adds html versions to targets

and creates an index, and makes html look good

R/replace_yaml.R

@@ -0,0 +1,24 @@
+replace_yaml = function(alt_dep, rmd_doc, yaml_doc,
+                        out_file = "docs/ici_kt_manuscript_html.Rmd")
+{
+  # alt_dep = tar_read(manuscript)
+  # rmd_doc = "docs/ici_kt_manuscript.Rmd"
+  # yaml_doc = "docs/html_document_opts.yaml"
+  # out_file = "docs/ici_kt_manuscript_html.Rmd"
+  rmd_contents = readLines(rmd_doc)
+  yaml_locs = grep("---", rmd_contents)
+  yaml_range = seq(yaml_locs[1], yaml_locs[2], 1)
+  rmd_noyaml = rmd_contents[-yaml_range]
+
+  new_yaml = readLines(yaml_doc)
+  new_yaml_delim = c("---", new_yaml, "---")
+  rmd_newyaml = c(new_yaml_delim, rmd_noyaml)
+  cat(rmd_newyaml, file = out_file, sep = "\n", append = FALSE)
+  return(out_file)
+}
+
+copy_figure = function(manuscript_dep, from_loc, to_loc)
+{
+  fs::file_copy(from_loc, to_loc)
+  to_loc
+}

README.md

@@ -21,7 +21,7 @@ If you use any content, you must give attribution to this original work.
 
 ## R Packages Needed
 
-The repository used R 4.1.0, and {renv} 1.0.0
+The repository used R 4.3.0, and {renv} 1.0.0
 For all of the other packages needed, see the file `renv.lock`.
 
 To setup to be able to rerun everything here, you can clone the repo from [github](https://github.com/MoseleyBioinformaticsLab/manuscript.ICIKendallTau) or download it from [Zenodo](https://zenodo.org/doi/10.5281/zenodo.6309187), and then from within that folder:
@@ -81,12 +81,14 @@ Having this cache, you have the state of the computations when we submitted the
 ```
 # make sure you are wherever you want the targets cache, like wherever
 # you cloned the github repo to, at the top level of the directory.
-wget https://zenodo.org/records/10570286/files/manuscript.ICIKendallTau.targets_cache.parts0.tar?download=1 --output-document=manuscript.ICIKendallTau.targets_cache.parts0.tar
-wget https://zenodo.org/records/10570286/files/manuscript.ICIKendallTau.targets_cache.parts1.tar?download=1 --output-document=manuscript.ICIKendallTau.targets_cache.parts1.tar
-wget https://zenodo.org/records/10570256/files/manuscript.ICIKendallTau.targets_cache.parts2.tar?download=1 --output-document=manuscript.ICIKendallTau.targets_cache.parts2.tar
+wget 'https://zenodo.org/records/13873347/files/manuscript.ICIKendallTau.targets_cache.parts0.tar?download=1' --output-document=manuscript.ICIKendallTau.targets_cache.parts0.tar
+wget 'https://zenodo.org/records/13873347/files/manuscript.ICIKendallTau.targets_cache.parts1.tar?download=1' --output-document=manuscript.ICIKendallTau.targets_cache.parts1.tar
+wget 'https://zenodo.org/records/13874988/files/manuscript.ICIKendallTau.targets_cache.parts2.tar?download=1' --output-document=manuscript.ICIKendallTau.targets_cache.parts2.tar
+wget 'https://zenodo.org/records/13874988/files/manuscript.ICIKendallTau.targets_cache.parts3.tar?download=1' --output-document=manuscript.ICIKendallTau.targets_cache.parts3.tar
 
 # now untar them. Note the "k", this keeps the directory from getting overwritten by subsequent un-tar
 tar -xkvf manuscript.ICIKendallTau.targets_cache.parts0.tar
 tar -xkvf manuscript.ICIKendallTau.targets_cache.parts1.tar
 tar -xkvf manuscript.ICIKendallTau.targets_cache.parts2.tar
+tar -xkvf manuscript.ICIKendallTau.targets_cache.parts3.tar
 ```

_targets.R

@@ -372,7 +372,22 @@ documents_plan = tar_plan(
   tar_render(manuscript,
            "docs/ici_kt_manuscript.Rmd"),
   tar_render(lod_stuff,
-             "docs/check_variable_lod.Rmd")
+             "docs/check_variable_lod.Rmd"),
+  tar_render(supp_html,
+             "docs/supplemental_materials.Rmd",
+             output_format = "rmarkdown::html_document"),
+  tar_target(manuscript_alt,
+             replace_yaml(manuscript, "docs/ici_kt_manuscript.Rmd",
+                          "docs/html_document_opts.yaml",
+                          "docs/ici_kt_manuscript_html.Rmd"),
+             format = "file"),
+  tar_render(manuscript_html,
+             "docs/ici_kt_manuscript_html.Rmd",
+             output_file = "ici_kt_manuscript.html"),
+  tar_render(readme_index,
+             "README.md",
+             output_file = "docs/index.html"),
+  copy_fig1 = copy_figure(manuscript, "docs/the_problem.png", "docs/ici_kt_manuscript_files/figure-docx/Figure_1-the-problem.png")
 
 )
 

docs/html_document_opts.yaml

@@ -0,0 +1,14 @@
+title: 'Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values'
+author: "Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley"
+output: 
+  rmarkdown::html_document:
+    self_contained: yes
+    toc: true
+    toc_float:
+      collapsed: false
+      smooth_scroll: false
+date: '`r Sys.time()`'
+bibliography: '`r here::here("docs/icikt_references.json")`'
+csl: plos-computational-biology.csl
+editor_options: 
+  chunk_output_type: console

docs/ici_kt_manuscript.Rmd

@@ -22,8 +22,6 @@ output:
     pandoc_args:
       - '--lua-filter=scholarly-metadata.lua'
       - '--lua-filter=author-info-blocks.lua'
-  rmarkdown::html_document:default:
-    self_contained: yes
 date: '`r Sys.time()`'
 bibliography: '`r here::here("docs/icikt_references.json")`'
 csl: plos-computational-biology.csl

docs/ici_kt_manuscript.md

@@ -22,9 +22,7 @@ output:
     pandoc_args:
       - '--lua-filter=scholarly-metadata.lua'
       - '--lua-filter=author-info-blocks.lua'
-  rmarkdown::html_document:default:
-    self_contained: yes
-date: '2024-09-30 17:38:15.03703'
+date: '2024-10-02 09:18:59.613449'
 bibliography: '/home/rmflight/Documents/manuscripts/in_progress/rmflight_ici-kendallt/docs/icikt_references.json'
 csl: plos-computational-biology.csl
 editor_options: