In sbalci/histopathR: Template and R Codes Used in Histopathologic Research

Codes for cross tables.^[See childRmd/_12crossTables.Rmd file for other codes]

Cross Tables

library(finalfit)

dependent <- c("dependent1",
               "dependent2"
              )

explanatory <- c("explanatory1",
                 "explanatory2"
                 )

source(here::here("R", "gc_table_cross.R"))

CreateTableOne(vars = myVars, strata = "columnname", data = pbc, factorVars = catVars)

print(tab, nonnormal = biomarkers, exact = "exactVariable", smd = TRUE)

write2html(
  knitr::kable(head(mockstudy)), paste0(tmpdir, "/test.kable.keep.rmd.html"),
  quiet = TRUE, # passed to rmarkdown::render
  keep.rmd = TRUE
)

ctable(tobacco$gender, tobacco$smoker, style = 'rmarkdown')

print(ctable(tobacco$gender, tobacco$smoker), method = 'render')
print(ctable(tobacco$smoker, tobacco$diseased, prop = "r"), method = "render")
with(tobacco, 
     print(ctable(smoker, diseased, prop = 'n', totals = FALSE, chisq = TRUE),
           headings = FALSE, method = "render"))

# devtools::install_github("ewenharrison/summarizer")
# library(summarizer)
# data(colon_s)
explanatory = c("age", "age.factor", "sex.factor", "obstruct.factor")
dependent = "perfor.factor"
colon_s %>%
  summary.factorlist(dependent, explanatory, p=TRUE) %>% 
    knitr::kable(row.names=FALSE, align=c("l", "l", "r", "r", "r"))

explanatory = c("age.factor", "sex.factor", "obstruct.factor", "perfor.factor")
dependent = 'mort_5yr'
colon_s %>%
  summary.factorlist(dependent, explanatory) %>% 
    knitr::kable(row.names=FALSE, align=c("l", "l", "r", "r", "r"))

library(DT)
datatable(mtcars, rownames = FALSE, filter="top", options = list(pageLength = 5, scrollX=T) )

sbalci/histopathR documentation built on Nov. 12, 2024, 12:28 p.m.