clears up issues with using docs

MoseleyBioinformaticsLab · Feb 1, 2024 · 06b6985 · 06b6985
1 parent 76f602f
commit 06b6985
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Showing 9 changed files with 30 additions and 29 deletions.
diff --git a/docs/ici_kt_manuscript.Rmd b/docs/ici_kt_manuscript.Rmd
@@ -25,7 +25,7 @@ output:
   rmarkdown::html_document:default:
     self_contained: yes
 date: '`r Sys.time()`'
-bibliography: '`r here::here("doc/icikt_references.json")`'
+bibliography: '`r here::here("docs/icikt_references.json")`'
 csl: plos-computational-biology.csl
 editor_options: 
   chunk_output_type: console
@@ -37,7 +37,7 @@ tar_source("R")
 
 doc_type = knitr::opts_knit$get("rmarkdown.pandoc.to")
 if (doc_type %in% "docx") {
-  unlink(here::here("doc", "ici_kt_manuscript_files"), recursive = TRUE)
+  unlink(here::here("docs", "ici_kt_manuscript_files"), recursive = TRUE)
 }
 
 
@@ -52,9 +52,9 @@ knitr::opts_chunk$set(echo = FALSE,
                       fig.process = figure_count$modify_path,
                       dpi = 600,
                       dev = "ragg_png")
-supp_figure_count = readRDS(here::here("doc/supp_figure_count.rds"))
-supp_table_count = readRDS(here::here("doc/supp_table_count.rds"))
-load(here::here("doc/supp_stuff.rda"))
+supp_figure_count = readRDS(here::here("docs/supp_figure_count.rds"))
+supp_table_count = readRDS(here::here("docs/supp_table_count.rds"))
+load(here::here("docs/supp_stuff.rda"))
 
 ```
 
@@ -136,7 +136,7 @@ Both dropping or imputing missing values are likely to cause the calculated samp
 ```{r}
 #| label: problem
 curr_dir = getwd()
-problem_loc = file.path(curr_dir, "doc", "the_problem.png")
+problem_loc = file.path(curr_dir, "docs", "the_problem.png")
 #message(problem_loc)
 #file.exists(problem_loc)
 knitr::include_graphics(problem_loc, rel_path = FALSE)

diff --git a/docs/ici_kt_manuscript.docx b/docs/ici_kt_manuscript.docx
diff --git a/docs/ici_kt_manuscript.html b/docs/ici_kt_manuscript.html
diff --git a/docs/ici_kt_manuscript.md b/docs/ici_kt_manuscript.md
@@ -24,8 +24,8 @@ output:
       - '--lua-filter=author-info-blocks.lua'
   rmarkdown::html_document:default:
     self_contained: yes
-date: '2024-01-31 15:05:33.795949'
-bibliography: '/home/rmflight/Documents/manuscripts/in_progress/rmflight_ici-kendallt/doc/icikt_references.json'
+date: '2024-02-01 08:30:47.557145'
+bibliography: '/home/rmflight/Documents/manuscripts/in_progress/rmflight_ici-kendallt/docs/icikt_references.json'
 csl: plos-computational-biology.csl
 editor_options: 
   chunk_output_type: console
@@ -76,7 +76,7 @@ The two most common approaches for ignoring (i.e. dropping) values is to only us
 Both dropping or imputing missing values are likely to cause the calculated sample-sample correlation values to deviate from the real sample-sample correlation values, especially with respect to specific data interpretation perspectives.
 
 
-![](/home/rmflight/Documents/manuscripts/in_progress/rmflight_ici-kendallt/doc/the_problem.png)<!-- -->
+![](/home/rmflight/Documents/manuscripts/in_progress/rmflight_ici-kendallt/docs/the_problem.png)<!-- -->
 
 Figure 1. 
 Graphical description of the left-censored data problem.

diff --git a/docs/supplemental_materials.Rmd b/docs/supplemental_materials.Rmd
@@ -5,7 +5,7 @@ date: '`r Sys.time()`'
 output: 
   rmarkdown::word_document:
     keep_md: true
-bibliography: '`r here::here("doc/icikt_references.json")`'
+bibliography: '`r here::here("docs/icikt_references.json")`'
 csl: plos-computational-biology.csl
 editor_options: 
   chunk_output_type: console
@@ -16,7 +16,7 @@ targets::tar_source(files = c("./packages.R", "R"))
 
 doc_type = knitr::opts_knit$get("rmarkdown.pandoc.to")
 if (doc_type %in% "docx") {
-  unlink(here::here("doc", "supplemental_materials_files"), recursive = TRUE)
+  unlink(here::here("docs", "supplemental_materials_files"), recursive = TRUE)
 }
 
 supp_figure_count = dn_counter$new("Figure ", "_", "S")
@@ -784,9 +784,9 @@ Difference of Ad lib feeding in high and low stamina medians and MADs  by correl
 Abbreviations for different measures and data are: IK: ICI-Kt; IKC: ICI-Kt * Completeness; Kt: Kendall-tau; PB: Pearson Base (raw values); PL: Pearson Log(x); PL1: Pearson Log(x + 1); PN0: Pearson No Zeros.
 
 ```{r save_supp_objects}
-saveRDS(supp_figure_count, file = here::here("doc/supp_figure_count.rds"))
-saveRDS(supp_table_count, file = here::here("doc/supp_table_count.rds"))
-save(yeast_table, egfrgenotype_table, adenocarcinoma_table, nsclc_table, ratstamina_table, adenocarcinoma_ratios, file = here::here("doc/supp_stuff.rda"))
+saveRDS(supp_figure_count, file = here::here("docs/supp_figure_count.rds"))
+saveRDS(supp_table_count, file = here::here("docs/supp_table_count.rds"))
+save(yeast_table, egfrgenotype_table, adenocarcinoma_table, nsclc_table, ratstamina_table, adenocarcinoma_ratios, file = here::here("docs/supp_stuff.rda"))
 ```
 
 ## References
diff --git a/docs/supplemental_materials.docx b/docs/supplemental_materials.docx
diff --git a/docs/supplemental_materials.html b/docs/supplemental_materials.html
diff --git a/docs/supplemental_materials.md b/docs/supplemental_materials.md
@@ -1,11 +1,11 @@
 ---
 title: 'Supplemental Materials'
 author: 'Robert M Flight, Praneeth S Bhatt, and Hunter NB Moseley'
-date: '2024-01-31 15:03:27.891435'
+date: '2024-02-01 08:27:52.604683'
 output: 
   rmarkdown::word_document:
     keep_md: true
-bibliography: '/home/rmflight/Documents/manuscripts/in_progress/rmflight_ici-kendallt/doc/icikt_references.json'
+bibliography: '/home/rmflight/Documents/manuscripts/in_progress/rmflight_ici-kendallt/docs/icikt_references.json'
 csl: plos-computational-biology.csl
 editor_options: 
   chunk_output_type: console

diff --git a/packages.R b/packages.R
@@ -30,3 +30,4 @@ future::plan(multicore)
 theme_set(cowplot::theme_cowplot())
 paint::mask_print()
 tar_option_set(memory = "transient")
+options(tflow.report_dir = "docs")