test/Error testing program.R

In UCL/mimix: Reference-Based Imputation for Longitudinal Clinical Trials with Protocol Deviation

#####################################################################
# Error testing program for RefBasedMI
# IW 4/11/2021
# updated 7mar2023 - works perfectly
# updated 31mar2023 - more tests; run from test directory
#####################################################################

# Install RefBasedMI if required
if(!require(RefBasedMI)) {
  if(!require(devtools)) install.packages('devtools') 
  library(devtools) 
  install_github("UCL/RefBasedMI")
}

if(!require(tidyverse)) install.packages('tidyverse') 

# Load RefBasedMI
library(RefBasedMI)
packageVersion("RefBasedMI")
library(mice)
packageVersion("mice")

# Open and modify data
load("../data/asthma.RData")
asthma$treat[1:200]<-3 # creates a 3rd arm
asthma$base2 <- asthma$base^2 # creates a 2nd covariate
asthma$fev<-asthma$fev*1000
head(asthma)

# non-existent covariate
impJ2R1 <- RefBasedMI(data=asthma,
                      covar=c(base,base3),
                      depvar=fev,
                      treatvar=treat,
                      idvar=id,
                      timevar=time,
                      M=2,
                      reference=1,
                      method="J2R",
                      seed=101,
                      prior="jeffreys",
                      burnin=1000,
                      bbetween=NULL,
                      methodvar=NULL
)

# non-existent depvar
impJ2R1 <- RefBasedMI(data=asthma,
                      covar=c(base,base2),
                      depvar=fev55,
                      treatvar=treat,
                      idvar=id,
                      timevar=time,
                      M=2,
                      reference=1,
                      method="J2R",
                      seed=101,
                      prior="jeffreys",
                      burnin=1000,
                      bbetween=NULL,
                      methodvar=NULL
)

# non-existent treatvar
impJ2R1 <- RefBasedMI(data=asthma,
                      covar=c(base,base2),
                      depvar=fev,
                      treatvar=treatx,
                      idvar=id,
                      timevar=time,
                      M=2,
                      reference=1,
                      method="J2R",
                      seed=101,
                      prior="jeffreys",
                      burnin=1000,
                      bbetween=NULL,
                      methodvar=NULL
)

# non-existent idvar
impJ2R1 <- RefBasedMI(data=asthma,
                      covar=c(base,base2),
                      depvar=fev,
                      treatvar=treat,
                      idvar=idx,
                      timevar=time,
                      M=2,
                      reference=1,
                      method="J2R",
                      seed=101,
                      prior="jeffreys",
                      burnin=1000,
                      bbetween=NULL,
                      methodvar=NULL
)

# non-existent timevar
impJ2R1 <- RefBasedMI(data=asthma,
                      covar=c(base,base2),
                      depvar=fev,
                      treatvar=treat,
                      idvar=id,
                      timevar=timex,
                      M=2,
                      reference=1,
                      method="J2R",
                      seed=101,
                      prior="jeffreys",
                      burnin=1000,
                      bbetween=NULL,
                      methodvar=NULL
)