Merge pull request #124 from scheidec/fix-article-links

Update article links in README, intro vignette
SomaLogic · May 15, 2024 · 9586713 · 9586713
2 parents bda55a1 + fafafd4
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diff --git a/README.Rmd b/README.Rmd
@@ -194,7 +194,7 @@ to users to run canned examples (or analyses). They can be accessed once
     + [dplyr](https://dplyr.tidyverse.org) and [tidyr](https://tidyr.tidyverse.org) verb
       S3 methods for the `soma_adat` class.
     + `?rownames` helpers that do not break `soma_adat` attributes.
-    + please see vignette `vignette("tips-loading-and-wrangling", package = "SomaDataIO")`
+    + please see the article [Loading and Wrangling 'SomaScan'](https://somalogic.github.io/SomaDataIO/articles/tips-loading-and-wrangling.html)
 
 * Exporting data (Output)
     + write out a `soma_adat` object as a `*.adat` text file.
@@ -217,7 +217,7 @@ is.soma_adat(my_adat)
 my_adat
 ```
 
-Please see vignette `vignette("tips-loading-and-wrangling", package = "SomaDataIO")`
+Please see the article [Loading and Wrangling SomaScan](https://somalogic.github.io/SomaDataIO/articles/tips-loading-and-wrangling.html)
 for more details and options.
 
 
@@ -233,7 +233,7 @@ S3 methods to the most popular
 methods(class = "soma_adat")
 ```
 
-Please see vignette `vignette("tips-loading-and-wrangling", package = "SomaDataIO")`
+Please see the article [Loading and Wrangling SomaScan](https://somalogic.github.io/SomaDataIO/articles/tips-loading-and-wrangling.html)
 for more details about available `soma_adat` methods.
 
 
@@ -254,20 +254,23 @@ For further detail please see:
 
 - Two-group comparison (e.g. differential expression) via *t*-test
   + see `stats::t.test()`
-  + see vignette `vignette("stat-two-group-comparison", package = "SomaDataIO")`
+  + see workflow: [Two-Group Comparison](https://somalogic.github.io/SomaDataIO/articles/stat-two-group-comparison.html)
 
 - Multi-group comparison (e.g. differential expression) via ANOVA
   + see `stats::aov()`
-  + see vignette `vignette("stat-three-group-analysis-anova", package = "SomaDataIO")`
+  + see workflow: [ANOVA Three-Group Analysis](https://somalogic.github.io/SomaDataIO/articles/stat-three-group-analysis-anova.html)
 
 - Binary classification
   + see `stats::glm()`
-  + see vignette `vignette("stat-binary-classification", package = "SomaDataIO")`
+  + see workflow: [Binary Classification](https://somalogic.github.io/SomaDataIO/articles/stat-binary-classification.html)
 
 - Linear regression
   + see `stats::lm()`
-  + see vignette `vignette("stat-linear-regression", package = "SomaDataIO")`
+  + see workflow: [Linear Regression](https://somalogic.github.io/SomaDataIO/articles/stat-linear-regression.html)
 
+Note that, in an effort to reduce package size and dependencies, these articles
+and workflows are only accessible via the `SomaDataIO` `pkgdown` website, and
+are not included with the installed package.
 
 ---------------------
 

diff --git a/README.md b/README.md
@@ -174,8 +174,8 @@ to run canned examples (or analyses). They can be accessed once
     [tidyr](https://tidyr.tidyverse.org) verb S3 methods for the
     `soma_adat` class.
   - `?rownames` helpers that do not break `soma_adat` attributes.
-  - please see vignette
-    `vignette("tips-loading-and-wrangling", package = "SomaDataIO")`
+  - please see the article [Loading and Wrangling
+    ‘SomaScan’](https://somalogic.github.io/SomaDataIO/articles/tips-loading-and-wrangling.html)
 - Exporting data (Output)
   - write out a `soma_adat` object as a `*.adat` text file.
 
@@ -230,9 +230,9 @@ my_adat
 #> ════════════════════════════════════════════════════════════════════════════════
 ```
 
-Please see vignette
-`vignette("tips-loading-and-wrangling", package = "SomaDataIO")` for
-more details and options.
+Please see the article [Loading and Wrangling
+SomaScan](https://somalogic.github.io/SomaDataIO/articles/tips-loading-and-wrangling.html)
+for more details and options.
 
 ## Wrangling
 
@@ -254,9 +254,9 @@ methods(class = "soma_adat")
 #> see '?methods' for accessing help and source code
 ```
 
-Please see vignette
-`vignette("tips-loading-and-wrangling", package = "SomaDataIO")` for
-more details about available `soma_adat` methods.
+Please see the article [Loading and Wrangling
+SomaScan](https://somalogic.github.io/SomaDataIO/articles/tips-loading-and-wrangling.html)
+for more details about available `soma_adat` methods.
 
 ## ADAT structure
 
@@ -273,20 +273,24 @@ detail please see:
 
 - Two-group comparison (e.g. differential expression) via *t*-test
   - see `stats::t.test()`
-  - see vignette
-    `vignette("stat-two-group-comparison", package = "SomaDataIO")`
+  - see workflow: [Two-Group
+    Comparison](https://somalogic.github.io/SomaDataIO/articles/stat-two-group-comparison.html)
 - Multi-group comparison (e.g. differential expression) via ANOVA
   - see `stats::aov()`
-  - see vignette
-    `vignette("stat-three-group-analysis-anova", package = "SomaDataIO")`
+  - see workflow: [ANOVA Three-Group
+    Analysis](https://somalogic.github.io/SomaDataIO/articles/stat-three-group-analysis-anova.html)
 - Binary classification
   - see `stats::glm()`
-  - see vignette
-    `vignette("stat-binary-classification", package = "SomaDataIO")`
+  - see workflow: [Binary
+    Classification](https://somalogic.github.io/SomaDataIO/articles/stat-binary-classification.html)
 - Linear regression
   - see `stats::lm()`
-  - see vignette
-    `vignette("stat-linear-regression", package = "SomaDataIO")`
+  - see workflow: [Linear
+    Regression](https://somalogic.github.io/SomaDataIO/articles/stat-linear-regression.html)
+
+Note that, in an effort to reduce package size and dependencies, these
+articles and workflows are only accessible via the `SomaDataIO`
+`pkgdown` website, and are not included with the installed package.
 
 ------------------------------------------------------------------------
 

diff --git a/vignettes/SomaDataIO.Rmd b/vignettes/SomaDataIO.Rmd
@@ -44,7 +44,7 @@ contributed packages from the Comprehensive R Archive Network (CRAN).
     + [dplyr](https://dplyr.tidyverse.org) and [tidyr](https://tidyr.tidyverse.org) verb
       S3 methods for the `soma_adat` class.
     + `?rownames` helpers that do not break `soma_adat` attributes.
-    + please see vignette `vignette("tips-loading-and-wrangling", package = "SomaDataIO")`
+    + please see the article [Loading and Wrangling 'SomaScan'](https://somalogic.github.io/SomaDataIO/articles/tips-loading-and-wrangling.html)
 
 * Exporting data (Output)
     + write out a `soma_adat` object as a `*.adat` text file.
@@ -61,20 +61,23 @@ primary statistical analyses that are commonly performed on
 
 - Two-group comparison (e.g. differential expression) via *t*-test
   + see `stats::t.test()`
-  + see vignette `vignette("stat-two-group-comparison", package = "SomaDataIO")`
+  + see workflow: [Two-Group Comparison](https://somalogic.github.io/SomaDataIO/articles/stat-two-group-comparison.html)
 
 - Multi-group comparison (e.g. differential expression) via ANOVA
   + see `stats::aov()`
-  + see vignette `vignette("stat-three-group-analysis-anova", package = "SomaDataIO")`
+  + see workflow: [ANOVA Three-Group Analysis](https://somalogic.github.io/SomaDataIO/articles/stat-three-group-analysis-anova.html)
 
 - Binary classification
   + see `stats::glm()`
-  + see vignette `vignette("stat-binary-classification", package = "SomaDataIO")`
+  + see workflow: [Binary Classification](https://somalogic.github.io/SomaDataIO/articles/stat-binary-classification.html)
 
 - Linear regression
   + see `stats::lm()`
-  + see vignette `vignette("stat-linear-regression", package = "SomaDataIO")`
+  + see workflow: [Linear Regression](https://somalogic.github.io/SomaDataIO/articles/stat-linear-regression.html)
 
+Note that, in an effort to reduce package size and dependencies, these articles
+and workflows are only accessible via the `SomaDataIO` `pkgdown` website, and
+are not included with the installed package.
 
 ---------------------