69: Function to compute empirical power for a list of simulated trials #70

holgstr · 2023-09-22T16:09:04Z

Fixes #69

github-actions · 2023-09-22T16:16:00Z

Unit Tests Summary

    1 files   14 suites 2m 9s ⏱️
  57 tests   57 ✔️ 0 💤 0 ❌
138 runs 138 ✔️ 0 💤 0 ❌

Results for commit 7fd7f94.

♻️ This comment has been updated with latest results.

github-actions · 2023-09-22T18:37:26Z

Code Coverage Summary

Filename                     Stmts    Miss  Cover    Missing
-------------------------  -------  ------  -------  ---------
R/assertions.R                  15       0  100.00%
R/eventTracking.R               88       2  97.73%   48, 244
R/getClinicalTrials.R           64       0  100.00%
R/getSimulatedData.R           107       0  100.00%
R/getWaitTimeSum.R              29       2  93.10%   45, 48
R/hazardFunctions.R             26       0  100.00%
R/piecewiseDistribution.R       32       0  100.00%
R/piecewiseHazards.R            18       0  100.00%
R/powerEmp.R                    59       0  100.00%
R/survivalFunctions.R           96       0  100.00%
R/transitionParameters.R        42       0  100.00%
TOTAL                          576       4  99.31%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/eventTracking.R               +8       0  +0.23%
R/getClinicalTrials.R           +6       0  +100.00%
R/getSimulatedData.R            +5       0  +100.00%
R/hazardFunctions.R            +26       0  +100.00%
R/piecewiseDistribution.R       -1       0  +100.00%
R/piecewiseHazards.R            +1       0  +100.00%
R/powerEmp.R                   +59       0  +100.00%
R/survivalFunctions.R          +96       0  +100.00%
TOTAL                         +200       0  +0.37%

Results for commit: e28dc85

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

danielinteractive

nice work, thanks @holgstr - please see few suggestions below

danielinteractive · 2023-09-22T18:39:29Z

R/powerEmp.R

+#' )[[1]]
+#' logRankTest(data = simTrial, typeEvent = "OS", critical = 3.4)
+logRankTest <- function(data, typeEvent, critical) {
+  # must be `1rowTransition`, i.e. have 10 (censored) or 11 columns


Suggested change

# must be `1rowTransition`, i.e. have 10 (censored) or 11 columns

# Must be `1rowTransition`, i.e. have 10 (censored) or 11 columns.

(best to use sentence style for all comments in the code)
re: what means "1rowTransition" ? would it be better to say a bit more here instead of using this abbreviation?

danielinteractive · 2023-09-22T18:40:34Z

R/powerEmp.R

+logRankTest <- function(data, typeEvent, critical) {
+  # must be `1rowTransition`, i.e. have 10 (censored) or 11 columns
+  assert_data_frame(data, min.cols = 10, max.cols = 11)
+  assert_choice(typeEvent, c("OS", "PFS"))


instead of this it is even more elegant to use typeEvent = c("OS", "PFS") in the function signature and then here typeEvent <- match.arg(typeEvent)

danielinteractive · 2023-09-22T18:41:33Z

R/powerEmp.R

+    event <- data$PFSevent
+  }
+
+  logRank <- survdiff(Surv(time, event) ~ trt, data)


Suggested change

logRank <- survdiff(Surv(time, event) ~ trt, data)

logRank <- survival::survdiff(Surv(time, event) ~ trt, data)

since it is not in base R

danielinteractive · 2023-09-22T18:43:10Z

R/powerEmp.R

+  assert_int(eventNumPFS, lower = 1L)
+  assert_int(eventNumOS, lower = 1L)


could also use assert_count(..., positive = TRUE)

danielinteractive · 2023-09-22T18:43:28Z

R/powerEmp.R

+  nRep <- length(simTrials)
+  simTrials <- lapply(simTrials, function(x) if (ncol(x) == 9) getDatasetWideFormat(x) else x)
+
+  # Censor simulated trials at time-point of OS/PFS analysis


Suggested change

# Censor simulated trials at time-point of OS/PFS analysis

# Censor simulated trials at time-point of OS/PFS analysis.

etc (sentence style)

danielinteractive · 2023-09-22T18:44:31Z

R/powerEmp.R

+  simTrials <- lapply(simTrials, function(x) if (ncol(x) == 9) getDatasetWideFormat(x) else x)
+
+  # Censor simulated trials at time-point of OS/PFS analysis
+  trialsAnaPFS <- lapply(simTrials, censoringByNumberEvents,


here we see repeated code for PFS and OS (3 calls which are basically the same for both) - here it would be useful to add an internal helper function that is then used twice here, once for PFS and once for OS to avoid the code duplication

danielinteractive · 2023-09-22T18:45:17Z

R/powerEmp.R

+  # Joint power: Both PFS/OS have significant log-rank tests
+  powerJoint <- sum(sumPassed == 2) / nRep
+
+  c("powerPFS" = powerPFS, "powerOS" = powerOS, "powerAtLeast" = powerAtLeast, "powerJoint" = powerJoint)


best to line break after each element, also consider returning a list instead of a vector - but check first the rest of the package what we use more so far in this kind of situation

danielinteractive · 2023-09-22T18:47:56Z

re: survival package - we have this currently in Suggests only (https://github.com/insightsengineering/simIDM/blob/main/DESCRIPTION#L34) I would move this to Imports and then import a single function in here: https://github.com/insightsengineering/simIDM/blob/main/R/package.R#L8 (does not matter which one, we always will prefix in our code with survival::)

danielinteractive · 2023-09-25T06:59:31Z

R/powerEmp.R

-    eventNum = eventNumOS, typeEvent = "OS"
-  )
+  # Helper function to conduct log-rank tests for either PFS or OS:
+  passedLogRank <- function(typeEvent, eventNum, critical) {


this could be good, but please move it out of the powerEmp function - because only then you can document and test separately

thx @danielinteractive. Can I infer from this that we want "any" function defined separately (i.e., outside the main function) if it is not just a one-liner or a very simple if-else structure (or sth. similar)?

danielinteractive

Thanks @holgstr please see last comments below

R/powerEmp.R

_pkgdown.yaml

holgstr · 2023-09-26T15:02:16Z

@danielinteractive I have implemented all of your suggestions :)

adds functions powerEmp() and logRankTest()

d87a293

holgstr added the enhancement New feature or request label Sep 22, 2023

holgstr requested a review from danielinteractive September 22, 2023 16:09

holgstr self-assigned this Sep 22, 2023

holgstr requested review from niessl and numbersman77 as code owners September 22, 2023 16:09

holgstr added 2 commits September 22, 2023 18:33

adds library call to examples

23638b9

add library(survival) to test

2f702e3

danielinteractive assigned danielinteractive and unassigned holgstr Sep 22, 2023

rename function args

f792478

danielinteractive reviewed Sep 22, 2023

View reviewed changes

holgstr added 2 commits September 23, 2023 21:34

add internal helper function inside powerEmp

d07c0c0

style file

a6dc1df

danielinteractive reviewed Sep 25, 2023

View reviewed changes

move passedLogRank out of powerEmp

4edb84b

danielinteractive reviewed Sep 25, 2023

View reviewed changes

R/powerEmp.R Show resolved Hide resolved

R/powerEmp.R Show resolved Hide resolved

R/powerEmp.R Outdated Show resolved Hide resolved

R/powerEmp.R Outdated Show resolved Hide resolved

R/powerEmp.R Show resolved Hide resolved

_pkgdown.yaml Outdated Show resolved Hide resolved

set passedLogRank to internal use

7fd7f94

danielinteractive approved these changes Sep 26, 2023

View reviewed changes

holgstr merged commit b74388f into main Sep 26, 2023
25 checks passed

holgstr deleted the power-idm branch September 26, 2023 15:09

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

69: Function to compute empirical power for a list of simulated trials #70

69: Function to compute empirical power for a list of simulated trials #70

holgstr commented Sep 22, 2023

github-actions bot commented Sep 22, 2023 •

edited

Loading

github-actions bot commented Sep 22, 2023 •

edited

Loading

danielinteractive left a comment

danielinteractive Sep 22, 2023

danielinteractive Sep 22, 2023

danielinteractive Sep 22, 2023

danielinteractive Sep 22, 2023

danielinteractive Sep 22, 2023

danielinteractive Sep 22, 2023

danielinteractive Sep 22, 2023

danielinteractive commented Sep 22, 2023

danielinteractive Sep 25, 2023

holgstr Sep 25, 2023 •

edited

Loading

danielinteractive left a comment

holgstr commented Sep 26, 2023

	# must be `1rowTransition`, i.e. have 10 (censored) or 11 columns
	# Must be `1rowTransition`, i.e. have 10 (censored) or 11 columns.

	logRank <- survdiff(Surv(time, event) ~ trt, data)
	logRank <- survival::survdiff(Surv(time, event) ~ trt, data)

		assert_int(eventNumPFS, lower = 1L)
		assert_int(eventNumOS, lower = 1L)

	# Censor simulated trials at time-point of OS/PFS analysis
	# Censor simulated trials at time-point of OS/PFS analysis.

69: Function to compute empirical power for a list of simulated trials #70

69: Function to compute empirical power for a list of simulated trials #70

Conversation

holgstr commented Sep 22, 2023

github-actions bot commented Sep 22, 2023 • edited Loading

Unit Tests Summary

github-actions bot commented Sep 22, 2023 • edited Loading

Code Coverage Summary

Diff against main

danielinteractive left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

danielinteractive commented Sep 22, 2023

Choose a reason for hiding this comment

holgstr Sep 25, 2023 • edited Loading

Choose a reason for hiding this comment

danielinteractive left a comment

Choose a reason for hiding this comment

holgstr commented Sep 26, 2023

github-actions bot commented Sep 22, 2023 •

edited

Loading

github-actions bot commented Sep 22, 2023 •

edited

Loading

holgstr Sep 25, 2023 •

edited

Loading