Fix img display in MRIreduce.Rmd

.Rproj.user/6A9A55E1/pcs/files-pane.pper

@@ -5,5 +5,5 @@
             "ascending": true
         }
     ],
-    "path": "~/Desktop/MRIreduce/R"
+    "path": "~/Desktop/MRIreduce/man"
 }

.Rproj.user/6A9A55E1/pcs/source-pane.pper

@@ -1,3 +1,3 @@
 {
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+    "activeTab": 3
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.Rproj.user/6A9A55E1/pcs/windowlayoutstate.pper

@@ -1,14 +1,14 @@
 {
     "left": {
-        "splitterpos": 290,
+        "splitterpos": 177,
         "topwindowstate": "NORMAL",
-        "panelheight": 663,
-        "windowheight": 701
+        "panelheight": 653,
+        "windowheight": 691
     },
     "right": {
-        "splitterpos": 195,
+        "splitterpos": 529,
         "topwindowstate": "NORMAL",
-        "panelheight": 663,
-        "windowheight": 701
+        "panelheight": 653,
+        "windowheight": 691
     }
 }

.Rproj.user/6A9A55E1/pcs/workbench-pane.pper

@@ -1,5 +1,5 @@
 {
-    "TabSet1": 0,
+    "TabSet1": 1,
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     "TabZoom": {}
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DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MRIreduce
 Type: Package
 Title: MRIreduce: An R Package for ROI-Based Transformation of Neuroimages into High-Dimensional Data Frames
-Version: 0.6.0
+Version: 1.0.0
 Authors@R: c(
     person("Joshua", "Milstein", email = "[email protected]", role = c("aut")),
     person("Jinyao", "Tian", email = "[email protected]", role = c("aut", "cre"))
@@ -38,4 +38,4 @@ Suggests:
     knitr,
     rmarkdown
 VignetteBuilder: knitr
-URL: https://github.com/USCbiostats/MRIreduce
+URL:https://uscbiostats.github.io/MRIreduce/

R/funcs.R

@@ -465,6 +465,13 @@ process_indep_variables <- function(indep_list, tissue_type, tind, roi, main_dir
   saveRDS(volume_dat, file = file.path(save_dir, paste0("volume.rds")))
 }
 
+# main_dir = '/Users/jinyaotian/Downloads/whims_test'
+# roi = 'inferior_frontal_gyrus_left'
+# indep_list_path = file.path(main_dir, "indep_list", paste0(roi,'.rds'))
+# indep_list <- readRDS(indep_list_path)
+# process_indep_variables(indep_list = indep_list, tissue_type = 2, tind = 5,
+#                         roi = roi, main_dir = main_dir)
+
 #Combine independent variables with reduced variables by tissue type by roi
 Cmb_indep_with_dep <- function(tissue_type, roi, thresh, main_dir){
   if (tissue_type == 3){

_pkgdown.yml

@@ -1,18 +1,18 @@
 url: https://uscbiostats.github.io/MRIreduce/
 template:
   bootstrap: 5
-  bootswatch: cosmo  # Using the Flatly theme from Bootswatch
-
+  bootswatch: cosmo
 navbar:
   title: MRIreduce
   left:
-    - text: Home
-      href: index.html
-    - text: Get Started
-      href: articles/MRIreduce.html  # Link directly to your vignette
-    - text: Reference
-      href: reference/index.html
+  - text: Home
+    href: index.html
+  - text: Get Started
+    href: articles/MRIreduce.html
+  - text: Reference
+    href: reference/index.html
   right:
-    - text: View on source code
-      href: https://github.com/USCbiostats/MRIreduce
-      icon: fab fa-github
+  - text: View on source code
+    href: https://github.com/USCbiostats/MRIreduce
+    icon: fab fa-github
+

vignettes/MRIreduce.Rmd

@@ -202,4 +202,5 @@ map2_eve(mask_img_path = "~/mask_nifti_GM_Volume_pm25_test1_avg_red.nii.gz",
 Note: `mask_img_path` should point to `loc_df` data generated by function `map_feature2_loc`.
 
 
-![Mask Image on the EVE Template with three cuts performed in orthogonal directions]("man/figures/test.png")
+![Mask Image on the EVE Template with three cuts performed in orthogonal directions](../man/figures/test.png)
+