Merge branch 'develop' into lemireg-add_quartiles-pairwise_test_cont

Author: slager

.github/workflows/R-CMD-check.yaml

@@ -22,7 +22,8 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: '4.0.4', pandoc-version: '2.11.4'}
+          - {os: ubuntu-latest,   r: '4.4.2', pandoc-version: '3.2'}
+          - {os: ubuntu-latest,   r: '4.1.0', pandoc-version: '2.11.4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -31,14 +32,14 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Setup statsrv pandoc
-        if: ${{ matrix.config.r == '4.0.4' }}
+      - name: Setup custom pandoc version
+        if: ${{ matrix.config.pandoc-version != null }}
         uses: r-lib/actions/setup-pandoc@v2
         with:
           pandoc-version: ${{ matrix.config.pandoc-version }}
 
-      - name: Setup default pandoc
-        if: ${{ matrix.config.r != '4.0.4' }}
+      - name: Setup default pandoc version
+        if: ${{ matrix.config.pandoc-version == null }}
         uses: r-lib/actions/setup-pandoc@v2
 
       - name: Set up tinytex
@@ -53,15 +54,15 @@ jobs:
 
       - name: Setup recent R
         uses: r-lib/actions/setup-r@v2
-        if: ${{ matrix.config.r != '4.0.4' }}
+        if: ${{ matrix.config.r != '4.1.0' && matrix.config.r != '4.4.2'}}
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - name: Setup R 4.0.4
+      - name: Setup older R
         uses: r-lib/actions/setup-r@v2
-        if: ${{ matrix.config.r == '4.0.4' }}
+        if: ${{ matrix.config.r == '4.1.0' || matrix.config.r == '4.4.2'}}
         with:
           r-version: ${{ matrix.config.r }}
           cran: 'https://packagemanager.posit.co/cran/__linux__/noble/2024-04-19'

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: VISCfunctions
 Title: VISC STP/SRA functions
-Version: 1.3.0.9000
+Version: 1.3.1.9000
 Authors@R: c(
     person("Bryan", "Mayer", , "bmayer@fredhutch.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2258-5276")),
     person("Dave", "Slager", , "dslager@fredhutch.org", role = "aut", comment = c(ORCID = "0000-0003-2525-2039")),
@@ -18,7 +18,7 @@ Description:
     Statistical, data processing, and annotation functions for VISC.
 License: MIT + file LICENSE
 Depends:
-    R (>= 3.5)
+    R (>= 4.1.0)
 Imports: 
     binom,
     coin,

NEWS.md

@@ -1,11 +1,18 @@
 # VISCfunctions (development version)
 
 * Add `Median_Quartiles` to `pairwise_test_cont()` output (#99)
-* Maintenance of package and CI (#114)
-* Add B cell example dataset from G001 flow and sequencing file (#108)
 * Minor Changes:
   * Update `Overview()` to include new `Median_Quartiles` (#99)
 
+# VISCfunctions 1.3.1
+
+* Report loaded and attached packages in package reproducibility table (#132)
+* Report nodename in platform reproducibility table (#121)
+* Add B cell example dataset from G001 flow and sequencing file (#108)
+* Maintenance of package and CI (#114, #116, #124)
+* VISCfunctions now depends on R >= 4.1.0 (#134)
+* Auto-generate VISCfunctions pkgdown website with GitHub Actions (#119)
+
 # VISCfunctions 1.3.0
 
 * Fix bug in `pairwise_test_bin()` and `pairwise_test_cont()` (#111)

R/collapse_group_row.R

@@ -19,8 +19,8 @@
 #'
 #' library(dplyr)
 #' options(knitr.kable.NA = '')
-#' collapse_group_row(sample_df, x, y, z) %>%
-#'  kableExtra::kable() %>%
+#' collapse_group_row(sample_df, x, y, z) |>
+#'  kableExtra::kable() |>
 #'  kableExtra::kable_styling()
 #' @export
 collapse_group_row <- function(.data, ..., reorder_cols = TRUE) {

R/pairwise_comparisons.R

@@ -83,8 +83,8 @@
 #' data(exampleData_BAMA)
 #'
 #' ## Group Comparison
-#'group_testing_tibble <- exampleData_BAMA %>%
-#'    group_by(antigen, visitno) %>%
+#'group_testing_tibble <- exampleData_BAMA |>
+#'    group_by(antigen, visitno) |>
 #'    reframe(pairwise_test_cont(x = magnitude,
 #'                               group = group,
 #'                               paired = FALSE,
@@ -97,8 +97,8 @@
 #'
 #'
 #' ## Timepoint Comparison
-#'timepoint_testing_dt <- exampleData_BAMA %>%
-#'                        group_by(antigen, group) %>%
+#'timepoint_testing_dt <- exampleData_BAMA |>
+#'                        group_by(antigen, group) |>
 #'                        reframe(pairwise_test_cont(x = magnitude,
 #'                                                   group = visitno,
 #'                                                   paired = TRUE,
@@ -118,8 +118,8 @@
 #'
 #' ## Group Comparison
 #' # using dplyr
-#'exampleData_ICS %>%
-#'group_by(Stim, Parent, Population, Visit) %>%
+#'exampleData_ICS |>
+#'group_by(Stim, Parent, Population, Visit) |>
 #'reframe(pairwise_test_cont(x = PercentCellNet,
 #'                           group = Group,
 #'                           paired = FALSE,
@@ -133,8 +133,8 @@
 #'                           verbose = TRUE))
 #'
 #' # Timepoint Comparison
-#'timepoint_testing_dt <- exampleData_ICS %>%
-#'                        group_by(Stim, Parent, Population, Group) %>%
+#'timepoint_testing_dt <- exampleData_ICS |>
+#'                        group_by(Stim, Parent, Population, Group) |>
 #'                        reframe(pairwise_test_cont(x = PercentCellNet,
 #'                                                   group = Visit,
 #'                                                   paired = TRUE,
@@ -483,8 +483,8 @@ pairwise_test_cont <- function(
 #' data(exampleData_BAMA)
 #'
 #' ## Group Comparison
-#'group_testing <- exampleData_BAMA %>%
-#'    group_by(antigen, visitno) %>%
+#'group_testing <- exampleData_BAMA |>
+#'    group_by(antigen, visitno) |>
 #'    group_modify(~ as.data.frame(
 #'        pairwise_test_bin(x = .$response, group = .$group,
 #'                method = 'barnard', alternative = 'less',
@@ -493,8 +493,8 @@ pairwise_test_cont <- function(
 #'
 #'
 #' ## Timepoint Comparison
-#'timepoint_testing <- exampleData_BAMA %>%
-#'    group_by(antigen, group) %>%
+#'timepoint_testing <- exampleData_BAMA |>
+#'    group_by(antigen, group) |>
 #'    group_modify(~ as.data.frame(
 #'        pairwise_test_bin(x = .$response, group = .$visitno, id = .$pubID,
 #'                method = 'mcnemar', num_needed_for_test = 3, digits = 1,
@@ -504,16 +504,16 @@ pairwise_test_cont <- function(
 #' data(exampleData_ICS)
 #'
 #' ## Group Comparison
-#'group_testing <- exampleData_ICS %>%
-#'    group_by(Stim, Parent, Population, Visit) %>%
+#'group_testing <- exampleData_ICS |>
+#'    group_by(Stim, Parent, Population, Visit) |>
 #'    group_modify(~ as.data.frame(
 #'        pairwise_test_bin(x = .$response, group = .$Group , alternative = 'greater',
 #'                method = 'barnard', num_needed_for_test = 3, digits = 1,
 #'                trailing_zeros = TRUE, sep_val = ' vs. ', verbose = TRUE)))
 #'
 #' ## Timepoint Comparison
-#'timepoint_testing <- exampleData_ICS %>%
-#'    group_by(Stim, Parent, Population, Group) %>%
+#'timepoint_testing <- exampleData_ICS |>
+#'    group_by(Stim, Parent, Population, Group) |>
 #'    group_modify(~ as.data.frame(
 #'        pairwise_test_bin(x = .$response, group = .$Visit, id = .$pubID,
 #'                method = 'mcnemar', num_needed_for_test = 3, digits = 1,
@@ -780,9 +780,9 @@ pairwise_test_bin <- function(x,
 #' data(exampleData_BAMA)
 #'
 #' ## Antigen Correlation
-#' exampleData_BAMA %>%
-#' filter(visitno != 0) %>%
-#' group_by(group, visitno) %>%
+#' exampleData_BAMA |>
+#' filter(visitno != 0) |>
+#' group_by(group, visitno) |>
 #'  summarize(
 #'    cor_test_pairs(x = magnitude, pair = antigen, id = pubID,
 #'    method = 'spearman', n_distinct_value = 3, digits = 1, verbose = TRUE),

R/pretty_output_functions.R

@@ -44,8 +44,8 @@
 #' library(tidyr)
 #' data(exampleData_BAMA)
 #'
-#' descriptive_stats_by_group <- exampleData_BAMA %>%
-#'   group_by(visitno,antigen) %>%
+#' descriptive_stats_by_group <- exampleData_BAMA |>
+#'   group_by(visitno,antigen) |>
 #'   reframe(
 #'     Group1 = unique(group[group == 1]), Group2 = unique(group[group == 2]),
 #'     Group1_n = length(magnitude[group == 1]), Group2_n = length(magnitude[group == 2]),
@@ -70,16 +70,16 @@
 #' # Same example wit tidyverse in single pipe
 #'
 #'
-#'exampleData_BAMA %>%
-#'  mutate(group = paste0("Group", group)) %>%
-#'  group_by(group, visitno, antigen) %>%
+#'exampleData_BAMA |>
+#'  mutate(group = paste0("Group", group)) |>
+#'  group_by(group, visitno, antigen) |>
 #'  reframe(N = n(), mean = mean(magnitude), sd = sd(magnitude),
 #'          median = median(magnitude), min = min(magnitude),
-#'          max = max(magnitude), q95_fun = quantile(magnitude, 0.95)) %>%
-#'  pivot_longer(-(group:antigen)) %>% # these three chains create a wide dataset
-#'  unite(temp, group, name) %>%
-#'  pivot_wider(names_from = temp, values_from = value) %>%
-#'  mutate(Group1 = "Group 1", Group2 = "Group 2") %>%
+#'          max = max(magnitude), q95_fun = quantile(magnitude, 0.95)) |>
+#'  pivot_longer(-(group:antigen)) |> # these three chains create a wide dataset
+#'  unite(temp, group, name) |>
+#'  pivot_wider(names_from = temp, values_from = value) |>
+#'  mutate(Group1 = "Group 1", Group2 = "Group 2") |>
 #'  paste_tbl_grp()
 #'
 #' @export
@@ -332,8 +332,8 @@ paste_tbl_grp <- function(
 #' stat_paste(c(rep(5,5),NA),c(1:5,NA),c(1,NA,2,NA,3,NA),bound_char = '[')
 #'
 #' library(dplyr)
-#' exampleData_BAMA %>%
-#' group_by(antigen, visitno, group) %>%
+#' exampleData_BAMA |>
+#' group_by(antigen, visitno, group) |>
 #' summarise(median_min_max = stat_paste(median(magnitude, na.rm = TRUE),
 #'                                         min(magnitude, na.rm = TRUE),
 #'                                         max(magnitude, na.rm = TRUE)),

R/reproducibility_tables.R

@@ -99,21 +99,21 @@ get_full_name <- function(id = NULL){
 #'
 #' # Simple HTML Display
 #' kableExtra::kable(my_session_info$platform_table, 'html',
-#'       caption = "Reproducibility Software Session Information") %>%
+#'       caption = "Reproducibility Software Session Information") |>
 #'       kableExtra::kable_styling()
 #'
 #' kableExtra::kable(my_session_info$packages_table, 'html',
-#'       caption = "Reproducibility Software Package Version Information") %>%
+#'       caption = "Reproducibility Software Package Version Information") |>
 #'       kableExtra::kable_styling()
 #'
 #'
 #' # Latex Display
 #' kableExtra::kable(my_session_info$platform_table, 'latex', booktabs = TRUE,
-#'       linesep = '', caption = "Reproducibility Software Session Information") %>%
+#'       linesep = '', caption = "Reproducibility Software Session Information") |>
 #'       kableExtra::kable_styling(font_size = 7)
 #'
 #' kableExtra::kable(my_session_info$packages_table, 'latex', booktabs = TRUE,
-#'       linesep = '', caption = "Reproducibility Software Package Version Information") %>%
+#'       linesep = '', caption = "Reproducibility Software Package Version Information") |>
 #'       kableExtra::kable_styling(font_size = 7)
 #'
 #' @export
@@ -127,10 +127,8 @@ get_session_info <- function(libpath = FALSE){
                                 Sys.getenv("USERNAME"),
                                 Sys.getenv("USER")))
 
-  my_session_info <- sessioninfo::session_info()
-
-  platform <- my_session_info[[1]]
-  packages <- my_session_info[[2]]
+  platform <- sessioninfo::platform_info()
+  packages <- sessioninfo::package_info(pkgs = 'loaded', include_base = FALSE)
 
   # TABLE 1
   my_session_info1 <- rbind(
@@ -222,8 +220,8 @@ get_session_info <- function(libpath = FALSE){
 
 
   # TABLE 2
-  my_session_info2 <- packages[packages$attached,] # Only want attached packages
-  my_session_info2 <- with(my_session_info2, {
+
+  my_session_info2 <- with(packages, {
     data.frame(package = package,
                version = loadedversion,
                # Pulling in Data Version numbers
@@ -238,6 +236,7 @@ get_session_info <- function(libpath = FALSE){
                  USE.NAMES = FALSE),
                date = date,
                source = source,
+               status = ifelse(attached, 'attached', 'loaded'),
                libpath = library)
   })
   if (! libpath) my_session_info2$libpath <- NULL
@@ -248,6 +247,9 @@ get_session_info <- function(libpath = FALSE){
   # Use short git hash
   my_session_info2$source <- shorten_git_hash(my_session_info2$source)
 
+  my_session_info2 <- my_session_info2[order(my_session_info2$status),]
+  rownames(my_session_info2) <- NULL
+
   list(platform_table = my_session_info1, packages_table = my_session_info2)
 }
 

R/step_curves.R

@@ -34,24 +34,24 @@
 #'                  event = c(1,1,0,1,1,0,0,1,1,1),
 #'                  ptid = c(1,1,2,2,3,3,3,3,3,3))
 #' plot_data <-
-#'  dat %>%
-#'   dplyr::group_by(ptid) %>%
+#'  dat |>
+#'   dplyr::group_by(ptid) |>
 #'   dplyr::group_modify(~ create_step_curve(x = .x$x, event = .x$event))
 #'
 #' ggplot2::ggplot(data = plot_data,
 #'                 ggplot2::aes(x = time, y = surv, color = factor(ptid))) +
 #'  ggplot2::geom_step(linetype = "dashed", direction = 'hv', lwd = .35) +
-#'  ggplot2::geom_point(data = plot_data %>% filter(n.censor == 1),
+#'  ggplot2::geom_point(data = plot_data |> filter(n.censor == 1),
 #'                      shape = 3, size = 6, show.legend = FALSE)
 #'
 #' #mAB example for reverse curves
 #' data(CAVD812_mAB)
 #'
 #' plot_data <-
-#' CAVD812_mAB %>%
-#'   filter(virus != 'SVA-MLV') %>%
-#'   tidyr::pivot_longer(cols = c(ic50, ic80)) %>%
-#'   dplyr::group_by(name, product) %>%
+#' CAVD812_mAB |>
+#'   filter(virus != 'SVA-MLV') |>
+#'   tidyr::pivot_longer(cols = c(ic50, ic80)) |>
+#'   dplyr::group_by(name, product) |>
 #'   dplyr::group_modify(~ create_step_curve(x = pmin(.x$value, 100),
 #'                                           event = as.numeric(.x$value < 50),
 #'                                           flip_surv = TRUE,
@@ -160,8 +160,8 @@ create_step_curve <- function(x,
 #'                  response = c(1,1,0,1,1,0,0,1,1,1),
 #'                  ptid = c(1,1,2,2,3,3,3,3,3,3))
 #' ind_results <-
-#'  dat %>%
-#'   dplyr::group_by(ptid) %>%
+#'  dat |>
+#'   dplyr::group_by(ptid) |>
 #'   dplyr::group_modify(~ mb_results(magnitude = .x$magnitude, response = .x$response))
 #'
 #' overall_results <-
@@ -179,17 +179,17 @@ create_step_curve <- function(x,
 #' data(exampleData_BAMA)
 #'
 #' data_here <-
-#'  exampleData_BAMA %>%
+#'  exampleData_BAMA |>
 #'  filter(visitno == 2)
 #'
 #' group_results <-
-#'   data_here %>%
-#'   dplyr::group_by(group) %>%
+#'   data_here |>
+#'   dplyr::group_by(group) |>
 #'   dplyr::group_modify(~ mb_results(magnitude = .x$magnitude , response = .x$response))
 #'
 #' ind_results <-
-#'   data_here %>%
-#'   dplyr::group_by(group, pubID) %>%
+#'   data_here |>
+#'   dplyr::group_by(group, pubID) |>
 #'   dplyr::group_modify(~ mb_results(magnitude = .x$magnitude , response = .x$response))
 #'
 #' ggplot2::ggplot(data = group_results,

data-raw/cds_datasets.R

@@ -5,13 +5,13 @@ library(DataSpaceR)
 con <- connectDS()
 
 cvd812 <- con$getStudy('cvd812')
-CAVD812_mAB <- cvd812$getDataset("NAB Ig") %>%
+CAVD812_mAB <- cvd812$getDataset("NAB Ig") |>
   distinct(
     product = mab_name_source,
     virus = cds_virus_name,
     ic50 = titer_curve_ic50,
     ic80 = titer_curve_ic80
-  ) %>% as.data.frame()
+  ) |> as.data.frame()
 
 usethis::use_data(CAVD812_mAB, overwrite = TRUE)