From fafafd4c949b0071cad7af74883bde8c432619b1 Mon Sep 17 00:00:00 2001 From: scheidec Date: Wed, 15 May 2024 13:05:12 -0400 Subject: [PATCH] Update article links in README, intro vignette - updated links to articles in README and introduction vignette to URLs to pkgdown website rather than `vignette()` code references - added clarification to above documents that articles are available on website only rather than traditional vignettes included with package in effort to reduce package size and dependencies - closes #123 --- README.Rmd | 17 ++++++++++------- README.md | 36 ++++++++++++++++++++---------------- vignettes/SomaDataIO.Rmd | 13 ++++++++----- 3 files changed, 38 insertions(+), 28 deletions(-) diff --git a/README.Rmd b/README.Rmd index 2356021..1683327 100644 --- 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 index 6584b01..6acb46b 100644 --- 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 index c53c8cc..31c9fcc 100644 --- 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. ---------------------