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Ensures required packages are in Imports section #774

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Ensures required packages are in Imports section #774

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e2275ab
chore: move required packages to imports
averissimo Aug 14, 2024
4590f44
fix: ensure optional requirements in tests
averissimo Aug 14, 2024
8484c82
Merge branch 'main' into 518-pkgs_imports@main
averissimo Dec 18, 2024
a87ccd1
chore: make sure all github are included
averissimo Dec 18, 2024
3015749
chore: remove require namespaces from examples
averissimo Dec 18, 2024
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chore: remove whitespace
averissimo Dec 18, 2024
fcedb3c
chore: remove unecessary skips
averissimo Dec 18, 2024
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[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
github-actions[bot] Dec 18, 2024
27a75ad
empty: trigger ci
averissimo Dec 19, 2024
8d1c172
test: action with custom max additional repos
averissimo Dec 20, 2024
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Revert "test: action with custom max additional repos"
averissimo Dec 20, 2024
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48 changes: 23 additions & 25 deletions DESCRIPTION
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I see changes in dependencies and I immediately think about verdepcheck. Can you please confirm that it is passing on this? If not - let's work on the deps versions.

This might need to wait for https://github.com/insightsengineering/teal.modules.general/pull/774/files#r1890465398

Original file line number Diff line number Diff line change
Expand Up @@ -31,16 +31,30 @@ Depends:
teal.transform (>= 0.5.0.9015)
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@averissimo averissimo Dec 18, 2024 •
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Teal requirement needs to be bumped with insightsengineering/teal#1432

Possibly to teal (>= 0.15.2.9091),

Keeping conversation open until the PR is closed

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I approved that PR, so working on this PR can continue.

Imports:
checkmate (>= 2.1.0),
colourpicker,
dplyr (>= 1.0.5),
DT (>= 0.13),
forcats (>= 1.0.0),
generics,
ggExtra,
ggpmisc (>= 0.4.3),
ggpp,
ggrepel,
goftest,
grid,
gridExtra,
htmlwidgets,
jsonlite,
lattice (>= 0.18-4),
MASS,
rtables (>= 0.6.8),
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lifecycle (>= 0.2.0),
scales,
shinyjs,
shinyTree (>= 0.2.8),
shinyvalidate,
shinyWidgets (>= 0.5.1),
sparkline,
stats,
stringr (>= 1.4.1),
teal.code (>= 0.5.0.9012),
Expand All @@ -54,50 +68,34 @@ Imports:
tools,
utils
Suggests:
broom (>= 0.7.10),
colourpicker,
ggExtra,
ggpmisc (>= 0.4.3),
ggpp,
ggrepel,
goftest,
gridExtra,
htmlwidgets,
jsonlite,
knitr (>= 1.42),
lattice (>= 0.18-4),
logger (>= 0.2.0),
MASS,
nestcolor (>= 0.1.0),
pkgload,
rlang (>= 1.0.0),
rmarkdown (>= 2.23),
roxy.shinylive,
rtables (>= 0.6.8),
rvest,
shinytest2,
sparkline,
testthat (>= 3.1.9),
withr (>= 2.0.0)
VignetteBuilder:
knitr,
rmarkdown
Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
rstudio/shiny, insightsengineering/teal,
insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
rstudio/DT, tidyverse/forcats, r-lib/lifecycle, r-lib/scales,
daattali/shinyjs, shinyTree/shinyTree, rstudio/shinyvalidate,
dreamRs/shinyWidgets, tidyverse/stringr,
rstudio/shiny, insightsengineering/teal, insightsengineering/teal.transform,
mllg/checkmate, daattali/colourpicker, tidyverse/dplyr, rstudio/DT,
tidyverse/forcats, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
slowkow/ggrepel, baddstats/goftest, ramnathv/htmlwidgets, jeroen/jsonlite,
deepayan/lattice, insightsengineering/rtables, r-lib/lifecycle,
r-lib/scales, daattali/shinyjs, shinyTree/shinyTree, rstudio/shinyvalidate,
dreamRs/shinyWidgets, htmlwidgets/sparkline, tidyverse/stringr,
insightsengineering/teal.code, insightsengineering/teal.data,
insightsengineering/teal.logger, insightsengineering/teal.reporter,
insightsengineering/teal.widgets, insightsengineering/tern,
tidyverse/tibble, tidyverse/tidyr, tidymodels/broom,
daattali/colourpicker, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
slowkow/ggrepel, baddstats/goftest, ramnathv/htmlwidgets,
jeroen/jsonlite, yihui/knitr, daroczig/logger, deepayan/lattice,
tidyverse/tibble, tidyverse/tidyr, yihui/knitr, daroczig/logger,
insightsengineering/nestcolor, r-lib/pkgload, r-lib/rlang,
rstudio/rmarkdown, insightsengineering/roxy.shinylive,
insightsengineering/rtables, tidyverse/rvest, htmlwidgets/sparkline,
rstudio/rmarkdown, insightsengineering/roxy.shinylive, tidyverse/rvest,
rstudio/shinytest2, r-lib/testthat, r-lib/withr
Config/Needs/website: insightsengineering/nesttemplate
Encoding: UTF-8
Expand Down
18 changes: 4 additions & 14 deletions R/tm_g_distribution.R
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@
#' interactive <- function() TRUE
#' {{ next_example }}
# nolint start: line_length_linter.
#' @examplesIf require("ggpmisc", quietly = TRUE) && require("ggpp", quietly = TRUE) && require("goftest", quietly = TRUE) && require("MASS", quietly = TRUE) && require("broom", quietly = TRUE)
#' @examples
# nolint end: line_length_linter.
#' # general data example
#' data <- teal_data()
Expand Down Expand Up @@ -89,7 +89,7 @@
#' interactive <- function() TRUE
#' {{ next_example }}
# nolint start: line_length_linter.
#' @examplesIf require("ggpmisc", quietly = TRUE) && require("ggpp", quietly = TRUE) && require("goftest", quietly = TRUE) && require("MASS", quietly = TRUE) && require("broom", quietly = TRUE)
#' @examples
# nolint end: line_length_linter.
#' # CDISC data example
#' data <- teal_data()
Expand Down Expand Up @@ -154,16 +154,6 @@ tm_g_distribution <- function(label = "Distribution Module",
decorators = NULL) {
message("Initializing tm_g_distribution")

# Requires Suggested packages
extra_packages <- c("ggpmisc", "ggpp", "goftest", "MASS", "broom")
missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)
if (length(missing_packages) > 0L) {
stop(sprintf(
"Cannot load package(s): %s.\nInstall or restart your session.",
toString(missing_packages)
))
}

# Normalize the parameters
if (inherits(dist_var, "data_extract_spec")) dist_var <- list(dist_var)
if (inherits(strata_var, "data_extract_spec")) strata_var <- list(strata_var)
Expand Down Expand Up @@ -1242,7 +1232,7 @@ srv_distribution <- function(id,
expr = {
test_table_data <- ANL %>%
dplyr::select(dist_var) %>%
with(., broom::glance(do.call(test, args))) %>%
with(., generics::glance(do.call(test, args))) %>%
dplyr::mutate_if(is.numeric, round, 3)
},
env = env
Expand All @@ -1256,7 +1246,7 @@ srv_distribution <- function(id,
test_table_data <- ANL %>%
dplyr::select(dist_var, s_var, g_var) %>%
dplyr::group_by_at(dplyr::vars(dplyr::any_of(groups))) %>%
dplyr::do(tests = broom::glance(do.call(test, args))) %>%
dplyr::do(tests = generics::glance(do.call(test, args))) %>%
tidyr::unnest(tests) %>%
dplyr::mutate_if(is.numeric, round, 3)
},
Expand Down
14 changes: 2 additions & 12 deletions R/tm_g_scatterplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
#' interactive <- function() TRUE
#' {{ next_example }}
# nolint start: line_length_linter.
#' @examplesIf require("ggpmisc", quietly = TRUE) && require("ggExtra", quietly = TRUE) && require("colourpicker", quietly = TRUE)
#' @examples
# nolint end: line_length_linter.
#' # general data example
#' data <- teal_data()
Expand Down Expand Up @@ -134,7 +134,7 @@
#' interactive <- function() TRUE
#' {{ next_example }}
# nolint start: line_length_linter.
#' @examplesIf require("ggpmisc", quietly = TRUE) && require("ggExtra", quietly = TRUE) && require("colourpicker", quietly = TRUE)
#' @examples
# nolint end: line_length_linter.
#' # CDISC data example
#' data <- teal_data()
Expand Down Expand Up @@ -243,16 +243,6 @@ tm_g_scatterplot <- function(label = "Scatterplot",
decorators = NULL) {
message("Initializing tm_g_scatterplot")

# Requires Suggested packages
extra_packages <- c("ggpmisc", "ggExtra", "colourpicker")
missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)
if (length(missing_packages) > 0L) {
stop(sprintf(
"Cannot load package(s): %s.\nInstall or restart your session.",
toString(missing_packages)
))
}

# Normalize the parameters
if (inherits(x, "data_extract_spec")) x <- list(x)
if (inherits(y, "data_extract_spec")) y <- list(y)
Expand Down
9 changes: 2 additions & 7 deletions R/tm_g_scatterplotmatrix.R
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
#' library(teal.modules.general)
#' interactive <- function() TRUE
#' {{ next_example }}
#' @examplesIf require("lattice", quietly = TRUE)
#' @examples
#' # general data example
#' data <- teal_data()
#' data <- within(data, {
Expand Down Expand Up @@ -118,7 +118,7 @@
#' library(teal.modules.general)
#' interactive <- function() TRUE
#' {{ next_example }}
#' @examplesIf require("lattice", quietly = TRUE)
#' @examples
#' # CDISC data example
#' data <- teal_data()
#' data <- within(data, {
Expand Down Expand Up @@ -181,11 +181,6 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
decorators = NULL) {
message("Initializing tm_g_scatterplotmatrix")

# Requires Suggested packages
if (!requireNamespace("lattice", quietly = TRUE)) {
stop("Cannot load lattice - please install the package or restart your session.")
}

# Normalize the parameters
if (inherits(variables, "data_extract_spec")) variables <- list(variables)

Expand Down
92 changes: 47 additions & 45 deletions R/tm_missing_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@
#' library(teal.modules.general)
#' interactive <- function() TRUE
#' {{ next_example }}
#' @examplesIf require("gridExtra", quietly = TRUE) && require("rlang", quietly = TRUE)
#' @examples
#' # general example data
#' data <- teal_data()
#' data <- within(data, {
Expand Down Expand Up @@ -85,7 +85,7 @@
#' library(teal.modules.general)
#' interactive <- function() TRUE
#' {{ next_example }}
#' @examplesIf require("gridExtra", quietly = TRUE) && require("rlang", quietly = TRUE)
#' @examples
#' # CDISC example data
#' data <- teal_data()
#' data <- within(data, {
Expand Down Expand Up @@ -121,14 +121,6 @@ tm_missing_data <- function(label = "Missing data",
decorators = NULL) {
message("Initializing tm_missing_data")

# Requires Suggested packages
if (!requireNamespace("gridExtra", quietly = TRUE)) {
stop("Cannot load gridExtra - please install the package or restart your session.")
}
if (!requireNamespace("rlang", quietly = TRUE)) {
stop("Cannot load rlang - please install the package or restart your session.")
}

# Normalize the parameters
if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)

Expand Down Expand Up @@ -1174,6 +1166,13 @@ srv_missing_data <- function(id,
ggtheme = input$ggtheme
)

# Unlikely that `rlang` is not available, new hashing may be expensive
hashing_function <- if (requireNamespace("rlang", quietly = TRUE)) {
quote(rlang::hash)
} else {
function(x) paste(as.integer(x), collapse = "")
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}

teal.code::eval_code(
common_code_q(),
substitute(
Expand All @@ -1188,41 +1187,44 @@ srv_missing_data <- function(id,
)
) %>%
teal.code::eval_code(
quote({
summary_plot_patients <- ANL[, c(parent_keys, analysis_vars)] %>%
dplyr::group_by_at(parent_keys) %>%
dplyr::mutate(id = dplyr::cur_group_id()) %>%
dplyr::ungroup() %>%
dplyr::group_by_at(c(parent_keys, "id")) %>%
dplyr::summarise_all(anyNA) %>%
dplyr::ungroup()

# order subjects by decreasing number of missing and then by
# missingness pattern (defined using sha1)
order_subjects <- summary_plot_patients %>%
dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
dplyr::transmute(
id = dplyr::row_number(),
number_NA = apply(., 1, sum),
sha = apply(., 1, rlang::hash)
) %>%
dplyr::arrange(dplyr::desc(number_NA), sha) %>%
getElement(name = "id")

# order columns by decreasing percent of missing values
ordered_columns <- summary_plot_patients %>%
dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
dplyr::summarise(
column = create_cols_labels(colnames(.)),
na_count = apply(., MARGIN = 2, FUN = sum),
na_percent = na_count / nrow(.) * 100
) %>%
dplyr::arrange(na_percent, dplyr::desc(column))

summary_plot_patients <- summary_plot_patients %>%
tidyr::gather("col", "isna", -"id", -dplyr::all_of(parent_keys)) %>%
dplyr::mutate(col = create_cols_labels(col))
})
substitute(
expr = {
summary_plot_patients <- ANL[, c(parent_keys, analysis_vars)] %>%
dplyr::group_by_at(parent_keys) %>%
dplyr::mutate(id = dplyr::cur_group_id()) %>%
dplyr::ungroup() %>%
dplyr::group_by_at(c(parent_keys, "id")) %>%
dplyr::summarise_all(anyNA) %>%
dplyr::ungroup()

# order subjects by decreasing number of missing and then by
# missingness pattern (defined using sha1)
order_subjects <- summary_plot_patients %>%
dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
dplyr::transmute(
id = dplyr::row_number(),
number_NA = apply(., 1, sum),
sha = apply(., 1, hashing_function)
) %>%
dplyr::arrange(dplyr::desc(number_NA), sha) %>%
getElement(name = "id")

# order columns by decreasing percent of missing values
ordered_columns <- summary_plot_patients %>%
dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
dplyr::summarise(
column = create_cols_labels(colnames(.)),
na_count = apply(., MARGIN = 2, FUN = sum),
na_percent = na_count / nrow(.) * 100
) %>%
dplyr::arrange(na_percent, dplyr::desc(column))

summary_plot_patients <- summary_plot_patients %>%
tidyr::gather("col", "isna", -"id", -dplyr::all_of(parent_keys)) %>%
dplyr::mutate(col = create_cols_labels(col))
},
env = list(hashing_function = hashing_function)
)
) %>%
teal.code::eval_code(
substitute(
Expand Down
9 changes: 2 additions & 7 deletions R/tm_t_crosstable.R
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
#' library(teal.modules.general)
#' interactive <- function() TRUE
#' {{ next_example }}
#' @examplesIf require("rtables", quietly = TRUE)
#' @examples
#' # general data example
#' data <- teal_data()
#' data <- within(data, {
Expand Down Expand Up @@ -87,7 +87,7 @@
#' library(teal.modules.general)
#' interactive <- function() TRUE
#' {{ next_example }}
#' @examplesIf require("rtables", quietly = TRUE)
#' @examples
#' # CDISC data example
#' data <- teal_data()
#' data <- within(data, {
Expand Down Expand Up @@ -147,11 +147,6 @@ tm_t_crosstable <- function(label = "Cross Table",
decorators = NULL) {
message("Initializing tm_t_crosstable")

# Requires Suggested packages
if (!requireNamespace("rtables", quietly = TRUE)) {
stop("Cannot load rtables - please install the package or restart your session.")
}

# Normalize the parameters
if (inherits(x, "data_extract_spec")) x <- list(x)
if (inherits(y, "data_extract_spec")) y <- list(y)
Expand Down
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