intended use #105

waddella · 2021-12-07T17:26:10Z

including data pre-processing

linting

…le-subtitle-and-footnotes@main

…refactor

adapt aet03 adapt aet04 adapt dmt01_1 adapt dst01 adapt ext01

eliminate intermediate variables rename arg

github-actions · 2021-12-07T18:46:22Z

File	Coverage		Missing
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R/aet02.R	`0%`	❌	`57-427`
R/aet03.R	`0%`	❌	`45-151`
R/aet04.R	`0%`	❌	`55-163`
R/assertthat.R	`0%`	❌	`3`
R/dmt01.R	`0%`	❌	`48-110`
R/dst01.R	`0%`	❌	`6-540`
R/ext01.R	`0%`	❌	`42-183`
R/gen_args.R	`0%`	❌	`20`
R/lbt01.R	`0%`	❌	`45-115`
R/standard_data_preprocessing.R	`0%`	❌	`29-325`
R/utils.R	`0%`	❌	`15-384`

Minimum allowed coverage is 80%

Generated by 🐒 cobertura-action against 6018f0d

wangh107 · 2021-12-08T02:49:20Z

@waddella
Is it possible to add example of how extra_args should be defined in the variable lopo in the intended_use vignettes?
If I need to change the arm and overall label, how would you suggest we specify them?

BFalquet

Minor comments otherwise ready to merge. Thank you for the hard work.

BFalquet · 2021-12-08T10:12:26Z

vignettes/layouts.Rmd

+Hence these layouts define a table pre-data. Note that pruning and sorting are currently not performed in the layout space in `rtables` but rather on the actual table objects.
+


I would add that in general, we try to make the layout function independent from the data, in the sense that they shouldn't take a dm or part of a dm object as an argument. Indeed, there is frequently a temptation to extract data from the dm object (for instances labels) inside the layout function and this is a bad idea.

see my suggestion above

BFalquet · 2021-12-08T10:13:35Z

vignettes/layouts.Rmd

+* `chevron` exports the layout functions for each table creating *tlg-function*
+* these layouts are useful to understand how table is created and what variables are required in the data to create a table using the layout
+* the table creation functions focus the main part of their code on building, sorting and pruning the table
+


Maybe a word about headers and footnotes.

please see my my suggestion below

BFalquet · 2021-12-08T10:15:14Z

vignettes/introduction.Rmd

+1. they produce a narrow defined output (currently standards in Roche GDS). Note, that the naming convention 
+   `<gds template id>_<i>` indicates that a Roche GDS defined standard may have different implementations. Or,
+    alternatively, a GDS template id can be regarded as a *guideline* and the function name in `chevron` as a
+    *standard*.
+1. have very few arguments to modify the standard. Generally, arguments may change the structure of the table (arm
+variable, which variables are summarized) but not parameterize the cell content (i.e. alpha-level for p-value).
+1. have always the first argument `adam_db` which is the collection of ADaM datasets (`ADSL`, `ADAE`,
+`ADRS`, etc.). Please read the *The adam_db Argument* vignette in this package for more details.
+1. have a `.study` argument, read the *The .study argument* vignette for more detail.


Suggested change

1. they produce a narrow defined output (currently standards in Roche GDS). Note, that the naming convention

`<gds template id>_<i>` indicates that a Roche GDS defined standard may have different implementations. Or,

alternatively, a GDS template id can be regarded as a *guideline* and the function name in `chevron` as a

*standard*.

1. have very few arguments to modify the standard. Generally, arguments may change the structure of the table (arm

variable, which variables are summarized) but not parameterize the cell content (i.e. alpha-level for p-value).

1. have always the first argument `adam_db` which is the collection of ADaM datasets (`ADSL`, `ADAE`,

`ADRS`, etc.). Please read the *The adam_db Argument* vignette in this package for more details.

1. have a `.study` argument, read the *The .study argument* vignette for more detail.

1. they produce a narrow defined output (currently standards in Roche GDS). Note, that the naming convention

`<gds template id>_<i>` indicates that a Roche GDS defined standard may have different implementations. Or,

alternatively, a GDS template id can be regarded as a *guideline* and the function name in `chevron` as a

*standard*.

2. have very few arguments to modify the standard. Generally, arguments may change the structure of the table (arm

variable, which variables are summarized) but not parameterize the cell content (i.e. alpha-level for p-value).

3. have always the first argument `adam_db` which is the collection of ADaM datasets (`ADSL`, `ADAE`,

`ADRS`, etc.). Please read the *The adam_db Argument* vignette in this package for more details.

4. have a `.study` argument, read the *The .study argument* vignette for more detail.

the numbering happens automatically in markdown

vignettes/adam_db_argument.Rmd

BFalquet · 2021-12-08T10:18:35Z

vignettes/adam_db_argument.Rmd

+validate_dm(adam_study_data)
+```
+
+Note that the keys are defined in the data analysis plan at Roche.


maybe a link with an example if it is possible.

I will leave it out as it is an internal resource. This is something to revisit though.

R/standard_data_preprocessing.R

waddella

@BFalquet thanks for reviewing, please have a look at my suggested changes

R/standard_data_preprocessing.R

vignettes/adam_db_argument.Rmd

waddella · 2021-12-08T10:29:27Z

vignettes/adam_db_argument.Rmd

+validate_dm(adam_study_data)
+```
+
+Note that the keys are defined in the data analysis plan at Roche.


I will leave it out as it is an internal resource. This is something to revisit though.

waddella · 2021-12-08T10:31:10Z

vignettes/introduction.Rmd

+1. they produce a narrow defined output (currently standards in Roche GDS). Note, that the naming convention 
+   `<gds template id>_<i>` indicates that a Roche GDS defined standard may have different implementations. Or,
+    alternatively, a GDS template id can be regarded as a *guideline* and the function name in `chevron` as a
+    *standard*.
+1. have very few arguments to modify the standard. Generally, arguments may change the structure of the table (arm
+variable, which variables are summarized) but not parameterize the cell content (i.e. alpha-level for p-value).
+1. have always the first argument `adam_db` which is the collection of ADaM datasets (`ADSL`, `ADAE`,
+`ADRS`, etc.). Please read the *The adam_db Argument* vignette in this package for more details.
+1. have a `.study` argument, read the *The .study argument* vignette for more detail.


the numbering happens automatically in markdown

vignettes/layouts.Rmd

waddella · 2021-12-08T10:32:27Z

vignettes/layouts.Rmd

+Hence these layouts define a table pre-data. Note that pruning and sorting are currently not performed in the layout space in `rtables` but rather on the actual table objects.
+


see my suggestion above

vignettes/layouts.Rmd

waddella · 2021-12-08T10:34:31Z

vignettes/layouts.Rmd

+* `chevron` exports the layout functions for each table creating *tlg-function*
+* these layouts are useful to understand how table is created and what variables are required in the data to create a table using the layout
+* the table creation functions focus the main part of their code on building, sorting and pruning the table
+


please see my my suggestion below

benoit and others added 30 commits November 2, 2021 15:54

refactor arguments organisation

c66b671

linting

linter correction

7c28f55

Document

fc1aa00

add_existing_table

32f35dc

Merge branch '79_split-gen_args_spec_study@main' into 84_maintain-tit…

a362a50

…le-subtitle-and-footnotes@main

linting

7e49f6c

add a setfooter function as a temporary fix

5dc770f

linting

dfb217e

add return description

e65d5d2

work in progress

92c9087

work on aet02.R

3fd0e7b

Merge branch '84_maintain-title-subtitle-and-footnotes@main' into 94_…

77e459e

…refactor

bugfix

63241fe

adapt aet03 adapt aet04 adapt dmt01_1 adapt dst01 adapt ext01

discussion with Adrian

77256aa

add filter for adex

fc88bcb

changes as discussed in the meeting

265d94a

simplify layout function

0ea94ef

eliminate intermediate variables rename arg

as per discussion

12f33ba

rename args

4381b71

start working on vignettes

5301645

added more content

d7ae31d

work on adam_db

1461784

work on intended use

ed0edd3

work on templates

2ce46eb

co-work with Gabe

e6dede3

some updates

367f21b

Merge remote-tracking branch 'origin/main' into 96_vignettes

1b8296c

work in progress

aeee055

wrap up the beam light concept

bb82851

fix error, warnings, notes

ff5537b

waddella requested a review from BFalquet December 7, 2021 17:26

update pkgdown configuration

6b56dc8

insightsengineering deleted a comment from github-actions bot Dec 7, 2021

update README

cd362d5

BFalquet approved these changes Dec 8, 2021

View reviewed changes

waddella commented Dec 8, 2021

View reviewed changes

waddella and others added 13 commits December 8, 2021 14:30

Update vignettes/adam_db_argument.Rmd

5513d05

Update vignettes/adam_db_argument.Rmd

45890fd

Update vignettes/layouts.Rmd

e576699

Update vignettes/layouts.Rmd

75429cd

work on typos and linting

ebcc140

remove trailing whitespaces

250ef2d

yet more trailing whitespace removal

3aba313

address more superlinter issues

a61af3b

more superlinter issues

3215bff

...

f0351c2

more linter issues addressed

8095288

more lintr issues

24bb155

add a modified standard

6018f0d

waddella merged commit 7b4ef11 into main Dec 9, 2021

waddella deleted the 96_vignettes branch December 9, 2021 08:39

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intended use #105

intended use #105

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		Hence these layouts define a table pre-data. Note that pruning and sorting are currently not performed in the layout space in `rtables` but rather on the actual table objects.

intended use #105

intended use #105

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