t1kable_and_rendering.R

require(devtools)
#devtools::install_github("benjaminrich/table1")

library(boot) 
library(table1)
library(kableExtra)

melanoma2 <- melanoma

# Factor the basic variables that
# we're interested in
melanoma2$status <- 
  factor(melanoma2$status, 
         levels=c(2,1,3),
         labels=c("Alive", # Reference
                  "Melanoma death", 
                  "Non-melanoma death"))

# table1(~ factor(sex) + age + factor(ulcer) + thickness | status, data=melanoma2)

melanoma2$sex <- 
  factor(melanoma2$sex, levels=c(1,0),
         labels=c("Male", 
                  "Female"))

melanoma2$ulcer <- 
  factor(melanoma2$ulcer, levels=c(0,1),
         labels=c("Absent", 
                  "Present"))

label(melanoma2$sex)       <- "Sex"
label(melanoma2$age)       <- "Age"
label(melanoma2$ulcer)     <- "Ulceration"
label(melanoma2$thickness) <- "Thickness"

units(melanoma2$age)       <- "years"
units(melanoma2$thickness) <- "mm"

#table1(~ sex + age + ulcer + thickness | status, data=melanoma2, overall="Total")


labels <- list(
  variables=list(sex="Sex",
                 age="Age (years)",
                 ulcer="Ulceration",
                 thickness="Thickness (mm)"),
  groups=list("", "", "Death"))

# Remove the word "death" from the labels, since it now appears above
levels(melanoma2$status) <- c("Alive", "Melanoma", "Non-melanoma")


strata <- c(list(Total=melanoma2), split(melanoma2, melanoma2$status))


my.render.cont <- function(x) {
  with(stats.apply.rounding(stats.default(x), digits=2), c("",
                                                           "Mean (SD)"=sprintf("%s (&plusmn; %s)", MEAN, SD)))
}
my.render.cat <- function(x) {
  c("", sapply(stats.default(x), function(y) with(y,
                                                  sprintf("%d (%0.0f %%)", FREQ, PCT))))
}



rendered_table1_object  <- table1(strata, labels, groupspan=c(1, 1, 2),
       render.continuous=my.render.cont, render.categorical=my.render.cat)


rendered_kable <- t1kable(rendered_table1_object ,format='latex')
#Error in rbind(deparse.level, ...) : 
# numbers of columns of arguments do not match
save_kable(rendered_kable,'rendered_kable.tex')


# t1kable command would work without the rendering parameters
rendered_table1 <- table1(strata, labels, groupspan=c(1, 1, 2))

##########33

test1 <- table1(strata, labels, groupspan=c(1, 3, 1),
       render.continuous=c(.="Mean (CV%)", .="Median [Min, Max]",
                           "Geo. mean (Geo. CV%)"="GMEAN (GCV%)"))
sessionInfo()

# R version 4.2.0 (2022-04-22 ucrt)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 19044)
# 
# Matrix products: default
# 
# locale:
#   [1] LC_COLLATE=Finnish_Finland.utf8 
# [2] LC_CTYPE=Finnish_Finland.utf8   
# [3] LC_MONETARY=Finnish_Finland.utf8
# [4] LC_NUMERIC=C                    
# [5] LC_TIME=Finnish_Finland.utf8    
# 
# attached base packages:
#   [1] stats     graphics  grDevices utils     datasets  methods  
# [7] base     
# 
# other attached packages:
#   [1] kableExtra_1.3.4 boot_1.3-28      devtools_2.4.3  
# [4] usethis_2.1.5    table1_1.4.2    
# 
# loaded via a namespace (and not attached):
#   [1] compiler_4.2.0    prettyunits_1.1.1 remotes_2.4.2    
# [4] tools_4.2.0       testthat_3.1.4    digest_0.6.29    
# [7] pkgbuild_1.3.1    pkgload_1.2.4     viridisLite_0.4.0
# [10] evaluate_0.15     memoise_2.0.1     lifecycle_1.0.1  
# [13] rlang_1.0.2       cli_3.3.0         rstudioapi_0.13  
# [16] curl_4.3.2        xfun_0.30         fastmap_1.1.0    
# [19] stringr_1.4.0     xml2_1.3.3        httr_1.4.2       
# [22] withr_2.5.0       knitr_1.39        systemfonts_1.0.4
# [25] desc_1.4.1        fs_1.5.2          webshot_0.5.3    
# [28] rprojroot_2.0.3   svglite_2.1.0     glue_1.6.2       
# [31] R6_2.5.1          processx_3.5.3    rmarkdown_2.14   
# [34] sessioninfo_1.2.2 Formula_1.2-4     callr_3.7.0      
# [37] purrr_0.3.4       magrittr_2.0.3    scales_1.2.0     
# [40] ps_1.7.0          ellipsis_0.3.2    htmltools_0.5.2  
# [43] rvest_1.0.2       colorspace_2.0-3  stringi_1.7.6    
# [46] munsell_0.5.0     cachem_1.0.6      crayon_1.5.1     
# [49] brio_1.1.3