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Creating ADBCVA • admiralophtha
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Skip to contents
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Introduction
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+
This article describes creating an ADBCVA ADaM with Best-Corrected
+Visual Acuity (BCVA) data for ophthalmology endpoints. It is to be used
+in conjunction with the article on creating
+a BDS dataset from SDTM. As such, derivations and processes that are
+not specific to ADBCVA are absent, and the user is invited to consult
+the aforementioned article for guidance.
+
Note: All examples assume CDISC SDTM and/or ADaM
+format as input unless otherwise specified.
+
+
Dataset Contents
+
+
As the name ADBCVA implies, admiralophtha suggests to
+populate ADBCVA solely with BCVA records from the OE SDTM.
+
+
+
Required Packages
+
+
The examples of this vignette require the following packages.
+
+
+
+
Programming Workflow
+
+
+
+
Initial set up of ADBCVA
+
+
As with all BDS ADaM datasets, one should start from the OE SDTM,
+where only the BCVA records are of interest. For the purposes of the
+next two sections, we shall be using the admiral OE and
+ADSL test data. We will also require a lookup table for the mapping of
+parameter codes.
+
Note: to simulate an ophthalmology study, we add a
+randomly generated STUDYEYE variable to ADSL, but in
+practice STUDYEYE will already have been derived using
+derive_var_studyeye().
+
+data("oe_ophtha")
+data("admiral_adsl")
+
+# Add STUDYEYE to ADSL to simulate an ophtha dataset
+adsl <- admiral_adsl %>%
+ as.data.frame() %>%
+ mutate(STUDYEYE = sample(c("LEFT", "RIGHT"), n(), replace = TRUE)) %>%
+ convert_blanks_to_na()
+
+oe <- convert_blanks_to_na(oe_ophtha) %>%
+ ungroup()
+
+# ---- Lookup table ----
+param_lookup <- tibble::tribble(
+ ~OETESTCD, ~OECAT, ~OESCAT, ~AFEYE, ~PARAMCD, ~PARAM, ~PARAMN,
+ "VACSCORE", "BEST CORRECTED VISUAL ACUITY", "OVERALL EVALUATION", "Study Eye", "SBCVA", "Study Eye Visual Acuity Score (letters)", 1, # nolint
+ "VACSCORE", "BEST CORRECTED VISUAL ACUITY", "OVERALL EVALUATION", "Fellow Eye", "FBCVA", "Fellow Eye Visual Acuity Score (letters)", 2, # nolint
+)
+
Following this setup, the programmer can start constructing ADBCVA.
+The first step is to subset OE to only BCVA parameters and merge with
+ADSL. This is required for two reasons: firstly, STUDYEYE
+is crucial in the mapping of AFEYE and
+PARAMCD’s. Secondly, the treatment start date
+(TRTSDT) is also a prerequisite for the derivation of
+variables such as Analysis Day (ADY).
+
+adsl_vars <- exprs(TRTSDT, TRTEDT, TRT01A, TRT01P, STUDYEYE)
+
+adbcva <- oe %>%
+ filter(
+ OETESTCD %in% c("VACSCORE")
+ ) %>%
+ derive_vars_merged(
+ dataset_add = adsl,
+ new_vars = adsl_vars,
+ by_vars = exprs(STUDYID, USUBJID)
+ )
+
The next item of business is to derive AVAL,
+AVALU, and DTYPE. In this example, due to the
+small number of parameters their derivation is trivial.
+AFEYE is also created in this step using the function
+derive_var_afeye().
+
+
Moving forwards, PARAM and PARAMCD can be
+assigned using derive_vars_merged() from
+admiral and the lookup table param_lookup
+generated above.
+
+adbcva <- adbcva %>%
+ derive_vars_merged(
+ dataset_add = param_lookup,
+ new_vars = exprs(PARAM, PARAMCD),
+ by_vars = exprs(OETESTCD, AFEYE),
+ filter_add = PARAMCD %in% c("SBCVA", "FBCVA")
+ )
+
+
+
Deriving LogMAR Score Parameters
+
+
Often ADBCVA datasets contain derived records for BCVA in LogMAR
+units. This can easily be achieved as follows using
+derive_param_computed(). The conversion of units is done
+using convert_etdrs_to_logmar(). Two separate calls are
+required due to the parameters being split by study and fellow eye. Once
+these extra parameters are added, all the records that will be in the
+end dataset are now present, so AVALC and day/date
+variables such as ADY and ADT can be
+derived.
+
+adbcva <- adbcva %>%
+ derive_param_computed(
+ by_vars = c(exprs(STUDYID, USUBJID, VISIT, VISITNUM, OEDY, OEDTC, AFEYE), adsl_vars),
+ parameters = c("SBCVA"),
+ set_values_to = exprs(
+ AVAL = convert_etdrs_to_logmar(AVAL.SBCVA),
+ PARAMCD = "SBCVALOG",
+ PARAM = "Study Eye Visual Acuity LogMAR Score",
+ DTYPE = NA_character_,
+ AVALU = "LogMAR"
+ )
+ ) %>%
+ derive_param_computed(
+ by_vars = c(exprs(STUDYID, USUBJID, VISIT, OEDY, OEDTC, AFEYE), adsl_vars),
+ parameters = c("FBCVA"),
+ set_values_to = exprs(
+ AVAL = convert_etdrs_to_logmar(AVAL.FBCVA),
+ PARAMCD = "FBCVALOG",
+ PARAM = "Fellow Eye Visual Acuity LogMAR Score",
+ DTYPE = NA_character_,
+ AVALU = "LogMAR"
+ )
+ ) %>%
+ mutate(AVALC = as.character(AVAL)) %>%
+ derive_vars_dt(
+ new_vars_prefix = "A",
+ dtc = OEDTC,
+ flag_imputation = "none"
+ ) %>%
+ derive_vars_dy(reference_date = TRTSDT, source_vars = exprs(ADT))
+
Importantly, the above calls to derive_param_computed()
+list the SDTM variables VISIT, VISITNUM,
+OEDY and OEDTC as by_vars for the
+function. This is because they will be necessary to derive ADaM
+variables such as AVISIT and ADY in successive
+steps. Once all the ADaM variables which require them are derived, the
+SDTM variables should be set to missing for the derived records, as per
+ADaM standards:
+
+adbcva <- adbcva %>%
+ mutate(
+ VISIT = ifelse(PARAMCD %in% c("SBCVALOG", "FBCVALOG"), NA_character_, VISIT),
+ VISITNUM = ifelse(PARAMCD %in% c("SBCVALOG", "FBCVALOG"), NA, VISITNUM),
+ OEDY = ifelse(PARAMCD %in% c("SBCVALOG", "FBCVALOG"), NA, OEDY),
+ OEDTC = ifelse(PARAMCD %in% c("SBCVALOG", "FBCVALOG"), NA_character_, OEDTC)
+ )
+
+
+
Further Derivations of Standard BDS Variables
+
+
The user is invited to consult the article on creating
+a BDS dataset from SDTM to learn how to add standard BDS variables
+to ADBCVA. Henceforth, for the purposes of this article, the following
+sections use the ADBCVA dataset generated by the corresponding
+admiralophtha template program as a starting point.
+
Note: This dataset already comes with some criterion
+flags and analysis value categorisation variables, so for illustration
+purposes these are removed.
+
+
+
+
Deriving Analysis Value Categories for Snellen Scores
+
+
Some ophthalmology studies may desire to subdivide BCVA records
+according to which Snellen category they fall into (eg, 20/320, 20/100,
+20/20 etc). This is best done through the use of
+AVALCATx/AVALCAxN variable pairs. Currently,
+admiralophtha does not provide specific functionality to
+create AVALCATx/AVALCAxN pairs, although this
+may be included in future releases of the package. With the current
+toolset, the suggested approach to derive such variables is to:
+
+- Create a lookup table which assigns numeric equivalents
+(i.e.
AVALCAxN) to Snellen categories.
+- Create a format function to map each
AVAL to a numeric
+category.
+- Add
AVALCAxN through a mutate statement using the
+format function.
+- Add
AVALCATx using derive_vars_merged in
+combination with the lookup table.
+
+
+avalcat_lookup <- tibble::tribble(
+ ~PARAMCD, ~AVALCA1N, ~AVALCAT1,
+ "SBCVA", 1000, "< 20/800",
+ "SBCVA", 800, "20/800",
+ "SBCVA", 640, "20/640",
+ "SBCVA", 500, "20/500",
+ "SBCVA", 400, "20/400",
+ "SBCVA", 320, "20/320",
+ "SBCVA", 250, "20/250",
+ "SBCVA", 200, "20/200",
+ "SBCVA", 160, "20/160",
+ "SBCVA", 125, "20/125",
+ "SBCVA", 100, "20/100",
+ "SBCVA", 80, "20/80",
+ "SBCVA", 63, "20/63",
+ "SBCVA", 50, "20/50",
+ "SBCVA", 40, "20/40",
+ "SBCVA", 32, "20/32",
+ "SBCVA", 25, "20/25",
+ "SBCVA", 20, "20/20",
+ "SBCVA", 16, "20/16",
+ "SBCVA", 12, "20/12",
+ "SBCVA", 1, "> 20/12",
+)
+
+avalcat_lookup <- avalcat_lookup %>%
+ mutate(PARAMCD = "FBCVA") %>%
+ rbind(avalcat_lookup)
+
+format_avalcat1n <- function(param, aval) {
+ case_when(
+ param %in% c("SBCVA", "FBCVA") & aval >= 0 & aval <= 3 ~ 1000,
+ param %in% c("SBCVA", "FBCVA") & aval >= 4 & aval <= 8 ~ 800,
+ param %in% c("SBCVA", "FBCVA") & aval >= 9 & aval <= 13 ~ 640,
+ param %in% c("SBCVA", "FBCVA") & aval >= 14 & aval <= 18 ~ 500,
+ param %in% c("SBCVA", "FBCVA") & aval >= 19 & aval <= 23 ~ 400,
+ param %in% c("SBCVA", "FBCVA") & aval >= 24 & aval <= 28 ~ 320,
+ param %in% c("SBCVA", "FBCVA") & aval >= 29 & aval <= 33 ~ 250,
+ param %in% c("SBCVA", "FBCVA") & aval >= 34 & aval <= 38 ~ 200,
+ param %in% c("SBCVA", "FBCVA") & aval >= 39 & aval <= 43 ~ 160,
+ param %in% c("SBCVA", "FBCVA") & aval >= 44 & aval <= 48 ~ 125,
+ param %in% c("SBCVA", "FBCVA") & aval >= 49 & aval <= 53 ~ 100,
+ param %in% c("SBCVA", "FBCVA") & aval >= 54 & aval <= 58 ~ 80,
+ param %in% c("SBCVA", "FBCVA") & aval >= 59 & aval <= 63 ~ 63,
+ param %in% c("SBCVA", "FBCVA") & aval >= 64 & aval <= 68 ~ 50,
+ param %in% c("SBCVA", "FBCVA") & aval >= 69 & aval <= 73 ~ 40,
+ param %in% c("SBCVA", "FBCVA") & aval >= 74 & aval <= 78 ~ 32,
+ param %in% c("SBCVA", "FBCVA") & aval >= 79 & aval <= 83 ~ 25,
+ param %in% c("SBCVA", "FBCVA") & aval >= 84 & aval <= 88 ~ 20,
+ param %in% c("SBCVA", "FBCVA") & aval >= 89 & aval <= 93 ~ 16,
+ param %in% c("SBCVA", "FBCVA") & aval >= 94 & aval <= 97 ~ 12,
+ param %in% c("SBCVA", "FBCVA") & aval >= 98 ~ 1
+ )
+}
+
+adbcva <- adbcva %>%
+ mutate(AVALCA1N = format_avalcat1n(param = PARAMCD, aval = AVAL)) %>%
+ derive_vars_merged(
+ avalcat_lookup,
+ by = exprs(PARAMCD, AVALCA1N)
+ )
+
The resulting output is shown below (limited to the first patient
+only):
+
+
+
+
+
Deriving Criterion Flags for BCVA Change
+
+
admiralophtha suggests the use of criterion flag
+variable pairs (CRITx/CRITxFL) to program BCVA
+endpoints such as Avoiding a loss of x letters or Gain of y
+letters or Gain of between x and y letters (relative to
+baseline or other basetypes). The package provides the function
+derive_var_bcvacritxfl() to program these endpoints
+efficiently and consistently. In terms of the logic to apply to the
+variable CHG, the endpoints fall into three classes, which
+can be represented by inequalities:
+
+- Class 1:
CHG value lying inside a range,
+a <= CHG <= b.
+- Class 2:
CHG value below an upper limit,
+CHG <= a.
+- Class 3:
CHG value above a lower limit,
+CHG => b.
+
+
By using derive_var_bcvacritxfl(), the ADaM programmer
+can implement all three types of endpoint at once. This is achieved by
+feeding the appropriate ranges, upper limits and lower limits to the
+bcva_ranges, bcva_uplims and
+bcva_lowlims arguments of the function. For instance, let’s
+suppose that the endpoints of interest are:
+
+-
+Gain of between 5 and 10 letters relative to baseline
+(Class 1:
5 <= CHG <= 10)
+-
+Gain of 25 letters or fewer relative to baseline (Class 2:
+
CHG <= 25)
+-
+Loss of 5 letters or more relative to baseline (Class 2:
+
CHG <= -5)
+-
+Gain of 15 letters or more relative to baseline (Class 3:
+
CHG >= 15)
+-
+Loss of 10 letters or fewer relative to baseline (Class 3:
+
CHG >= -10).
+
+
Then, the following call will implement criterion variable/flag pairs
+for the endpoints above. The CRITx variables will
+automatically encode the correct inequality. Note that that
+restrict_derivation() is wrapped around the call so as to
+only derive the variables for the relevant parameters. In this way, the
+filter argument can be altered to restrict derivation to
+only relevant records. Note also that the argument
+crit_var = exprs(CHG) has to be specified so that the
+criterion flags are derived with respect to the correct variable.
+
+adbcva <- adbcva %>% restrict_derivation(
+ derivation = derive_var_bcvacritxfl,
+ args = params(
+ crit_var = exprs(CHG),
+ bcva_ranges = list(c(5, 10)),
+ bcva_uplims = list(25, -5),
+ bcva_lowlims = list(15, -10)
+ ),
+ filter = PARAMCD %in% c("SBCVA", "FBCVA")
+)
+
The resulting output is shown below (limited to the first patient
+only):
+
+
It is also possible to assign significance to the “x” in
+CRITxFL. For instance, one could designate all criterion
+flags of Class 1 as CRIT1yFL, Class 2 as
+CRIT2yFL, and Class 3 as CRIT3yFL. The
+argument critxfl_index allows a simple implementation of
+this in conjunction with three separate calls to
+derive_var_bcvacritxfl():
+
+adbcva <- adbcva %>%
+ restrict_derivation(
+ derivation = derive_var_bcvacritxfl,
+ args = params(
+ crit_var = exprs(CHG),
+ bcva_ranges = list(c(5, 10)),
+ critxfl_index = 10
+ ),
+ filter = PARAMCD %in% c("SBCVA", "FBCVA")
+ ) %>%
+ restrict_derivation(
+ derivation = derive_var_bcvacritxfl,
+ args = params(
+ crit_var = exprs(CHG),
+ bcva_uplims = list(25, -5),
+ critxfl_index = 20
+ ),
+ filter = PARAMCD %in% c("SBCVA", "FBCVA")
+ ) %>%
+ restrict_derivation(
+ derivation = derive_var_bcvacritxfl,
+ args = params(
+ crit_var = exprs(CHG),
+ bcva_lowlims = list(15, -10),
+ critxfl_index = 30
+ ),
+ filter = PARAMCD %in% c("SBCVA", "FBCVA")
+ )
+
+
+
Additional Notes
+
+
+When interpreting endpoints such as Loss of 5 letters or
+fewer relative to baseline, it is implicitly assumed in this
+article that this also includes the case where letters are
+gained, so that the inequality reads CHG >= -5.
+One would then use the bcva_lowlims = list(-5) argument of
+derive_var_bcvacritxfl() to program such an endpoint. If
+this is not the case, i.e. one wishes to exclude cases of letter gains,
+then the inequality of interest would instead be
+-5 <= CHG <= -1. Importantly,
+derive_var_bcvacritxfl() could still be used, but with the
+argument bcva_ranges = list(c(-5, -1)).
This vignette extensively showcases the use of
+derive_var_bcvacritxfl() applied to the variable
+CHG, but through the argument crit_var the
+function can also be used to create criterion flag relative to other
+variables (e.g. crit_var = exprs(AVAL) for
+AVAL).
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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@@ -2,7 +2,7 @@
// some helper functions: using a global object DTWidget so that it can be used
// in JS() code, e.g. datatable(options = list(foo = JS('code'))); unlike R's
-// dynamic scoping, when 'code' is eval()'ed, JavaScript does not know objects
+// dynamic scoping, when 'code' is eval'ed, JavaScript does not know objects
// from the "parent frame", e.g. JS('DTWidget') will not work unless it was made
// a global object
var DTWidget = {};
@@ -71,12 +71,20 @@ DTWidget.formatDate = function(data, method, params) {
window.DTWidget = DTWidget;
-// A helper function to update the lims of the existing filters
-var set_filter_lims = function(td, new_vals) {
+// A helper function to update the properties of existing filters
+var setFilterProps = function(td, props) {
+ // Update enabled/disabled state
+ var $input = $(td).find('input').first();
+ var searchable = $input.data('searchable');
+ $input.prop('disabled', !searchable || props.disabled);
+
// Based on the filter type, set its new values
- if (['factor', 'logical'].includes(td.getAttribute('data-type'))) {
+ var type = td.getAttribute('data-type');
+ if (['factor', 'logical'].includes(type)) {
// Reformat the new dropdown options for use with selectize
- new_vals = new_vals.map(function(item) {return {text: item, value: item}});
+ var new_vals = props.params.options.map(function(item) {
+ return { text: item, value: item };
+ });
// Find the selectize object
var dropdown = $(td).find('.selectized').eq(0)[0].selectize;
@@ -93,12 +101,16 @@ var set_filter_lims = function(td, new_vals) {
// Preserve the existing values
dropdown.setValue(old_vals);
- } else if (['number', 'integer', 'date', 'time'].includes(td.getAttribute('data-type'))) {
+ } else if (['number', 'integer', 'date', 'time'].includes(type)) {
+ // Apply internal scaling to new limits. Updating scale not yet implemented.
+ var slider = $(td).find('.noUi-target').eq(0);
+ var scale = Math.pow(10, Math.max(0, +slider.data('scale') || 0));
+ var new_vals = [props.params.min * scale, props.params.max * scale];
+
// Note what the new limits will be just for this filter
- var new_lims = [...new_vals];
+ var new_lims = new_vals.slice();
// Determine the current values and limits
- var slider = $(td).find('.noUi-target').eq(0);
var old_vals = slider.val().map(Number);
var old_lims = slider.noUiSlider('options').range;
old_lims = [old_lims.min, old_lims.max];
@@ -151,6 +163,13 @@ HTMLWidgets.widget({
type: "output",
renderOnNullValue: true,
initialize: function(el, width, height) {
+ // in order that the type=number inputs return a number
+ $.valHooks.number = {
+ get: function(el) {
+ var value = parseFloat(el.value);
+ return isNaN(value) ? "" : value;
+ }
+ };
$(el).html(' ');
return {
data: null,
@@ -406,13 +425,6 @@ HTMLWidgets.widget({
return $.inArray(val, $.makeArray(array)) > -1;
};
- // encode + to %2B when searching in the table on server side, because
- // shiny::parseQueryString() treats + as spaces, and DataTables does not
- // encode + to %2B (or % to %25) when sending the request
- var encode_plus = function(x) {
- return server ? x.replace(/%/g, '%25').replace(/\+/g, '%2B') : x;
- };
-
// search the i-th column
var searchColumn = function(i, value) {
var regex = false, ci = true;
@@ -420,7 +432,7 @@ HTMLWidgets.widget({
regex = options.search.regex,
ci = options.search.caseInsensitive !== false;
}
- return table.column(i).search(encode_plus(value), regex, !regex, ci);
+ return table.column(i).search(value, regex, !regex, ci);
};
if (data.filter !== 'none') {
@@ -429,7 +441,10 @@ HTMLWidgets.widget({
var $td = $(td), type = $td.data('type'), filter;
var $input = $td.children('div').first().children('input');
- $input.prop('disabled', !table.settings()[0].aoColumns[i].bSearchable || type === 'disabled');
+ var disabled = $input.prop('disabled');
+ var searchable = table.settings()[0].aoColumns[i].bSearchable;
+ $input.prop('disabled', !searchable || disabled);
+ $input.data('searchable', searchable); // for updating later
$input.on('input blur', function() {
$input.next('span').toggle(Boolean($input.val()));
});
@@ -478,7 +493,9 @@ HTMLWidgets.widget({
$input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus();
},
input: function() {
- if ($input.val() === '') filter[0].selectize.setValue([]);
+ var v1 = JSON.stringify(filter[0].selectize.getValue()), v2 = $input.val();
+ if (v1 === '[]') v1 = '';
+ if (v1 !== v2) filter[0].selectize.setValue(v2 === '' ? [] : JSON.parse(v2));
}
});
var $input2 = $x.children('select');
@@ -494,7 +511,7 @@ HTMLWidgets.widget({
if (value.length) $input.trigger('input');
$input.attr('title', $input.val());
if (server) {
- table.column(i).search(value.length ? encode_plus(JSON.stringify(value)) : '').draw();
+ table.column(i).search(value.length ? JSON.stringify(value) : '').draw();
return;
}
// turn off filter if nothing selected
@@ -808,6 +825,7 @@ HTMLWidgets.widget({
var disableCols = data.editable.disable ? data.editable.disable.columns : null;
var numericCols = data.editable.numeric;
var areaCols = data.editable.area;
+ var dateCols = data.editable.date;
for (var i = 0; i < target.length; i++) {
(function(cell, current) {
var $cell = $(cell), html = $cell.html();
@@ -817,6 +835,8 @@ HTMLWidgets.widget({
$input = $('
');
} else if (inArray(index, areaCols)) {
$input = $('
');
+ } else if (inArray(index, dateCols)) {
+ $input = $('
');
} else {
$input = $('
');
}
@@ -834,7 +854,7 @@ HTMLWidgets.widget({
if (immediate) $input.on('blur', function(e) {
var valueNew = $input.val();
- if (valueNew != value) {
+ if (valueNew !== value) {
_cell.data(valueNew);
if (HTMLWidgets.shinyMode) {
changeInput('cell_edit', [cellInfo(cell)], 'DT.cellInfo', null, {priority: 'event'});
@@ -1380,7 +1400,7 @@ HTMLWidgets.widget({
console.log('The search keyword for column ' + i + ' is undefined')
return;
}
- $(td).find('input').first().val(v);
+ $(td).find('input').first().val(v).trigger('input');
searchColumn(i, v);
});
table.draw();
@@ -1416,16 +1436,19 @@ HTMLWidgets.widget({
}
// update table filters (set new limits of sliders)
- methods.updateFilters = function(newLims) {
+ methods.updateFilters = function(newProps) {
// loop through each filter in the filter row
filterRow.each(function(i, td) {
var k = i;
- if (filterRow.length > newLims.length) {
+ if (filterRow.length > newProps.length) {
if (i === 0) return; // first column is row names
k = i - 1;
}
- // Update the filters to reflect the updated data
- set_filter_lims(td, newLims[k]);
+ // Update the filters to reflect the updated data.
+ // Allow "falsy" (e.g. NULL) to signify a no-op.
+ if (newProps[k]) {
+ setFilterProps(td, newProps[k]);
+ }
});
};
diff --git a/articles/adbcva_files/datatables-css-0.0.0/datatables-crosstalk.css b/articles/adbcva_files/datatables-css-0.0.0/datatables-crosstalk.css
new file mode 100644
index 00000000..bd1159c8
--- /dev/null
+++ b/articles/adbcva_files/datatables-css-0.0.0/datatables-crosstalk.css
@@ -0,0 +1,32 @@
+.dt-crosstalk-fade {
+ opacity: 0.2;
+}
+
+html body div.DTS div.dataTables_scrollBody {
+ background: none;
+}
+
+
+/*
+Fix https://github.com/rstudio/DT/issues/563
+If the `table.display` is set to "block" (e.g., pkgdown), the browser will display
+datatable objects strangely. The search panel and the page buttons will still be
+in full-width but the table body will be "compact" and shorter.
+In therory, having this attributes will affect `dom="t"`
+with `display: block` users. But in reality, there should be no one.
+We may remove the below lines in the future if the upstream agree to have this there.
+See https://github.com/DataTables/DataTablesSrc/issues/160
+*/
+
+table.dataTable {
+ display: table;
+}
+
+
+/*
+When DTOutput(fill = TRUE), it receives a .html-fill-item class (via htmltools::bindFillRole()), which effectively amounts to `flex: 1 1 auto`. That's mostly fine, but the case where `fillContainer=TRUE`+`height:auto`+`flex-basis:auto` and the container (e.g., a bslib::card()) doesn't have a defined height is a bit problematic since the table wants to fit the parent but the parent wants to fit the table, which results pretty small table height (maybe because there is a minimum height somewhere?). It seems better in this case to impose a 400px height default for the table, which we can do by setting `flex-basis` to 400px (the table is still allowed to grow/shrink when the container has an opinionated height).
+*/
+
+.html-fill-container > .html-fill-item.datatables {
+ flex-basis: 400px;
+}
diff --git a/devel/articles/adbcva_files/dt-core-1.11.3/css/jquery.dataTables.extra.css b/articles/adbcva_files/dt-core-1.13.4/css/jquery.dataTables.extra.css
similarity index 100%
rename from devel/articles/adbcva_files/dt-core-1.11.3/css/jquery.dataTables.extra.css
rename to articles/adbcva_files/dt-core-1.13.4/css/jquery.dataTables.extra.css
diff --git a/articles/adbcva_files/dt-core-1.13.4/css/jquery.dataTables.min.css b/articles/adbcva_files/dt-core-1.13.4/css/jquery.dataTables.min.css
new file mode 100644
index 00000000..aff1ca67
--- /dev/null
+++ b/articles/adbcva_files/dt-core-1.13.4/css/jquery.dataTables.min.css
@@ -0,0 +1 @@
+:root{--dt-row-selected: 13, 110, 253;--dt-row-selected-text: 255, 255, 255;--dt-row-selected-link: 9, 10, 11}table.dataTable td.dt-control{text-align:center;cursor:pointer}table.dataTable td.dt-control:before{height:1em;width:1em;margin-top:-9px;display:inline-block;color:white;border:.15em solid white;border-radius:1em;box-shadow:0 0 .2em #444;box-sizing:content-box;text-align:center;text-indent:0 !important;font-family:"Courier New",Courier,monospace;line-height:1em;content:"+";background-color:#31b131}table.dataTable tr.dt-hasChild td.dt-control:before{content:"-";background-color:#d33333}table.dataTable thead>tr>th.sorting,table.dataTable thead>tr>th.sorting_asc,table.dataTable thead>tr>th.sorting_desc,table.dataTable thead>tr>th.sorting_asc_disabled,table.dataTable thead>tr>th.sorting_desc_disabled,table.dataTable thead>tr>td.sorting,table.dataTable thead>tr>td.sorting_asc,table.dataTable thead>tr>td.sorting_desc,table.dataTable thead>tr>td.sorting_asc_disabled,table.dataTable thead>tr>td.sorting_desc_disabled{cursor:pointer;position:relative;padding-right:26px}table.dataTable thead>tr>th.sorting:before,table.dataTable thead>tr>th.sorting:after,table.dataTable thead>tr>th.sorting_asc:before,table.dataTable thead>tr>th.sorting_asc:after,table.dataTable thead>tr>th.sorting_desc:before,table.dataTable thead>tr>th.sorting_desc:after,table.dataTable thead>tr>th.sorting_asc_disabled:before,table.dataTable thead>tr>th.sorting_asc_disabled:after,table.dataTable thead>tr>th.sorting_desc_disabled:before,table.dataTable thead>tr>th.sorting_desc_disabled:after,table.dataTable thead>tr>td.sorting:before,table.dataTable thead>tr>td.sorting:after,table.dataTable thead>tr>td.sorting_asc:before,table.dataTable thead>tr>td.sorting_asc:after,table.dataTable thead>tr>td.sorting_desc:before,table.dataTable thead>tr>td.sorting_desc:after,table.dataTable thead>tr>td.sorting_asc_disabled:before,table.dataTable thead>tr>td.sorting_asc_disabled:after,table.dataTable thead>tr>td.sorting_desc_disabled:before,table.dataTable thead>tr>td.sorting_desc_disabled:after{position:absolute;display:block;opacity:.125;right:10px;line-height:9px;font-size:.8em}table.dataTable thead>tr>th.sorting:before,table.dataTable thead>tr>th.sorting_asc:before,table.dataTable thead>tr>th.sorting_desc:before,table.dataTable thead>tr>th.sorting_asc_disabled:before,table.dataTable thead>tr>th.sorting_desc_disabled:before,table.dataTable thead>tr>td.sorting:before,table.dataTable thead>tr>td.sorting_asc:before,table.dataTable thead>tr>td.sorting_desc:before,table.dataTable thead>tr>td.sorting_asc_disabled:before,table.dataTable thead>tr>td.sorting_desc_disabled:before{bottom:50%;content:"▲";content:"▲"/""}table.dataTable thead>tr>th.sorting:after,table.dataTable thead>tr>th.sorting_asc:after,table.dataTable thead>tr>th.sorting_desc:after,table.dataTable thead>tr>th.sorting_asc_disabled:after,table.dataTable thead>tr>th.sorting_desc_disabled:after,table.dataTable thead>tr>td.sorting:after,table.dataTable thead>tr>td.sorting_asc:after,table.dataTable thead>tr>td.sorting_desc:after,table.dataTable thead>tr>td.sorting_asc_disabled:after,table.dataTable thead>tr>td.sorting_desc_disabled:after{top:50%;content:"▼";content:"▼"/""}table.dataTable thead>tr>th.sorting_asc:before,table.dataTable thead>tr>th.sorting_desc:after,table.dataTable thead>tr>td.sorting_asc:before,table.dataTable thead>tr>td.sorting_desc:after{opacity:.6}table.dataTable thead>tr>th.sorting_desc_disabled:after,table.dataTable thead>tr>th.sorting_asc_disabled:before,table.dataTable thead>tr>td.sorting_desc_disabled:after,table.dataTable thead>tr>td.sorting_asc_disabled:before{display:none}table.dataTable thead>tr>th:active,table.dataTable thead>tr>td:active{outline:none}div.dataTables_scrollBody>table.dataTable>thead>tr>th:before,div.dataTables_scrollBody>table.dataTable>thead>tr>th:after,div.dataTables_scrollBody>table.dataTable>thead>tr>td:before,div.dataTables_scrollBody>table.dataTable>thead>tr>td:after{display:none}div.dataTables_processing{position:absolute;top:50%;left:50%;width:200px;margin-left:-100px;margin-top:-26px;text-align:center;padding:2px}div.dataTables_processing>div:last-child{position:relative;width:80px;height:15px;margin:1em auto}div.dataTables_processing>div:last-child>div{position:absolute;top:0;width:13px;height:13px;border-radius:50%;background:rgb(13, 110, 253);background:rgb(var(--dt-row-selected));animation-timing-function:cubic-bezier(0, 1, 1, 0)}div.dataTables_processing>div:last-child>div:nth-child(1){left:8px;animation:datatables-loader-1 .6s infinite}div.dataTables_processing>div:last-child>div:nth-child(2){left:8px;animation:datatables-loader-2 .6s 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th.dt-body-left,table.dataTable tbody td.dt-body-left{text-align:left}table.dataTable tbody th.dt-body-center,table.dataTable tbody td.dt-body-center{text-align:center}table.dataTable tbody th.dt-body-right,table.dataTable tbody td.dt-body-right{text-align:right}table.dataTable tbody th.dt-body-justify,table.dataTable tbody td.dt-body-justify{text-align:justify}table.dataTable tbody th.dt-body-nowrap,table.dataTable tbody td.dt-body-nowrap{white-space:nowrap}table.dataTable{width:100%;margin:0 auto;clear:both;border-collapse:separate;border-spacing:0}table.dataTable thead th,table.dataTable tfoot th{font-weight:bold}table.dataTable thead th,table.dataTable thead td{padding:10px;border-bottom:1px solid rgba(0, 0, 0, 0.3)}table.dataTable thead th:active,table.dataTable thead td:active{outline:none}table.dataTable tfoot th,table.dataTable tfoot td{padding:10px 10px 6px 10px;border-top:1px solid rgba(0, 0, 0, 0.3)}table.dataTable tbody tr{background-color:transparent}table.dataTable tbody 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new file mode 100644
index 00000000..c89263c6
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