In modelistatistik/deneme: Template of R Codes Used in Histopathology Research

mydata$int <- lubridate::interval(
  lubridate::ymd(mydata$CerrahiTarih),
  lubridate::ymd(mydata$SonTarih)
  )
mydata$OverallTime <- lubridate::time_length(mydata$int, "month")
mydata$OverallTime <- round(mydata$OverallTime, digits = 1)

mydata$OverallTime <- mydata$genel_sagkalim

## Recoding mydata$Outcome into mydata$Outcome2
mydata$Outcome2 <- recode(mydata$Outcome,
               "Alive" = "0",
               "Dead" = "1")
mydata$Outcome2 <- as.numeric(mydata$Outcome2)

Survival Analysis

library(survival)
km <- with(mydata, Surv(OverallTime, Outcome2))
# head(km,80)
# plot(km)

dependentKM <-  "Surv(OverallTime, Outcome2)"

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

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

mydependent <-  "Surv(time, status)"
explanatory <- "Organ"

mysurvival <- function(mydata, mydependent, explanatory) {
    {{mydata}} %>%
        finalfit::surv_plot(dependent = {{mydependent}},
                            explanatory = {{explanatory}},
                            xlab='Time (months)',
                            pval=TRUE,
                            legend = 'none',
                            break.time.by = 12,
                            xlim = c(0,60)
        )
}


library(tidyverse)
mysurvival(mydata = whippleables, mydependent = mydependent, explanatory = explanatory)

explanatory <- c("Organ", "LVI")

deneme <- purrr::map(explanatory, mysurvival, mydata = whippleables, mydependent = mydependent)

Pairwise comparison

survminer::pairwise_survdiff(formula = Surv(time, Outcome) ~ ShellAnteriorOnly, 
                             data = mydata,
                             p.adjust.method = "BH")

Multivariate Analysis Survival

library(finalfit)
library(survival)
explanatoryMultivariate <- explanatoryKM
dependentMultivariate <- dependentKM

mydata %>%
  finalfit(dependentMultivariate, explanatoryMultivariate) -> tMultivariate

knitr::kable(tMultivariate, row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))