From a2548501e7aa99223cb98f5e615da02eb8cafae0 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Mon, 24 Jan 2022 22:45:43 +1100 Subject: [PATCH] Rename package TransparentSOFIA -> SOFIA --- DESCRIPTION | 8 +++---- NEWS.md | 9 +------- ...sparentSOFIA-package.R => SOFIA-package.R} | 8 +++---- R/addDriors.R | 2 +- R/addEffort.R | 2 +- R/calcCat.R | 2 +- R/plotCat.R | 2 +- README.md | 23 ++++++++----------- ...arentSOFIA-package.Rd => SOFIA-package.Rd} | 12 +++++----- man/addDriors.Rd | 2 +- man/addEffort.Rd | 2 +- man/calcCat.Rd | 2 +- man/plotCat.Rd | 2 +- 13 files changed, 33 insertions(+), 43 deletions(-) rename R/{TransparentSOFIA-package.R => SOFIA-package.R} (77%) rename man/{TransparentSOFIA-package.Rd => SOFIA-package.Rd} (69%) diff --git a/DESCRIPTION b/DESCRIPTION index 3bd0f24..128edd2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,13 +1,13 @@ -Package: TransparentSOFIA -Version: 1.0.1 -Date: 2022-01-21 +Package: SOFIA +Version: 1.0.2 +Date: 2022-01-24 Title: Tools to Work with SOFIA Analyses Authors@R: c(person("Rishi", "Sharma", role="aut"), person("Arni", "Magnusson", role=c("aut","cre"), email="thisisarni@gmail.com")) Imports: stats, ggplot2, sraplus Description: Tools that support the Transparent SOFIA framework. License: GPL-3 -URL: https://github.com/sofia-tsaf/TransparentSOFIA +URL: https://github.com/sofia-tsaf/SOFIA Encoding: UTF-8 RoxygenNote: 7.1.2 Roxygen: list(old_usage=TRUE) diff --git a/NEWS.md b/NEWS.md index f2da734..4cbb76a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,3 @@ -# TransparentSOFIA 1.0.1 (2022-01-21) - -* Renamed package TSAF -> TransparentSOFIA. - - - - -# TransparentSOFIA 1.0.0 (2021-12-10) +# SOFIA 1.0.2 (2022-01-24) * Initial release. diff --git a/R/TransparentSOFIA-package.R b/R/SOFIA-package.R similarity index 77% rename from R/TransparentSOFIA-package.R rename to R/SOFIA-package.R index 5ef9614..04912b2 100644 --- a/R/TransparentSOFIA-package.R +++ b/R/SOFIA-package.R @@ -1,8 +1,8 @@ #' @docType package #' -#' @name TransparentSOFIA-package +#' @name SOFIA-package #' -#' @aliases TransparentSOFIA +#' @aliases SOFIA #' #' @title Tools to Work with SOFIA Analyses #' @@ -27,10 +27,10 @@ #' @author Rishi Sharma and Arni Magnusson. #' #' @references -#' \url{https://github.com/sofia-tsaf/TransparentSOFIA} +#' \url{https://github.com/sofia-tsaf/SOFIA} #' #' @seealso -#' \pkg{TransparentSOFIA} is used in combination with the packages \pkg{sraplus} +#' \pkg{SOFIA} is used in combination with the packages \pkg{sraplus} #' (analytical model) and \pkg{TAF} (workflow). NA diff --git a/R/addDriors.R b/R/addDriors.R index 47140af..439cd74 100644 --- a/R/addDriors.R +++ b/R/addDriors.R @@ -33,7 +33,7 @@ #' #' \code{\link{addEffort}} adds an effort column to catch data. #' -#' \code{\link{TransparentSOFIA-package}} gives an overview of the package. +#' \code{\link{SOFIA-package}} gives an overview of the package. #' #' @examples #' \dontrun{ diff --git a/R/addEffort.R b/R/addEffort.R index c780aa2..4b99731 100644 --- a/R/addEffort.R +++ b/R/addEffort.R @@ -26,7 +26,7 @@ #' #' \code{\link{addDriors}} adds a driors column to stocks. #' -#' \code{\link{TransparentSOFIA-package}} gives an overview of the package. +#' \code{\link{SOFIA-package}} gives an overview of the package. #' #' @examples #' \dontrun{ diff --git a/R/calcCat.R b/R/calcCat.R index e365221..b8ea197 100644 --- a/R/calcCat.R +++ b/R/calcCat.R @@ -50,7 +50,7 @@ #' @seealso #' \code{\link{plotCat}} plots a summary of stock status categories. #' -#' \code{\link{TransparentSOFIA-package}} gives an overview of the package. +#' \code{\link{SOFIA-package}} gives an overview of the package. #' #' @examples #' \dontrun{ diff --git a/R/plotCat.R b/R/plotCat.R index 7a8f526..045f9d3 100644 --- a/R/plotCat.R +++ b/R/plotCat.R @@ -28,7 +28,7 @@ #' #' \code{\link{calcCat}} calculates stock status categories. #' -#' \code{\link{TransparentSOFIA-package}} gives an overview of the package. +#' \code{\link{SOFIA-package}} gives an overview of the package. #' #' @examples #' \dontrun{ diff --git a/README.md b/README.md index 4a07b2a..8715239 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,16 @@ -TransparentSOFIA -================ +SOFIA +===== -The TransparentSOFIA package provides tools that support the SOFIA analyses. +The SOFIA package provides tools that support the Transparent SOFIA framework. Installation ------------ -TransparentSOFIA can be installed from GitHub using the `install_github` -command: +SOFIA can be installed from GitHub using the `install_github` command: ```R library(remotes) -install_github("sofia-tsaf/TransparentSOFIA") +install_github("sofia-tsaf/SOFIA") ``` Usage @@ -20,16 +19,14 @@ Usage For a summary of the package: ```R -library(TransparentSOFIA) -?TransparentSOFIA +library(SOFIA) +?SOFIA ``` Development ----------- -TransparentSOFIA is developed openly on -[GitHub](https://github.com/sofia-tsaf/TransparentSOFIA). +SOFIA is developed openly on [GitHub](https://github.com/sofia-tsaf/SOFIA). -Feel free to open an -[issue](https://github.com/sofia-tsaf/TransparentSOFIA/issues) there if you -encounter problems or have suggestions for future versions. +Feel free to open an [issue](https://github.com/sofia-tsaf/SOFIA/issues) there +if you encounter problems or have suggestions for future versions. diff --git a/man/TransparentSOFIA-package.Rd b/man/SOFIA-package.Rd similarity index 69% rename from man/TransparentSOFIA-package.Rd rename to man/SOFIA-package.Rd index 4075aee..f89f12a 100644 --- a/man/TransparentSOFIA-package.Rd +++ b/man/SOFIA-package.Rd @@ -1,9 +1,9 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/TransparentSOFIA-package.R +% Please edit documentation in R/SOFIA-package.R \docType{package} -\name{TransparentSOFIA-package} -\alias{TransparentSOFIA-package} -\alias{TransparentSOFIA} +\name{SOFIA-package} +\alias{SOFIA-package} +\alias{SOFIA} \title{Tools to Work with SOFIA Analyses} \description{ Tools that support the Transparent SOFIA framework. @@ -24,10 +24,10 @@ Tools that support the Transparent SOFIA framework. } } \references{ -\url{https://github.com/sofia-tsaf/TransparentSOFIA} +\url{https://github.com/sofia-tsaf/SOFIA} } \seealso{ -\pkg{TransparentSOFIA} is used in combination with the packages \pkg{sraplus} +\pkg{SOFIA} is used in combination with the packages \pkg{sraplus} (analytical model) and \pkg{TAF} (workflow). } \author{ diff --git a/man/addDriors.Rd b/man/addDriors.Rd index 8333743..db33be5 100644 --- a/man/addDriors.Rd +++ b/man/addDriors.Rd @@ -55,7 +55,7 @@ addDriors(stocks, priors, stocks.combined=FALSE) \code{\link{addEffort}} adds an effort column to catch data. -\code{\link{TransparentSOFIA-package}} gives an overview of the package. +\code{\link{SOFIA-package}} gives an overview of the package. } \author{ Arni Magnusson. diff --git a/man/addEffort.Rd b/man/addEffort.Rd index 76f33b2..65cfe0f 100644 --- a/man/addEffort.Rd +++ b/man/addEffort.Rd @@ -41,7 +41,7 @@ frames. \code{\link{addDriors}} adds a driors column to stocks. -\code{\link{TransparentSOFIA-package}} gives an overview of the package. +\code{\link{SOFIA-package}} gives an overview of the package. } \author{ Arni Magnusson. diff --git a/man/calcCat.Rd b/man/calcCat.Rd index b0b7043..8c4cdd9 100644 --- a/man/calcCat.Rd +++ b/man/calcCat.Rd @@ -64,7 +64,7 @@ calcCat(newResTab, method="effDepP") \seealso{ \code{\link{plotCat}} plots a summary of stock status categories. -\code{\link{TransparentSOFIA-package}} gives an overview of the package. +\code{\link{SOFIA-package}} gives an overview of the package. } \author{ Rishi Sharma, with a contribution by Arni Magnusson. diff --git a/man/plotCat.Rd b/man/plotCat.Rd index 41c0fb1..8df1e73 100644 --- a/man/plotCat.Rd +++ b/man/plotCat.Rd @@ -46,7 +46,7 @@ plotCat(newResTab, method="effEdepP", cats=3, type="all") \code{\link{calcCat}} calculates stock status categories. -\code{\link{TransparentSOFIA-package}} gives an overview of the package. +\code{\link{SOFIA-package}} gives an overview of the package. } \author{ Rishi Sharma, with a contribution by Arni Magnusson.