v0.3.4 (#10)

man/var.relations.Rd

@@ -15,7 +15,7 @@ var.relations(
   num.threads = NULL,
   status = NULL,
   save.ranger = FALSE,
-  create.forest = TRUE,
+  create.forest = is.null(forest),
   forest = NULL,
   save.memory = FALSE,
   case.weights = NULL,
@@ -48,9 +48,9 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{save.ranger}{set TRUE if ranger object should be saved. Default is that ranger object is not saved (FALSE).}
 
-\item{create.forest}{set FALSE if you want to analyze an existing forest. Default is TRUE.}
+\item{create.forest}{Default: TRUE if `forest` is NULL, FALSE otherwise. Whether to create or use an existing forest.}
 
-\item{forest}{the random forest that should be analyzed if create.forest is set to FALSE. (x and y still have to be given to obtain variable names)}
+\item{forest}{the random forest that should be analyzed}
 
 \item{save.memory}{Use memory saving (but slower) splitting mode. No effect for survival and GWAS data. Warning: This option slows down the tree growing, use only if you encounter memory problems. (This parameter is transfered to ranger)}
 

man/var.relations.mfi.Rd

@@ -15,7 +15,7 @@ var.relations.mfi(
   num.threads = NULL,
   status = NULL,
   save.ranger = FALSE,
-  create.forest = TRUE,
+  create.forest = is.null(forest),
   forest = NULL,
   save.memory = FALSE,
   case.weights = NULL,
@@ -49,9 +49,9 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{save.ranger}{set TRUE if ranger object should be saved. Default is that ranger object is not saved (FALSE).}
 
-\item{create.forest}{set FALSE if you want to analyze an existing forest. Default is TRUE.}
+\item{create.forest}{Default: TRUE if `forest` is NULL, FALSE otherwise. Whether to create or use an existing forest.}
 
-\item{forest}{the random forest that should be analyzed if create.forest is set to FALSE. (x and y still have to be given to obtain variable names)}
+\item{forest}{the random forest that should be analyzed}
 
 \item{save.memory}{Use memory saving (but slower) splitting mode. No effect for survival and GWAS data. Warning: This option slows down the tree growing, use only if you encounter memory problems. (This parameter is transfered to ranger)}
 

man/var.select.md.Rd

@@ -14,7 +14,7 @@ var.select.md(
   num.threads = NULL,
   status = NULL,
   save.ranger = FALSE,
-  create.forest = TRUE,
+  create.forest = is.null(forest),
   forest = NULL,
   save.memory = FALSE,
   case.weights = NULL
@@ -41,9 +41,9 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{save.ranger}{Set TRUE if ranger object should be saved. Default is that ranger object is not saved (FALSE).}
 
-\item{create.forest}{set FALSE if you want to analyze an existing forest. Default is TRUE.}
+\item{create.forest}{Default: TRUE if `forest` is NULL, FALSE otherwise. Whether to create or use an existing forest.}
 
-\item{forest}{the random forest that should be analyzed if create.forest is set to FALSE. (x and y still have to be given to obtain variable names)}
+\item{forest}{the random forest that should be analyzed.}
 
 \item{save.memory}{Use memory saving (but slower) splitting mode. No effect for survival and GWAS data. Warning: This option slows down the tree growing, use only if you encounter memory problems. (This parameter is transfered to ranger)}
 

man/var.select.smd.Rd

@@ -15,7 +15,7 @@ var.select.smd(
   num.threads = NULL,
   status = NULL,
   save.ranger = FALSE,
-  create.forest = TRUE,
+  create.forest = is.null(forest),
   forest = NULL,
   save.memory = FALSE,
   case.weights = NULL
@@ -44,9 +44,9 @@ classification mode is used). For survival forests this is the time variable.}
 
 \item{save.ranger}{set TRUE if ranger object should be saved. Default is that ranger object is not saved (FALSE).}
 
-\item{create.forest}{set FALSE if you want to analyze an existing forest. Default is TRUE.}
+\item{create.forest}{Default: TRUE if `forest` is NULL, FALSE otherwise. Whether to create or use an existing forest.}
 
-\item{forest}{the random forest that should be analyzed if create.forest is set to FALSE. (x and y still have to be given to obtain variable names)}
+\item{forest}{the random forest that should be analyzed}
 
 \item{save.memory}{Use memory saving (but slower) splitting mode. No effect for survival and GWAS data. Warning: This option slows down the tree growing, use only if you encounter memory problems. (This parameter is transfered to ranger)}
 

tests/testthat/test-meanAdjAgree_index.mean.R

@@ -10,7 +10,7 @@ test_that("mean.index always returns a numeric vector of length(index.variables)
       list(`5` = c(0.3, 0.0, 0.5, 0.6), `100` = c(0.7, 0.6, 0.0, 0.9))
     )
   )
-  index.variables = c(1, 5, 100, 10000)
+  index.variables <- c(1, 5, 100, 10000)
 
   # 1 would not go out of bounds, thus should always pass
   testthat::expect_length(mean.index(1, list.res, index.variables), length(index.variables))
@@ -23,6 +23,6 @@ test_that("mean.index always returns a numeric vector of length(index.variables)
 
 test_that("mean.index returns NA vector when i is out of bounds of index.variables", {
   list.res <- list()
-  index.variables = 1:4
+  index.variables <- 1:4
   testthat::expect_equal(mean.index(5, list.res, index.variables), rep(NA, length(index.variables)))
 })