Running examples in ‘papeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: prettify
> ### Title: Make Pretty Summary and Anova Tables
> ### Aliases: prettify prettify.anova prettify.data.frame
> ###   prettify.summary.lm prettify.summary.glm prettify.summary.coxph
> ###   prettify.summary.lme prettify.summary.mer prettify.summary.merMod
> ###   prettifyPValue
> ### Keywords: methods models
> 
> ### ** Examples
> 
> ## Example requires package nlme to be installed and loaded
> if (require("nlme")) {
+     ## Load data set Orthodont
+     data(Orthodont, package = "nlme")
+ 
+     ######################################################################
+     # Linear model
+     ######################################################################
+ 
+     ## Fit a linear model
+     linmod <- lm(distance ~ age + Sex, data = Orthodont)
+     ## Extract pretty summary
+     prettify(summary(linmod))
+ 
+     ## Extract anova (sequential tests)
+     anova(linmod)
+     ## now prettify it
+     prettify(anova(linmod))
+ 
+     ######################################################################
+     # Random effects model (nlme)
+     ######################################################################
+ 
+     ### (fit a more suitable model with random effects)
+     ## With package nlme:
+     require("nlme")
+     ## Fit a model for distance with random intercept for Subject
+     mod <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1 | Subject)
+     summary(mod)
+     ## Extract fixed effects table, add confidence interval and make it pretty
+     prettify(summary(mod))
+     ## Extract fixed effects table only and make it pretty
+     prettify(summary(mod), confint = FALSE)
+ 
+     ######################################################################
+     # Random effects model (lme4)
+     ######################################################################
+ 
+     set.seed(130913)
+ 
+     ## With package lme4:
+     if (require("lme4") && require("car")) {
+         ## Fit a model for distance with random intercept for Subject
+         mod4 <- lmer(distance ~ age + Sex + (1|Subject), data = Orthodont)
+         summary(mod4)
+         ## Extract fixed effects table and make it pretty
+         prettify(summary(mod4))
+ 
+         ## Extract and prettify anova (sequential tests)
+         prettify(anova(mod4))
+ 
+         ## Better: extract Anova (partial instead of sequential tests)
+         library("car")
+         Anova(mod4)
+         ## now prettify it
+         prettify(Anova(mod4))
+     }
+ 
+     ######################################################################
+     # Cox model
+     ######################################################################
+ 
+     ## survival models
+     if (require("survival")) {
+         ## Load data set ovarian
+         data(ovarian, package = "survival")
+ 
+         ## fit a Cox model
+         mod5 <- coxph(Surv(futime, fustat) ~ age, data=ovarian)
+         summary(mod5)
+         ## Make pretty summary
+         prettify(summary(mod5))
+ 
+         ## Make pretty summary
+         prettify(Anova(mod5))
+     }
+ 
+ 
+     ######################################################################
+     # ATTENTION when confint = TRUE: Do not modify or delete data
+     ######################################################################
+ 
+     ## Fit a linear model (same as above)
+     linmod <- lm(distance ~ age + Sex, data = Orthodont)
+     ## Extract pretty summary
+     prettify(summary(linmod))
+ 
+     ## Change the data (age in month instead of years)
+     Orthodont$age <- Orthodont$age * 12
+     prettify(summary(linmod))  ## confidence intervals for age have changed
+                                ## but coefficients stayed the same; a
+                                ## warning is issued
+ 
+     ## Remove data in fitting environment
+     rm(Orthodont)
+     prettify(summary(linmod))  ## confidence intervals are missing as no
+                                ## data set was available to refit the model
+ 
+ 
+ 
+     ######################################################################
+     # Use confint to specify confidence interval without refitting
+     ######################################################################
+ 
+     ## make labels without using the data set
+     labels <- c("distance", "age", "Subject", "Sex")
+     names(labels) <- labels
+ 
+     ## usually easier via: labels(Orthodont)
+ 
+     prettify(summary(linmod), confint = confint(linmod),
+              labels = labels)
+ }
Loading required package: nlme
Loading required package: lme4
Loading required package: Matrix

Attaching package: ‘lme4’

The following object is masked from ‘package:nlme’:

    lmList

Computing profile confidence intervals ...
Confidence intervals are experimental only;
Model refitted but original environment not available.

Loading required package: survival
Warning in data(ovarian, package = "survival") :
  data set ‘ovarian’ not found
Error in prettify.summary.coxph(summary(mod5)) : 
  Model can't be refitted and no labels are specified. Please specify labels.
Calls: prettify -> prettify.summary.coxph
Execution halted