diff --git a/DESCRIPTION b/DESCRIPTION
index 50b3241..2a90813 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,12 +1,12 @@
Package: icesTAF
-Version: 4.2.0
+Version: 4.3.0
Title: Functions to Support the ICES Transparent Assessment Framework
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")
)
@@ -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/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',
diff --git a/R/TAF.R b/R/TAF.R
index 514462c..9c154c0 100644
--- a/R/TAF.R
+++ b/R/TAF.R
@@ -4,437 +4,454 @@
#' 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]{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 makeAll
+#' @importFrom TAF already.in.taf.library
#' @name taf-reexports
#' @keywords internal
#' @export
-makeAll <- TAF::makeAll
+already.in.taf.library <- TAF::already.in.taf.library
-#' @importFrom TAF taf.install
+#' @importFrom TAF boot.dir
#' @rdname taf-reexports
#' @export
-taf.install <- TAF::taf.install
+boot.dir <- TAF::boot.dir
-#' @importFrom TAF parse.repo
+#' @importFrom TAF boot.dir.inside
#' @rdname taf-reexports
#' @export
-parse.repo <- TAF::parse.repo
+boot.dir.inside <- TAF::boot.dir.inside
-#' @importFrom TAF taf2long
+#' @importFrom TAF boot.exists
#' @rdname taf-reexports
#' @export
-taf2long <- TAF::taf2long
+boot.exists <- TAF::boot.exists
-#' @importFrom TAF write.taf
+#' @importFrom TAF check.software
#' @rdname taf-reexports
#' @export
-write.taf <- TAF::write.taf
+check.software <- TAF::check.software
-#' @importFrom TAF utf8.to.latin1
+#' @importFrom TAF clean
#' @rdname taf-reexports
#' @export
-utf8.to.latin1 <- TAF::utf8.to.latin1
+clean <- TAF::clean
-#' @importFrom TAF download
+#' @importFrom TAF clean.boot
#' @rdname taf-reexports
#' @export
-download <- TAF::download
+clean.boot <- TAF::clean.boot
-#' @importFrom TAF clean.boot
+#' @importFrom TAF clean.data
#' @rdname taf-reexports
#' @export
-clean.boot <- TAF::clean.boot
+clean.data <- TAF::clean.data
-#' @importFrom TAF flr2taf
+#' @importFrom TAF clean.library
#' @rdname taf-reexports
#' @export
-flr2taf <- TAF::flr2taf
+clean.library <- TAF::clean.library
-#' @importFrom TAF get.remote.sha
+#' @importFrom TAF clean.software
#' @rdname taf-reexports
#' @export
-get.remote.sha <- TAF::get.remote.sha
+clean.software <- TAF::clean.software
-#' @importFrom TAF taf.bootstrap
+#' @importFrom TAF convert.spaces
#' @rdname taf-reexports
#' @export
-taf.bootstrap <- TAF::taf.bootstrap
+convert.spaces <- TAF::convert.spaces
-#' @importFrom TAF xtab2taf
+#' @importFrom TAF cp
#' @rdname taf-reexports
#' @export
-xtab2taf <- TAF::xtab2taf
+cp <- TAF::cp
-#' @importFrom TAF long2taf
+#' @importFrom TAF ddim
#' @rdname taf-reexports
#' @export
-long2taf <- TAF::long2taf
+ddim <- TAF::ddim
-#' @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.libraries
#' @rdname taf-reexports
#' @export
-stamp.description <- TAF::stamp.description
+taf.libraries <- TAF::taf.libraries
-#' @importFrom TAF make.all
+#' @importFrom TAF taf.library
#' @rdname taf-reexports
#' @export
-make.all <- TAF::make.all
+taf.library <- TAF::taf.library
-#' @importFrom TAF make.taf
+#' @importFrom TAF taf.png
#' @rdname taf-reexports
#' @export
-make.taf <- TAF::make.taf
+taf.png <- TAF::taf.png
-#' @importFrom TAF make
+#' @importFrom TAF taf.session
#' @rdname taf-reexports
#' @export
-make <- TAF::make
+taf.session <- TAF::taf.session
-#' @importFrom TAF boot.dir.inside
+#' @importFrom TAF taf.sources
#' @rdname taf-reexports
#' @export
-boot.dir.inside <- TAF::boot.dir.inside
+taf.sources <- TAF::taf.sources
-#' @importFrom TAF model.dir
+#' @importFrom TAF taf.unzip
#' @rdname taf-reexports
#' @export
-model.dir <- TAF::model.dir
+taf.unzip <- TAF::taf.unzip
-#' @importFrom TAF line.endings
+#' @importFrom TAF taf2html
#' @rdname taf-reexports
#' @export
-line.endings <- TAF::line.endings
+taf2html <- TAF::taf2html
-#' @importFrom TAF already.in.taf.library
+#' @importFrom TAF taf2long
#' @rdname taf-reexports
#' @export
-already.in.taf.library <- TAF::already.in.taf.library
+taf2long <- TAF::taf2long
-#' @importFrom TAF taf.unzip
+#' @importFrom TAF taf2xtab
#' @rdname taf-reexports
#' @export
-taf.unzip <- TAF::taf.unzip
+taf2xtab <- TAF::taf2xtab
-#' @importFrom TAF process.bibfile
+#' @importFrom TAF tafpng
#' @rdname taf-reexports
#' @export
-process.bibfile <- TAF::process.bibfile
+tafpng <- TAF::tafpng
-#' @importFrom TAF cp
+#' @importFrom TAF tt
#' @rdname taf-reexports
#' @export
-cp <- TAF::cp
+tt <- TAF::tt
-#' @importFrom TAF makeTAF
+#' @importFrom TAF unix2dos
#' @rdname taf-reexports
#' @export
-makeTAF <- TAF::makeTAF
+unix2dos <- TAF::unix2dos
-#' @importFrom TAF rmdir
+#' @importFrom TAF utf8.to.latin1
#' @rdname taf-reexports
#' @export
-rmdir <- TAF::rmdir
+utf8.to.latin1 <- TAF::utf8.to.latin1
-#' @importFrom TAF source.dir
+#' @importFrom TAF write.taf
#' @rdname taf-reexports
#' @export
-source.dir <- TAF::source.dir
+write.taf <- TAF::write.taf
-#' @importFrom TAF sam2taf
+#' @importFrom TAF xtab2long
#' @rdname taf-reexports
#' @export
-sam2taf <- TAF::sam2taf
+xtab2long <- TAF::xtab2long
+
+#' @importFrom TAF xtab2taf
+#' @rdname taf-reexports
+#' @export
+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
#' @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/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"
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/README.md b/README.md
index 6a4507e..a9690cb 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
[](https://cran.r-project.org/package=icesTAF)
[](https://cran.r-project.org/package=icesTAF)
-[
](https://ices.dk)
+[
](https://www.ices.dk)
icesTAF
=======
diff --git a/TAF-exports/create-TAF-exports.R b/TAF-exports/create-TAF-exports.R
index 0682719..9b5f5ad 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) {
@@ -34,8 +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/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..f0b5eec 100644
--- a/man/taf-reexports.Rd
+++ b/man/taf-reexports.Rd
@@ -2,290 +2,301 @@
% 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")
+taf.skeleton(path = ".", force = FALSE, pkgs = "icesTAF",
+ model.script = "model.R", gitignore = TRUE)
}
\description{
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}
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.
}