Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup, include=FALSE-----------------------------------------------------
library(dplyr)
library(tidyr)
library(magrittr)
library(Tplyr)
library(knitr)
## ----table_creation-----------------------------------------------------------
t <- tplyr_table(tplyr_adsl, TRT01P, where = SAFFL == "Y") %>%
add_layer(
group_count(RACE)
) %>%
add_layer(
group_desc(AGE, where = EFFFL == "Y")
)
dat <- t %>% build(metadata=TRUE)
kable(dat)
## ----meta_subset--------------------------------------------------------------
get_meta_subset(t, 'c2_1', 'var1_Placebo') %>%
kable()
## ----add_vars-----------------------------------------------------------------
get_meta_subset(t, 'c2_1', 'var1_Placebo', add_cols = vars(USUBJID, SEX)) %>%
kable()
## ----desc_stats---------------------------------------------------------------
get_meta_subset(t, 'd1_2', 'var1_Xanomeline High Dose') %>%
head(10) %>%
kable()
## ----tplyr_meta---------------------------------------------------------------
get_meta_result(t, 'd1_2', 'var1_Xanomeline High Dose')
## ----unpack-------------------------------------------------------------------
m <- get_meta_result(t, 'd1_2', 'var1_Xanomeline High Dose')
tplyr_adsl %>%
filter(!!!m$filters) %>%
select(!!!m$names) %>%
head(10) %>%
kable()
## ----to string print, eval=FALSE----------------------------------------------
# cat(c("tplyr_adsl %>%\n",
# " filter(\n ",
# paste(purrr::map_chr(m$filters, ~ rlang::as_label(.)), collpase=",\n "),
# ") %>%\n",
# paste(" select(", paste(purrr::map_chr(m$names, rlang::as_label), collapse=", "), ")", sep="")
# ))
## ----anti_join1---------------------------------------------------------------
t <- tplyr_table(tplyr_adae, TRTA) %>%
set_pop_data(tplyr_adsl) %>%
set_pop_treat_var(TRT01A) %>%
add_layer(
group_count(vars(AEBODSYS, AEDECOD)) %>%
set_distinct_by(USUBJID) %>%
add_missing_subjects_row(f_str("xx (XX.x%)", distinct_n, distinct_pct), sort_value = Inf)
)
x <- build(t, metadata=TRUE)
tail(x) %>%
select(starts_with('row'), var1_Placebo) %>%
kable()
## ----anti_join2---------------------------------------------------------------
m <- get_meta_result(t, 'c23_1', 'var1_Placebo')
m
## ----anti_join3---------------------------------------------------------------
head(get_meta_subset(t, 'c23_1', 'var1_Placebo'))
## ----anti_join4---------------------------------------------------------------
head(get_meta_subset(t$metadata, 'c23_1', 'var1_Placebo',
target=t$target, pop_data=t$pop_data))
## ----to string content, results='asis', echo=FALSE----------------------------
cat(c("tplyr_adsl %>%\n",
" filter(\n ",
paste(purrr::map_chr(m$filters, ~ rlang::as_label(.)), collpase=",\n "),
") %>%\n",
paste(" select(", paste(purrr::map_chr(m$names, rlang::as_label), collapse=", "), ")", sep="")
))
## ---- out.width=850, out.extra='style="border: 1px solid #464646;" allowfullscreen="" allow="autoplay"', echo=FALSE----
knitr::include_app("https://michael-stackhouse.shinyapps.io/Tplyr-shiny-demo/", height = "900px")
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