Added pkgdown website

.Rbuildignore

@@ -37,3 +37,6 @@ vignettes/_region_.tex
 vignettes/Sweave.sty
 ^revdep$
 ^man-roxygen$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -22,3 +22,4 @@ R/#*
 /temp/
 /revdep/
 inst/doc
+

DESCRIPTION

@@ -2,7 +2,7 @@ Package: flexsurv
 Type: Package
 Title: Flexible Parametric Survival and Multi-State Models
 Version: 2.3
-Date: 2023-05-26
+Date: 2023-08-22
 Authors@R: c(person("Christopher", "Jackson",
          email="chris.jackson@mrc-bsu.cam.ac.uk",
          role=c("aut", "cre")),
@@ -62,7 +62,8 @@ Suggests:
     testthat,
     TH.data,
     broom
-URL: https://github.com/chjackson/flexsurv-dev
+URL: https://github.com/chjackson/flexsurv-dev,
+    http://chjackson.github.io/flexsurv-dev/
 BugReports: https://github.com/chjackson/flexsurv-dev/issues
 VignetteBuilder: knitr
 LazyData: yes

R/flexsurvmix.R

@@ -863,6 +863,17 @@ inv.transform.res <- function(x, dlists) {
   c(probs, pcov, unlist(est))
 }
 
+##' Model frame from a flexsurvmix object
+##'
+##' Returns a list of data frames, with each component containing the
+##' data that were used for the model fit for that mixture component.
+##'
+##' @param formula Fitted model object from \code{\link{flexsurvmix}}.
+##'
+##' @param ... Further arguments (currently unused).
+##'
+##' @return A list of data frames
+##' 
 ##' @export
 model.frame.flexsurvmix <- function(formula, ...)
 {

R/flexsurvreg.R

@@ -1068,6 +1068,14 @@ form.model.matrix <- function(object, newdata, na.action=na.pass, forms=NULL){
 }
 
 
+##' Variance-covariance matrix from  a flexsurvreg model
+##'
+##' @inheritParams logLik.flexsurvreg
+##'
+##' @return Variance-covariance matrix of the estimated parameters, on
+##'   the scale that they were estimated on (for positive parameters
+##'   this is the log scale).
+##' 
 ##' @export
 vcov.flexsurvreg <- function (object, ...)
 {
@@ -1124,6 +1132,18 @@ model.matrix.flexsurvreg <- function(object, par=NULL, ...)
     if (is.null(par)) compress.model.matrices(x$data$mml) else x$data$mml[[par]]
 }
 
+##' Log likelihood from a flexsurvreg model
+##'
+##' @param object A fitted model object of class
+##'   \code{\link{flexsurvreg}}, e.g. as returned by
+##'   \code{flexsurvreg} or \code{flexsurvspline}.
+##'
+##' @param ... Other arguments (currently unused).
+##'
+##' @return Log-likelihood (numeric) with additional attributes \code{df} (degrees of freedom, or number
+##' of parameters that were estimated), and number of observations \code{nobs} (including observed
+##' events and censored observations).
+##' 
 ##' @export
 logLik.flexsurvreg <- function(object, ...){
     val <- object$loglik

R/mstate.R

@@ -1347,6 +1347,18 @@ print.fmsm <- function(x, ...){
     }
 }
 
+##' Akaike's information criterion from a flexible parametric multistate model
+##'
+##' Defined as the sum of the AICs of the transition-specific models.
+##'
+##' @param object Object returned by \code{\link{fmsm}} representing a multistate model.
+##'
+##' @param k Penalty applied to number of parameters (defaults to the standard 2).
+##'
+##' @param ... Further arguments (currently unused).
+##'
+##' @return The sum of the AICs of the transition-specific models.
+##' 
 ##' @export
 AIC.fmsm <- function(object,...,k=2){
     nmods <- length(object)

R/predict.flexsurvreg.R

@@ -71,9 +71,10 @@
 #'
 #' @param ... Not currently used.
 #'
-#' @return A \code{\link{tibble}} with same number of rows as \code{newdata}
-#'   and in the same order. If multiple predictions are requested, a
-#'   \code{\link{tibble}} containing a single list-column of data frames.
+#' @return A \code{\link{tibble}} with same number of rows as
+#'   \code{newdata} and in the same order. If multiple predictions are
+#'   requested, a \code{\link{tibble}} containing a single list-column
+#'   of data frames.
 #'
 #'   For the list-column of data frames - the dimensions of each data frame
 #'   will be identical. Rows are added for each value of \code{times} or

R/survsplinek.R

@@ -1,4 +1,4 @@
-##' Royston/Parmar spline survival distribution functions 
+##' Royston/Parmar spline survival distribution functions with one argument per parameter
 ##' 
 ##' Probability density, distribution, quantile, random generation, hazard, 
 ##' cumulative hazard, mean and restricted mean functions for the Royston/Parmar

R/utils.R

@@ -73,13 +73,13 @@ rbase <- function(dname, n, ...){
 }
 
 
-##' Generic function to find restricted mean survival of a distribution
+##' Generic function to find restricted mean survival time for some distribution
 ##'
 ##' Generic function to find the restricted mean of a distribution, given the
-##' equivalent probability distribution function using numeric integration.
+##' equivalent probability distribution function, using numeric integration.
 ##'
 ##' This function is used by default for custom distributions for which an
-##' rmst function is not provided.
+##' \code{rmst} function is not provided.
 ##'
 ##' This assumes a suitably smooth, continuous distribution.
 ##'

README.md

@@ -1,7 +1,29 @@
-flexsurv-dev
-============
+flexsurv
+========
 
-The development repository for the [flexsurv](http://cran.r-project.org/package=flexsurv) R package for parametric survival modelling.
+The [flexsurv](http://cran.r-project.org/package=flexsurv) R package for parametric survival and multi-state modelling.
+
+
+## Key features
+
+* Parametric models for time-to-event (survival) data.  Data may be right-censored, and/or left-censored, and/or left-truncated.  Several built-in parametric distributions are available, including a very flexible model based on splines (Royston and Parmar). 
+
+* Any user-defined parametric model can be employed by supplying R functions defining the distribution.
+
+* Covariates can be included using a (log-)linear model on any parameter of any distribution.  This typically defines an accelerated failure time or proportional hazards model.
+
+* Multi-state models for continuously-observed data can be defined by piecing together transition-specific parametric models of any kind.   (For intermittently-observed data, see instead the [msm](http://CRAN.R-project.org/package=msm) package.)
+
+
+## Learn more 
+
+[User guide (PDF)](articles/flexsurv.pdf).
+
+[Guide to multi-state modelling in flexsurv](articles/multistate.pdf).
+
+[Full reference manual](reference/index.html) for all the package's functions.
+
+[Paper in Journal of Statistical Software (Jackson 2016)](https://www.jstatsoft.org/article/view/v070i08).  Mostly the same as the user guide, but not kept up to date.
 
 
 ## Installation (stable CRAN version)

_pkgdown.yml

@@ -0,0 +1,105 @@
+url: http://chjackson.github.io/flexsurv-dev/
+template:
+  bootstrap: 5
+reference:
+- title: Fitting survival models
+- contents:
+  - flexsurvreg
+  - flexsurvspline
+  - flexsurvrtrunc
+  - survrtrunc
+- title: Getting results from survival models
+- contents:
+  - summary.flexsurvreg
+  - standsurv
+  - coef.flexsurvreg
+  - normboot.flexsurvreg
+  - hr_flexsurvreg
+  - vcov.flexsurvreg
+  - simulate.flexsurvreg
+  - plot.flexsurvreg
+  - lines.flexsurvreg
+  - plot.standsurv
+  - summary.flexsurvrtrunc
+  - plot.survrtrunc
+  - lines.survrtrunc
+- title: Multi-state models based on transition-specific hazards
+- contents:
+  - fmsm
+  - pars.fmsm
+  - pmatrix.fs
+  - pmatrix.simfs
+  - totlos.fs
+  - totlos.simfs
+  - sim.fmsm
+  - simfs_bytrans
+  - bootci.fmsm
+  - pfinal_fmsm
+  - simfinal_fmsm
+  - ajfit_fmsm
+  - msfit.flexsurvreg
+- title: Competing risks and multi-state models based on mixtures
+- contents:
+  - flexsurvmix
+  - get_basepars
+  - mean_flexsurvmix
+  - pdf_flexsurvmix
+  - probs_flexsurvmix
+  - p_flexsurvmix
+  - quantile_flexsurvmix
+  - rmst_flexsurvmix
+  - simt_flexsurvmix
+  - fmixmsm
+  - meanfinal_fmixmsm
+  - ppath_fmixmsm
+  - qfinal_fmixmsm
+  - ajfit
+  - ajfit_flexsurvmix
+- title: Model comparison and checking
+- contents:
+  - logLik.flexsurvreg
+  - AICc.flexsurvreg
+  - AICc
+  - BIC.flexsurvreg
+  - AIC.fmsm
+  - nobs.flexsurvreg
+  - residuals.flexsurvreg
+  - coxsnell_flexsurvreg
+- title: Probability distributions
+- contents:
+  - Survspline
+  - Survsplinek
+  - WeibullPH
+  - GenGamma
+  - GenGamma.orig
+  - GenF
+  - GenF.orig
+  - Gompertz
+  - Llogis
+  - hexp
+  - Hexp
+  - mean_exp
+  - rmst_exp
+  - qgeneric
+- title: Tools for using flexsurv with tidyverse
+- contents:
+  - predict.flexsurvreg
+  - tidy.flexsurvreg
+  - tidy.standsurv
+  - augment.flexsurvreg
+  - glance.flexsurvreg
+- title: Datasets
+- contents:
+  - bc
+  - bos
+- title: Miscellaneous / advanced tools
+- contents:
+  - model.frame.flexsurvreg
+  - model.matrix.flexsurvreg
+  - model.frame.flexsurvmix
+  - basis
+  - rmst_generic
+  - unroll.function
+- title: Package overview
+- contents:
+  - flexsurv-package