Adding agument `estimate_KM(formula=)` #390

ddsjoberg · 2022-05-29T16:19:43Z

What changes are proposed in this pull request?

Adding formula argument to estimate_KM(). When the formula argument is used, the AVAL, CNSR, and strata args are not used to construct the formula. (Add estimate_KM.formula() method #379)

Did you include unit tests for the proposed change/bug fix (https://testthat.r-lib.org/)?
Yes

If there is an GitHub issue associated with this pull request, please provide link.
closes #379

Checklist for PR reviewer

…into formula_argument

SHAESEN2

Looks great but needs more work for UAT. Also the documentation needs to highlight that our main focus is data standards. We tolerate non-standard formats through the formula argument, not the other way around :)

SHAESEN2 · 2022-06-05T07:33:51Z

R/estimate_KM.R

 #'
-#' @description This function is a wrapper around \code{survival::survfit.formula} to perform a Kaplan-Meier analysis, assuming right-censored data.
-#'    The function expects that the data has been filtered on the parameter (PARAM/PARAMCD) of interest. All NA values in the CNSR, AVAL and strata


This should be kept. You can generalize it if you prefer, but it is important information for the programmer.

I moved this text to a section in the help file

I'll recheck later this week.

One proposal is to mention CDISC compliant data model and explicitly ADTTE and how the function leverages it in the decription. For example, we could add the following qualifer:

The function is designed to leverage the \link[CDISC ADaM ADTTE data model](https://www.cdisc.org/standards/foundational/adam/adam-basic-data-structure-bds-time-event-tte-analyses-v1-0) and more explicity the conventions and controlled vocabulary of the data model. Functionality is also supplied to handle non ADTTE compiant data sets.

SHAESEN2 · 2022-06-05T07:34:40Z

R/estimate_KM.R

@@ -17,15 +14,19 @@
 #'
 #' @seealso \code{\link[survival]{survfit.formula} \link[survival]{survfitCI}}
 #'
-#' @param data The name of the dataset for Time-to-Event analysis based on the Analysis Data Model (ADaM) principles. The dataset is expected to have


Should be kept. Our main focus still is data standards. Non-standard data is the exception that we are allowing for, not what we design for.

CDISC is mentioned 1 million times in the documentation: there is no missing is. This argument now applies to both non-CDISC data and CDISC, and there is no value added adding details about CDISC here as well.

There is added value for statistical programmers. They like things explicit.

there are 5 references to CDISC data in this single help file. The line directly below is "default values follow the naming conventions in CDISC." This is quite explicit

See above - I think a statement at the start then is enough throughout the rest of the help file.

An update to the vignette - one that is not about CDISC - should be sufficient IMO.

SHAESEN2 · 2022-06-05T07:37:36Z

R/estimate_KM.R

+    }
+  }
+  else if (!inherits(formula, "formula")) {
+    stop("Argument `formula=` must be class 'formula'.")


Can you include a requirement test for this: 1. That we allow for the argument. That the argument is tested, the argument cancels out aval and cnsr, ...

I'll recheck later this week.

R/estimate_KM.R

SHAESEN2 · 2022-06-05T07:40:16Z

tests/testthat/test-estimate_KM.R

@@ -43,6 +43,9 @@
 #' T7.2 The function prefixes the function call with survival
 #' T8. Piped datasets still return accurate results
 #' T8.1 Piped datasets still return accurate results
+#' T9. The user can specify formula argument
+#' T9.1 The formula method returns the same results and the data method.


rephrase as we dont work with methods anymore.

I'll recheck later this week.

SHAESEN2 · 2022-06-05T07:40:32Z

tests/testthat/test-estimate_KM.R

@@ -43,6 +43,9 @@
 #' T7.2 The function prefixes the function call with survival
 #' T8. Piped datasets still return accurate results
 #' T8.1 Piped datasets still return accurate results
+#' T9. The user can specify formula argument
+#' T9.1 The formula method returns the same results and the data method.
+#' T9.2 The formula method triggers error messages.


? what does this mean?

I'll recheck later this week.

SHAESEN2 · 2022-06-05T07:41:09Z

tests/testthat/test-estimate_KM.R

@@ -43,6 +43,9 @@
 #' T7.2 The function prefixes the function call with survival
 #' T8. Piped datasets still return accurate results
 #' T8.1 Piped datasets still return accurate results
+#' T9. The user can specify formula argument


I saw more things you implemented as safety nets and requirements eg when the string is empty you put the formula to NULL.

You will have to review above testing to be more specific eg we say "The function relies on the presence of two numeric variables, specified through AVAL and CNSR, to be present in data" but this is now only true when the formula is NULL.

how are we testing the presence of the actual variables inside the formula argument? Are the NAs also removed from those variables, ...

eg when the string is empty you put the formula to NULL.

i am not sure what you're speaking to, this is not done

You will have to review above testing to be more specific eg we say "The function relies on the presence of two numeric variables, specified through AVAL and CNSR, to be present in data" but this is now only true when the formula is NULL.

formula is marked experimental...no need to update these in case implementation is changed

how are we testing the presence of the actual variables inside the formula argument? Are the NAs also removed from those variables, ...

test added to ensure error. NAs are removed.

tests/testthat/test-estimate_KM.R

ddsjoberg · 2022-06-05T12:35:02Z

Looks great but needs more work for UAT.

All comments have been addressed.

Also the documentation needs to highlight that our main focus is data standards. We tolerate non-standard formats through the formula argument, not the other way around :)

The documentation already heavily highlights CDSIC format, and the formula argument is not merely "tolerated": it will in fact be the method the vast majority of the users use to interact with this function.

ddsjoberg · 2022-06-05T12:35:28Z

@bailliem do you want to provide any further review before the PR is merged?

ddsjoberg · 2022-06-08T12:11:58Z

@SHAESEN2 @bailliem let's discuss any outstanding items on the call tomorrow. I am sure we can resolve everything in under 10 minutes.

bailliem · 2022-06-09T09:15:12Z

R/estimate_KM.R

 #'
-#' @description This function is a wrapper around \code{survival::survfit.formula} to perform a Kaplan-Meier analysis, assuming right-censored data.
-#'    The function expects that the data has been filtered on the parameter (PARAM/PARAMCD) of interest. All NA values in the CNSR, AVAL and strata


One proposal is to mention CDISC compliant data model and explicitly ADTTE and how the function leverages it in the decription. For example, we could add the following qualifer:

The function is designed to leverage the \link[CDISC ADaM ADTTE data model](https://www.cdisc.org/standards/foundational/adam/adam-basic-data-structure-bds-time-event-tte-analyses-v1-0) and more explicity the conventions and controlled vocabulary of the data model. Functionality is also supplied to handle non ADTTE compiant data sets.

bailliem · 2022-06-09T09:15:46Z

R/estimate_KM.R

@@ -17,15 +14,19 @@
 #'
 #' @seealso \code{\link[survival]{survfit.formula} \link[survival]{survfitCI}}
 #'
-#' @param data The name of the dataset for Time-to-Event analysis based on the Analysis Data Model (ADaM) principles. The dataset is expected to have


See above - I think a statement at the start then is enough throughout the rest of the help file.

bailliem · 2022-06-09T09:24:50Z

R/estimate_KM.R

@@ -17,15 +14,19 @@
 #'
 #' @seealso \code{\link[survival]{survfit.formula} \link[survival]{survfitCI}}
 #'
-#' @param data The name of the dataset for Time-to-Event analysis based on the Analysis Data Model (ADaM) principles. The dataset is expected to have


An update to the vignette - one that is not about CDISC - should be sufficient IMO.

bailliem · 2022-06-09T09:29:42Z

@SHAESEN2 @bailliem let's discuss any outstanding items on the call tomorrow. I am sure we can resolve everything in under 10 minutes.

Lets discuss today. I proposed one clarification at the start of the description to make it clear that an aim is to leverage a standard data model. But we also accomodation other data. Given the conventions in the survival package, I think this functionality adds value to the package. Maybe we can provide a clearer vignette that goes through this. I think this will be helpful also when we are working with ADAE data and want to do a TTE or competing risks analysis and ADTTE is not set up for it.

@nord

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Tidycmprisk should deal with confint variations - add more informative messages - Do we want to add an overall strata? We can put Overall instead of 1 inside the formula and then add a column strat99= Overall - %||% is not defined. When strata is NULL then the formula becomes ...... ~ NULL in the final object without any error => used ifelse statement testing ------- - we need to focus on what the wrapper is doing, not on what the tidycmprisk function -- test arguments -- test excecuting surrounding the main function -- do not test how the main function works - downstream processing of this object needs to be tested in the respective test files, not in the estimate function - we expect tidycmprisk to do the heavy lifting and testing on the final object. We only verify wether the wrapper does not change the object. If it do * Re-build README.Rmd * review updates * Update _pkgdown.yml * adding `visR::` prefix in examples * review updates from call * Re-build README.Rmd * update for conf.int * Re-build README.Rmd * redocument Co-authored-by: shaesen2 <shaesen2@its.jnj.com> Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * Test/add annotation cuminc updates (#364) * update T1 to include cuminc test * update T2 to include cuminc tests * update T3 to include cuminc * update T5 to include cuminc * update T6 * Fix T3.2 extracted_lbl * spell check updates (#372) * spell check updates * Re-build README.Rmd Co-authored-by: GitHub Actions <actions@github.com> * Update README.Rmd by tableone (#369) * Update README.Rmd by tableone * Re-build README.Rmd * installing and rendering readme * Re-build README.Rmd * updates * Update README.md * Update NEWS.md * Increment version number to 0.2.0.9002 * Re-build README.Rmd Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * Added table.height to add_risktable (#353) * Added table.height to add_risktable * Re-build README.Rmd * unit tests were added * Complete tests + rename var + doc * Added small fixes * Delete test-estimate_CUMINC.R * fix doc reference * Re-build README.Rmd * Update rowgutter default value Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: shaesen2 <shaesen2@its.jnj.com> Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * Update readme tableone display (#376) * update readme tableone display * Re-build README.Rmd * Re-build README.Rmd Co-authored-by: GitHub Actions <actions@github.com> * Add na.rm option to remove the strata variable in rows (#368) * Add na.rm option to remove the strata variable in rows * update unit tests * Re-build README.Rmd * remove na.rm and applied strata filteration * Re-build README.Rmd * Update test-get_tableone.R * Update WORDLIST * increment version number * Re-build README.Rmd Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> Co-authored-by: GitHub Actions <actions@github.com> * Removing warning in `visr()` when PARAMCD not present (#380) * Update visr.R * Update test-visr_survfit.R * Re-build README.Rmd * documentation update * doc updates * increment version number * Re-build README.Rmd Co-authored-by: GitHub Actions <actions@github.com> * Replaced `survfit` call with quo (#366) * replace survfit call with quo * Re-build README.Rmd * Update test-get_pvalue.R * Re-build README.Rmd * Update get_COX_HR.R * Re-build README.Rmd * Update test-watchdog_testfiles.R * Re-build README.Rmd * small adjustments to improve readability * Re-build README.Rmd * updates from review * Re-build README.Rmd * Re-build README.Rmd * doc update * Re-build README.Rmd * Re-build README.Rmd * Added prefix for testthat. Updated documentation for estimate_KM. Removed warning param/paramcd. * Re-build README.Rmd * review updates * Re-build README.Rmd * increment version number Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: shaesen2 <shaesen2@its.jnj.com> * Adding unit tests with cumulative inc. (#387) * adding unit tests * Update get_risktable.Rd * visr survfit check (#389) * WIP: start documenting all functions in render.R * WIP: add roygen skeleton * WIP: remove export for all summarize functions * WIP: remove export for align_plots function * WIP: remove export from get_tableone function * WIP: remove export from get_summary function * WIP: remove export from lhs/pipe function * WIP: remove export for get_risktable and quantilte funcs * Remove lifecycle badge and text. Move remaining badges under installation. * Re-build README.Rmd * add lifecycle to description and experimental badge to render function * document royxgen headings for all functions in render.R. compile documentation. * export what is needed * export what is needed * Re-build README.Rmd * move badge location to under first section - * Re-build README.Rmd * adding lifecycle to wordlist * bump package increment * export * get_summary * align_plots * package bump * tidy up methods of the same s3 class and remove duplication in docs * Re-build README.Rmd * roll back some of the export deletions. trigging test failures and also required for vignettes, examples. * get_* * utils pipe * utilts table * Re-build README.Rmd * WIP: connect the s3 methods for summarize through document. * Tidy up tags * clean up typo and build docs * bump package add experimental tag to get_tableone * Adding agument `estimate_KM(formula=)` (#390) * adding formula argument * adding lifecycle badges * doc update * Re-build README.Rmd * Update test-estimate_KM.R * Re-build README.Rmd * cleaning up before requesting review * review comment updates * typo * Update estimate_KM.R * doc update * Re-build README.Rmd * updates * increment version number Co-authored-by: GitHub Actions <actions@github.com> * Updated to GH Actions V2 * Re-build README.Rmd * Add instruction to check if the readme has been rendered manually. (#404) * Add instruction to check if the readme has been rendered manually. * build readme * Updates from review estimate_KM (#405) * Updated estimate KM testing Updated estimate KM documentation to ensure to user knows that we allow non-CDISC. This was not clear. * Ran `usethis::use_tidy_description()` to put DESCRIPTION entries in standard order * docs * re-adding the error message that was removed. * docs Co-authored-by: shaesen2 <shaesen2@its.jnj.com> Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * Documentation updates (#409) * doc updates * doc updates * Adding `Surv_CNSR()` function (#397) * Create Surv_CDISC.R * updates * doc update * Re-build README.Rmd * Update Surv_CDISC.R * Re-build README.Rmd * Update Surv_CDISC.R * Re-build README.Rmd * doc updates * Re-build README.Rmd * Update NAMESPACE * merge conflict fix * Re-build README.Rmd * updates * Re-build README.Rmd * Update test-Surv_CDISC.R * Re-build README.Rmd * readme * doc updates from review * doc updates * Update test-Surv_CDISC.R * Update testing: - consistent with CDISC philosophy - check the actual requirement - remove req T2.5 as this is not a requirement of our function, but something tested in the backend of survival * removed requirement 2.3 in TOC * change function name * Update testing Included CNSR info in estimate_KM to ensure user will restrict to 0/1 * re-documenting Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: Mark Baillie <bailliem@gmail.com> Co-authored-by: shaesen2 <shaesen2@its.jnj.com> * Update test-Surv_CNSR.R (#410) * fix issues associated with this function * issue fix * Add @nord to internal functions. (#412) Add questioning to functions under development / review * Added test for case when not all colours are defined. * Tiny bugfix, two more tests * Update testing of theming * Updated code/testing for coverage * Include legend title testing * Knit readme Move lifecycle badges to under description Add questioning badge to tabelone * add update to news,md * styler + spell check (#414) * Update pull_request_template.md Co-authored-by: Tim Treis <tim.treis@outlook.de> Co-authored-by: James Black <james@epijim.uk> Co-authored-by: shaesen2 <haesendonckx.steven@gmail.com> Co-authored-by: Tim Treis <tim.treis@stud.uni-heidelberg.de> Co-authored-by: shaesen2 <shaesen2@its.jnj.com> Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: Steven Haesendonckx <47894155+SHAESEN2@users.noreply.github.com> Co-authored-by: Mark Baillie <bailliem@gmail.com> Co-authored-by: Joana M. Barros <94060211+joanacmbarros@users.noreply.github.com> Co-authored-by: ardeeshany <ardeeshany@gmail.com>

ddsjoberg and others added 4 commits May 29, 2022 12:14

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Added estimate_KM.formula() method #386

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Adding agument `estimate_KM(formula=)` #390

Adding agument `estimate_KM(formula=)` #390

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bailliem Jun 9, 2022

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bailliem Jun 9, 2022

bailliem commented Jun 9, 2022

Adding agument estimate_KM(formula=) #390

Adding agument estimate_KM(formula=) #390

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bailliem commented Jun 9, 2022

Adding agument `estimate_KM(formula=)` #390

Adding agument `estimate_KM(formula=)` #390

ddsjoberg commented May 29, 2022 •

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