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Teal refactor (#598)
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Part of insightsengineering/teal#731

FYI @shajoezhu once this goes in SME will be able to test the refactor
hasn't broken anything

Signed-off-by: Nikolas Burkoff <nikolas.burkoff@roche.com>
Signed-off-by: Marek Blazewicz <110387997+BLAZEWIM@users.noreply.github.com>
Co-authored-by: Dawid Kałędkowski <6959016+gogonzo@users.noreply.github.com>
Co-authored-by: Mahmoud Hallal <mahmoud.hallal@roche.com>
Co-authored-by: Maciej Nasinski <nasinski.maciej@gmail.com>
Co-authored-by: Nikolas Burkoff <nikolas.burkoff@roche.com>
Co-authored-by: Mahmoud Hallal <86970066+mhallal1@users.noreply.github.com>
Co-authored-by: Marek Blazewicz <110387997+BLAZEWIM@users.noreply.github.com>
Co-authored-by: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>
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@pawelru @gogonzo
@mhallal1 @Polkas @BLAZEWIM
8 people authored Nov 4, 2022
1 parent 92b4506 commit f79d2c4
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -38,6 +38,7 @@ Imports:
ggplot2,
ggrepel,
grid,
lifecycle,
logger (>= 0.2.0),
magrittr,
methods,
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8 changes: 7 additions & 1 deletion NEWS.md
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@@ -1,5 +1,10 @@
# teal.modules.clinical 0.8.14.9002

### Breaking changes

* Replaced `chunks` with simpler `qenv` class.
* Replaced `datasets` argument containing `FilteredData` with the new arguments `data` (`tdata` object) and `filter_panel_api` (`FilterPanelAPI`).

### Enhancements
* Replaced `synthetic_cdisc_data` with refactored `synthetic_cdisc_dataset` function to speed up dataset loading in tests/examples.

Expand All @@ -10,6 +15,7 @@

### Enhancements
* Updated all synthetic data for tests to version `rcd_2022_02_28`.
* Updated all test files in `tests/testthat/` to `synthetic_cdisc_data("2022_02_28")`
* Reverted missing data checkbox in `tm_t_summary` (encoding and filtering should be separate).
* Implemented a new widget that allows dragging and dropping to select comparison groups.
* Added the `teal.reporter` functionality to all modules.
Expand All @@ -28,7 +34,7 @@

### Bug fixes

* Fixed bug in `tm_g_barchart_simple` which prevented graph from showing.
* Fixed bug in `tm_g_barchart_simple` which prevented graph from being shown.
* Fixed broken example for `tm_t_abnormality_by_worst_grade`.
* Fixed bug in `tm_a_mmrm` which prevented table headers from displaying.
* Fixed bug in `tm_g_forest_rsp` when deselecting endpoint.
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3 changes: 2 additions & 1 deletion R/argument_convention.R
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Expand Up @@ -113,7 +113,8 @@ NULL
#' @param arm_var (`choices_selected` or `data_extract_spec`)\cr
#' object with all available choices
#' and preselected option for variable names that can be used as `arm_var`.
#' It defines the grouping variable(s) in the results table. If there are two elements selected for `arm_var`,
#' It defines the grouping variable(s) in the results table.
#' If there are two elements selected for `arm_var`,
#' second variable will be nested under the first variable.
#' @param arm_ref_comp optional, (`list`)\cr
#' If specified it must be a named list with each element corresponding to
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109 changes: 45 additions & 64 deletions R/arm_ref_comp.R
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Expand Up @@ -9,8 +9,8 @@
#' @param id_ref (`character`) id of reference Treatment input ui element
#' @param id_comp (`character`) id of comparison group input ui element
#' @param id_arm_var (`character`) id of Treatment variable input ui element
#' @param datasets (`FilteredData`) object from the module
#' @param dataname (`character`) dataset name
#' @param data (`reactive` or `data.frame`) dataset used to validate Treatment reference inputs and
#' set `id_ref` input.
#' @param arm_ref_comp (`unknown`) Treatment reference and compare variables provided as a
#' nested list where each Treatment variable corresponds a list specifying the default levels for the
#' reference and comparison treatments.
Expand All @@ -24,66 +24,60 @@
#' @keywords internal
#'
#' @examples
#' \dontrun{
#' ds <- teal:::get_dummy_datasets()
#'
#' arm_ref_comp <- list(ARMCD = list(ref = "ARM A", comp = c("ARM B")))
#' arm_var <- choices_selected(c("ARM", "ARMCD"), "ARM")
#' shinyApp(
#' ui = fluidPage(
#' teal.widgets::optionalSelectInput(
#' "arm",
#' "Treatment Variable",
#' choices = arm_var$choices,
#' selected = arm_var$selected
#' if (interactive()) {
#' shinyApp(
#' ui = fluidPage(
#' teal.widgets::optionalSelectInput(
#' "arm",
#' "Treatment Variable",
#' choices = arm_var$choices,
#' selected = arm_var$selected
#' ),
#' shiny::uiOutput("arms_buckets"),
#' ),
#' shiny::uiOutput("arms_buckets"),
#' ),
#' server = function(input, output, session) {
#' shiny::isolate({
#' teal.modules.clinical:::arm_ref_comp_observer(
#' session,
#' input,
#' output,
#' id_arm_var = "arm",
#' datasets = ds,
#' arm_ref_comp = arm_ref_comp,
#' module = "example"
#' )
#' })
#' }
#' )
#' server = function(input, output, session) {
#' shiny::isolate({
#' teal.modules.clinical:::arm_ref_comp_observer(
#' session,
#' input,
#' output,
#' id_arm_var = "arm",
#' datasets = ds,
#' arm_ref_comp = arm_ref_comp,
#' module = "example"
#' )
#' })
#' }
#' )
#' }
arm_ref_comp_observer <- function(session,
input,
output,
id_ref = "Ref",
id_comp = "Comp",
id_arm_var,
datasets,
dataname = "ADSL",
data,
arm_ref_comp,
module,
on_off = shiny::reactive(TRUE),
input_id = "buckets",
output_id = "arms_buckets") {
if (any(unlist(lapply(arm_ref_comp, lapply, inherits, "delayed_data")))) {
stopifnot(
all(vapply(arm_ref_comp, function(x) identical(sort(names(x)), c("comp", "ref")), logical(1)))
)
# when a delayed object is used for arm_ref_comp, the entire FilteredData
# object must be passed to resolve it
arm_ref_comp <- teal.transform::resolve_delayed(arm_ref_comp, datasets)
}

df <- datasets$get_data(dataname, filtered = FALSE)

check_arm_ref_comp(arm_ref_comp, df, module) ## throws an error if there are issues

# uses observe because observeEvent evaluates only when on_off() is switched
# not necessarily when variables are dropped
output[[output_id]] <- shiny::renderUI({
if (!is.null(on_off()) && on_off()) {
df <- if (shiny::is.reactive(data)) {
data()
} else {
data
}

check_arm_ref_comp(arm_ref_comp, df, module) ## throws an error if there are issues

arm_var <- input[[id_arm_var]]

# validations here don't produce nice UI message (it's observe and not render output) but it prevent red errors
Expand All @@ -97,7 +91,6 @@ arm_ref_comp_observer <- function(session,
} else {
unique(arm)
}

default_settings <- arm_ref_comp[[arm_var]]

if (is.null(default_settings)) {
Expand Down Expand Up @@ -150,29 +143,17 @@ check_arm_ref_comp <- function(x, df_to_check, module) {
}


Map(function(xi, var) {
if (!is.list(xi)) {
stop(
msg, "definition for Treatment variable ",
var, " list element needs to be lists with ref and comp elements"
)
}

rc <- names(xi)
if (is.null(rc) || !identical(sort(rc), c("comp", "ref"))) {
stop(msg, "definition for Treatment variable ", var, " nested list needs to have the elements ref and comp")
}


arm_levels <- unlist(xi)

if (!all(arm_levels %in% df_to_check[[var]])) {
stop(
msg, "definition for Treatment variable ",
var, " refers to treatment levels that do not exist in the data"
)
Map(
x, vars,
f = function(xi, var) {
if (!checkmate::check_list(xi) || !setequal(names(xi), c("comp", "ref"))) {
stop(
msg, "definition for Treatment variable ",
var, " list element needs to be lists with ref and comp elements"
)
}
}
}, x, vars)
)
}

invisible(TRUE)
Expand Down
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