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fix bug for check population and observation grouping NA #137

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merged 4 commits into from
Mar 27, 2023
Merged

fix bug for check population and observation grouping NA #137

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98b2b48
fix bug for check population and observation grouping NA
wangben718 Mar 24, 2023
ca03e52
Style code
wangben718 Mar 24, 2023
c9b1ccf
Generate snapshots with latest r2rtf version on CRAN
nanxstats Mar 24, 2023
cbcb7b4
remove comment out code
wangben718 Mar 24, 2023
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51 changes: 25 additions & 26 deletions R/prepare_ae_specific.R
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Original file line number Diff line number Diff line change
Expand Up @@ -49,32 +49,6 @@ prepare_ae_specific <- function(meta,
parameter,
components = c("soc", "par"),
reference_group = NULL) {
# Check if the grouping variable is missing
pop_grp <- vapply(meta$population, "[[", FUN.VALUE = character(1), "group")
obs_grp <- vapply(meta$population, "[[", FUN.VALUE = character(1), "group")
grp <- unique(c(pop_grp, obs_grp))

for (i in seq(grp)) {
if (any(is.na(meta$data_population[[grp[i]]]))) {
stop(
paste0(
"There are >= 1 subjects with missing grouping variable '", grp[i],
"' in the population dataset."
),
call. = FALSE
)
}
if (any(is.na(meta$data_observation[[grp[i]]]))) {
stop(
paste0(
"There are >= 1 subjects with missing grouping variable '", grp[i],
"' in the observation dataset."
),
call. = FALSE
)
}
}

# Obtain variables
pop_var <- collect_adam_mapping(meta, population)$var
obs_var <- collect_adam_mapping(meta, observation)$var
Expand All @@ -93,6 +67,31 @@ prepare_ae_specific <- function(meta,
pop_group <- collect_adam_mapping(meta, population)$group
obs_group <- collect_adam_mapping(meta, observation)$group

# Check if the grouping variable is missing
# pop_grp <- vapply(meta$population, "[[", FUN.VALUE = character(1), "group")
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Please don't have commented out code.

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Please don't have commented out code.

I haved removed the code. Thanks for review!

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Hi @nanxstats , since @wangben718 already removed the comments, I directly merged this PR to the master, considering there are two teammates who need the package for slide preparation early this week...

# obs_grp <- vapply(meta$population, "[[", FUN.VALUE = character(1), "group")
# grp <- unique(c(pop_grp, obs_grp))


if (any(is.na(pop[[pop_group]]))) {
stop(
paste0(
"There are >= 1 subjects with missing grouping variable '", pop_group,
"' in the population dataset."
),
call. = FALSE
)
}
if (any(is.na(obs[[obs_group]]))) {
stop(
paste0(
"There are >= 1 subjects with missing grouping variable '", obs_group,
"' in the observation dataset."
),
call. = FALSE
)
}

# Ensure group is a factor
if (!"factor" %in% class(pop[[pop_group]])) {
warning("In population level data, force group variable '", pop_group, "' be a factor")
Expand Down
26 changes: 0 additions & 26 deletions R/prepare_ae_summary.R
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Original file line number Diff line number Diff line change
Expand Up @@ -38,32 +38,6 @@ prepare_ae_summary <- function(meta,
observation,
parameter,
...) {
# Check if the grouping variable is missing
pop_grp <- vapply(meta$population, "[[", FUN.VALUE = character(1), "group")
obs_grp <- vapply(meta$population, "[[", FUN.VALUE = character(1), "group")
grp <- unique(c(pop_grp, obs_grp))

for (i in seq(grp)) {
if (any(is.na(meta$data_population[[grp[i]]]))) {
stop(
paste0(
"There are >= 1 subjects with missing grouping variable '", grp[i],
"' in the population dataset."
),
call. = FALSE
)
}
if (any(is.na(meta$data_observation[[grp[i]]]))) {
stop(
paste0(
"There are >= 1 subjects with missing grouping variable '", grp[i],
"' in the observation dataset."
),
call. = FALSE
)
}
}

parameters <- unlist(strsplit(parameter, ";"))

res <- lapply(parameters, function(x) {
Expand Down