updating urls to nmautoverse

NMautoverse · Oct 30, 2024 · c394f3f · c394f3f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: NMdata
 Type: Package
 Title: Preparation, Checking and Post-Processing Data for PK/PD Modeling
-Version: 0.1.7.910
+Version: 0.1.7.911
 Authors@R:
   c(person(given="Philip", family="Delff",
      email = "philip@delff.dk",
@@ -33,6 +33,6 @@ Suggests:
   htmltools,
   spelling
 Encoding: UTF-8
-BugReports: https://github.com/philipdelff/NMdata/issues
+BugReports: https://github.com/nmautoverse/NMdata/issues
 Language: en-US
-URL: https://philipdelff.github.io/NMdata/
+URL: https://nmautoverse.github.io/NMdata/
diff --git a/R/zzz.R b/R/zzz.R
@@ -7,5 +7,5 @@ NMdataConf(reset=TRUE)
 
 ##' @importFrom utils packageVersion
 .onAttach <- function(libname,pkgname){
-    packageStartupMessage(paste0("NMdata ",packageVersion("NMdata"),". Browse NMdata documentation at\nhttps://philipdelff.github.io/NMdata/"))
+    packageStartupMessage(paste0("NMdata ",packageVersion("NMdata"),". Browse NMdata documentation at\nhttps://nmautoverse.github.io/NMdata/"))
 }
diff --git a/README.Rmd b/README.Rmd
@@ -19,12 +19,12 @@ NMscanData <- function(x,...)NMdata::NMscanData(file.path(system.file(paste0("ex
 
 ```
 
-# NMdata<a href='https://philipdelff.github.io/NMdata/'><img src='man/figures/logo.png' align="right" height="120" /></a>
+# NMdata<a href='https://nmautoverse.github.io/NMdata/'><img src='man/figures/logo.png' align="right" height="120" /></a>
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
-[![R-CMD-check](https://github.com/philipdelff/NMdata/workflows/R-CMD-check/badge.svg)](https://github.com/philipdelff/NMdata/actions)
-[![Codecov test coverage](https://codecov.io/gh/philipdelff/NMdata/branch/master/graph/badge.svg)](https://app.codecov.io/gh/philipdelff/NMdata?branch=master)
+[![R-CMD-check](https://github.com/nmautoverse/NMdata/workflows/R-CMD-check/badge.svg)](https://github.com/nmautoverse/NMdata/actions)
+[![Codecov test coverage](https://codecov.io/gh/NMautoverse/NMdata/branch/master/graph/badge.svg)](https://app.codecov.io/gh/nmautoverse/NMdata?branch=master)
 [![CRAN status](https://www.r-pkg.org/badges/version/NMdata)](https://CRAN.R-project.org/package=NMdata)
 [![CRAN downloads](https://cranlogs.r-pkg.org/badges/NMdata)](https://cran.r-project.org/package=NMdata)
 <!-- badges: end -->
@@ -53,13 +53,13 @@ already use.
 
 ### More information
 The best place to browse information about the package is
-[here](https://philipdelff.github.io/NMdata/). The quickest way in is
+[here](https://nmautoverse.github.io/NMdata/). The quickest way in is
 the
-[Cheatsheet](https://htmlpreview.github.io/?https://github.com/philipdelff/NMdata/blob/master/vignettes/NMdata-cheat.html). 
+[Cheatsheet](https://htmlpreview.github.io/?https://github.com/nmautoverse/NMdata/blob/master/vignettes/NMdata-cheat.html). 
 
 <!-- ![Cheatsheet](man/figures/cheatsheet_icon_0010.png){width="15%"} -->
-<!-- [Cheatsheet](https://htmlpreview.github.io/?https://github.com/philipdelff/NMdata/blob/master/devel/NMdata-cheat.html) -->
-<a href="https://htmlpreview.github.io/?https://github.com/philipdelff/NMdata/blob/master/vignettes/NMdata-cheat.html"><img src="man/figures/cheatsheet_icon_0010.png" alt="CheatSheet" width="200"/></a>
+<!-- [Cheatsheet](https://htmlpreview.github.io/?https://github.com/nmautoverse/NMdata/blob/master/devel/NMdata-cheat.html) -->
+<a href="https://htmlpreview.github.io/?https://github.com/nmautoverse/NMdata/blob/master/vignettes/NMdata-cheat.html"><img src="man/figures/cheatsheet_icon_0010.png" alt="CheatSheet" width="200"/></a>
 
 ### How to install
 `NMdata` is on [CRAN](https://cran.r-project.org/package=NMdata) and [MPN](https://mpn.metworx.com/docs/packages/NMdata). To install from the package archive you are already using, do:
@@ -73,7 +73,7 @@ See further below for instructions on how to install from other sources than you
 ## Prepare, check, and export PK/PD data 
 On the data-generation side, functionality is provided for
 documentation of the datasets while generating them. Check out [this
-vignette](https://philipdelff.github.io/NMdata/articles/DataPrepare.html)
+vignette](https://nmautoverse.github.io/NMdata/articles/DataPrepare.html)
 on the topic. There are functions for automatic checks of (some) data
 merges, handling and counting of exclusions flags, final preparations
 for ensuring readability in NONMEM, and ensuring traceability of
@@ -120,7 +120,7 @@ res.dt <- NMscanData("xgxr001.lst",quiet=TRUE)
 `NMscanData` is very general, and should work with all kinds of models,
 and all kinds of other software and configurations. Take a look at
 [this
-vignette](https://philipdelff.github.io/NMdata/articles/NMscanData.html)
+vignette](https://nmautoverse.github.io/NMdata/articles/NMscanData.html)
 for more info on the NONMEM data reader. Then you will learn how to
 access the meta data that will allow you to trace every step that was
 taken combining the data and the many checks that were done along the
@@ -158,19 +158,19 @@ library(NMdata)
 
 ## Option 3: Install from github
 library(remotes)
-install_github("philipdelff/NMdata")
+install_github("nmautoverse/NMdata")
 library(NMdata)
 ```
 If you use the Github version, you may want to see the
-[FAQ](https://philipdelff.github.io/NMdata/articles/NMdata-FAQ.html)
+[FAQ](https://nmautoverse.github.io/NMdata/articles/NMdata-FAQ.html)
 for how to install specific releases from Github (ensuring reproducibility).
 
 
 ## Questions?
-Check the [FAQ](https://philipdelff.github.io/NMdata/articles/NMdata-FAQ.html), or ask on [github](https://github.com/philipdelff/NMdata/)
+Check the [FAQ](https://nmautoverse.github.io/NMdata/articles/NMdata-FAQ.html), or ask on [github](https://github.com/nmautoverse/NMdata/)
 
 ## Issues?
-The best way to report a bug or to request features is on [github](https://github.com/philipdelff/NMdata/).
+The best way to report a bug or to request features is on [github](https://github.com/nmautoverse/NMdata/).
 
 ## Code of Conduct
-Please note that the patchwork project is released with a [Contributor Code of Conduct](https://philipdelff.github.io/NMdata/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+Please note that the patchwork project is released with a [Contributor Code of Conduct](https://nmautoverse.github.io/NMdata/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: https://philipdelff.github.io/NMdata/
+url: https://nmautoverse.github.io/NMdata/
 template:
   opengraph:
     image:
@@ -31,7 +31,7 @@ navbar:
       text: Vignettes
       menu:
       - text: Cheat Sheet
-        href: https://htmlpreview.github.io/?https://github.com/philipdelff/NMdata/blob/master/vignettes/NMdata-cheat.html
+        href: https://htmlpreview.github.io/?https://github.com/nmautoverse/NMdata/blob/master/vignettes/NMdata-cheat.html
       - text: 'NMscanData: find and combine all output and input data'
         href: articles/NMscanData.html
       - text: Data Preparation Tools
@@ -118,8 +118,8 @@ news:
   href: news/index.html
 github:
   icon: fab fa-github fa-lg
-  href: https://github.com/philipdelff/NMdata
+  href: https://github.com/nmautoverse/NMdata
 cheatsheet:
   text: CheatSheet
-  href: https://htmlpreview.github.io/?https://github.com/philipdelff/NMdata/blob/master/devel/NMdata-cheat.html
+  href: https://htmlpreview.github.io/?https://github.com/nmautoverse/NMdata/blob/master/devel/NMdata-cheat.html
 
diff --git a/vignettes/DataPrepare.Rmd b/vignettes/DataPrepare.Rmd
@@ -38,7 +38,7 @@ Built `r Sys.Date()` using NMdata `r packageVersion("NMdata")`.
 
 This vignette is still under development. Please make sure to see
 latest version available
-[here](https://philipdelff.github.io/NMdata/).
+[here](https://nmautoverse.github.io/NMdata/).
 
 ## Objectives
 This vignettes aims at enabling you at 

diff --git a/vignettes/NMdata-FAQ.Rmd b/vignettes/NMdata-FAQ.Rmd
@@ -21,7 +21,7 @@ Built `r Sys.Date()` using NMdata `r packageVersion("NMdata")`.
 
 This vignette is still under development. Please make sure to see
 latest version available
-[here](https://philipdelff.github.io/NMdata/).
+[here](https://nmautoverse.github.io/NMdata/).
 
 ## General NMdata questions
 
@@ -57,23 +57,23 @@ within R:
 
 ```{r,eval=FALSE}
 library(remotes)
-install_github("philipdelff/NMdata")
+install_github("nmautoverse/NMdata")
 library(NMdata)
 ```
 
 In a production environment, use a [github
-release](https://github.com/philipdelff/NMdata/releases) To install
+release](https://github.com/nmautoverse/NMdata/releases) To install
 `NMdata X.Y.Z` release, do (notice "@v":)
 
 ```{r,eval=FALSE}
 library(remotes)
-install_github("philipdelff/NMdata@vX.Y.Z")
+install_github("nmautoverse/NMdata@vX.Y.Z")
 library(NMdata)
 ```
 
 This example is not automatically updated to latest available
 release. Please make sure to check for latest version on
-(https://github.com/philipdelff/NMdata/releases)
+(https://github.com/nmautoverse/NMdata/releases)
 
 If you need to archive a script that is dependent on a feature or bug
 fix which is only in the master branch, you can request a release. 
@@ -188,7 +188,7 @@ technically inherit from the data.frame class).
 
 
 ### Can I request a feature?
-Please open an issue on [github](https://github.com/philipdelff/NMdata/issues).
+Please open an issue on [github](https://github.com/nmautoverse/NMdata/issues).
 
 ### Any plans on including some plotting functions?
 No. See the question above about dependencies. If NMdata were extended

diff --git a/vignettes/NMdata-cheat.Rmd b/vignettes/NMdata-cheat.Rmd
@@ -89,7 +89,7 @@ htmltools::img(src = knitr::image_uri("apple-touch-icon-180x180.png"),
 Built `r Sys.Date()` using NMdata `r packageVersion("NMdata")`.
 
 Please make sure to see latest version available
-[here](https://philipdelff.github.io/NMdata/). 
+[here](https://nmautoverse.github.io/NMdata/). 
 
 This cheat sheet is
 intented to provide an overview and remind of command names. Please

diff --git a/vignettes/NMscanData.Rmd b/vignettes/NMscanData.Rmd
@@ -28,7 +28,7 @@ knitr::opts_chunk$set(
 
 Built `r Sys.Date()` using NMdata `r packageVersion("NMdata")`.
 
-Please make sure to see latest vignette version available [here](https://philipdelff.github.io/NMdata/).
+Please make sure to see latest vignette version available [here](https://nmautoverse.github.io/NMdata/).
 
 ## Objectives
 This vignettes aims at enabling you at 
@@ -139,7 +139,7 @@ your control streams and list files differently than this
 vignette. Here, we use the `NMdata` default which is `.mod` and
 `.lst`. You can easily configure `NMdata` to match your
 preferences. See the
-[FAQ](https://philipdelff.github.io/NMdata/articles/NMdata-FAQ.html)
+[FAQ](https://nmautoverse.github.io/NMdata/articles/NMdata-FAQ.html)
 for how. So for now, rest assured that this is easy to adjust and read
 on.
 
@@ -495,7 +495,7 @@ so file/network access (I/O) is likely to be the main bottleneck.
 If you write Nonmem datasets with the `NMdata::NMwriteData`, you can
 get an `rds` file automatically, exactly where `NMscanData` will look
 for it. Preparing datasets using `NMdata` is described in [this
-vignette](https://philipdelff.github.io/NMdata/articles/DataPrepare.html).
+vignette](https://nmautoverse.github.io/NMdata/articles/DataPrepare.html).
 
 You probably want to use `NMdataConf` to change the default behavior
 if you don't want to use `rds` files.

diff --git a/vignettes/ParameterTables.Rmd b/vignettes/ParameterTables.Rmd
@@ -49,7 +49,7 @@ A manual or even semi-automated approach to establishing these relationships are
 
 * Automatic translation of Nonmem code related to direct use of the parameters (`NMrelate()`). This may be a pretty good approach trying to report a Nonmem model without structured labeling in the parameter sections. If you keep a  coding standard, it may allow you to skip manual parameter translation altogether. And lastly, it may be a powerful QC tool in any case.
 
-Notice, this vignette zooms in on how to read, label and format "parameter estimates". It does not deal with reading input and output data (see the [NMscanData()](https://philipdelff.github.io/NMdata/articles/NMscanData.html) vignette). `NMdata` contains the following functions to read estimates from Nonmem:
+Notice, this vignette zooms in on how to read, label and format "parameter estimates". It does not deal with reading input and output data (see the [NMscanData()](https://nmautoverse.github.io/NMdata/articles/NMscanData.html) vignette). `NMdata` contains the following functions to read estimates from Nonmem:
 
 * `NMreadExt()` A feature-rich processor of ext files. Provides final parameter estimates with uncertainties and everything else provided in the ext file, iterations, objective function value and termination status
 * `NMreadPhi()` Reads individual posthoc estimates into a `data.frame`