roche / global-hta-evidence-open Goto Github PK

runPSM function does not allow to implement weights in the regressions, which could be useful in the case of MAICs etc

I'm trying to check this package before use and was running into a few issues.

I'm receiving errors when trying to run the examples for this package, either independently via tools::testInstalledPackage("MAIC", types = "examples") or as part of R CMD check (via devtools::check("./MAIC")).

Using testInstalledPackage

When using testInstalledPackage, I get an error about the use of T. During example execution, T and F are masked with code that will throw these errors when they're used (from R email list).

> KM_plot <- ggsurvplot(KM_list,
+                       combine = TRUE,
+                       risk.table=T, # numbers at risk displayed on the plot
+                       break.x.by=50,
+                       xlab="Time (days)",
+                       censor=FALSE,
+                       legend.title = "Treatment",
+                       title = "Kaplan-Meier plot of overall survival",
+                       legend.labs=c("Intervention",
+                                     "Intervention weighted",
+                                     "Comparator"),
+                       font.legend = list(size = 10)) +
+   guides(colour=guide_legend(nrow = 2))
Error in ggsurvplot(KM_list, combine = TRUE, risk.table = T, break.x.by = 50,  : 
  T used instead of TRUE

Using R CMD check

A simple enough issue, but currently throwing errors. Fixed by adding Suggests: knitr to DESCRIPTION

VignetteBuilder package not declared: ‘knitr’

Using devtools::check("./MAIC", vignettes = FALSE)

When running R CMD check I get namespace errors, which may be due to the masking of .oldSearch in the check environment.

  > library(MAIC)
  > library(ggplot2)
  > library(survminer)
  Loading required package: ggpubr
  Error: package or namespace load failed for ‘ggpubr’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   there is no package called ‘foreign’
  Error: package ‘ggpubr’ could not be loaded
  Execution halted

I think that this might be a result of these undeclared dependencies required to run the examples. Even if these are installed in my library, they aren't being picked up while running the examples during R CMD check. I was able to fix this by adding these three dependencies as Suggests: dependencies. With these added, I get the same error as when running tools::testInstalledPackages (the issue with using T in examples)

* checking for unstated dependencies in examples ... WARNING
'library' or 'require' calls not declared from:
  ‘flextable’ ‘officer’ ‘survminer’

The estimate_weights() function does not have a ... argument allowing a user to pass arguments to optim() even though the documentation says this is possible.

In the vignette (https://roche.github.io/Global-HTA-Evidence-Open/Rpackages/flexsurvPlus/docs/articles/Survival_analysis_theory.html) it is suggested that the following function should be used in excel:
1-((EXP(GAMMALN(rate)) * GAMMA.DIST(shape * time,rate,1,TRUE))/GAMMA(rate)

This is incorrect. The following formula should be used:
1-GAMMA.DIST(time, shape, 1/(rate),TRUE)

Functions correct but documentation needs updating