publish.coxph: Tabulize hazard ratios with confidence intervals and...

In Publish: Format Output of Various Routines in a Suitable Way for Reports and Publication

Tabulize hazard ratios with confidence intervals and p-values.

Description

Tabulize the part of the result of a Cox regression analysis which is commonly shown in publications.

Usage

## S3 method for class 'coxph'
publish(
  object,
  confint.method,
  pvalue.method,
  print = TRUE,
  factor.reference = "extraline",
  units = NULL,
  probindex = FALSE,
  ...
)

Arguments

object	A coxph object.
confint.method	See regressionTable
pvalue.method	See regressionTable
print	If FALSE do not print results.
factor.reference	See regressionTable
units	See regressionTable
probindex	Logical. If TRUE show coefficients on probabilistic index scale instead of hazard ratio scale.
...	passed to summary.regressionTable and also to labelUnits.

Details

Transforms the log hazard ratios to hazard ratios and returns them with confidence limits and p-values. If explanatory variables are log transformed or log2 transformed, a scaling factor is multiplied to both the log-hazard ratio and its standard-error.

Value

Table with hazard ratios, confidence intervals and p-values.

Author(s)

Thomas Alexander Gerds

Examples

library(survival)
data(pbc)
pbc$edema <- factor(pbc$edema,
             levels=c("0","0.5","1"), labels=c("0","0.5","1"))
fit = coxph(Surv(time,status!=0)~age+sex+edema+log(bili)+log(albumin),
            data=na.omit(pbc))
publish(fit)
## forest plot
plot(publish(fit),cex=1.3)

publish(fit,ci.digits=2,pvalue.eps=0.01,pvalue.digits=2,pvalue.stars=TRUE)
publish(fit,ci.digits=2,ci.handler="prettyNum",pvalue.eps=0.01,
        pvalue.digits=2,pvalue.stars=TRUE)
publish(fit, ci.digits=2, ci.handler="sprintf", pvalue.eps=0.01,
        pvalue.digits=2,pvalue.stars=TRUE, ci.trim=FALSE)

fit2 = coxph(Surv(time,status!=0)~age+sex+edema+log(bili,base=2)+log(albumin)+log(protime),
    data=na.omit(pbc))
publish(fit2)

# with cluster variable
fit3 = coxph(Surv(time,status!=0)~age+cluster(sex)+edema+log(bili,base=2)
                                    +log(albumin)+log(protime),
    data=na.omit(pbc))
publish(fit3)

# with strata and cluster variable
fit4 = coxph(Surv(time,status!=0)~age+cluster(sex)+strata(edema)+log(bili,base=2)
                 +log(albumin)+log(protime),
    data=pbc)
publish(fit4)

Publish documentation built on Jan. 18, 2023, 1:08 a.m.