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Pass CRAN checks #149

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Nov 23, 2023
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1 change: 1 addition & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
^inst/extdata/vaccine_jags\.RData$
^inst/extdata/statins_base\.RData$
^inst/extdata/statins_HC\.RData$
^inst/extdata/smoking_output\.RData$
^paper\.bib$
^paper\.md$
^CONTRIBUTING\.md$
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3 changes: 2 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,5 @@ BCEA.Rcheck/
*.Rproj
inst/doc
renv/
BCEA_book.pdf - Shortcut
revdep/
BCEA_book.pdf - Shortcut
9 changes: 3 additions & 6 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ Authors@R: c(
Imports:
cli (>= 3.3.0),
dplyr,
ggplot2,
ggplot2 (>= 3.4.0),
graphics,
gridExtra,
MASS,
Expand All @@ -32,6 +32,7 @@ Imports:
Rdpack,
reshape2,
rlang,
rstan,
scales,
voi
Depends:
Expand All @@ -47,14 +48,12 @@ Suggests:
RColorBrewer,
rjags,
rmarkdown,
rstan,
splancs,
testthat (>= 2.1.0),
vdiffr,
withr
RdMacros: Rdpack
VignetteBuilder: knitr
Additional_repositories: https://inla.r-inla-download.org/R/testing/
Description: Produces an economic evaluation of a sample of suitable variables of
cost and effectiveness / utility for two or more interventions,
e.g. from a Bayesian model in the form of MCMC simulations.
Expand All @@ -69,8 +68,6 @@ NeedsCompilation: no
RoxygenNote: 7.2.3.9000
Encoding: UTF-8
BugReports: https://github.com/n8thangreen/BCEA/issues/
Remotes:
chjackson/voi,
plotrix/plotrix
LazyData: false
Roxygen: list(markdown = TRUE)

1 change: 1 addition & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,7 @@ importFrom(purrr,pluck)
importFrom(reshape2,melt)
importFrom(rlang,.data)
importFrom(rlang,int)
importFrom(rstan,extract)
importFrom(scales,label_dollar)
importFrom(stats,as.formula)
importFrom(stats,cov)
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2 changes: 1 addition & 1 deletion R/add_contour_quadrants.R
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ add_contour_quadrants <- function(he, params) {
#' Geom Quadrant Text
#'
#' @template args-he
#' @template args-graph
#' @param graph_param Plot parameters; list
#' @keywords internal aplot
#'
geom_quad_txt <- function(he, graph_params) {
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1 change: 1 addition & 0 deletions R/bcea.default.R
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Expand Up @@ -108,6 +108,7 @@ bcea.rjags <- function(eff, ...) {

#' @rdname bcea
#' @param ... Additional arguments
#' @importFrom rstan extract
#' @export
bcea.rstan <- function(eff, ...) {

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4 changes: 4 additions & 0 deletions R/ce_table.R
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Expand Up @@ -49,6 +49,10 @@ ce_table <- function(he,
#' comparison label and associated ICER
#'
#' @export
#' @examples
#' data("Smoking")
#' he <- BCEA::bcea(eff, cost)
#' tabulate_means(he)
#'
tabulate_means <- function(he,
comp_label = NULL,
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2 changes: 1 addition & 1 deletion R/ceac_plot_graph.R
Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ ceac_ggplot <- function(he,

ggplot(data_psa, aes(x = .data$k, y = .data$ceac)) +
geom_line(aes(linetype = .data$comparison,
size = factor(.data$comparison),
linewidth = factor(.data$comparison),
colour = factor(.data$comparison))) +
theme_ceac() +
theme_add + # theme
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1 change: 0 additions & 1 deletion R/contour_ggplot_params.R
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@
#' Contour ggplot Parameters
#'
#' @template args-he
#' @param pos_legend Position of legend
#' @param graph_params Other graphical parameters
#' @param ... Additional arguments
#'
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13 changes: 11 additions & 2 deletions R/ib.plot.R
Original file line number Diff line number Diff line change
Expand Up @@ -25,14 +25,23 @@
#' @author Gianluca Baio, Andrea Berardi
#' @seealso [bcea()],
#' [ceplane.plot()]
#' @importFrom Rdpack reprompt
#'
#' @references
#'
#' \insertRef{Baio2011}{BCEA}
#'
#' \insertRef{Baio2013}{BCEA}
#'
#' @keywords hplot
#' @export
#'
#' @import ggplot2
#' @importFrom Rdpack reprompt
#'
#' @examples
#' data("Vaccine")
#' he <- BCEA::bcea(eff, cost)
#' ib.plot(he)
#'
ib.plot.bcea <- function(he,
comparison = NULL,
wtp = 25000,
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29 changes: 3 additions & 26 deletions cran-comments.md
Original file line number Diff line number Diff line change
@@ -1,30 +1,7 @@

# Resubmission (2.4.4)

* Suggested package wasn't used conditionally in unit test causing CRAN check error. `MCMCvis` is now moved to Required packages.
* Fixed R package CRAN webpage canonical form in README

## R CMD check results

0 errors | 0 warnings | 1 note

* Any notes about using INLA has been condoned in previous versions, as they are only suggested.

CHECK message:

Suggests or Enhances not in mainstream repositories:
INLA
Availability using Additional_repositories specification:
INLA yes https://inla.r-inla-download.org/R/stable/

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: package dependencies, Result: NOTE
Package suggested but not available for checking: 'INLA'

## Downstream dependencies

We checked 2 reverse dependencies (missingHE, heesim), comparing R CMD check results across CRAN and dev versions of this package.
0 errors | 0 warnings | 0 note

* We saw 0 new problems
* We failed to check 0 packages
* This is an updated release.

Previous versions depended directly on INLA which is now not the case
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21 changes: 0 additions & 21 deletions inst/rmarkdown/report/section_ceplane.Rmd.save

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2 changes: 0 additions & 2 deletions man/contour_ggplot_params.Rd

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5 changes: 1 addition & 4 deletions man/geom_quad_txt.Rd

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8 changes: 8 additions & 0 deletions man/ib.plot.Rd

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6 changes: 6 additions & 0 deletions man/tabulate_means.Rd

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7 changes: 0 additions & 7 deletions revdep/.gitignore

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