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Not sure why the visible=FALSE, does not drop the variables in the report

jagadishkatam opened this issue · comments

commented

library(Tplyr)
library(reporter)
library(tidyCDISC)

data(list=c('adsl','adae'), package='tidyCDISC')

adsl <- adsl %>% filter(SAFFL=='Y') %>% select(USUBJID, TRTA=TRT01A, TRTAN=TRT01AN)

adae <- adae %>% select(-c(TRTA, TRTAN)) %>% inner_join(adsl, by='USUBJID')

adae <- adae %>% select(USUBJID, TRTA, TRTAN, AEBODSYS, AEDECOD) %>% distinct() %>%
mutate(all='Subjects with any Adverse Events',
across(c(AEBODSYS, AEDECOD), ~ str_to_title(.)))

t <- Tplyr::tplyr_table(adae, TRTA) %>%
set_pop_data(adsl) %>%
set_pop_treat_var(TRTA) %>%
set_pop_where(TRUE) %>%
Tplyr::add_layer(group_count(all, by='Subjects with any Adverse Events')) %>%
set_distinct_by(USUBJID) %>%
Tplyr::add_layer(group_count(vars(AEBODSYS,AEDECOD))) %>%
set_distinct_by(USUBJID)

dt <- t %>% Tplyr::build() #%>% View()
dt <- dt %>% mutate(ord_layer_1=ifelse(row_number()!=1,ord_layer_1+1,ord_layer_1))

names(dt) <- str_replace_all(names(dt),'\s','_')

tbl <- create_table(dt, show_cols = 1:8) %>%
define(row_label1, visible = FALSE) %>%
define(row_label2, label = "", indent = .25) %>%
define(var1_Placebo, label = "Placebo", align = "center", n = 86) %>%
define(var1_Xanomeline_High_Dose, label = "Xanomeline High Dose", align = "center", n = 84) %>%
define(var1_Xanomeline_Low_Dose, label = "Xanomeline Low Dose", align = "center", n = 84) %>%
define(ord_layer_index, visible = FALSE) %>%
define(ord_layer_1, visible = FALSE) %>%
define(ord_layer_2, visible = FALSE)

pth <- file.path(tempdir(), "test1.rtf")

rpt <- create_report(pth,
output_type = "RTF",
orientation = "landscape") %>%
titles("Table 1.0",
"Adverse Events",
"Population: Safety") %>%
set_margins(top = 1, bottom = 1) %>%
add_content(tbl)

write_report(rpt)

commented

Hi @jagadishkatam,

It looks like this is a question on reporter and not Tplyr.

But looking at your code, the issue is using the show_cols argument in the create_table() function. It seems that this will override the visible=FALSE parameters withing define().

Try this:

tbl <- create_table(dt) %>%
  define(row_label1, visible = FALSE) %>%
  define(row_label2, label = "", indent = .25) %>%
  define(var1_Placebo, label = "Placebo", align = "center", n = 86) %>%
  define(var1_Xanomeline_High_Dose, label = "Xanomeline High Dose", align = "center", n = 84) %>%
  define(var1_Xanomeline_Low_Dose, label = "Xanomeline Low Dose", align = "center", n = 84) %>%
  define(ord_layer_index, visible = FALSE) %>%
  define(ord_layer_1, visible = FALSE) %>%
  define(ord_layer_2, visible = FALSE)
commented

Hi @mstackhouse,
Appreciate your prompt response, it worked for me as per your suggestion.

However i am struck with another issue, the 'subjects with any adverse events' does not align with adverse event counts and percentage. I am not sure of the reason.

I am using the same code as given earlier except for below update

tbl <- create_table(dt) %>%
define(row_label1, visible = FALSE) %>%
define(row_label2, label = "", indent = .25) %>%
define(var1_Placebo, label = "Placebo", align = "left", n = 86) %>%
define(var1_Xanomeline_High_Dose, label = "Xanomeline High Dose", align = "left", n = 84) %>%
define(var1_Xanomeline_Low_Dose, label = "Xanomeline Low Dose", align = "left", n = 84) %>%
define(ord_layer_index, visible = FALSE) %>%
define(ord_layer_1, visible = FALSE, blank_after = TRUE) %>%
define(ord_layer_2, visible = FALSE)

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