poor reproducibility

Author: yuw444

R/utils.R

@@ -30,7 +30,6 @@ vimp <- function(object, ...) {
 #' @param forest An Rforce object
 #' @return A matrix containing variable importance statistics for each variable in each tree of the forest,
 #' row correspond to trees and columns correspond to variables.
-
 vimp.Rforce <- function(forest) {
   if (!inherits(forest, "Rforce")) {
     stop("forest must be an Rforce object.")

TODO

@@ -30,3 +30,20 @@ fit <- Rforce(
   mtry          = 2,
   n_splits      = 5
 )
+
+
+Rforce train -d ./raw/Intervals_designMatrixY_wide.csv \
+  -a ./raw/Intervals_auxiliaryFeature_wide.csv \
+  -u ./raw/units_of_cpiu.csv \
+  -o ./rst \
+  -m 8 \
+  -n 10 \
+  -g 0.01 \
+  -t 5 \
+  -s 6 \
+  -k 99 \
+  -r 100 \
+  -e 926 \
+  --pseudorisk2 \
+  --phi2 \
+  --threads 10

vignettes/get-started.Rmd

@@ -81,10 +81,10 @@ break_points <- stats::quantile(
 )
 break_points[1] <- 0.0 # ensure starting at 0
 break_points[n_intervals + 1] <- max(observed_times, na.rm = TRUE) * 1.001 # ensure ending at max time
-units_of_cpius <- diff(break_points)
+intervals <- diff(break_points)
 cpiu_wide <- patients_to_cpius(
   data_to_convert = df,
-  units_of_cpiu = units_of_cpiu
+  units_of_cpiu = intervals
 )
 names(cpiu_wide)
 class(cpiu_wide)
@@ -128,7 +128,14 @@ cpiu_wide <- cpius_to_dummy(cpiu_wide, cols_to_keep = NULL)
 ```{r}
 fit <- Rforce(
   cpius = cpiu_wide,
-  split_rule = "Rforce-QLR"
+  split_rule = "Rforce-QLR",
+  n_trees = 1
+)
+
+fitt <- Rforce(
+  cpius = cpiu_wide,
+  split_rule = "Rforce-QLR",
+  n_trees = 1
 )
 ```
 
@@ -138,12 +145,26 @@ fit <- Rforce(
 * `Rforce` is also a bigger wrapper function for `Step 1 - 3`
 
 ```{r}
-fit <- Rforce(
+fit1 <- Rforce(
+  data = df,
+  formula = Surv(Id, X, Status) ~ ., 
+  n_intervals = 10,
+  split_rule = "Rforce-QLR",
+  n_trees = 200
+)
+
+fit2 <- Rforce(
   data = df,
   formula = Surv(Id, X, Status) ~ ., 
   n_intervals = 10,
-  split_rule = "Rforce-QLR"
+  split_rule = "Rforce-QLR",
+  n_trees = 200
 )
+all.equal(fit1, fit2)
+saveRforce(fit1, "output/fit1/")
+saveRforce(fit2, "output/fit2/")
+
+fit1 <- loadRforce("/home/yu89975/r-dev/Rforce/output/fit1/")
 ```
 
 ## Reference