Merge pull request #33 from SchlossLab/improve-docs

Improve docs

.github/workflows/check.yaml

@@ -33,7 +33,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}

NEWS.md

@@ -4,6 +4,7 @@
     - New column `label_html` provides HTML to correctly italicize genus names but not OTU labels.
     - Added an example the intro vignette to demonstrate using this feature with `ggtext`.
     - Changed taxonomy data frame column names to lowercase and reordered them.
+- Minor documentation improvements (#33, @kelly-sovacool)
 
 # schtools 0.1.1
 

README.Rmd

@@ -51,6 +51,23 @@ or the development version from [GitHub](https://github.com/SchlossLab/schtools)
 devtools::install_github("SchlossLab/schtools")
 ```
 
+or install from a terminal using
+[conda](https://docs.conda.io/projects/conda/en/latest/index.html)
+or [mamba](https://mamba.readthedocs.io/en/latest/):
+
+```{bash conda, eval = FALSE}
+mamba install -c conda-forge r-schtools
+```
+
+
+## Usage
+
+Check out the 
+[introductory vignette](http://www.schlosslab.org/schtools/articles/introduction.html) 
+for a quick start tutorial or take a look at the 
+[reference documentation](http://www.schlosslab.org/schtools/reference/index.html) 
+for a comprehensive list of functions.
+
 ## Help & Contributing
 
 If you come across a bug, [open an

README.md

@@ -41,6 +41,22 @@ or the development version from
 devtools::install_github("SchlossLab/schtools")
 ```
 
+or install from a terminal using
+[conda](https://docs.conda.io/projects/conda/en/latest/index.html) or
+[mamba](https://mamba.readthedocs.io/en/latest/):
+
+``` bash
+mamba install -c conda-forge r-schtools
+```
+
+## Usage
+
+Check out the [introductory
+vignette](http://www.schlosslab.org/schtools/articles/introduction.html)
+for a quick start tutorial or take a look at the [reference
+documentation](http://www.schlosslab.org/schtools/reference/index.html)
+for a comprehensive list of functions.
+
 ## Help & Contributing
 
 If you come across a bug, [open an

_pkgdown.yml

@@ -12,3 +12,29 @@ authors:
         href: "https://github.com/NLesniak"
     Patrick Schloss:
         href: "https://github.com/pschloss"
+reference:
+- title:
+  contents:
+  - schtools
+- title: Readers
+  desc: >
+    Read microbiome-related files.
+  contents:
+  - starts_with('read_')
+  - starts_with('parse_')
+- title: R Markdown helpers
+  desc: >
+    Format publication-quality documents.
+  contents:
+  - set_knitr_opts
+  - inline_hook
+  - paste_oxford_list
+  - format_number
+- title: Everything else
+  desc: >
+    Useful tools for miscellaneous tasks.
+  contents:
+  - close_enough
+  - is_nearly_whole
+  - is_nondesc
+  - load_deps

docs/pkgdown.yml

@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   logo: logo.html
   introduction: introduction.html
-last_built: 2022-04-27T18:41Z
+last_built: 2022-05-11T21:22Z
 urls:
   reference: http://www.schlosslab.org/schtools/reference
   article: http://www.schlosslab.org/schtools/articles

vignettes/articles/logo.Rmd

@@ -28,15 +28,13 @@ showtext_auto()
 
 ## Emojis
 
-From OpenMoji, [licensed under CC BY SA 4.0](https://github.com/hfg-gmuend/openmoji/blob/master/LICENSE.txt)
+From OpenMoji, [licensed under CC BY-SA 4.0](https://github.com/hfg-gmuend/openmoji/blob/master/LICENSE.txt)
 
 - poop: https://openmoji.org/library/#search=poo&emoji=1F4A9
 - wrench: https://openmoji.org/library/#search=tool&emoji=1F527
 - hammer: https://openmoji.org/library/#search=tool&emoji=1F528
 
-## Schtools Logo
-
-```{r logo, dpi=300}
+```{r emojis, dpi=300, out.width='50%'}
 poo_file <- here('vignettes', 'articles','1F4A9_color.png')
 wrench_file <- here('vignettes', 'articles', '1F527_color.png')
 hammer_file <- here('vignettes', 'articles', '1F528_color.png')
@@ -49,18 +47,26 @@ ggsave2(img,
         height = 2,
         width = 2,
         units = 'in')
+img
+```
+
 
+## Schtools Logo
+
+```{r logo, dpi=300, out.width='50%'}
 mint <- '#A2EAE0'
 pink <- '#FA9DC5'
 orange <- '#FFDBAD'
 black <- '#000000'
-
+logo_filename <-  here('vignettes', 'articles', 'schtools-logo.png')
 sticker(img, package = 'schtools', 
         s_x = 1, s_y = 0.85, s_width = 1.6, s_height = 1.6,
         p_x = 1, p_y = 1.55, p_color = black, 
         p_size = 23, p_family = 'Source Sans Pro', 
         h_fill = mint, h_color = orange,
         url = 'schlosslab.org/schtools', u_size = 3.5,
-        filename = here('vignettes', 'articles', 'schtools-logo.png'))
+        filename = logo_filename)
+ggdraw() +
+    draw_image(logo_filename)
 ```