fix: replace if(interactive) with \donttest

Author: RobinDenz1

.Rbuildignore

@@ -8,3 +8,4 @@
 ^docs$
 ^pkgdown$
 ^cran-comments\.md$
+^CRAN-SUBMISSION$

codemeta.json

@@ -414,7 +414,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "2371.954KB",
+  "fileSize": "2372.788KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -448,10 +448,5 @@
         }
       }
     }
-  ],
-  "releaseNotes": "https://github.com/RobinDenz1/adjustedCurves/blob/master/NEWS.md",
-  "readme": "https://github.com/RobinDenz1/adjustedCurves/blob/main/README.md",
-  "contIntegration": ["https://github.com/RobinDenz1/adjustedCurves/actions", "https://app.codecov.io/gh/RobinDenz1/adjustedCurves?branch=main"],
-  "developmentStatus": "https://www.repostatus.org/#active",
-  "keywords": ["adjusted", "survival-curves", "cumulative-incidence", "confidence-intervals"]
+  ]
 }

cran-comments.md

@@ -7,3 +7,6 @@
 The package was tested on Windows 10, macOS and ubuntu using github actions and rhub as well as local machines.
 There were no errors or warnings and two notes. The first note is due to this being a new release.
 The second note only appears on some rhub checks: "checking for detritus in the temp directory Found the following files/directories: 'lastMiKTeXException'"
+
+Most if(interactive()) statements have been replaced by \donttest as adviced.
+I only kept the if(interactive()) calls in the man pages of surv_iptw_cox, surv_iptw_km and surv_iptw_pseudo to avoid the dependency on the "optweight" package.

man/adjustedcif.Rd

@@ -218,7 +218,7 @@ adjcif <- adjustedcif(data=sim_dat,
                       n_boot=10)
 
 # not run because those are too slow
-if(interactive()){
+\donttest{
 # using bootstrapping with direct adjustment, run in parallel
 # on two cores
 library(foreach)
@@ -234,7 +234,7 @@ adjcif <- adjustedcif(data=sim_dat,
                       outcome_model=cox_mod,
                       conf_int=TRUE,
                       bootstrap=TRUE,
-                      n_boot=10,
+                      n_boot=4,
                       n_cores=2)
 
 # using multiple imputation
@@ -251,7 +251,7 @@ sim_dat$group <- as.factor(sim_dat$group)
 sim_dat$x1 <- ifelse(runif(n=50) < 0.5, sim_dat$x1, NA)
 
 # perform multiple imputation
-mids <- mice::mice(data=sim_dat, method="pmm", m=5, printFlag=FALSE)
+mids <- mice::mice(data=sim_dat, method="pmm", m=2, printFlag=FALSE)
 
 # IPTW Pseudo using WeightIt on imputed data, for cause = 1
 adj <- adjustedcif(data=mids,

man/adjustedsurv.Rd

@@ -220,7 +220,7 @@ adjsurv <- adjustedsurv(data=sim_dat,
                         n_boot=10)
 
 # not run because those are too slow
-if(interactive()){
+\donttest{
 # using bootstrapping with direct adjustment, run in parallel
 # on two cores
 adjsurv <- adjustedsurv(data=sim_dat,
@@ -231,7 +231,7 @@ adjsurv <- adjustedsurv(data=sim_dat,
                         outcome_model=cox_mod,
                         conf_int=TRUE,
                         bootstrap=TRUE,
-                        n_boot=10,
+                        n_boot=4,
                         n_cores=2)
 
 # using multiple imputation
@@ -248,7 +248,7 @@ sim_dat$group <- as.factor(sim_dat$group)
 sim_dat$x1 <- ifelse(runif(n=50) < 0.5, sim_dat$x1, NA)
 
 # perform multiple imputation
-mids <- mice::mice(data=sim_dat, method="pmm", m=5, printFlag=FALSE)
+mids <- mice::mice(data=sim_dat, method="pmm", m=2, printFlag=FALSE)
 
 # IPTW KM using WeightIt on imputed data
 adj <- adjustedsurv(data=mids,

man/cif_tmle.Rd

@@ -78,14 +78,14 @@ The wrapper function was written by Robin Denz, the \pkg{survtmle} package (whic
 }
 \examples{
 # not run because any meaningful example is too slow
-if(interactive()){
+\donttest{
 library(adjustedCurves)
 library(survtmle)
 
 set.seed(42)
 
 # simulate some data as example
-sim_dat <- sim_confounded_crisk(n=50, max_t=5)
+sim_dat <- sim_confounded_crisk(n=30, max_t=5)
 sim_dat$group <- as.factor(sim_dat$group)
 
 # only works with integer time, only unbiased with small amounts of them

man/surv_ostmle.Rd

@@ -87,7 +87,7 @@ The wrapper function was written by Robin Denz, the \code{MOSS} package (which t
 }
 \examples{
 # not run because any meaningful example is too slow
-if(interactive()){
+\donttest{
 library(adjustedCurves)
 
 # simulate some data as example

man/surv_tmle.Rd

@@ -81,14 +81,14 @@ The wrapper function was written by Robin Denz, the \code{survtmle} package (whi
 }
 \examples{
 # not run because any meaningful example is too slow
-if(interactive()){
+\donttest{
 library(adjustedCurves)
 library(survtmle)
 
 set.seed(42)
 
 # simulate some data as example
-sim_dat <- sim_confounded_surv(n=50, max_t=1.2)
+sim_dat <- sim_confounded_surv(n=30, max_t=1.2)
 sim_dat$group <- as.factor(sim_dat$group)
 
 # only works with integer time, only unbiased with small amounts of them