From 502dacdd67f2a53fd69f23614380596b8cf633f9 Mon Sep 17 00:00:00 2001
From: Andrew Hooker <andrew.c.hooker@gmail.com>
Date: Thu, 22 Feb 2024 08:41:49 +0100
Subject: [PATCH] update URL links

---
 R/compute.cwres.R    |  2 +-
 README.Rmd           |  4 ++--
 README.md            | 27 +++++++++++++--------------
 man/compute.cwres.Rd |  2 +-
 4 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/R/compute.cwres.R b/R/compute.cwres.R
index 277f147..cdf2761 100644
--- a/R/compute.cwres.R
+++ b/R/compute.cwres.R
@@ -440,7 +440,7 @@ ind.cwres <-
 #' This procedure can be done automatically using Perl Speaks NONMEM (PsN) and
 #' we highly recommend using PsN for this purpose.  After installing PsN just
 #' type '\code{execute [modelname] -cwres}'.  See
-#' \url{http://psn.sourceforge.net} for more details.  
+#' \url{https://uupharmacometrics.github.io/PsN/} for more details.  
 #' 
 #' There are five main insertions needed in your NONMEM control file:
 #' \enumerate{ \item$ABB COMRES=X.
diff --git a/README.Rmd b/README.Rmd
index a5b6730..170b236 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -23,7 +23,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/xpose4)](https://CRAN.R-project.org/package=xpose4) 
-[![codecov.io](https://codecov.io/github/UUPharmacometrics/xpose4/coverage.svg?branch=master)](https://codecov.io/github/UUPharmacometrics/xpose4?branch=master)
+[![codecov.io](https://codecov.io/github/UUPharmacometrics/xpose4/coverage.svg?branch=master)](https://app.codecov.io/github/UUPharmacometrics/xpose4?branch=master)
 [![R-CMD-check](https://github.com/UUPharmacometrics/xpose4/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UUPharmacometrics/xpose4/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
@@ -114,7 +114,7 @@ typing (for example) `?xpose4` at the R command line.
 
 A more detailed description of Xpose with example plots and explanaitions for
 most of the functions in the package is available in our Bestiarium: 
-http://xpose.sourceforge.net/bestiarium_v1.0.pdf
+https://xpose.sourceforge.net/bestiarium_v1.0.pdf
 
 
 ## Don't Panic
diff --git a/README.md b/README.md
index 41e350d..9e6d856 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/xpose4)](https://CRAN.R-project.org/package=xpose4)
-[![codecov.io](https://codecov.io/github/UUPharmacometrics/xpose4/coverage.svg?branch=master)](https://codecov.io/github/UUPharmacometrics/xpose4?branch=master)
+[![codecov.io](https://codecov.io/github/UUPharmacometrics/xpose4/coverage.svg?branch=master)](https://app.codecov.io/github/UUPharmacometrics/xpose4?branch=master)
 [![R-CMD-check](https://github.com/UUPharmacometrics/xpose4/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UUPharmacometrics/xpose4/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
@@ -24,21 +24,20 @@ diagnostics, candidate covariate identification and model comparison.
 To install xpose you will need R (\>= version 2.2.0).  
 To install Xpose in R use one of the following methods:
 
--   latest stable release – From CRAN. Write at the R command line:
+- latest stable release – From CRAN. Write at the R command line:
 
-    ``` r
-    install.packages("xpose4")
-    ```
+  ``` r
+  install.packages("xpose4")
+  ```
 
--   Latest development version – from Github. Note that the command
-    below installs the “master” (development) branch; if you want the
-    release branch from Github add `ref="release"` to the
-    `install_github()` call.
+- Latest development version – from Github. Note that the command below
+  installs the “master” (development) branch; if you want the release
+  branch from Github add `ref="release"` to the `install_github()` call.
 
-    ``` r
-    # install.packages("devtools")
-    devtools::install_github("UUPharmacometrics/xpose4")
-    ```
+  ``` r
+  # install.packages("devtools")
+  devtools::install_github("UUPharmacometrics/xpose4")
+  ```
 
 ## Running Xpose 4
 
@@ -94,7 +93,7 @@ by typing (for example) `?xpose4` at the R command line.
 
 A more detailed description of Xpose with example plots and
 explanaitions for most of the functions in the package is available in
-our Bestiarium: <http://xpose.sourceforge.net/bestiarium_v1.0.pdf>
+our Bestiarium: <https://xpose.sourceforge.net/bestiarium_v1.0.pdf>
 
 ## Don’t Panic
 
diff --git a/man/compute.cwres.Rd b/man/compute.cwres.Rd
index be48b0f..b63c3ed 100644
--- a/man/compute.cwres.Rd
+++ b/man/compute.cwres.Rd
@@ -149,7 +149,7 @@ so this function is rarely needed.
 This procedure can be done automatically using Perl Speaks NONMEM (PsN) and
 we highly recommend using PsN for this purpose.  After installing PsN just
 type '\code{execute [modelname] -cwres}'.  See
-\url{http://psn.sourceforge.net} for more details.  
+\url{https://uupharmacometrics.github.io/PsN/} for more details.  
 
 There are five main insertions needed in your NONMEM control file:
 \enumerate{ \item$ABB COMRES=X.