In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(ClinicoPath)

data("histopathology")

#| glimpse histopathology

dplyr::glimpse(histopathology)

ClinicoPath::survival(
    data = histopathology,
    elapsedtime = "OverallTime",
    tint = TRUE,
    dxdate = SurgeryDate,
    fudate = LastFollowUpDate,
    explanatory = LVI,
    outcome = Outcome,
    outcomeLevel = NULL,
    dod = NULL,
    dooc = NULL,
    awd = NULL,
    awod = NULL,
    timetypedata = "ymdhms",
    sc = TRUE,
    ce = TRUE,
    ch = TRUE
    )

overall_survival <-
ClinicoPath::survival(
    data = histopathology,
    elapsedtime = "OverallTime",
    tint = TRUE,
    dxdate = SurgeryDate,
    fudate = LastFollowUpDate,
    explanatory = LVI,
    outcome = Outcome,
    outcomeLevel = NULL,
    dod = NULL,
    dooc = NULL,
    awd = NULL,
    awod = NULL,
    timetypedata = "ymdhms",
    sc = TRUE,
    ce = TRUE,
    ch = TRUE
    )

ls(overall_survival)

overall_survival$tCoxtext2

overall_survival$survTableSummary

overall_survival$survTable

overall_survival$subtitle

overall_survival$plot3

overall_survival$plot2

overall_survival$plot

overall_survival$medianTable

overall_survival$medianSummary

overall_survival$coxTable

overall_survival$coxTable$asDF

overall_survival$coxSummary

overall_survival$plot

# overall_survival$plot$saveAs("overall_survival.png")
# 
# overall_survival <- png::readPNG("overall_survival.png")
# 
# tiff::writeTIFF(what = overall_survival, where = "overall_survival.tiff", compression = "none")

# htmlTable::htmlTable(
#   kableExtra::kable(
#     overall_survival$coxTable$asDF
#     ))

All functions

histopathology

histopathology

jsurvival-package _PACKAGE jsurvival

jsurvival: Analysis for jsurvivalological Research

multisurvival()

Multivariable Survival Analysis

multisurvivalClass

Multivariable Survival Analysis

oddsratio()

Odds Ratio Table and Plot

oddsratioClass

Odds Ratio Table and Plot

singlearm()

Single Arm Survival

singlearmClass

Single Arm Survival

survival()

Survival Analysis

survivalClass

Survival Analysis

survivalcont()

Survival Analysis for Continuous Variable

survivalcontClass

Survival Analysis for Continuous Explanatory Variable Contents

Reference

sbalci/ClinicoPathJamoviModule documentation built on Feb. 25, 2025, 6:34 a.m.