Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup, include=FALSE-----------------------------------------------------
library(tidyverse)
library(magrittr)
library(Tplyr)
library(knitr)
## ----missing------------------------------------------------------------------
tplyr_adsl$TRT01P <- as.factor(tplyr_adsl$TRT01P)
tplyr_adlb$TRTA <- as.factor(tplyr_adlb$TRTA)
tplyr_adlb_2 <- tplyr_adlb %>%
filter(TRTA != "Placebo")
tplyr_table(tplyr_adlb_2, TRTA) %>%
set_pop_data(tplyr_adsl) %>%
set_pop_treat_var(TRT01P) %>%
add_layer(
group_desc(AVAL, by=PARAMCD) %>%
set_format_strings('Mean (SD)' = f_str('xxx (xxx)', mean, sd))
) %>%
build() %>%
head() %>%
select(-starts_with("ord")) %>%
kable()
## ----missing1-----------------------------------------------------------------
tplyr_table(tplyr_adlb_2, TRTA) %>%
set_pop_data(tplyr_adsl) %>%
set_pop_treat_var(TRT01P) %>%
add_layer(
group_desc(AVAL, by=PARAMCD) %>%
set_format_strings('Mean (SD)' = f_str('xxx.xx (xxx.xxx)', mean, sd, empty=c(.overall="MISSING")))
) %>%
build() %>%
head() %>%
select(-starts_with("ord")) %>%
kable()
## ----missing2-----------------------------------------------------------------
tplyr_table(tplyr_adlb_2, TRTA) %>%
set_pop_data(tplyr_adsl) %>%
set_pop_treat_var(TRT01P) %>%
add_layer(
group_desc(AVAL, by=PARAMCD) %>%
set_format_strings('Mean (SD)' = f_str('xxx.xx (xxx.xxx)', mean, sd, empty=c("NA")))
) %>%
build() %>%
head() %>%
select(-starts_with("ord")) %>%
kable()
## ----autoprecision1-----------------------------------------------------------
tplyr_table(tplyr_adlb, TRTA) %>%
add_layer(
group_desc(AVAL, by = PARAMCD) %>%
set_format_strings(
'Mean (SD)' = f_str('a.a+1 (a.a+2)', mean, sd)
)
) %>%
build() %>%
head(20) %>%
select(-starts_with("ord")) %>%
kable()
## ----autoprecision2-----------------------------------------------------------
tplyr_table(tplyr_adlb, TRTA) %>%
add_layer(
group_desc(AVAL, by = PARAMCD) %>%
set_format_strings(
'Mean (SD)' = f_str('a.a+1 (a.a+2)', mean, sd),
cap = c(int=3, dec=2)
)
) %>%
build() %>%
head(20) %>%
select(-starts_with("ord")) %>%
kable()
## ----precision3---------------------------------------------------------------
tplyr_table(tplyr_adlb, TRTA) %>%
add_layer(
group_desc(vars(AVAL, CHG, BASE), by = PARAMCD) %>%
set_format_strings(
'Mean (SD)' = f_str('a.a+1 (a.a+2)', mean, sd, empty="NA"),
cap = c(int=3, dec=2)
) %>%
set_precision_on(AVAL) %>%
set_precision_by(PARAMCD)
) %>%
build() %>%
head() %>%
select(-starts_with("ord")) %>%
kable()
## ----external-precision-------------------------------------------------------
prec_data <- tibble::tribble(
~PARAMCD, ~max_int, ~max_dec,
"BUN", 1, 0,
"CA", 2, 4,
"CK", 3, 1,
"GGT", 3, 0,
"URATE", 3, 1,
)
tplyr_table(tplyr_adlb, TRTA) %>%
add_layer(
group_desc(AVAL, by = PARAMCD) %>%
set_format_strings(
'Mean (SD)' = f_str('a.a+1 (a.a+2)', mean, sd, empty="NA")
) %>%
set_precision_on(AVAL) %>%
set_precision_by(PARAMCD) %>%
set_precision_data(prec_data)
) %>%
build() %>%
head() %>%
select(-starts_with("ord")) %>%
kable()
## ----external-precision2------------------------------------------------------
prec_data <- tibble::tribble(
~PARAMCD, ~max_int, ~max_dec,
"BUN", 1, 0,
"CA", 2, 4,
"CK", 3, 1,
"GGT", 3, 0,
)
tplyr_table(tplyr_adlb, TRTA) %>%
add_layer(
group_desc(AVAL, by = PARAMCD) %>%
set_format_strings(
'Mean (SD)' = f_str('a.a+1 (a.a+2)', mean, sd, empty="NA")
) %>%
set_precision_on(AVAL) %>%
set_precision_by(PARAMCD) %>%
set_precision_data(prec_data, default="auto")
) %>%
build() %>%
head() %>%
select(-starts_with("ord")) %>%
kable()
## ----standard-----------------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_desc(AGE, by = "Age (years)", where= SAFFL=="Y") %>%
set_format_strings(
"n" = f_str("xx", n),
"Mean (SD)"= f_str("xx.x (xx.xx)", mean, sd),
"Median" = f_str("xx.x", median),
"Q1, Q3" = f_str("xx, xx", q1, q3),
"Min, Max" = f_str("xx, xx", min, max),
"Missing" = f_str("xx", missing)
)
) %>%
build() %>%
select(-starts_with('ord'))
## ----manual_hugging-----------------------------------------------------------
tplyr_table(tplyr_adlb, TRTA, PARAMCD == "CK") %>%
add_layer(
group_desc(AVAL, by=vars(PARAMCD, AVISIT)) %>%
set_format_strings(
TEST = f_str("xxx.x (XXX.x)", mean, sd, empty="NA")
) %>%
set_precision_by(PARAMCD)
) %>%
build() %>%
head() %>%
select(-starts_with('ord'))
## ----auto_hugging-------------------------------------------------------------
tplyr_table(tplyr_adlb, TRTA, PARAMCD == "CK") %>%
add_layer(
group_desc(AVAL, by=vars(PARAMCD, AVISIT)) %>%
set_format_strings(
TEST = f_str("a.a (A.a)", mean, sd, empty="NA")
) %>%
set_precision_by(PARAMCD)
) %>%
build() %>%
head() %>%
select(-starts_with('ord'))
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