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Fix bug for multiple variables in observation #46

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Merged
wangben718 merged 2 commits into from
Dec 10, 2025
Merged

Fix bug for multiple variables in observation #46

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ab59560
Fix bug for multiple variables in observation
fukuhiro2023 Dec 5, 2025
f48a7bd
Style code (GHA)
fukuhiro2023 Dec 5, 2025
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15 changes: 8 additions & 7 deletions R/meta_boxly.R
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Original file line number Diff line number Diff line change
Expand Up @@ -41,13 +41,14 @@
#' observation_term = "wk12"
#' )
meta_boxly <- function(
dataset_adsl,
dataset_param,
population_term,
population_subset = SAFFL == "Y",
observation_term,
observation_subset = SAFFL == "Y",
parameters = unique(dataset_param$PARAMCD)) {
dataset_adsl,
dataset_param,
population_term,
population_subset = SAFFL == "Y",
observation_term,
observation_subset = SAFFL == "Y",
parameters = unique(dataset_param$PARAMCD)
) {
# Input Checking
require_param <- c("PARAM", "PARAMCD", "AVISITN", "CHG")

Expand Down
27 changes: 21 additions & 6 deletions R/prepare_boxly.R
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@
#' The term name is used as key to link information.
#' @param analysis A character value of analysis term name.
#' The term name is used as key to link information.
#' @param filter_var A character value of variable name used for filtering.
#' Default is "PARAM".
#' @param hover_var_outlier A character vector of hover variables for outlier.
#'
#' @return Metadata list with plotting dataset.
Expand All @@ -48,6 +50,7 @@ prepare_boxly <- function(meta,
population = NULL,
observation = NULL,
analysis = NULL,
filter_var = "PARAM",
hover_var_outlier = c("USUBJID", metalite::collect_adam_mapping(meta, analysis)$y)) {
if (is.null(population)) {
if (length(meta$population) == 1) {
Expand Down Expand Up @@ -109,11 +112,23 @@ prepare_boxly <- function(meta,
obs[[obs_group]] <- factor(obs[[obs_group]], levels = sort(unique(obs[[obs_group]])))
}

if (!"factor" %in% class(obs[[obs_var]])) {
message("In observation level data, the facet variable '", obs_var, "' is automatically transformed into a factor.")
obs[[obs_var]] <- factor(obs[[obs_var]], levels = sort(unique(obs[[obs_var]])))
if (!filter_var %in% obs_var) {
stop(paste(
"The filter variable '", filter_var, "' is not found in the observation data.",
Comment on lines +116 to +117
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Copilot AI Dec 5, 2025

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The error message uses inconsistent spacing in the paste() function, resulting in extra spaces around the filter variable name in the output. Remove the trailing space after the filter_var placeholder:

stop(paste(
  "The filter variable '", filter_var, "' is not found in the observation data.",
  "Please check the metadata for observation and `filter_var`."
))

Should be:

stop(paste0(
  "The filter variable '", filter_var, "' is not found in the observation data. ",
  "Please check the metadata for observation and `filter_var`."
))

Using paste0() gives better control over spacing.

Suggested change
stop(paste(
"The filter variable '", filter_var, "' is not found in the observation data.",
stop(paste0(
"The filter variable '", filter_var, "' is not found in the observation data. ",

Copilot uses AI. Check for mistakes.
"Please check the metadata for observation and `filter_var`."
))
}

obs[, obs_var] <- lapply(obs_var, function(var) {
x <- obs[[var]]
if (!is.factor(x)) {
message("In observation level data, the facet variable '", var, "' is automatically transformed into a factor.")
factor(x, levels = sort(unique(x)))
} else {
x
}
})
Comment on lines +122 to +130
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Copilot AI Dec 5, 2025

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The assignment obs[, obs_var] <- lapply(...) will create a list column in the data frame instead of properly updating the individual columns. This is because lapply() returns a list, and assigning a list to multiple columns creates a single list-column.

To fix this, use a loop to assign each column individually:

for (var in obs_var) {
  x <- obs[[var]]
  if (!is.factor(x)) {
    message("In observation level data, the facet variable '", var, "' is automatically transformed into a factor.")
    obs[[var]] <- factor(x, levels = sort(unique(x)))
  }
}

Alternatively, use obs[obs_var] <- lapply(...) (without the comma) to properly assign the list elements to respective columns.

Suggested change
obs[, obs_var] <- lapply(obs_var, function(var) {
x <- obs[[var]]
if (!is.factor(x)) {
message("In observation level data, the facet variable '", var, "' is automatically transformed into a factor.")
factor(x, levels = sort(unique(x)))
} else {
x
}
})
for (var in obs_var) {
x <- obs[[var]]
if (!is.factor(x)) {
message("In observation level data, the facet variable '", var, "' is automatically transformed into a factor.")
obs[[var]] <- factor(x, levels = sort(unique(x)))
}
}

Copilot uses AI. Check for mistakes.

if (!"factor" %in% class(obs[[x]])) {
message("In observation level data, the group variable '", x, "' is automatically transformed into a factor.")
obs[[x]] <- factor(obs[[x]], levels = sort(unique(obs[[x]])))
Expand Down Expand Up @@ -163,8 +178,8 @@ prepare_boxly <- function(meta,
ans
}
},
split(tbl, list(tbl[[obs_var]], tbl[[obs_group]], tbl[[x]])),
names(split(tbl, list(tbl[[obs_var]], tbl[[obs_group]], tbl[[x]]), sep = ", ")),
split(tbl, tbl[, c(obs_var, obs_group, x)]),
names(split(tbl, tbl[, c(obs_var, obs_group, x)], sep = ", ")),
SIMPLIFY = FALSE
)

Expand Down Expand Up @@ -198,7 +213,7 @@ prepare_boxly <- function(meta,
# Return value
metalite::outdata(meta, population, observation, parameter,
x_var = x, y_var = y, group_var = obs_group,
param_var = obs_var, hover_var_outlier = hover_var_outlier,
param_var = filter_var, hover_var_outlier = hover_var_outlier,
n = n_tbl, order = NULL, group = NULL, reference_group = NULL,
plotds = plotds
)
Expand Down
4 changes: 4 additions & 0 deletions man/prepare_boxly.Rd
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