diff --git a/DESCRIPTION b/DESCRIPTION index f0e9034..78999a7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,6 +15,8 @@ Authors@R: role = "aut", email = "annanev@umich.edu")) License: MIT + file LICENSE +URL: https://metrumresearchgroup.github.io/pmforest, https://github.com/metrumresearchgroup/pmforest +BugReports: https://github.com/metrumresearchgroup/pmforest/issues Imports: assertthat, dplyr, @@ -34,8 +36,6 @@ Imports: Suggests: devtools, knitr, - mrgvalidate, - mrgvalprep (>= 0.0.4), svglite, testthat (>= 3.0.0), vdiffr, @@ -48,13 +48,4 @@ Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 7.2.3 VignetteBuilder: knitr -Collate: - 'classicforest.R' - 'table-plot.R' - 'forest-constructor.R' - 'AAAA.R' - 'helpers-for-tests.R' - 'plot-forest.R' - 'summarize-data.R' - 'utils-null.R' - 'utils-pipe.R' + diff --git a/R/AAAA.R b/R/AAAA.R index 48a77ad..c1a7a99 100644 --- a/R/AAAA.R +++ b/R/AAAA.R @@ -18,9 +18,6 @@ #' @importFrom stats median quantile #' @importFrom RColorBrewer brewer.pal #' -#' @include forest-constructor.R -#' @include table-plot.R -#' @include classicforest.R #' NULL diff --git a/R/utils-null.R b/R/utils-null.R deleted file mode 100644 index 63991ff..0000000 --- a/R/utils-null.R +++ /dev/null @@ -1,14 +0,0 @@ -# if the value of x is null, use y -# for example, given a val that, if -# null should be an NA of type character -# either: -# `nullable(val, NA_character_)` -# `val %||% NA_character_` -nullable <- function(x, y) { - if (is.null(x)) { - return(y) - } - return(x) -} - -`%||%` <- nullable diff --git a/inst/validation/.gitignore b/inst/validation/.gitignore deleted file mode 100644 index 1a1dc4c..0000000 --- a/inst/validation/.gitignore +++ /dev/null @@ -1,5 +0,0 @@ -*.html -*.docx -*.pdf -*.md -test_results/ diff --git a/inst/validation/build-validation-docs.R b/inst/validation/build-validation-docs.R deleted file mode 100644 index 23e248c..0000000 --- a/inst/validation/build-validation-docs.R +++ /dev/null @@ -1,66 +0,0 @@ -####################################################### -## This script runs the test suite and builds -## the validation documents from the test outputs -## -## The script expects the following: -## * Validation stories in mrgvalprep YAML format in "inst/validation/{PKGNAME}-stories.yaml" -## * A standard testthat test suite than can be run with devtools::test() -## -## It will write the validation documents to -## "inst/validation/{PKGNAME}-{PKGVERSION}-validation-docs/") -## -####################################################### - -PKGNAME <- "pmforest" -PKGVERSION <- "0.0.1" -STYLE_REF_DIR <- "docx-ref-header-image" # set to NULL if not using style ref - -# set up directories and clear existing output dirs, if they exist -val_dir <- system.file("validation", package = PKGNAME) -print(val_dir) - -style_ref_path <- NULL -if (!is.null(STYLE_REF_DIR)) { - style_ref_path <- file.path(val_dir, STYLE_REF_DIR) -} - -test_dir <- file.path(val_dir, "test_results") -if (fs::dir_exists(test_dir)) fs::dir_delete(test_dir) -fs::dir_create(test_dir) - -docs_dir <- file.path(val_dir, paste0(PKGNAME, "-", PKGVERSION, "-validation-docs")) -if (fs::dir_exists(docs_dir)) fs::dir_delete(docs_dir) -fs::dir_create(docs_dir) - -# run tests and write res to disk -test_res <- mrgvalprep::parse_testthat_list_reporter( - devtools::test(Reporter = testthat::ListReporter), - roll_up_ids = TRUE -) - -write.csv( - test_res, - file.path(test_dir, paste0(PKGNAME, "-tests.csv")) -) - -# capture commit hash and other system info -git_hash <- system("git rev-parse HEAD", intern=TRUE) -Sys.setenv("COMMIT_HASH" = git_hash) - -mrgvalprep::get_sys_info( - out_path = file.path(test_dir, paste0(PKGNAME, "-tests.json")), - env_vars = c("METWORX_VERSION", "COMMIT_HASH") -) - -# read in stories -spec <- mrgvalprep::read_spec_yaml(file.path(val_dir, paste0(PKGNAME, "-stories.yaml"))) - -# make docs -mrgvalidate::create_validation_docs( - PKGNAME, - PKGVERSION, - spec, - auto_test_dir = test_dir, - output_dir = docs_dir, - style_dir = style_ref_path -) diff --git a/inst/validation/pmforest-stories.yaml b/inst/validation/pmforest-stories.yaml deleted file mode 100644 index 4a82bcd..0000000 --- a/inst/validation/pmforest-stories.yaml +++ /dev/null @@ -1,126 +0,0 @@ -PLOT-S001: - name: Create basic forest plot - description: As a user, I want to be able to generate forest plots using previously-simulated - data for a model with various covariates set to fixed values, so that I can evaluate - the potential for effects of covariates on model properties. - ProductRisk: high - tests: - - PMF-PLOT-017 - - PMF-PLOT-018 -DATA-S001: - name: summary methods - description: As a user, I want to be able to specify the type of summaries presented - for each covariate level in the forest plot, including the location type (mean - vs median) and width of the confidence interval (e.g., 90% vs 95%). - ProductRisk: high - tests: - - PMF-DATA-001 - - PMF-DATA-002 - - PMF-DATA-003 -PLOT-S004: - name: metagroup specification - description: As a user, I want to be able to generate multiple forest plots from - the same set of simulations, e.g., for multiple model parameters (CL and V) or - multiple responses (AUC and Cmax) or a combination of both (CL, AUC, Cmax). - ProductRisk: low - tests: - - PMF-PLOT-004 - - PMF-PLOT-005 -PLOT-S005: - name: CI table - description: As a user, I would like each plot to optionally include accompanying - text showing the location (mean/median) and CI for each covariate level. - ProductRisk: high - tests: - - PMF-PLOT-006 - - PMF-PLOT-007 -PLOT-S006: - name: Plot/table width - description: As a user, I would like to be able to specify the relative widths of - the plot and accompanying text. - ProductRisk: low - tests: PMF-PLOT-008 -PLOT-S007: - name: Set vertical intercept - description: As a user, I would like the forest plots to show a vertical line at - a specified value to show the reference value for comparison. - ProductRisk: medium - tests: PMF-PLOT-009 -PLOT-S008: - name: shaded interval - description: As a user, I would like to have the option to include a shaded interval - for the value being plotted, for the range that I specify. - ProductRisk: medium - tests: PMF-PLOT-010 -PLOT-S009: - name: update labels via yaml file - description: As a user, I would like to be able to provide custom labels for the - covariates and response/parameter. - ProductRisk: low - tests: PMF-PLOT-011 -PLOT-S010: - name: plot multiple simulations - description: As a user, I would like to be able to (when providing data from nested - simulations) have the forest plots reflect the variability between replicates - by showing additional confidence interval line segments above the overall values - (i.e., above the mean/median and upper/lower percentiles). - ProductRisk: high - tests: - - PMF-PLOT-012 - - PMF-PLOT-013 -PLOT-S011: - name: label adjustments and positioning - description: As a user, I would like to have control over axis labels, breaks, and - limits, as well as text size for all text elements. - ProductRisk: medium - tests: - - PMF-PLOT-014 - - PMF-PLOT-015 - - PMF-PLOT-016 - - PMF-PLOT-023 -PLOT-S012: - name: Formatting options, ggplot themes - description: As a user, I would like to have be able to change the shape and size - of the median value. I would also like to modify the default ggplot theme. - ProductRisk: medium - tests: - - PMF-PLOT-020 - - PMF-PLOT-021 - - PMF-PLOT-022 -DATA-S002: - name: Column selection, summary - description: As a user, I want to be able to specify which model property (i.e., - predicted response (e.g., AUC or Cmax) or parameter value (e.g., CL or V)) will - be summarized in the forest plot. - ProductRisk: high - tests: - - PMF-DATA-001 - - PMF-DATA-003 -DATA-S003: - name: Summarize data by group - description: As a user, I want to pass in raw data and summarize by group, and optionally - level and metagroup. - ProductRisk: high - tests: - - PMF-DATA-001 - - PMF-DATA-002 - - PMF-PLOT-019 - - PMF-PLOT-024 -DATA-S004: - name: Summarize across replicates - description: As a user, I want to calculate median, lower, and upper quantile, for - each replicate and optionally across multiple replicates. - ProductRisk: high - tests: PMF-DATA-003 -DATA-S005: - name: Control significant digits - description: As a user, I want to be able specify the number of significant digits - for my summary statistics, and control whether to use scientific or numeric notation. - ProductRisk: low - tests: PMF-PLOT-018 -DATA-S006: - name: Check input data - description: As a user, I want to be notified if I do not have the required input - data for plotting. - ProductRisk: low - tests: PMF-DATA-004 diff --git a/pkgr.yml b/pkgr.yml index e705a6c..aa4d129 100644 --- a/pkgr.yml +++ b/pkgr.yml @@ -11,7 +11,7 @@ Packages: Repos: - CRAN: https://cran.rstudio.com # used for most things - - MPN: https://mpn.metworx.com/snapshots/stable/2022-02-11 # used for pmtables and mrgval + - MPN: https://mpn.metworx.com/snapshots/stable/2023-08-24 # used for specific Metrum packages (such as pmtables & yspec) Lockfile: Type: renv diff --git a/tests/testthat/_snaps/base-plot/axis-labels-and-captions.svg b/tests/testthat/_snaps/base-plot/axis-labels-and-captions.svg index 0158b33..1ed199e 100644 --- a/tests/testthat/_snaps/base-plot/axis-labels-and-captions.svg +++ b/tests/testthat/_snaps/base-plot/axis-labels-and-captions.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/base-plot.svg b/tests/testthat/_snaps/base-plot/base-plot.svg index 04b1969..a34753a 100644 --- a/tests/testthat/_snaps/base-plot/base-plot.svg +++ b/tests/testthat/_snaps/base-plot/base-plot.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/change-ci-interval-format-change-both.svg b/tests/testthat/_snaps/base-plot/change-ci-interval-format-change-both.svg index 3c2dda5..cc9f17b 100644 --- a/tests/testthat/_snaps/base-plot/change-ci-interval-format-change-both.svg +++ b/tests/testthat/_snaps/base-plot/change-ci-interval-format-change-both.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/change-ci-interval-format-mixed.svg b/tests/testthat/_snaps/base-plot/change-ci-interval-format-mixed.svg index 610fb98..0935249 100644 --- a/tests/testthat/_snaps/base-plot/change-ci-interval-format-mixed.svg +++ b/tests/testthat/_snaps/base-plot/change-ci-interval-format-mixed.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/character-interpretation-of-numeric-group-level.svg b/tests/testthat/_snaps/base-plot/character-interpretation-of-numeric-group-level.svg index bd8d8ec..4d9f180 100644 --- a/tests/testthat/_snaps/base-plot/character-interpretation-of-numeric-group-level.svg +++ b/tests/testthat/_snaps/base-plot/character-interpretation-of-numeric-group-level.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/ci-table-mean.svg b/tests/testthat/_snaps/base-plot/ci-table-mean.svg index 31f98d3..064e33a 100644 --- a/tests/testthat/_snaps/base-plot/ci-table-mean.svg +++ b/tests/testthat/_snaps/base-plot/ci-table-mean.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/ci-table-median.svg b/tests/testthat/_snaps/base-plot/ci-table-median.svg index 2c3457f..85f4627 100644 --- a/tests/testthat/_snaps/base-plot/ci-table-median.svg +++ b/tests/testthat/_snaps/base-plot/ci-table-median.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/full-test-big.svg b/tests/testthat/_snaps/base-plot/full-test-big.svg index 819b90e..df69f63 100644 --- a/tests/testthat/_snaps/base-plot/full-test-big.svg +++ b/tests/testthat/_snaps/base-plot/full-test-big.svg @@ -24,46 +24,54 @@ - - + + - + + + + + + + + + - - + + - - + + - + - + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + @@ -79,38 +87,38 @@ - - - - - - + + + + + + - - - + + + - - - - + + + + - + - + Weight 85 kg 55 kg Renal Function Severe -Moderate +Moderate Mild Albumin 5 g/dL @@ -121,8 +129,8 @@ - - + + @@ -130,14 +138,14 @@ - - - - - - - - + + + + + + + + 0.4 0.6 0.8 @@ -145,31 +153,31 @@ 1.2 1.4 Fraction and 95% CI -Relative to Reference +Relative to Reference CL (L/hr) - - + + - - + + - + - + Weight 1.2 [1.2, 1.2] 0.83 [0.83, 0.83] -Renal Function -0.51 [0.47, 0.56] +Renal Function +0.51 [0.47, 0.56] 0.70 [0.66, 0.73] 0.92 [0.90, 0.93] Albumin @@ -177,20 +185,20 @@ 0.87 [0.84, 0.90] Age 0.99 [0.96, 1.0] -1.0 [0.97, 1.1] - +1.0 [0.97, 1.1] + - + - - - - - - - + + + + + + + 1.0 1.1 1.2 diff --git a/tests/testthat/_snaps/base-plot/full-test-small.svg b/tests/testthat/_snaps/base-plot/full-test-small.svg index 1367d8f..e99bf79 100644 --- a/tests/testthat/_snaps/base-plot/full-test-small.svg +++ b/tests/testthat/_snaps/base-plot/full-test-small.svg @@ -24,51 +24,59 @@ - - + + - + + + + + + + + + - - + + - - + + - + - + - - - - - - - - - - - - + + + + + + + + + + + + - - + + @@ -89,7 +97,7 @@ - + @@ -104,20 +112,20 @@ - + Weight 85 kg 55 kg Renal Function -Severe +Severe Moderate Mild Albumin -5 g/dL +5 g/dL 3.25 g/dL -Age +Age 45 years -20 years +20 years @@ -131,13 +139,13 @@ - - - - - - - + + + + + + + 0.4 0.6 0.8 @@ -145,25 +153,25 @@ 1.2 1.4 Fraction and 95% CI -Relative to Reference +Relative to Reference CL (L/hr) - - + + - - + + - + - + Weight 1.2 [1.2, 1.2] @@ -178,19 +186,19 @@ Age 0.99 [0.96, 1.0] 1.0 [0.97, 1.1] - + - + - - - - - - - + + + + + + + 1.0 1.1 1.2 diff --git a/tests/testthat/_snaps/base-plot/full-test.svg b/tests/testthat/_snaps/base-plot/full-test.svg index 357aa5a..6758005 100644 --- a/tests/testthat/_snaps/base-plot/full-test.svg +++ b/tests/testthat/_snaps/base-plot/full-test.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/modify-ggplot-theme.svg b/tests/testthat/_snaps/base-plot/modify-ggplot-theme.svg index 80d72ff..1e4d151 100644 --- a/tests/testthat/_snaps/base-plot/modify-ggplot-theme.svg +++ b/tests/testthat/_snaps/base-plot/modify-ggplot-theme.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/modify-shape-size.svg b/tests/testthat/_snaps/base-plot/modify-shape-size.svg index 0f7d7d3..802b325 100644 --- a/tests/testthat/_snaps/base-plot/modify-shape-size.svg +++ b/tests/testthat/_snaps/base-plot/modify-shape-size.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/modify-shape.svg b/tests/testthat/_snaps/base-plot/modify-shape.svg index 0b6a744..185b4cd 100644 --- a/tests/testthat/_snaps/base-plot/modify-shape.svg +++ b/tests/testthat/_snaps/base-plot/modify-shape.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/modify-text-size.svg b/tests/testthat/_snaps/base-plot/modify-text-size.svg index 336fa56..8a48b09 100644 --- a/tests/testthat/_snaps/base-plot/modify-text-size.svg +++ b/tests/testthat/_snaps/base-plot/modify-text-size.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/multiple-lines-for-ci-label.svg b/tests/testthat/_snaps/base-plot/multiple-lines-for-ci-label.svg index 40d7d29..eff1d03 100644 --- a/tests/testthat/_snaps/base-plot/multiple-lines-for-ci-label.svg +++ b/tests/testthat/_snaps/base-plot/multiple-lines-for-ci-label.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/no-group-level.svg b/tests/testthat/_snaps/base-plot/no-group-level.svg index 35935ef..8845220 100644 --- a/tests/testthat/_snaps/base-plot/no-group-level.svg +++ b/tests/testthat/_snaps/base-plot/no-group-level.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/numeric-group-level.svg b/tests/testthat/_snaps/base-plot/numeric-group-level.svg index 844c5e4..fbafc39 100644 --- a/tests/testthat/_snaps/base-plot/numeric-group-level.svg +++ b/tests/testthat/_snaps/base-plot/numeric-group-level.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/plot-table-width.svg b/tests/testthat/_snaps/base-plot/plot-table-width.svg index 48bf584..33b0d2b 100644 --- a/tests/testthat/_snaps/base-plot/plot-table-width.svg +++ b/tests/testthat/_snaps/base-plot/plot-table-width.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/shaded-interval.svg b/tests/testthat/_snaps/base-plot/shaded-interval.svg index 89098ac..72acf3b 100644 --- a/tests/testthat/_snaps/base-plot/shaded-interval.svg +++ b/tests/testthat/_snaps/base-plot/shaded-interval.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/test-breaks-and-limits-of-x-axis.svg b/tests/testthat/_snaps/base-plot/test-breaks-and-limits-of-x-axis.svg index efd1914..42a0622 100644 --- a/tests/testthat/_snaps/base-plot/test-breaks-and-limits-of-x-axis.svg +++ b/tests/testthat/_snaps/base-plot/test-breaks-and-limits-of-x-axis.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/test-metagroup-with-labels.svg b/tests/testthat/_snaps/base-plot/test-metagroup-with-labels.svg index 5697d8c..a1dedc7 100644 --- a/tests/testthat/_snaps/base-plot/test-metagroup-with-labels.svg +++ b/tests/testthat/_snaps/base-plot/test-metagroup-with-labels.svg @@ -20,6 +20,15 @@ + + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/test-metagroup-with-nrow.svg b/tests/testthat/_snaps/base-plot/test-metagroup-with-nrow.svg index 9af0811..cdd091b 100644 --- a/tests/testthat/_snaps/base-plot/test-metagroup-with-nrow.svg +++ b/tests/testthat/_snaps/base-plot/test-metagroup-with-nrow.svg @@ -20,6 +20,15 @@ + + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/test-metagroup.svg b/tests/testthat/_snaps/base-plot/test-metagroup.svg index ba195c8..d0c75bc 100644 --- a/tests/testthat/_snaps/base-plot/test-metagroup.svg +++ b/tests/testthat/_snaps/base-plot/test-metagroup.svg @@ -20,6 +20,15 @@ + + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/update-labels-via-yaml-file.svg b/tests/testthat/_snaps/base-plot/update-labels-via-yaml-file.svg index 6cd89d0..290af94 100644 --- a/tests/testthat/_snaps/base-plot/update-labels-via-yaml-file.svg +++ b/tests/testthat/_snaps/base-plot/update-labels-via-yaml-file.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/base-plot/vertical-intercept.svg b/tests/testthat/_snaps/base-plot/vertical-intercept.svg index 826698d..a69b926 100644 --- a/tests/testthat/_snaps/base-plot/vertical-intercept.svg +++ b/tests/testthat/_snaps/base-plot/vertical-intercept.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/nsim-plot/multiple-ci-s-with-jitter.svg b/tests/testthat/_snaps/nsim-plot/multiple-ci-s-with-jitter.svg index b534769..fe7501c 100644 --- a/tests/testthat/_snaps/nsim-plot/multiple-ci-s-with-jitter.svg +++ b/tests/testthat/_snaps/nsim-plot/multiple-ci-s-with-jitter.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/_snaps/nsim-plot/multiple-simulations.svg b/tests/testthat/_snaps/nsim-plot/multiple-simulations.svg index 2e75e46..d7492b0 100644 --- a/tests/testthat/_snaps/nsim-plot/multiple-simulations.svg +++ b/tests/testthat/_snaps/nsim-plot/multiple-simulations.svg @@ -29,6 +29,14 @@ + + + + + + + + diff --git a/tests/testthat/test-base-plot.R b/tests/testthat/test-base-plot.R index 3346b84..e1095f6 100644 --- a/tests/testthat/test-base-plot.R +++ b/tests/testthat/test-base-plot.R @@ -31,7 +31,7 @@ describe("Base plots", { group_level = LVL ) - it("Test metagroup (Cl and V2) [PMF-PLOT-004]", { + it("Test metagroup (Cl and V2)", { skip_on_cran() skip_vdiffr() plt1 <- sumData2 %>% @@ -45,7 +45,7 @@ describe("Base plots", { }) - it("Test metagroup (Cl and V2) with labels [PMF-PLOT-005]", { + it("Test metagroup (Cl and V2) with labels", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData2, @@ -56,7 +56,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Test metagroup with labels", plt) }) - it("CI Table - mean [PMF-PLOT-006]", { + it("CI Table - mean", { skip_on_cran() skip_vdiffr() plt <- plotData %>% @@ -72,7 +72,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("CI Table - mean", plt) }) - it("CI Table - median [PMF-PLOT-007]", { + it("CI Table - median", { skip_on_cran() skip_vdiffr() plt <- plotData %>% @@ -88,7 +88,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("CI Table - median", plt) }) - it("Plot/Table width [PMF-PLOT-008]", { + it("Plot/Table width", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -97,7 +97,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Plot/Table width", plt) }) - it("Vertical Intercept [PMF-PLOT-009]", { + it("Vertical Intercept", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -106,7 +106,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Vertical Intercept", plt) }) - it("shaded interval displays over correct range [PMF-PLOT-010]", { + it("shaded interval displays over correct range", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -115,7 +115,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("shaded interval", plt) }) - it("update labels via yaml file [PMF-PLOT-011]", { + it("update labels via yaml file", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -124,7 +124,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("update labels via yaml file", plt) }) - it("Axis labels and captions [PMF-PLOT-014]", { + it("Axis labels and captions", { skip_on_cran() skip_vdiffr() plt <- plotData %>% @@ -142,7 +142,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Axis labels and captions", plt) }) - it("Test breaks and limits of x-axis [PMF-PLOT-015]", { + it("Test breaks and limits of x-axis", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -153,7 +153,7 @@ describe("Base plots", { }) - it("Modify text size [PMF-PLOT-016]", { + it("Modify text size", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -162,7 +162,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Modify text size", plt) }) - it("Base plot [PMF-PLOT-017]", { + it("Base plot", { skip_on_cran() skip_vdiffr() plt <- plotData %>% @@ -175,7 +175,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Base plot", plt) }) - it("Full Test [PMF-PLOT-018]", { + it("Full Test", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -198,7 +198,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Full Test", plt) }) - it("plots without group_level [PMF-PLOT-019]", { + it("plots without group_level", { skip_on_cran() skip_vdiffr() df <- @@ -212,7 +212,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("No group_level", plt) }) - it("modify shape of median value [PMF-PLOT-020]", { + it("modify shape of median value", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -221,7 +221,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Modify shape", plt) }) - it("modify shape size of median value [PMF-PLOT-021]", { + it("modify shape size of median value", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -230,7 +230,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Modify shape size", plt) }) - it("modify ggplot theme [PMF-PLOT-022]", { + it("modify ggplot theme", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -239,7 +239,7 @@ describe("Base plots", { vdiffr::expect_doppelganger("Modify ggplot theme", plt) }) - it("Multiple lines for CI_label [PMF-PLOT-023]", { + it("Multiple lines for CI_label", { skip_on_cran() skip_vdiffr() expect_error( @@ -254,7 +254,7 @@ describe("Base plots", { }) - it("Plot alignment with different saving to different sizes [PMF-PLOT-024]", { + it("Plot alignment with different saving to different sizes", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, @@ -286,7 +286,7 @@ describe("Base plots", { }) - it("group_level works with numeric data [PMF-PLOT-024]", { + it("group_level works with numeric data", { skip_on_cran() skip_vdiffr() df <- plotData %>% @@ -309,7 +309,7 @@ describe("Base plots", { }) - it("Change CI interval format [PMF-PLOT-025]", { + it("Change CI interval format", { skip_on_cran() skip_vdiffr() plt <- plot_forest(data = sumData, diff --git a/tests/testthat/test-input-data.R b/tests/testthat/test-input-data.R index 421b85a..7e82395 100644 --- a/tests/testthat/test-input-data.R +++ b/tests/testthat/test-input-data.R @@ -1,4 +1,4 @@ -test_that("plot_forest() input data check errors with missing value column [PMF-DATA-004]", { +test_that("plot_forest() input data check errors with missing value column", { df <- data.frame( group = c("a", "b", "c"), @@ -11,7 +11,7 @@ test_that("plot_forest() input data check errors with missing value column [PMF- ) }) -test_that("plot_forest() input data check errors with missing group column [PMF-DATA-004]", { +test_that("plot_forest() input data check errors with missing group column", { df <- data.frame( lo = c(1, 2, 3), @@ -24,7 +24,7 @@ test_that("plot_forest() input data check errors with missing group column [PMF- ) }) -test_that("plot_forest() input data check warns with extra columns [PMF-DATA-004]", { +test_that("plot_forest() input data check warns with extra columns", { df <- data.frame( group = c("a", "b", "c"), diff --git a/tests/testthat/test-nsim-plot.R b/tests/testthat/test-nsim-plot.R index 72ffe49..cb59503 100644 --- a/tests/testthat/test-nsim-plot.R +++ b/tests/testthat/test-nsim-plot.R @@ -17,7 +17,7 @@ describe("Multiple simulations", { plotData2 <- readRDS(file.path(dataDir, "plotDataEXP.RDS")) %>% mutate(stat = stat + (nsim/300)) # make larger to test jitter - it("Multiple simulations base test [PMF-PLOT-012]", { + it("Multiple simulations base test", { skip_on_cran() skip_vdiffr() plt <- plotData %>% @@ -39,7 +39,7 @@ describe("Multiple simulations", { vdiffr::expect_doppelganger("Multiple simulations", plt) }) - it("Multiple CI's with jitter [PMF-PLOT-013]", { + it("Multiple CI's with jitter", { skip_on_cran() skip_vdiffr() plt <- plotData2 %>% diff --git a/tests/testthat/test-summary.R b/tests/testthat/test-summary.R index 2d1c59c..11b41a1 100644 --- a/tests/testthat/test-summary.R +++ b/tests/testthat/test-summary.R @@ -31,18 +31,18 @@ describe("Column selection, summary", { lo = quantile(stat, lci), hi = quantile(stat, uci)) - it("correct column is summarized [PMF-DATA-001]", { + it("correct column is summarized", { expect_equal(sumdat_med$lo, sumdat$lo) # test lower quartile expect_equal(sumdat_med$hi, sumdat$hi) # test upper quartile }) - it("Can switch between mean/median [PMF-DATA-002]", { + it("Can switch between mean/median", { expect_equal(sumdat_med$mid, sumdat$med) # Test medians expect_equal(sumdat_mn$mid, sumdat$mean) # Test means }) - it("Summary for multiple CI's [PMF-DATA-003]", { + it("Summary for multiple CI's", { sumdat_med <- summarize_data( plotData2,