update vignettes #705

mhallal1 · 2022-07-26T15:26:36Z

part of #700

transferred join_keys and preprocessing data vignettes to teal.data
Replaced instances as [XXX()] with XXX
Removed the long printed datasets when possible and the unnecessary messages

github-actions · 2022-07-26T15:32:18Z

Code Coverage Summary

Filename                         Stmts    Miss  Cover    Missing
-----------------------------  -------  ------  -------  -------------------------------------------
R/default_filter.R                   7       7  0.00%    17-27
R/dummy_functions.R                 74      61  17.57%   12-95
R/example_module.R                  17      17  0.00%    19-35
R/get_rcode_utils.R                 52       2  96.15%   94, 99
R/get_rcode.R                      131      51  61.07%   66, 73, 78, 139-148, 186, 212-261
R/include_css_js.R                  24       0  100.00%
R/init.R                            39      21  46.15%   171, 182-183, 236-257
R/log_app_usage.R                   38      38  0.00%    34-119
R/logging.R                         13      13  0.00%    11-28
R/module_nested_tabs.R             113      16  85.84%   57, 96, 100-117, 163, 212, 257
R/module_tabs_with_filters.R        65       0  100.00%
R/module_teal_with_splash.R         33       2  93.94%   62, 74
R/module_teal.R                    119      20  83.19%   49, 52, 142-143, 156-162, 168-174, 197, 227
R/modules_debugging.R               19      19  0.00%    41-60
R/modules.R                        115       9  92.17%   218, 423-448
R/reporter_previewer_module.R       12       2  83.33%   18, 22
R/show_rcode_modal.R                20      20  0.00%    17-38
R/utils.R                            6       0  100.00%
R/validations.R                     62      39  37.10%   103-355
R/zzz.R                             11       7  36.36%   3-14
TOTAL                              970     344  64.54%

Results for commit: 12e45bf

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2022-07-26T15:33:10Z

Unit Tests Summary

    1 files   10 suites 15s ⏱️
107 tests 107 ✔️ 0 💤 0 ❌
207 runs 207 ✔️ 0 💤 0 ❌

Results for commit 2a54a1d.

♻️ This comment has been updated with latest results.

nikolas-burkoff

You need to update the articles list in the pkgdown_yml file
At the bottom of the including -x-data-in-teal vignettes we should have a link to here

nikolas-burkoff · 2022-07-27T09:53:30Z

vignettes/including-adam-data-in-teal.Rmd

+and dataset connector. These can be specified on the most general dataset constructor `dataset` as
 shown below.

-```{r}
+```{r, message=FALSE}
 library(teal)
 library(scda)

-# specify keys x and y on a general dataset
-dataset("x", data.frame(x = c(1, 1:9), y = 2:11, z = 1), keys = c("x", "y"))
-
-# or for ADSL
+# specify keys for ADSL using dataset
 adsl <- synthetic_cdisc_data("latest")$adsl
-dataset("ADSL", adsl, keys = c("STUDYID", "USUBJID"))
+dataset_adsl <- dataset("ADSL", adsl, keys = c("STUDYID", "USUBJID"))
+class(dataset_adsl)


Do we really want users to care about this? Surely we want them to use cdisc_dataset (so they get a parent) - and they can specify a keys argument there?

only cdisc_dataset example is kept.

nikolas-burkoff · 2022-07-27T09:54:26Z

vignettes/including-adam-data-in-teal.Rmd

-
-Note that it is assumed that join keys are symmetric, i.e. `join_key("x", "y", "x_col" = "y_col")` will enable merge
-from "x" to "y" and vice versa.
+If you want to learn more about basics of join keys, please refer to `vignette("join-keys", package = "teal.data")`.


Do we want it to be a vignette call or a link to the github pages?

replaced by this:

For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the `teal.data.` [vignette](https://insightsengineering.github.io/teal.data)

nikolas-burkoff · 2022-07-27T09:56:04Z

vignettes/including-general-data-in-teal.Rmd

@@ -38,7 +38,7 @@ For more information, see documentation in `teal.data`.
 To learn more about DDL, visit `vignette("delayed-data-loading", package = "teal.data")`. All the features of DDL


we should also mention specifying relationships between datasets can be included - see join_keys vignette for details

For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the `teal.data.` [vignette](https://insightsengineering.github.io/teal.data)

added

nikolas-burkoff · 2022-07-27T09:57:15Z

vignettes/including-mae-data-in-teal.Rmd


-```{r}
+```{r, eval = FALSE}


line 41 there's a space before the comma. And I think in line 39 we should refer to tmh specifically as modules which do work with MAE data

…nettes@main

nikolas-burkoff

Looking good - a few tweaks and this can go in

nikolas-burkoff · 2022-07-28T10:20:38Z

vignettes/including-general-data-in-teal.Rmd

@@ -76,3 +76,5 @@ if (interactive()) {
  shinyApp(app$ui, app$server)
 }
 ```
+
+For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the `teal.data.` [vignette](https://insightsengineering.github.io/teal.data)


Suggested change

For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the `teal.data.` [vignette](https://insightsengineering.github.io/teal.data)

For more information about preprocessing, reproducibility, relationships between datasets and DDL, please refer to the [`teal.data` package](https://insightsengineering.github.io/teal.data)

Or point explicitly to the vignette...

Same in other vignettes

nikolas-burkoff · 2022-07-28T10:22:51Z

vignettes/including-mae-data-in-teal.Rmd

@@ -37,5 +37,7 @@ if (interactive()) {
 ```

 The filter panel supports `MAE` data out of the box, but `teal` itself does not guarantee that any module will work with `MAE` data the same way it works with other types of data (e.g. `ADaM`) because `MAE` has a unique structure that needs to be considered when developing a module.
+The package [`teal.modules.hemres`](https://github.com/insightsengineering/teal.modules.hermes) has been specifically developed for the 


Refer to github pages not repo?

vignettes/preprocessing-data.Rmd

…nettes@main

update vignettes

bc0a74e

mhallal1 added the core label Jul 26, 2022

mhallal1 requested a review from nikolas-burkoff July 26, 2022 15:28

nikolas-burkoff self-assigned this Jul 26, 2022

Merge branch 'main' into 700_vignettes@main

65854f7

nikolas-burkoff reviewed Jul 27, 2022

View reviewed changes

mhallal1 and others added 3 commits July 28, 2022 10:30

review

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Merge remote-tracking branch 'origin/700_vignettes@main' into 700_vig…

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…nettes@main

Merge branch 'main' into 700_vignettes@main

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nikolas-burkoff approved these changes Jul 28, 2022

View reviewed changes

mhallal1 and others added 3 commits July 28, 2022 15:29

review 2

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Merge remote-tracking branch 'origin/700_vignettes@main' into 700_vig…

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…nettes@main

Merge branch 'main' into 700_vignettes@main

2a54a1d

mhallal1 merged commit 845d75f into main Jul 29, 2022

mhallal1 deleted the 700_vignettes@main branch July 29, 2022 12:15

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update vignettes #705

update vignettes #705

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		@@ -38,7 +38,7 @@ For more information, see documentation in `teal.data`.
		To learn more about DDL, visit `vignette("delayed-data-loading", package = "teal.data")`. All the features of DDL


		```{r}
		```{r, eval = FALSE}

update vignettes #705

update vignettes #705

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mhallal1 commented Jul 26, 2022 •

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