Merge pull request #12 from Merck/Nextrel

Update package installations at top of vignettes

Author: dom-muston

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: psm3mkv
 Title: Fit and Evaluate Three-State Partitioned Survival Analysis and Markov Models to Progression-Free and Overall Survival Data
-Version: 0.2.0
+Version: 0.2.0.9000
 Authors@R: c(
     person("Dominic", "Muston", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-4876-7940")),
@@ -22,6 +22,7 @@ Imports:
     flexsurv,
     ggplot2,
     purrr,
+    remotes,
     rlang,
     SimplicialCubature,
     stats,

NEWS.md

@@ -1,3 +1,5 @@
+# psm3mkv (development version)
+
 # 26 Jan 2024 - Version 0.2
 
 This version provides additional functionality to the calculation of restricted mean durations in `calc_allrmds`. These estimates may now be constrained by a lifetable (see `calc_ltsurv`) and discounting may now be applied. A vignette describing how to use this functionality is provided: `vignette("background-mortality")`.

README.Rmd

@@ -80,8 +80,10 @@ The package requires version 4.1 of R (due to use of the [native pipe](https://w
 The development version of *psm3mkv* may be downloaded as follows:
 
 ``` r
-# Install from Github as follows (with the vignette)
-remotes::install_github("Merck/psm3mkv", build_vignettes=TRUE)
+# Install version 0.2 from Github as follows, with the vignette
+remotes::install_github("Merck/psm3mkv",
+    ref="v0.2",
+    build_vignettes=TRUE)
 ```
 
 ## Licensing

README.md

@@ -94,8 +94,10 @@ ensure R is updated first.
 The development version of *psm3mkv* may be downloaded as follows:
 
 ``` r
-# Install from Github as follows (with the vignette)
-remotes::install_github("Merck/psm3mkv", build_vignettes=TRUE)
+# Install version 0.2 from Github as follows, with the vignette
+remotes::install_github("Merck/psm3mkv",
+    ref="v0.2",
+    build_vignettes=TRUE)
 ```
 
 ## Licensing

vignettes/background-mortality.Rmd

@@ -122,13 +122,28 @@ The calculation of restricted mean durations in *psm3mkv* default to assume no l
 
 ### Initializing
 
-First we load the packages we need - all of which are suggested for or imported to *psm3mkv*.
+First we load the packages we need - all of which are suggested for or imported to *psm3mkv*. With thanks again to @vbaliga for [this helpful code](https://vbaliga.github.io/posts/2019-04-28-verify-that-r-packages-are-installed-and-loaded/)).
 
 ```{r packages, message=FALSE}
-library(psm3mkv) # Load psm3mkv itself
-library(dplyr) # for data wrangling
-library(flexsurv) # for the datasets attached
-library(HMDHFDplus) # to create lifetables from the Human Mortality Database
+# Install psm3mkv version 0.2 from github
+require("remotes")
+remotes::install_github("Merck/psm3mkv",
+                        ref="v0.2",
+                        build_vignettes=TRUE)
+
+# First specify the packages of interest
+packages = c("psm3mkv", "dplyr", "flexsurv", "HMDHFDplus", "remotes")
+
+# Now load or install & load all
+package.check <- lapply(
+  packages,
+  FUN = function(x) {
+    if (!require(x, character.only = TRUE)) {
+      install.packages(x, dependencies = TRUE)
+      library(x, character.only = TRUE)
+    }
+  }
+)
 ```
 
 ### Creating the life table

vignettes/example.Rmd

@@ -16,18 +16,30 @@ knitr::opts_chunk$set(
 
 ## Introduction
 
-This vignette walks through evaluating the partitioned survival model (PSM) and state transition model structures (either clock reset, STM-CR, or clock forward types, STM-CF) to a dataset derived from the *bosms3* dataset that comes with the *flexsurv* package.[1] A review of PSMs and STMs in oncology cost-effectiveness models is provided by Woods et al.[2]
+This vignette walks through evaluating the partitioned survival model (PSM) and state transition model structures (either clock reset, STM-CR, or clock forward types, STM-CF) to a dataset derived from the *bosms3* dataset that comes with the [flexsurv::flexsurv-package()].[1] A review of PSMs and STMs in oncology cost-effectiveness models is provided by Woods et al.[2]
+
+First we need to install and load the packages of interest (with thanks to @vbaliga for [this helpful code](https://vbaliga.github.io/posts/2019-04-28-verify-that-r-packages-are-installed-and-loaded/)).
 
 ```{r packages, message=FALSE}
-# Load psm3mkv itself
-library(psm3mkv)
-
-# Other packages
-library(dplyr) # for data wrangling
-library(boot) # for bootstrapping
-library(ggsci) # for nice graphics
-library(flexsurv) # for data to work
-library(survival) # for data to work
+# Install psm3mkv version 0.2 from github
+require("remotes")
+remotes::install_github("Merck/psm3mkv",
+                        ref="v0.2",
+                        build_vignettes=TRUE)
+
+# First specify the packages of interest
+packages = c("psm3mkv", "dplyr", "boot", "ggsci", "flexsurv", "survival")
+
+# Now load or install & load all
+package.check <- lapply(
+  packages,
+  FUN = function(x) {
+    if (!require(x, character.only = TRUE)) {
+      install.packages(x, dependencies = TRUE)
+      library(x, character.only = TRUE)
+    }
+  }
+)
 ```
 
 ## Obtaining a suitable dataset