## ----echo=FALSE,results='hide',warning=FALSE,message=FALSE------------------------------------------------------------------------------------------ library(knitr) knitr::opts_chunk$set(comment="", message=FALSE, warning=FALSE,fig.align="center",fig.height=10,fig.width=10,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=1200)) options(width=150) library(kableExtra) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- library(compareGroups) ## --------------------------------------------------------------------------------------------------------------------------------------------------- data(regicor) ## ----echo=FALSE,results="asis"---------------------------------------------------------------------------------------------------------------------- dicc <- data.frame( "Name"=I(names(regicor)), "Label"=I(unlist(lapply(regicor, attr, which="label", exact=TRUE))), "Codes"=I(unlist(lapply(regicor, function(x) paste(levels(x),collapse="; ")))) ) dicc$Codes <- sub(">=","$\\\\geq$",dicc$Codes) kable(dicc, align=rep("l",4), row.names=FALSE, format = "html") ## --------------------------------------------------------------------------------------------------------------------------------------------------- library(survival) regicor$tmain <- with(regicor, Surv(tocv, cv == 'Yes')) attr(regicor$tmain,"label") <- "Time to CV event or censoring" ## ----results='hide'--------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ . , data=regicor) ## ----results='hide'--------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ . - id, data=regicor) ## --------------------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(year ~ age + sex + bmi, data=regicor) res ## --------------------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + smoker + bmi, data=regicor, subset = sex=='Female') ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + bmi + smoker, data=regicor, selec = list(age= sex=="Female", bmi = age>50 )) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + smoker + bmi, data=regicor, selec = list(bmi=age>50), subset = sex=="Female") ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + sex + bmi + bmi, data=regicor, selec = list(bmi.1=txhtn=='Yes')) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + smoker + triglyc, data=regicor, method = c(triglyc=2)) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + smoker + triglyc, data=regicor, method = c(triglyc=NA), alpha= 0.01) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- regicor$age7gr<-as.integer(cut(regicor$age, breaks=c(-Inf,40,45,50,55,65,70,Inf), right=TRUE)) compareGroups(year ~ age7gr, data=regicor, method = c(age7gr=NA)) compareGroups(year ~ age7gr, data=regicor, method = c(age7gr=NA), min.dis=8) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # regicor$var6cat <- factor(sample(1:5, nrow(regicor), replace=TRUE)) # compareGroups(age7gr ~ sex + bmi + smoker, data=regicor) ## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- cat("Error in compareGroups.fit(X = X, y = y, include.label = include.label, : number of groups must be less or equal to 5") ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(age7gr ~ sex + bmi + smoker, data=regicor, max.ylev=7) ## ----echo=TRUE, eval=FALSE-------------------------------------------------------------------------------------------------------------------------- # compareGroups(year ~ sex + age7gr, method=c(age7gr=3), data=regicor, max.xlev=5) ## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- cat("Warning in compareGroups.fit(X = X, y = y, include.label = include.label, : Variables 'age7gr' have been removed since some errors occurred") ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + smoker + bmi, data=regicor, include.label= FALSE) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- resu1<-compareGroups(year ~ age + triglyc, data=regicor, method = c(triglyc=2)) createTable(resu1) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- resu2<-compareGroups(year ~ age + triglyc, data=regicor, method = c(triglyc=2), Q1=0.025, Q3=0.975) createTable(resu2) ## ----echo=TRUE, results='hide'---------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + triglyc, data=regicor, method = c(triglyc=2), Q1=0, Q3=1) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- regicor$smk<-regicor$smoker levels(regicor$smk)<- c("Never smoker", "Current or former < 1y", "Former >= 1y", "Unknown") attr(regicor$smk,"label")<-"Smoking 4 cat." cbind(table(regicor$smk)) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + smk + bmi, data=regicor) ## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- cat("Warning in compare.i(X[, i], y = y, selec.i = selec[i], method.i = method[i], : Some levels of 'smk' are removed since no observation in that/those levels") ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- compareGroups(year ~ age + smk + bmi, data=regicor, simplify=FALSE) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(year ~ age + sex + smoker + bmi + triglyc, method = c(triglyc=2), data=regicor) summary(res[c(1, 2, 5)]) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- plot(res[c(1,2)], file="./figures/univar/", type="png") ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- plot(res[c(1,2)], bivar=TRUE, file="./figures/bivar/", type="png") ## --------------------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(year ~ age + sex + smoker + bmi, data=regicor) res ## ----echo=TRUE, results='hide'---------------------------------------------------------------------------------------------------------------------- res<-update(res, . ~. - sex + triglyc + cv + tocv, subset = sex=='Female', method = c(triglyc=2, tocv=2), selec = list(triglyc=txchol=='No')) res ## --------------------------------------------------------------------------------------------------------------------------------------------------- data(SNPs) tab <- createTable(compareGroups(casco ~ snp10001 + snp10002 + snp10005 + snp10008 + snp10009, SNPs)) pvals <- getResults(tab, "p.overall") p.adjust(pvals, method = "BH") ## --------------------------------------------------------------------------------------------------------------------------------------------------- cg <- compareGroups(casco ~ snp10001 + snp10002 + snp10005 + snp10008 + snp10009, SNPs) createTable(padjustCompareGroups(cg, method="BH")) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res1<-compareGroups(cv ~ age + sex + bmi + smoker, data=regicor, ref=1) createTable(res1, show.ratio=TRUE) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res2<-compareGroups(cv ~ age + sex + bmi + smoker, data=regicor, ref=c(smoker=1, sex=2)) createTable(res2, show.ratio=TRUE) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(cv ~ age + sex + bmi + histhtn + txhtn, data=regicor, ref.no='NO') createTable(res, show.ratio=TRUE) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(cv ~ age + bmi, data=regicor) createTable(res, show.ratio=TRUE) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(cv ~ age + bmi, data=regicor, fact.ratio= c(age=10, bmi=2)) createTable(res, show.ratio=TRUE) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(cv ~ age + sex + bmi + txhtn, data=regicor) createTable(res, show.ratio=TRUE) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(cv ~ age + sex + bmi + txhtn, data=regicor, ref.y=2) createTable(res, show.ratio=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- plot(compareGroups(tmain ~ sex, data=regicor), bivar=TRUE, file="./figures/bivarsurv/", type="png") plot(compareGroups(tmain ~ age, data=regicor), bivar=TRUE, file="./figures/bivarsurv/", type="png") ## ----echo=TRUE, results='hide'---------------------------------------------------------------------------------------------------------------------- res<-compareGroups(sex ~ age + tmain, timemax=c(tmain=3*365.25), data=regicor) res ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- plot(res[2], file="./figures/univar/", type="png") plot(res[2], bivar=TRUE, file="./figures/bivar/", type="png") ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(year ~ age + sex + smoker + bmi + sbp, data=regicor, selec = list(sbp=txhtn=="No")) restab<-createTable(res) ## ----echo=TRUE-------------------------------------------------------------------------------------------------------------------------------------- print(restab,which.table='descr') ## ----echo=TRUE, eval=FALSE-------------------------------------------------------------------------------------------------------------------------- # print(restab,which.table='avail') ## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- print(restab,which.table='avail') ## --------------------------------------------------------------------------------------------------------------------------------------------------- update(restab, hide = c(sex="Male")) ## --------------------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(year ~ age + sex + histchol + histhtn, data=regicor) createTable(res, hide.no='no', hide = c(sex="Male")) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(res, digits= c(age=2, sex = 3)) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(res, type=1) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(res, type=3) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(res, show.n=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(res, show.descr=FALSE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(res, show.all=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(res, show.p.overall=FALSE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(res, show.p.trend=TRUE) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # createTable(res, show.p.mul=TRUE) ## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- createTable(res, show.p.mul=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(update(res, subset= year!=1995), show.ratio=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(compareGroups(tmain ~ year + age + sex, data=regicor), show.ratio=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(compareGroups(tmain ~ year + age + sex, data=regicor), show.ratio=TRUE, digits.ratio= 3) ## --------------------------------------------------------------------------------------------------------------------------------------------------- tab<-createTable(compareGroups(tmain ~ year + age + sex, data=regicor), show.all = TRUE) print(tab, header.labels = c("p.overall" = "p-value", "all" = "All")) ## --------------------------------------------------------------------------------------------------------------------------------------------------- restab1 <- createTable(compareGroups(year ~ age + sex, data=regicor)) restab2 <- createTable(compareGroups(year ~ bmi + smoker, data=regicor)) rbind("Non-modifiable risk factors"=restab1, "Modifiable risk factors"=restab2) ## --------------------------------------------------------------------------------------------------------------------------------------------------- x <- rbind("Non-modifiable"=restab1,"Modifiable"=restab2) rbind("Non-modifiable"=restab1,"Modifiable"=restab2)[c(1,4)] ## --------------------------------------------------------------------------------------------------------------------------------------------------- rbind("Modifiable"=restab1,"Non-modifiable"=restab2)[c(4,3,2,1)] ## --------------------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(year ~ age + smoker + bmi + histhtn , data=regicor) alltab <- createTable(res, show.p.overall = FALSE) femaletab <- createTable(update(res,subset=sex=='Female'), show.p.overall = FALSE) maletab <- createTable(update(res,subset=sex=='Male'), show.p.overall = FALSE) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # cbind("ALL"=alltab,"FEMALE"=femaletab,"MALE"=maletab) ## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- cbind("ALL"=alltab,"FEMALE"=femaletab,"MALE"=maletab) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # cbind(alltab,femaletab,maletab) ## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- cbind(alltab,femaletab,maletab) ## --------------------------------------------------------------------------------------------------------------------------------------------------- res <- compareGroups(year ~ age + bmi + smoker + histchol + histhtn, regicor) restab <- createTable(res, hide.no="no") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # strataTable(restab, "sex") ## ----echo=FALSE------------------------------------------------------------------------------------------------------------------------------------- strataTable(restab, "sex") ## --------------------------------------------------------------------------------------------------------------------------------------------------- print(createTable(compareGroups(year ~ age + sex + smoker + bmi, data=regicor)), which.table='both') ## --------------------------------------------------------------------------------------------------------------------------------------------------- print(createTable(compareGroups(year ~ age + sex + smoker + bmi, data=regicor)), nmax=FALSE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- summary(createTable(compareGroups(year ~ age + sex + smoker + bmi, data=regicor))) ## --------------------------------------------------------------------------------------------------------------------------------------------------- res<-compareGroups(year ~ age + sex + smoker + bmi, data=regicor) restab<-createTable(res, type=1) restab update(restab, show.n=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- update(restab, x = update(res, subset=c(sex=='Female')), show.n=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(compareGroups(year ~ age + sex + smoker + bmi + histhtn, data=regicor)) ## --------------------------------------------------------------------------------------------------------------------------------------------------- createTable(compareGroups(year ~ age + sex + smoker + bmi + histhtn, data=regicor))[1:2, ] ## --------------------------------------------------------------------------------------------------------------------------------------------------- descrTable(regicor) ## --------------------------------------------------------------------------------------------------------------------------------------------------- descrTable(~ age + sex, regicor) ## --------------------------------------------------------------------------------------------------------------------------------------------------- descrTable(regicor, hide.no="no") ## --------------------------------------------------------------------------------------------------------------------------------------------------- descrTable(year ~ ., regicor, hide.no="no", show.all=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- descrTable(regicor, subset=age>65) ## --------------------------------------------------------------------------------------------------------------------------------------------------- restab<-createTable(compareGroups(year ~ age + sex + smoker + bmi + histchol, data=regicor)) export2latex(restab) ## --------------------------------------------------------------------------------------------------------------------------------------------------- res <- compareGroups(year ~ ., regicor) restab <- createTable(res, hide.no="no") ## --------------------------------------------------------------------------------------------------------------------------------------------------- export2md(restab) ## --------------------------------------------------------------------------------------------------------------------------------------------------- export2md(restab, strip=TRUE, first.strip=TRUE) ## --------------------------------------------------------------------------------------------------------------------------------------------------- export2md(restab, size=6) ## --------------------------------------------------------------------------------------------------------------------------------------------------- export2md(restab, width="400px") ## --------------------------------------------------------------------------------------------------------------------------------------------------- restab <- strataTable(descrTable(year ~ . -id, regicor), "sex") ## --------------------------------------------------------------------------------------------------------------------------------------------------- export2md(restab, size=8) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # # to know more about report function # ?report # # # info about REGICOR data set # ?regicor ## --------------------------------------------------------------------------------------------------------------------------------------------------- # from a compareGroups object data(regicor) res <- compareGroups(year ~ .-id, regicor) missingTable(res) ## ----eval=FALSE,results='hide'---------------------------------------------------------------------------------------------------------------------- # # or from createTable objects # restab <- createTable(res, hide.no = 'no') # missingTable(restab) ## --------------------------------------------------------------------------------------------------------------------------------------------------- # first create time-to-cardiovascular event regicor$tcv<-with(regicor,Surv(tocv,cv=='Yes')) # create the table res <- compareGroups(tcv ~ . -id-tocv-cv-todeath-death, regicor, include.miss = TRUE) restab <- createTable(res, hide.no = 'no') restab ## --------------------------------------------------------------------------------------------------------------------------------------------------- data(SNPs) head(SNPs) ## --------------------------------------------------------------------------------------------------------------------------------------------------- res<-compareSNPs(casco ~ snp10001 + snp10002 + snp10003, data=SNPs) res ## --------------------------------------------------------------------------------------------------------------------------------------------------- res<-compareSNPs(~ snp10001 + snp10002 + snp10003, data=SNPs) res ## ----echo=FALSE, results='asis'--------------------------------------------------------------------------------------------------------------------- export2md(descrTable(year ~ age + sex + smoker + sbp + dbp + histhtn + txhtn + chol + hdl + triglyc + ldl + histchol + txchol + bmi, data=regicor, method=c(triglyc=2), hide.no="No",hide = c(sex="Male"))) ## ----echo=FALSE, results='asis'--------------------------------------------------------------------------------------------------------------------- export2md(descrTable(cv ~ age + sex + smoker + bmi + chol + triglyc + ldl + sbp + dbp + txhtn, data=regicor, method=c(triglyc=2), hide.no="No",hide = c(sex="Male"), show.ratio=TRUE, show.descr=FALSE)) ## ----echo=FALSE, results='asis'--------------------------------------------------------------------------------------------------------------------- export2md(createTable(compareGroups(tcv ~ year + age + sex, data=regicor), show.ratio=TRUE))