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130 DST01 sample data review #131

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merged 3 commits into from
Mar 11, 2022
Merged

130 DST01 sample data review #131

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d2403b9
correct format
Feb 4, 2022
6653b2d
Merge branch 'main' into 130_dst01-sample-data-review@main
Mar 10, 2022
c841d14
styler
Mar 10, 2022
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39 changes: 24 additions & 15 deletions R/dst01.R
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ dst01_1 <- function(adam_db,
deco = std_deco("DST01"),
.study = list(
armvar = "ARM",
lbl_overall = "All patients",
lbl_overall = "All Patients",
disc_reason_var = "DCSREAS"
)) {
check_dst01_1_args(
Expand Down Expand Up @@ -147,7 +147,7 @@ dst01_1_lyt <- function(armvar = .study$armvar,
deco = std_deco("DST01"),
.study = list(
armvar = "ARM",
lbl_overall = "All patients",
lbl_overall = "All Patients",
status = "EOSSTT",
disc_reason_var = "DCSREAS"
)) {
Expand All @@ -161,25 +161,28 @@ dst01_1_lyt <- function(armvar = .study$armvar,
count_values(
vars = status,
values = completed_lbl,
.labels = c(count_fraction = "Completed Study")
.labels = c(count_fraction = "Completed Study"),
.formats = "xx (xx.x%)"
)

layout_table_other <-
layout_table %>%
count_values(
vars = status,
values = ongoing_lbl,
.labels = c(count_fraction = "Ongoing Study")
.labels = c(count_fraction = "Ongoing"),
.formats = "xx (xx.x%)"
) %>%
split_rows_by(
status,
split_fun = keep_split_levels(discontinued_lbl),
) %>%
summarize_row_groups(label_fstr = "Discontinued Study") %>%
summarize_row_groups(label_fstr = "Discontinued Study", format = "xx (xx.x%)") %>%
summarize_vars(
disc_reason_var,
.stats = "count_fraction",
denom = "N_col"
denom = "N_col",
formats = "xx (xx.x%)"
)

list(layout_table_completed, layout_table_other)
Expand Down Expand Up @@ -231,7 +234,7 @@ dst01_2 <- function(adam_db,
deco = std_deco("DST01"),
.study = list(
armvar = "ARM",
lbl_overall = "All patients",
lbl_overall = "All Patients",
disc_reason_var = "DCSREAS"
)) {
check_dst01_1_args(
Expand Down Expand Up @@ -316,7 +319,7 @@ dst01_2_lyt <- function(armvar = .study$armvar,
deco = std_deco("DST01"),
.study = list(
armvar = "ARM",
lbl_overall = "All patients",
lbl_overall = "All Patients",
status = "EOSSTT",
disc_reason_var = "DCSREAS"
)) {
Expand All @@ -329,14 +332,16 @@ dst01_2_lyt <- function(armvar = .study$armvar,
count_values(
vars = status,
values = completed_lbl,
.labels = c(count_fraction = "Completed Study")
.labels = c(count_fraction = "Completed Study"),
.formats = "xx (xx.x%)"
)

layout_table_other <- layout_table %>%
count_values(
vars = status,
values = ongoing_lbl,
.labels = c(count_fraction = "Ongoing Study")
.labels = c(count_fraction = "Ongoing"),
.formats = "xx (xx.x%)"
) %>%
split_rows_by(
var = status,
Expand All @@ -345,13 +350,14 @@ dst01_2_lyt <- function(armvar = .study$armvar,
summarize_row_groups(label_fstr = "Discontinued Study") %>%
split_rows_by(
"reasonGP",
split_fun = reorder_split_levels(neworder = c("Safety", "Non Safety"))
split_fun = reorder_split_levels(neworder = c("Safety", "Non-safety"))
) %>%
summarize_row_groups() %>%
summarize_row_groups(format = "xx (xx.x%)") %>%
summarize_vars(
disc_reason_var,
.stats = "count_fraction",
denom = "N_col"
denom = "N_col",
formats = "xx (xx.x%)"
)

list(completed = layout_table_completed, other = layout_table_other)
Expand Down Expand Up @@ -408,7 +414,7 @@ dst01_3 <- function(adam_db,
.study = list(
armvar = "ARM",
disc_reason_var = "DCSREAS",
lbl_overall = "All patients"
lbl_overall = "All Patients"
)) {
check_dst01_1_args(
reason = disc_reason_var,
Expand Down Expand Up @@ -515,7 +521,7 @@ dst01_3_lyt <- function(armvar = .study$armvar,
deco = std_deco("DST01"),
.study = list(
armvar = "ARM",
lbl_overall = "All patients",
lbl_overall = "All Patients",
status_treatment = "EOTSTT"
)) {
layout_table <- basic_table_deco(deco) %>%
Expand All @@ -526,18 +532,21 @@ dst01_3_lyt <- function(armvar = .study$armvar,
vars = status_treatment,
values = completed_lbl,
.labels = c(count_fraction = "Completed Treatment"),
.formats = "xx (xx.x%)",
table_names = c("COMPLETED")
) %>%
count_values(
vars = status_treatment,
values = ongoing_lbl,
.labels = c(count_fraction = "Ongoing Treatment"),
.formats = "xx (xx.x%)",
table_names = c("ONGOING")
) %>%
count_values(
vars = status_treatment,
values = discontinued_lbl,
.labels = c(count_fraction = "Discontinued Treatment"),
.formats = "xx (xx.x%)",
table_names = c("DISCONTINUED")
)
}
2 changes: 1 addition & 1 deletion R/standard_data_preprocessing.R
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Expand Up @@ -366,7 +366,7 @@ mutate_adsl_gp <- function(adam_db,
mutate(reasonGP = case_when(
!!sym_reason %in% c("ADVERSE EVENT", "DEATH") ~ "Safety",
!!sym_reason == "<Missing>" ~ "<Missing>",
TRUE ~ "Non Safety"
TRUE ~ "Non-safety"
)) %>%
dm_update_zoomed()
}
Expand Down
4 changes: 2 additions & 2 deletions man/dst01_1.Rd
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4 changes: 2 additions & 2 deletions man/dst01_2.Rd
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4 changes: 2 additions & 2 deletions man/dst01_3.Rd
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