Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- include = FALSE, setup--------------------------------------------------
library(Tplyr)
library(dplyr, warn.conflicts = FALSE)
library(knitr)
## -----------------------------------------------------------------------------
tplyr_table(tplyr_adae, TRTA) %>%
add_layer(
group_count(AEDECOD) %>%
set_distinct_by(USUBJID) %>%
set_format_strings(f_str('xx (xx.x%)', distinct_n, distinct_pct))
) %>%
build() %>%
head() %>%
kable()
## -----------------------------------------------------------------------------
tplyr_table(tplyr_adae, TRTA) %>%
set_pop_data(tplyr_adsl) %>%
set_pop_treat_var(TRT01A) %>%
add_layer(
group_count(AEDECOD) %>%
set_distinct_by(USUBJID) %>%
set_format_strings(f_str('xx (xx.x%)', distinct_n, distinct_pct))
) %>%
build() %>%
head() %>%
kable()
## -----------------------------------------------------------------------------
tplyr_adsl <- tplyr_adsl %>%
mutate(DCSREAS = ifelse(DCSREAS == '', 'Completed', DCSREAS))
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(DCSREAS)
) %>%
build() %>%
kable()
## -----------------------------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(DCSREAS, by=SEX)
) %>%
build() %>%
kable()
## -----------------------------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(DCSREAS, by=SEX) %>%
set_denoms_by(SEX, TRT01P)
) %>%
build() %>%
kable()
## -----------------------------------------------------------------------------
tplyr_table(tplyr_adlb, TRTA, where=PARAMCD == "CK") %>%
add_layer(
group_shift(vars(row = BNRIND, column = ANRIND), by = vars(PARAM, AVISIT)) %>%
set_format_strings(f_str("xx (xxx.x%)", n, pct)) %>%
# This is the default, the 3x3 box formed by the target variables
set_denoms_by(TRTA, PARAM, AVISIT)
) %>%
build() %>%
kable()
## -----------------------------------------------------------------------------
tplyr_table(tplyr_adlb, TRTA, where=PARAMCD == "CK") %>%
add_layer(
group_shift(vars(row = BNRIND, column = ANRIND), by = vars(PARAM, AVISIT)) %>%
set_format_strings(f_str("xx (xxx.x%)", n, pct)) %>%
set_denoms_by(TRTA, PARAM, AVISIT, BNRIND) # Each row made by TRTA, BNRIND
) %>%
build() %>%
arrange(ord_layer_1, ord_layer_2, ord_layer_3) %>%
head() %>%
kable()
## -----------------------------------------------------------------------------
tplyr_table(tplyr_adlb, TRTA, where = PARAMCD == "CK") %>%
add_layer(
group_shift(vars(row = BNRIND, column = ANRIND), by = vars(PARAM, AVISIT)) %>%
set_format_strings(f_str("xx (xx.xx%)", n, pct)) %>%
set_denoms_by(TRTA, ANRIND) # Use the column total as the denominator
) %>%
build() %>%
arrange(ord_layer_1, ord_layer_2, ord_layer_3) %>%
head() %>%
kable()
## -----------------------------------------------------------------------------
tplyr_adsl2 <- tplyr_adsl %>%
mutate(DISCONTEXT = if_else(DISCONFL == 'Y', 'DISCONTINUED', 'COMPLETED'))
t <- tplyr_table(tplyr_adsl2, TRT01P, where = SAFFL == 'Y') %>%
add_layer(
group_count(DISCONTEXT)
) %>%
add_layer(
group_count(DCSREAS, where = DISCONFL == 'Y')
) %>%
add_layer(
group_count(DCSREAS, where = DISCONFL == 'Y') %>%
set_denom_where(TRUE)
) %>%
build() %>%
arrange(ord_layer_index, ord_layer_1)
t %>%
kable()
## -----------------------------------------------------------------------------
tplyr_adae2 <- tplyr_adae
tplyr_adae2[sample(nrow(tplyr_adae2), 50), "AESEV"] <- NA
t <- tplyr_table(tplyr_adae2, TRTA) %>%
add_layer(
group_count(AESEV) %>%
set_format_strings(f_str("xxx (xx.xx%)", n, pct)) %>%
set_missing_count(f_str("xxx", n), sort_value=Inf, denom_ignore=TRUE, Missing = NA)
) %>%
build() %>%
arrange(ord_layer_1)
t %>%
kable()
## ----missing_subs1------------------------------------------------------------
missing_subs <- tplyr_table(tplyr_adae, TRTA) %>%
set_pop_data(tplyr_adsl) %>%
set_pop_treat_var(TRT01A) %>%
add_layer(
group_count(vars(AEBODSYS, AEDECOD)) %>%
set_nest_count(TRUE) %>%
set_distinct_by(USUBJID) %>%
add_missing_subjects_row(f_str("xx (XX.x%)", distinct_n, distinct_pct), sort_value = Inf) %>%
set_missing_subjects_row_label("Missing Subjects")
) %>%
build()
tail(missing_subs) %>%
select(-starts_with('ord')) %>%
kable()
## -----------------------------------------------------------------------------
tplyr_adsl2 <- tplyr_adsl
tplyr_adsl2[sample(nrow(tplyr_adsl2), 50), "AGEGR1"] <- NA
tplyr_table(tplyr_adsl2, TRT01P) %>%
add_layer(
group_count(AGEGR1, by=SEX) %>%
set_denoms_by(TRT01P, SEX) %>% # This gives me a Total row each group
add_total_row(f_str("xxx", n), count_missings=TRUE, sort_value=-Inf) %>%
set_total_row_label("All Age Groups") %>%
set_missing_count(f_str("xx (xx.x%)", n, pct), Missing = NA, sort_value=Inf)
) %>%
build() %>%
arrange(ord_layer_1, ord_layer_2) %>%
kable()
## -----------------------------------------------------------------------------
tplyr_table(tplyr_adsl2, TRT01P) %>%
add_layer(
group_count(AGEGR1, by=SEX) %>%
set_denoms_by(TRT01P, SEX) %>% # This gives me a Total row each group
add_total_row(f_str("xxx", n), count_missings=FALSE, sort_value=-Inf) %>%
set_total_row_label("All Age Groups") %>%
set_missing_count(f_str("xxx", n), Missing = NA, sort_value=Inf, denom_ignore=TRUE)
) %>%
build() %>%
arrange(ord_layer_1, ord_layer_2) %>%
kable()
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