From cd33853b51dbb1a6c4cd6811ef60c512b80d8d0b Mon Sep 17 00:00:00 2001
From: Lucas Kook <lucasheinrich.kook@gmail.com>
Date: Wed, 10 Jul 2024 11:53:11 +0200
Subject: [PATCH 1/2] fix path

---
 inst/code/dependencies.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/code/dependencies.R b/inst/code/dependencies.R
index bb586dd..1679d5a 100644
--- a/inst/code/dependencies.R
+++ b/inst/code/dependencies.R
@@ -6,7 +6,7 @@ install.packages("remotes", repos = "https://cloud.r-project.org")
 
 ### GitHub packages
 remotes::install_github("igraph/rigraph")
-remotes::install_github("strobl/RCIT")
+remotes::install_github("ericstrobl/RCIT")
 
 ### Bioconductor packages
 remotes::install_bioc(c("graph", "Rgraphviz", "RBGL"))

From 7d2c9c3c0d259b43dc80835b61c11dd7869f3ad8 Mon Sep 17 00:00:00 2001
From: Lucas Kook <lucasheinrich.kook@gmail.com>
Date: Thu, 11 Jul 2024 12:12:47 +0200
Subject: [PATCH 2/2] paths

---
 inst/code/run-simulation.R | 20 ++++++++++----------
 inst/code/vis-simulation.R | 29 +++--------------------------
 2 files changed, 13 insertions(+), 36 deletions(-)

diff --git a/inst/code/run-simulation.R b/inst/code/run-simulation.R
index 2437a09..fea639b 100644
--- a/inst/code/run-simulation.R
+++ b/inst/code/run-simulation.R
@@ -4,7 +4,6 @@
 
 set.seed(27) # Seed
 parall <- FALSE # Parallel computing?
-.libPaths(c("~/tutu/lib", .libPaths()))
 
 ### Command line args and defaults
 args <- as.numeric(commandArgs(TRUE))
@@ -110,14 +109,15 @@ fobs <- list(types = types, fml = fml, resp = resp, env = env, preds = preds,
              affect_variance = affect_variance)
 
 if (save) {
-  pvec <- c("nanc", nanc, "ndec", ndec, "panc", panc, "pdec", pdec, "penv", penv,
-            "stdz", stdz, "sde", round(sde, 2), "errDist", errDistAnY, errDistDeY,
-            "spec", spec)
-  outdir <- file.path(
-    "inst", "results", Sys.Date(), paste0(paste0(
-      names(pvec), pvec, collapse = ""), collapse = "_"))
+  specname <- switch(spec, "correct" = "results_main",
+                     "link" = "results_link", "hidden" = "results_hidden",
+                     "roc" = "results_binary-roc", "larger" = "results_larger")
+  outdir <- file.path("inst", "results", specname)
+  resdir <- file.path(outdir, "results")
   if (!dir.exists(outdir))
     dir.create(outdir, recursive = TRUE)
+  if (!dir.exists(resdir))
+    dir.create(resdir, recursive = TRUE)
 
   write_rds(fobs, file.path(outdir, "fobs.rds"))
 }
@@ -138,7 +138,6 @@ if (TEST) {
   Design <- Design[ROW <- 1, ]
 }
 
-
 # Run ---------------------------------------------------------------------
 
 suppressWarnings(file.remove(list.files(pattern = "SIMDESIGN-TEMPFILE")))
@@ -158,7 +157,8 @@ res <- runSimulation(
   packages = pkgs,
   filename = file.path(outdir, paste0("sim-results", ROW, ".rds")),
   save_details = list(
-    safe = TRUE, save_results_dirname = file.path(outdir, paste0("results-row-", ROW)),
-    save_seeds_dirname = file.path(outdir, "seeds")
+    safe = TRUE, save_results_dirname = file.path(resdir, paste0("results-row-", ROW)),
+    save_results_filename = paste0("results-row-", ROW),
+    save_seeds_dirname = file.path(resdir, "seeds")
   )
 )
diff --git a/inst/code/vis-simulation.R b/inst/code/vis-simulation.R
index e1b01b7..01403d9 100644
--- a/inst/code/vis-simulation.R
+++ b/inst/code/vis-simulation.R
@@ -2,7 +2,7 @@
 # Visualize simulation results
 # LK 2023
 
-settings <- c("main", "app", "hidden", "link", "wald-extended", "larger")
+settings <- c("main", "app", "hidden", "link", "larger")
 
 setting <- settings[as.numeric(commandArgs(TRUE))[1]]
 if (is.na(setting))
@@ -112,29 +112,6 @@ if (setting == "main") {
   fobs <- readRDS(file.path(bpath, "fobs.rds"))
   res <- read_sim_results(file.path(bpath, "results"))
   res$oicp[res$oicp == "empty"] <- "Empty"
-} else if (setting == "wald-extended") {
-  ### paths
-  bpath <- file.path(rpath, "results_main")
-  tmods <- c(mods[-1], amods)
-  ttests <- tests
-  out <- "sim-wald-extended.pdf"
-  th <- 4.5
-  tw <- 11
-
-  fobs <- readRDS(file.path(bpath, "fobs.rds"))
-  res <- read_sim_results(file.path(bpath, "results"))
-  res$oicp[res$oicp == "empty"] <- "Empty"
-  res <- dplyr::filter(res, test == "wald")
-
-  bpath <- file.path(rpath, "results_wald-extended")
-  bfobs <- readRDS(file.path(bpath, "fobs.rds"))
-  bres <- read_sim_results(file.path(bpath, "results"))
-  bres$oicp[bres$oicp == "empty"] <- "Empty"
-  bres <- dplyr::filter(bres, test == "wald")
-  bres$test <- "wald.test"
-
-  res <- full_join(res, bres)
-
 }
 
 ### Summarize for plotting
@@ -163,5 +140,5 @@ if (setting == "hidden") {
 # Vis ---------------------------------------------------------------------
 
 p1 <- vis(tmods, ttests)
-ggsave(file.path(rpath, out), p1, height = th, width = tw, scale = 1)
-ggsave(file.path("inst", "figures", out), p1, height = th, width = tw, scale = 1)
+ggsave(file.path(rpath, out), p1, height = th, width = tw, scale = 1, create.dir = TRUE)
+ggsave(file.path("inst", "figures", out), p1, height = th, width = tw, scale = 1, create.dir = TRUE)