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Update article links in README, intro vignette #124

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Update article links in README, intro vignette #124

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17 changes: 10 additions & 7 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand All @@ -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.


Expand All @@ -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.


Expand All @@ -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.

---------------------

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36 changes: 20 additions & 16 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down Expand Up @@ -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

Expand All @@ -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

Expand All @@ -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.

------------------------------------------------------------------------

Expand Down
13 changes: 8 additions & 5 deletions vignettes/SomaDataIO.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand All @@ -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.

---------------------

Expand Down
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