Merge branch 'release/v0.7.2' into develop

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "multinma" in publications use:'
 type: software
 license: GPL-3.0-only
 title: 'multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data'
-version: 0.7.1.9000
+version: 0.7.2
 doi: 10.5281/zenodo.3904454
 abstract: Network meta-analysis and network meta-regression models for aggregate data,
   individual patient data, and mixtures of both individual and aggregate data using
@@ -28,7 +28,7 @@ preferred-citation:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-2672-7841
   year: '2024'
-  notes: R package version 0.7.1.9000
+  notes: R package version 0.7.2
   url: https://dmphillippo.github.io/multinma/
   doi: 10.5281/zenodo.3904454
 repository: https://CRAN.R-project.org/package=multinma

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: multinma
 Title: Bayesian Network Meta-Analysis of Individual and Aggregate Data
-Version: 0.7.1.9004
+Version: 0.7.2
 Authors@R: 
     person(given = c("David", "M."),
            family = "Phillippo",
@@ -53,7 +53,7 @@ LinkingTo:
     rstan (>= 2.26.0),
     StanHeaders (>= 2.32.9)
 SystemRequirements: GNU make
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Suggests: 
     testthat (>= 2.1.0),

NEWS.md

@@ -1,4 +1,4 @@
-# multinma 0.7.1.9000
+# multinma 0.7.2
 
 * Fix: Predictions for non-proportional hazards IPD NMA or ML-NMR survival 
 models using `aux_regression = ~.trt` were incorrectly omitting the treatment 

R/integration.R

@@ -25,7 +25,7 @@
 #'   \code{\link[randtoolbox:quasiRNG]{sobol()}}
 #'
 #' @return For the `nma_data` method, an object of class [nma_data]. For the
-#'   `data.frame` method, the input data frame is returned (as a [tibble]) with
+#'   `data.frame` method, the input data frame is returned (as a `tibble`) with
 #'   an added column for each covariate (prefixed with ".int_"), containing the
 #'   numerical integration points nested as length-`n_int` vectors within each
 #'   row. For `unnest_integration()`, a data frame with integration points

R/nma.R

@@ -7,7 +7,8 @@
 #'   `combine_network()`, or `add_integration()`
 #' @param consistency Character string specifying the type of (in)consistency
 #'   model to fit, either `"consistency"`, `"ume"`, or `"nodesplit"`
-#' @param trt_effects Character string specifying either `"fixed"` or `"random"` effects
+#' @param trt_effects Character string specifying either `"fixed"` or `"random"`
+#'   effects
 #' @param regression A one-sided model formula, specifying the prognostic and
 #'   effect-modifying terms for a regression model. Any references to treatment
 #'   should use the `.trt` special variable, for example specifying effect
@@ -28,7 +29,8 @@
 #'   multiple treatment comparisons to split in turn. By default, all possible
 #'   comparisons will be chosen (see [get_nodesplits()]).
 #' @param prior_intercept Specification of prior distribution for the intercept
-#' @param prior_trt Specification of prior distribution for the treatment effects
+#' @param prior_trt Specification of prior distribution for the treatment
+#'   effects
 #' @param prior_het Specification of prior distribution for the heterogeneity
 #'   (if `trt_effects = "random"`)
 #' @param prior_het_type Character string specifying whether the prior
@@ -106,8 +108,8 @@
 #'   For the advanced user, the additional specials `.study` and `.trtclass` are
 #'   also available, and refer to studies and (if specified) treatment classes
 #'   respectively. When node-splitting models are fitted (`consistency =
-#'   "nodesplit"`) the special `.omega` is available, indicating the arms
-#'   to which the node-splitting inconsistency factor is added.
+#'   "nodesplit"`) the special `.omega` is available, indicating the arms to
+#'   which the node-splitting inconsistency factor is added.
 #'
 #'   See \code{\link[multinma:priors]{?priors}} for details on prior
 #'   specification. Default prior distributions are available, but may not be
@@ -231,7 +233,8 @@
 #'
 #' @return `nma()` returns a [stan_nma] object, except when `consistency =
 #'   "nodesplit"` when a [nma_nodesplit] or [nma_nodesplit_df] object is
-#'   returned. `nma.fit()` returns a [stanfit] object.
+#'   returned. `nma.fit()` returns a \code{\link[rstan:stanfit-class]{stanfit}}
+#'   object.
 #' @export
 #'
 #' @references

R/nma_data-class.R

@@ -237,8 +237,9 @@ green <- function(...) {
 #' Convert networks to graph objects
 #'
 #' The method `as.igraph()` converts `nma_data` objects into the form used by
-#' the [igraph] package. The method `as_tbl_graph()` converts `nma_data` objects
-#' into the form used by the [ggraph] and
+#' the \link[igraph:igraph-package]{igraph} package. The method `as_tbl_graph()`
+#' converts `nma_data` objects into the form used by the
+#' \link[ggraph:ggraph-package]{ggraph} and
 #' \link[tidygraph:tidygraph-package]{tidygraph} packages.
 #'
 #' @param x An [nma_data] object to convert
@@ -682,13 +683,16 @@ has_indirect <- function(network, trt1, trt2) {
 #' Create a network plot from a `nma_data` network object.
 #'
 #' @param x A [nma_data] object to plot
-#' @param ... Additional arguments passed to [ggraph()] and on to the layout
-#'   function
-#' @param layout The type of layout to create. Any layout accepted by [ggraph()]
-#'   may be used, including all of the layout functions provided by [igraph].
-#' @param circular Whether to use a circular representation. See [ggraph()].
+#' @param ... Additional arguments passed to
+#'   \code{\link[ggraph:ggraph]{ggraph()}} and on to the layout function
+#' @param layout The type of layout to create. Any layout accepted by
+#'   \code{\link[ggraph:ggraph]{ggraph()}} may be used, including all of the
+#'   layout functions provided by \link[igraph:igraph-package]{igraph}.
+#' @param circular Whether to use a circular representation. See
+#'   \code{\link[ggraph:ggraph]{ggraph()}}.
 #' @param weight_edges Weight edges by the number of studies? Default is `TRUE`.
-#' @param weight_nodes Weight nodes by the total sample size? Default is `FALSE`.
+#' @param weight_nodes Weight nodes by the total sample size? Default is
+#'   `FALSE`.
 #' @param show_trt_class Colour treatment nodes by class, if `trt_class` is set?
 #'   Default is `FALSE`.
 #' @param nudge Numeric value to nudge the treatment labels away from the nodes
@@ -705,7 +709,8 @@ has_indirect <- function(network, trt1, trt2) {
 #'   any aggregate data in the network, using the `sample_size` option of
 #'   `set_agd_*()`.
 #'
-#' @return A `ggplot` object, as produced by [ggraph()].
+#' @return A `ggplot` object, as produced by
+#'   \code{\link[ggraph:ggraph]{ggraph()}}.
 #' @export
 #'
 #' @examples ## Stroke prevention in atrial fibrillation

R/nma_nodesplit-class.R

@@ -28,7 +28,7 @@ NULL
 #' Print `nma_nodesplit_df` objects
 #'
 #' @param x A [nma_nodesplit_df] object
-#' @param ... Further arguments passed to [print.stanfit()]
+#' @param ... Further arguments passed to \code{\link[rstan:print.stanfit]{print.stanfit()}}
 #'
 #' @seealso The summary method [summary.nma_nodesplit_df()] summarises the
 #'   node-splitting results.

R/nma_summary-class.R

@@ -150,10 +150,10 @@ print.nma_summary <- function(x, ..., digits = 2, pars, include = TRUE) {
 #' @param ref_line Numeric vector of positions for reference lines, by default
 #'   no reference lines are drawn
 #'
-#' @details Plotting is handled by [ggplot2] and the stats and geoms provided in
-#'   the [ggdist] package. As a result, the output is very flexible. Any
-#'   plotting stats provided by `ggdist` may be used, via the argument
-#'   `stat`.
+#' @details Plotting is handled by \link[ggplot2:ggplot2-package]{ggplot2} and
+#'   the stats and geoms provided in the \link[ggdist:ggdist-package]{ggdist}
+#'   package. As a result, the output is very flexible. Any plotting stats
+#'   provided by `ggdist` may be used, via the argument `stat`.
 #'
 #'   The default uses
 #'   \code{\link[ggdist:stat_pointinterval]{ggdist::stat_pointinterval()}}, to
@@ -179,7 +179,8 @@ print.nma_summary <- function(x, ..., digits = 2, pars, include = TRUE) {
 #'   bands, specify `point_interval = "mean_qi"` and `.width = 0.95`.
 #'
 #'   A `ggplot` object is returned which can be further modified through the
-#'   usual [ggplot2] functions to add further aesthetics, geoms, themes, etc.
+#'   usual \link[ggplot2:ggplot2-package]{ggplot2} functions to add further
+#'   aesthetics, geoms, themes, etc.
 #'
 #' @return A `ggplot` object.
 #'

R/nodesplit_summary-class.R

@@ -146,13 +146,14 @@ as.data.frame.nodesplit_summary <- function(x, ...) {
 #' @param ref_line Numeric vector of positions for reference lines, by default
 #'   no reference lines are drawn.
 #'
-#' @details Plotting is handled by [ggplot2] and the stats and geoms provided in
-#'   the [ggdist] package. As a result, the output is very flexible. Any
-#'   plotting stats provided by `ggdist` may be used, via the argument `stat`.
-#'   The default `"dens_overlay"` is a special exception, which uses
-#'   \code{\link[ggplot2:geom_density]{ggplot2::geom_density()}}, to plot overlaid
-#'   densities. Additional arguments in `...` are passed to the `ggdist` stat,
-#'   to customise the output.
+#' @details Plotting is handled by \link[ggplot2:ggplot2-package]{ggplot2} and
+#'   the stats and geoms provided in the \link[ggdist:ggdist-package]{ggdist}
+#'   package. As a result, the output is very flexible. Any plotting stats
+#'   provided by `ggdist` may be used, via the argument `stat`. The default
+#'   `"dens_overlay"` is a special exception, which uses
+#'   \code{\link[ggplot2:geom_density]{ggplot2::geom_density()}}, to plot
+#'   overlaid densities. Additional arguments in `...` are passed to the
+#'   `ggdist` stat, to customise the output.
 #'
 #'   Alternative stats can be specified to produce different summaries. For
 #'   example, specify `stat = "[half]eye"` to produce (half) eye plots, or `stat
@@ -162,7 +163,8 @@ as.data.frame.nodesplit_summary <- function(x, ...) {
 #'   `vignette("slabinterval", package = "ggdist")`.
 #'
 #'   A `ggplot` object is returned which can be further modified through the
-#'   usual [ggplot2] functions to add further aesthetics, geoms, themes, etc.
+#'   usual \link[ggplot2:ggplot2-package]{ggplot2} functions to add further
+#'   aesthetics, geoms, themes, etc.
 #'
 #' @return A `ggplot` object.
 #' @seealso [summary.nma_nodesplit_df()]

R/stan_nma-class.R

@@ -38,7 +38,7 @@ NULL
 #' Print `stan_nma` objects
 #'
 #' @param x A [stan_nma] object
-#' @param ... Further arguments passed to [print.stanfit()]
+#' @param ... Further arguments passed to \code{\link[rstan:print.stanfit]{print.stanfit()}}
 #'
 #' @return `x` is returned invisibly.
 #'
@@ -722,7 +722,7 @@ as.stanfit.default <- function(x, ...) {
 #' array, matrix, or data frame.
 #'
 #' @param x A `stan_nma` object
-#' @param ... Additional arguments passed to [as.array.stanfit()]
+#' @param ... Additional arguments passed to \code{\link[rstan:as.array.stanfit]{as.array.stanfit()}}
 #' @param pars Optional character vector of parameter names to include in output. If not specified, all parameters are used.
 #' @param include Logical, are parameters in `pars` to be included (`TRUE`, default) or excluded (`FALSE`)?
 #'

README.md

@@ -78,7 +78,7 @@ papers:
 The `multinma` package can be cited as follows:
 
 > Phillippo, D. M. (2024). *multinma: Bayesian Network Meta-Analysis of
-> Individual and Aggregate Data*. R package version 0.7.1.9000, doi:
+> Individual and Aggregate Data*. R package version 0.7.2, doi:
 > [10.5281/zenodo.3904454](https://doi.org/10.5281/zenodo.3904454).
 
 When fitting ML-NMR models, please cite the methods paper:

cran-comments.md

@@ -1,16 +1,10 @@
-Require StanHeaders version 2.32.9 or later in LinkingTo, as requested, which 
-fixes the UBSAN warnings.
-
-Confirmed that this fixes the sanitizer warnings with rocker/r-devel-san and 
-rhub clang-asan.
+This is a minor bugfix release. Also addresses new CRAN check note "Rd \link{} 
+targets missing package anchors".
 
 ## Test environments
-* rocker/r-devel-san
-* rhub clang-asan
-* local R installation (Windows 10), R 4.4.0
-* win-builder (release, devel)
+* local R installation (Windows 10), R 4.4.1
 * Ubuntu 22.04.4 on GitHub Actions (release, devel, oldrel)
-* Mac OS 14.4.1 on GitHub Actions (release)
+* Mac OS 14.6.1 on GitHub Actions (release)
 * Windows Server 2022 10.0.20348 on GitHub Actions (release)
 
 ## R CMD check results