\link[TAF]{clean}}, \code{\link[TAF]{model.script}}, \code{\link[TAF]{taf.libPaths}}, \code{\link[TAF]{draft.software}}, \code{\link[TAF]{sourceDir}}, \code{\link[TAF]{taf.boot}}, \code{\link[TAF]{file.encoding}}, \code{\link[TAF]{latin1.to.utf8}}, \code{\link[TAF]{clean.library}}, \code{\link[TAF]{tafpng}}, \code{\link[TAF]{sourceTAF}}, \code{\link[TAF]{taf2html}}, \code{\link[TAF]{source.all}}, \code{\link[TAF]{extract.subdir}}, \code{\link[TAF]{taf.library}}, \code{\link[TAF]{read.bib}}, \code{\link[TAF]{boot.exists}}, \code{\link[TAF]{boot.dir}}, \code{\link[TAF]{stamp.description}}, \code{\link[TAF]{make.all}}, \code{\link[TAF]{make.taf}}, \code{\link[TAF]{make}}, \code{\link[TAF]{boot.dir.inside}}, \code{\link[TAF]{model.dir}}, \code{\link[TAF]{line.endings}}, \code{\link[TAF]{already.in.taf.library}}, \code{\link[TAF]{taf.unzip}}, \code{\link[TAF]{process.bibfile}}, \code{\link[TAF]{cp}}, \code{\link[TAF]{makeTAF}}, \code{\link[TAF]{rmdir}}, \code{\link[TAF]{source.dir}}, \code{\link[TAF]{sam2taf}} +\code{\link[TAF]{already.in.taf.library}}, \code{\link[TAF]{boot.dir}}, \code{\link[TAF]{boot.dir.inside}}, \code{\link[TAF]{boot.exists}}, \code{\link[TAF]{check.software}}, \code{\link[TAF]{clean}}, \code{\link[TAF]{clean.boot}}, \code{\link[TAF]{clean.data}}, \code{\link[TAF]{clean.library}}, \code{\link[TAF]{clean.software}}, \code{\link[TAF]{convert.spaces}}, \code{\link[TAF]{cp}}, \code{\link[TAF]{ddim}}, \code{\link[TAF]{deps}}, \code{\link[TAF]{detach.packages}}, \code{\link[TAF]{div}}, \code{\link[TAF]{dos2unix}}, \code{\link[TAF]{download}}, \code{\link[TAF]{download.github}}, \code{\link[TAF]{draft.data}}, \code{\link[TAF]{draft.software}}, \code{\link[TAF]{ds.file}}, \code{\link[TAF]{ds.package}}, \code{\link[TAF]{extract.subdir}}, \code{\link[TAF]{file.encoding}}, \code{\link[TAF]{flr2taf}}, \code{\link[TAF]{get.remote.sha}}, \code{\link[TAF]{is.r.package}}, \code{\link[TAF]{latin1.to.utf8}}, \code{\link[TAF]{lim}}, \code{\link[TAF]{line.endings}}, \code{\link[TAF]{long2taf}}, \code{\link[TAF]{long2xtab}}, \code{\link[TAF]{make}}, \code{\link[TAF]{make.all}}, \code{\link[TAF]{make.taf}}, \code{\link[TAF]{makeAll}}, \code{\link[TAF]{makeTAF}}, \code{\link[TAF]{mkdir}}, \code{\link[TAF]{model.dir}}, \code{\link[TAF]{model.script}}, \code{\link[TAF]{msg}}, \code{\link[TAF]{os}}, \code{\link[TAF]{os.linux}}, \code{\link[TAF]{os.macos}}, \code{\link[TAF]{os.unix}}, \code{\link[TAF]{os.windows}}, \code{\link[TAF]{parse.repo}}, \code{\link[TAF]{period}}, \code{\link[TAF]{plus}}, \code{\link[TAF]{process.bibfile}}, \code{\link[TAF]{process.entry}}, \code{\link[TAF]{read.bib}}, \code{\link[TAF]{read.taf}}, \code{\link[TAF]{rmdir}}, \code{\link[TAF]{rnd}}, \code{\link[TAF]{sam2taf}}, \code{\link[TAF]{source.all}}, \code{\link[TAF]{source.dir}}, \code{\link[TAF]{source.taf}}, \code{\link[TAF]{sourceAll}}, \code{\link[TAF]{sourceDir}}, \code{\link[TAF]{sourceTAF}}, \code{\link[TAF]{stamp.description}}, \code{\link[TAF]{taf.boot}}, \code{\link[TAF]{taf.boot.path}}, \code{\link[TAF]{taf.bootstrap}}, \code{\link[TAF]{taf.data.path}}, \code{\link[TAF]{taf.install}}, \code{\link[TAF]{taf.libPaths}}, \code{\link[TAF]{taf.libraries}}, \code{\link[TAF]{taf.library}}, \code{\link[TAF]{taf.png}}, \code{\link[TAF]{taf.session}}, \code{\link[TAF]{taf.sources}}, \code{\link[TAF]{taf.unzip}}, \code{\link[TAF]{taf2html}}, \code{\link[TAF]{taf2long}}, \code{\link[TAF]{taf2xtab}}, \code{\link[TAF]{tafpng}}, \code{\link[TAF]{tt}}, \code{\link[TAF]{unix2dos}}, \code{\link[TAF]{utf8.to.latin1}}, \code{\link[TAF]{write.taf}}, \code{\link[TAF]{xtab2long}}, \code{\link[TAF]{xtab2taf}}, \code{\link[TAF]{zoom}}, \code{\link[TAF]{zoom.trellis}} } \keyword{internal} From 826142239a2ddd47be89a3aba7ea4c268456b655 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 26 Sep 2024 14:21:12 +1100 Subject: [PATCH 07/10] Update ICES logo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 6a4507e..a9690cb 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![CRAN Monthly](https://cranlogs.r-pkg.org/badges/icesTAF)](https://cran.r-project.org/package=icesTAF) [![CRAN Total](https://cranlogs.r-pkg.org/badges/grand-total/icesTAF)](https://cran.r-project.org/package=icesTAF) -[ICES Logo](https://ices.dk) +[ICES Logo](https://www.ices.dk) icesTAF ======= From 6f4947590e893cca0f28589a5ebf7243a6ec9b05 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 26 Sep 2024 15:12:21 +1100 Subject: [PATCH 08/10] Sync taf.skeleton() with TAF 4.3.0 --- R/TAF.R | 6 ++++-- TAF-exports/create-TAF-exports.R | 6 ++++-- man/taf-reexports.Rd | 3 ++- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/R/TAF.R b/R/TAF.R index 4abe2e7..9c154c0 100644 --- a/R/TAF.R +++ b/R/TAF.R @@ -450,6 +450,8 @@ zoom.trellis <- TAF::zoom.trellis #' @importFrom TAF taf.skeleton #' @rdname taf-reexports #' @export -taf.skeleton <- function(path = ".", force = FALSE, pkgs = "icesTAF") { - TAF::taf.skeleton(path = path, force = force, pkgs = pkgs) +taf.skeleton <- function(path = ".", force = FALSE, pkgs = "icesTAF", + model.script = "model.R", gitignore = TRUE) { + TAF::taf.skeleton(path = path, force = force, pkgs = pkgs, + model.script = model.script, gitignore = gitignore) } diff --git a/TAF-exports/create-TAF-exports.R b/TAF-exports/create-TAF-exports.R index 7c3b757..9b5f5ad 100644 --- a/TAF-exports/create-TAF-exports.R +++ b/TAF-exports/create-TAF-exports.R @@ -35,8 +35,10 @@ taf.skeleton.txt <- "#' @importFrom TAF taf.skeleton #' @rdname taf-reexports #' @export -taf.skeleton <- function(path = \".\", force = FALSE, pkgs = \"icesTAF\") { - TAF::taf.skeleton(path = path, force = force, pkgs = pkgs) +taf.skeleton <- function(path = \".\", force = FALSE, pkgs = \"icesTAF\", + model.script = \"model.R\", gitignore = TRUE) { + TAF::taf.skeleton(path = path, force = force, pkgs = pkgs, + model.script = model.script, gitignore = gitignore) } " diff --git a/man/taf-reexports.Rd b/man/taf-reexports.Rd index 6439941..f0b5eec 100644 --- a/man/taf-reexports.Rd +++ b/man/taf-reexports.Rd @@ -289,7 +289,8 @@ zoom(x, ...) axis = size, strip = size, sub = 0.9 * size, legend = 0.9 * size, splom = 0.9 * size, ...) -taf.skeleton(path = ".", force = FALSE, pkgs = "icesTAF") +taf.skeleton(path = ".", force = FALSE, pkgs = "icesTAF", + model.script = "model.R", gitignore = TRUE) } \description{ These functions are re-exported from the TAF package. From 40f05cb9e7abea2529181f64fa42d70b19bc36b8 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Mon, 30 Sep 2024 11:27:14 +1100 Subject: [PATCH 09/10] Add Iago as package author --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 56fc21e..2a90813 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,8 +5,8 @@ Authors@R: c( person("Colin", "Millar", role = c("aut", "cre"), email="colin.millar@ices.dk"), person("Arni", "Magnusson", role = "aut"), + person("Iago", "Mosqueira", role = "aut"), person("Alexandros", "Kokkalis", role = "ctb"), - person("Iago", "Mosqueira", role = "ctb"), person("Ibrahim", "Umar", role = "ctb"), person("Hjalte", "Parner", role = "ctb") ) From 1a3436ff07d321d8e0d5142695adc61025917bc4 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Tue, 22 Oct 2024 14:20:17 +1100 Subject: [PATCH 10/10] Link to icesTAF package help page --- R/taf.colors.R | 2 +- R/taf.skeleton.sa.org.R | 2 +- man/taf.colors.Rd | 2 +- man/taf.skeleton.sa.org.Rd | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/taf.colors.R b/R/taf.colors.R index 34142c5..6896265 100644 --- a/R/taf.colors.R +++ b/R/taf.colors.R @@ -16,7 +16,7 @@ #' taf.light #' #' @seealso -#' \code{\link{TAF-package}} gives an overview of the package. +#' \code{\link{icesTAF-package}} gives an overview of the package. #' #' @examples #' taf.green diff --git a/R/taf.skeleton.sa.org.R b/R/taf.skeleton.sa.org.R index 87b5ca0..0da7485 100644 --- a/R/taf.skeleton.sa.org.R +++ b/R/taf.skeleton.sa.org.R @@ -13,7 +13,7 @@ #' @seealso #' \code{\link{package.skeleton}} creates an empty template for a new R package. #' -#' \code{\link{TAF-package}} gives an overview of the package. +#' \code{\link{icesTAF-package}} gives an overview of the package. #' #' @examples #' \dontrun{ diff --git a/man/taf.colors.Rd b/man/taf.colors.Rd index b004b22..1fe63bc 100644 --- a/man/taf.colors.Rd +++ b/man/taf.colors.Rd @@ -34,5 +34,5 @@ barplot(7:1, main="Seven", col=c("black", taf.dark, taf.light, par(opar) } \seealso{ -\code{\link{TAF-package}} gives an overview of the package. +\code{\link{icesTAF-package}} gives an overview of the package. } diff --git a/man/taf.skeleton.sa.org.Rd b/man/taf.skeleton.sa.org.Rd index 4e383f8..702678c 100644 --- a/man/taf.skeleton.sa.org.Rd +++ b/man/taf.skeleton.sa.org.Rd @@ -30,5 +30,5 @@ taf.skeleton.sa.org(stockname = "WBCod_2021_cand01") \seealso{ \code{\link{package.skeleton}} creates an empty template for a new R package. -\code{\link{TAF-package}} gives an overview of the package. +\code{\link{icesTAF-package}} gives an overview of the package. }