Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup, include=FALSE-----------------------------------------------------
library(tidyverse)
library(magrittr)
library(Tplyr)
library(knitr)
## ----tplyr_table--------------------------------------------------------------
t <- tplyr_table(tplyr_adsl, TRT01P, where = SAFFL == "Y")
t
## ----tplyr_layer--------------------------------------------------------------
cnt <- group_count(t, AGEGR1)
cnt
dsc <- group_desc(t, AGE)
dsc
shf <- group_shift(t, vars(row=COMP8FL, column=COMP24FL))
shf
## ----add_layer----------------------------------------------------------------
t <- tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(AGEGR1, by = "Age categories n (%)")
)
## ----add_layer_with_piping----------------------------------------------------
t <- tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(AGEGR1, by = "Age categories n (%)") %>%
set_format_strings(f_str("xx (xx.x%)", n, pct)) %>%
add_total_row()
)
## ----add_layers---------------------------------------------------------------
t <- tplyr_table(tplyr_adsl, TRT01P)
l1 <- group_count(t, AGEGR1, by = "Age categories n (%)")
l2 <- group_desc(t, AGE, by = "Age (years)")
t <- add_layers(t, l1, l2)
## ----build--------------------------------------------------------------------
t <- tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(AGEGR1, by = "Age categories n (%)")
)
t %>%
build() %>%
kable()
## ----get_numeric_data---------------------------------------------------------
get_numeric_data(t) %>%
head() %>%
kable()
## ----format_strings_1---------------------------------------------------------
t <- tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_desc(AGE, by = "Age (years)") %>%
set_format_strings(
'n' = f_str('xx', n),
'Mean (SD)' = f_str('xx.xx (xx.xxx)', mean, sd)
)
)
t %>%
build() %>%
kable()
## ----format_strings_2---------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(AGEGR1, by = "Age categories") %>%
set_format_strings(f_str('xx (xx.x)',n,pct))
) %>%
build() %>%
kable()
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(AGEGR1, by = "Age categories") %>%
set_format_strings(f_str('xx',n))
) %>%
build() %>%
kable()
## ----format_strings_3---------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(AGEGR1, by = "Age categories") %>%
set_format_strings(f_str('xx (•◡•) xx.x%',n,pct))
) %>%
build() %>%
kable()
## ----desc1--------------------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_desc(AGE, by = "Age (years)")
) %>%
build() %>%
kable()
## ----custom_summaries---------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_desc(AGE, by = "Sepal Length") %>%
set_custom_summaries(
geometric_mean = exp(sum(log(.var[.var > 0]), na.rm=TRUE) / length(.var))
) %>%
set_format_strings(
'Geometric Mean (SD)' = f_str('xx.xx (xx.xxx)', geometric_mean, sd)
)
) %>%
build() %>%
kable()
## ----desc2--------------------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_desc(vars(AGE, AVGDD), by = "Age and Avg. Daily Dose")
) %>%
build() %>%
kable()
## ----count_total1-------------------------------------------------------------
tplyr_table(tplyr_adsl, TRT01P) %>%
add_layer(
group_count(AGEGR1, by = "Age categories") %>%
add_total_row()
) %>%
build() %>%
kable()
## ----count_distinct-----------------------------------------------------------
tplyr_table(tplyr_adae, TRTA) %>%
add_layer(
group_count('Subjects with at least one adverse event') %>%
set_distinct_by(USUBJID) %>%
set_format_strings(f_str('xx', n))
) %>%
build() %>%
kable()
## ----count_nested-------------------------------------------------------------
tplyr_table(tplyr_adae, TRTA) %>%
add_layer(
group_count(vars(AEBODSYS, AEDECOD))
) %>%
build() %>%
head() %>%
kable()
## ----shift1-------------------------------------------------------------------
# Tplyr can use factor orders to dummy values and order presentation
tplyr_adlb$ANRIND <- factor(tplyr_adlb$ANRIND, c("L", "N", "H"))
tplyr_adlb$BNRIND <- factor(tplyr_adlb$BNRIND, c("L", "N", "H"))
tplyr_table(tplyr_adlb, TRTA, where = PARAMCD == "CK") %>%
add_layer(
group_shift(vars(row=BNRIND, column=ANRIND), by=PARAM) %>%
set_format_strings(f_str("xx (xxx%)", n, pct))
) %>%
build() %>%
kable()
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