Introduce jstable

In jstable: Create Tables from Different Types of Regression

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = TRUE, message = F, warning = F
)
library(jstable)

Regression Tables from 'GLM', 'GEE', 'GLMM', 'Cox' and 'survey' Results for Publication.

Install

remotes::install_github('jinseob2kim/jstable')
library(jstable)

GLM Table

## Gaussian
glm_gaussian <- glm(mpg~cyl + disp, data = mtcars)
glmshow.display(glm_gaussian, decimal = 2)

## Binomial
glm_binomial <- glm(vs~cyl + disp, data = mtcars, family = binomial)
glmshow.display(glm_binomial, decimal = 2)

GEE Table: from geeglm object from geepack package

library(geepack)  ## for dietox data
data(dietox)
dietox$Cu <- as.factor(dietox$Cu)
dietox$ddn = as.numeric(rnorm(nrow(dietox)) > 0)
gee01 <- geeglm (Weight ~ Time + Cu , id = Pig, data = dietox, family = gaussian, corstr = "ex")
geeglm.display(gee01)

gee02 <- geeglm (ddn ~ Time + Cu , id = Pig, data = dietox, family = binomial, corstr = "ex")
geeglm.display(gee02)

Mixed model Table: lmerMod or glmerMod object from lme4 package

library(lme4)
l1 = lmer(Weight ~ Time + Cu + (1|Pig), data = dietox) 
lmer.display(l1, ci.ranef = T)

l2 = glmer(ddn ~  Time + Cu + (1|Pig), data= dietox, family= "binomial")
lmer.display(l2)

Cox model with frailty or cluster options

library(survival)
fit1 <- coxph(Surv(time, status) ~ ph.ecog + age, cluster = inst, lung, model = T)  ## model = T: to extract original data
fit2 <- coxph(Surv(time, status) ~ ph.ecog + age + frailty(inst), lung, model = T)
cox2.display(fit1)
cox2.display(fit2)

Cox mixed effect model Table: coxme object from coxme package

library(coxme)
fit <- coxme(Surv(time, status) ~ ph.ecog + age + (1|inst), lung)
coxme.display(fit) 

GLM for survey data : svyglm object from survey package

library(survey)
data(api)
apistrat$tt = c(rep(1, 20), rep(0, nrow(apistrat) -20))
apistrat$tt2 = factor(c(rep(0, 40), rep(1, nrow(apistrat) -40)))

dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
ds <- svyglm(api00~ell+meals + tt2, design=dstrat)
ds2 <- svyglm(tt~ell+meals+ tt2, design=dstrat, family = quasibinomial())
svyregress.display(ds)
svyregress.display(ds2)

Cox model for survey data :svycoxph object from survey package

data(pbc, package="survival")
pbc$sex = factor(pbc$sex)
pbc$stage = factor(pbc$stage)
pbc$randomized<-with(pbc, !is.na(trt) & trt>0)
biasmodel<-glm(randomized~age*edema,data=pbc,family=binomial)
pbc$randprob<-fitted(biasmodel)

if (is.null(pbc$albumin)) pbc$albumin<-pbc$alb ##pre2.9.0

dpbc <- svydesign(id=~1, prob=~randprob, strata=~edema, data=subset(pbc,randomized))

model <- svycoxph(Surv(time,status>0)~ sex + protime + albumin + stage,design=dpbc)
svycox.display(model)

Sub-group analysis for Cox/svycox model

library(dplyr)
lung %>% 
mutate(status = as.integer(status == 1),
       sex = factor(sex),
       kk = factor(as.integer(pat.karno >= 70)),
       kk1 = factor(as.integer(pat.karno >= 60))) -> lung

#TableSubgroupMultiCox(Surv(time, status) ~ sex, var_subgroups = c("kk", "kk1"), data=lung, line = T)

## Survey data
library(survey)
data.design <- svydesign(id = ~1, data = lung, weights = ~1)
#TableSubgroupMultiCox(Surv(time, status) ~ sex, var_subgroups = c("kk", "kk1"), data = data.design, line = F)

jstable documentation built on May 31, 2023, 8:06 p.m.