New commit for additional statistics #663

Prerana17 · 2023-08-16T13:19:34Z

closes ##656

danielinteractive

Thanks @Prerana17 and @0liver0815 please see comments below

R/Design-methods.R

danielinteractive · 2023-08-16T14:13:18Z

R/Design-methods.R

+        )
+
+        # Create list with median MTD and CV.
+        additional_stats <- list(


this is nice I think, however I wonder if we can make this more flexible for the user - e.g. how about accepting a list of functions as part of the simulate() call and then the user can define median, cv functions etc. to apply to target_dose_samples?

Great proposal. I really like that idea. This will add much flexibility e.g. if someone want to see the mean instead of the median etc.. We just have to evaluate, if it is straight forward to implement.

@danielinteractive @0liver0815 Sure, as the next step, I will try to implement the functions where user can define median, cv, mean etc. functions.

danielinteractive · 2023-08-17T08:14:04Z

@Prerana17 @ClaraBeckBayer @0liver0815 I am assuming this is the PR moving forward now and not #661 ? or is that not the case? ... please clarify

0liver0815 · 2023-08-17T11:16:02Z

After talking to @Prerana17, the other PR is closed and the changes that @ClaraBeckBayer added, that were not part of this PR will be added here, so that this PR is up to date. @danielinteractive I think a review makes only sense for you, if the all checks completed without error.

danielinteractive · 2023-08-17T11:17:20Z

Thanks @0liver0815 and @Prerana17 for the clarification :) all good. I did initial review here, please have a look since that could change structure a bit.

…ggetions by Clara

github-actions · 2023-08-17T15:26:02Z

Unit Tests Summary

      1 files     36 suites 2m 33s ⏱️
1 174 tests 1 045 ✔️ 129 💤 0 ❌
6 191 runs 6 027 ✔️ 164 💤 0 ❌

Results for commit 9cdeabe.

♻️ This comment has been updated with latest results.

R/Design-methods.R

0liver0815 · 2023-08-30T15:41:49Z

R/Design-methods.R

+        if (is.null(derive)) {
+          additional_stats <- list()
+        } else {
+          additional_stats <- lapply(derive, function(f) f(target_dose_samples))
+        }


If default is an empty list, I think you can get rid of the if statement

Suggested change

if (is.null(derive)) {

additional_stats <- list()

} else {

additional_stats <- lapply(derive, function(f) f(target_dose_samples))

}

additional_stats <- lapply(derive, function(f) f(target_dose_samples))

0liver0815 · 2023-08-30T15:44:45Z

R/Design-methods.R

+        if (is.null(derive)) {
+          additional_stats <- list()
+        } else {
+          additional_stats <- lapply(derive, function(f) f(target_dose_samples))
+        }


I think it is the same here. lapply works with an empty list.

Suggested change

if (is.null(derive)) {

additional_stats <- list()

} else {

additional_stats <- lapply(derive, function(f) f(target_dose_samples))

}

additional_stats <- lapply(derive, function(f) f(target_dose_samples))

0liver0815 · 2023-08-30T15:46:30Z

R/Design-methods.R

+        # Create a function for additional statistical summary.
+        if (is.null(derive)) {
+          additional_stats <- list()
+        } else {
+          additional_stats <- lapply(derive, function(f) f(target_dose_samples))
+        }


I think you need to add derive = list()to the function as done in line 212 above.

R/Simulations-class.R

R/Design-methods.R

danielinteractive

thanks @Prerana17 , nice work! please see comments below, can you also add a NEWS entry?

R/Design-methods.R

danielinteractive · 2023-08-30T13:48:21Z

R/Design-methods.R

-          median_mtd = median(target_dose_samples),
-          cv_mtd = mad(target_dose_samples) / median(target_dose_samples)
-        )
+        # Create a function for additional statistical summary.


examples/Simulations-method-summary.R

R/Design-methods.R

danielinteractive · 2023-09-08T13:58:39Z

R/Design-methods.R

@@ -209,7 +212,7 @@ setMethod("simulate",
             truth, args = NULL, firstSeparate = FALSE,
             mcmcOptions = McmcOptions(),
             parallel = FALSE, nCores =
-               min(parallel::detectCores(), 5),
+               min(parallel::detectCores(), 5), derive = list(),
             ...) {
      nsim <- safeInteger(nsim)


please assert derive properties here (list, named, unique names, elements are functions) using checkmate package functions

danielinteractive · 2023-09-08T13:59:09Z

R/Design-methods.R

+
+        # Create a function for additional statistical summary.
+
+        additional_stats <- lapply(derive, function(f) f(target_dose_samples))


Suggested change

additional_stats <- lapply(derive, function(f) f(target_dose_samples))

additional_stats <- lapply(derive, f, target_dose_samples)

should work too I guess?

It's throwing error. So I kept same.

yep makes sense actually

danielinteractive · 2023-09-08T14:00:08Z

R/Simulations-class.R

+        o$check(
+          identical(length(object@additional_stats), nSims),
+          "additional_stats must have same length as the number of simulations"
+        )


also check that it has names?

danielinteractive · 2023-09-08T14:00:46Z

R/Simulations-methods.R

+
+        cat(
+          "Results of Additional Statistical Calculation : \n",
+          paste(names(summary_stat_op), ":", round(summary_stat_op), "\n")


ok as a first version, just wondering if we should follow up in another PR to make this printing more flexible

github-actions · 2023-10-09T08:16:44Z

Code Coverage Summary

Filename                    Stmts    Miss  Cover    Missing
------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/checkmate.R                  49       0  100.00%
R/crmPack-package.R             4       0  100.00%
R/Data-class.R                 91       4  95.60%   466-467, 473-478
R/Data-methods.R              203       0  100.00%
R/Data-validity.R             144       1  99.31%   21
R/Design-class.R               75       0  100.00%
R/Design-methods.R           2763    2328  15.74%   111, 136-139, 147-158, 162-181, 193-197, 203-216, 392-969, 1034-1375, 1426, 1616, 1787-4592, 4711
R/Design-validity.R            20       0  100.00%
R/fromQuantiles.R             178      69  61.24%   237-378
R/helpers_covr.R               23       0  100.00%
R/helpers_data.R               84       1  98.81%   139
R/helpers_design.R             75      36  52.00%   22, 77-129
R/helpers_jags.R               77       0  100.00%
R/helpers_model.R              78       4  94.87%   38, 89-90, 139
R/helpers_rules.R             447       0  100.00%
R/helpers.R                   244      80  67.21%   107-127, 140, 153-167, 203-323, 353-402
R/logger.R                     11       0  100.00%
R/mcmc.R                      287      18  93.73%   90-95, 374-375, 385, 387-388, 391-394, 577-578, 667, 673, 731
R/McmcOptions-class.R          18       0  100.00%
R/McmcOptions-methods.R         8       1  87.50%   43
R/McmcOptions-validity.R       42       0  100.00%
R/Model-class.R               962     155  83.89%   135-137, 205-207, 211-213, 272-274, 346-348, 352-354, 433-435, 502-504, 566-570, 573-576, 679-682, 686-687, 802-806, 926-928, 932-940, 1085-1087, 1092-1095, 1099-1102, 1218-1222, 1224-1227, 1231-1234, 1237, 1398-1408, 1413-1419, 1574-1577, 1583-1590, 1747, 1756, 1765, 1774, 1783-1788, 1924, 1933, 1942, 1950-1952, 2693-2722, 2726-2732, 2739-2743, 2748, 2855-2868, 2894, 2990-2992, 2996, 3089-3091, 3095, 3164-3176, 3194
R/Model-methods.R             376      34  90.96%   78, 155, 208, 675-720, 1039-1048
R/Model-validity.R            435       8  98.16%   430-433, 442-445
R/ModelParams-class.R          13       0  100.00%
R/ModelParams-validity.R       21       0  100.00%
R/Rules-class.R               416       2  99.52%   3102, 3169
R/Rules-methods.R            1429     164  88.52%   741, 744, 887, 890, 893, 1008, 1011, 1014, 1134-1137, 1171, 1274-1277, 1312, 2475-2483, 2507-2514, 3017-3260
R/Rules-validity.R            418       0  100.00%
R/Samples-class.R               1       0  100.00%
R/Samples-methods.R          1104      45  95.92%   406-416, 644, 1358-1393, 1616, 1629, 1794, 2124-2129
R/Samples-validity.R           10       0  100.00%
R/Simulations-class.R          51      32  37.25%   408-727
R/Simulations-methods.R      1604    1460  8.98%    65-350, 406, 416-435, 448-453, 500-509, 675-2944
R/Simulations-validity.R       75      75  0.00%    20-168
R/utils.R                       6       0  100.00%
TOTAL                       11842    4517  61.86%

Diff against main

Filename                    Stmts    Miss  Cover
------------------------  -------  ------  --------
R/Design-methods.R            +29     +18  +0.24%
R/Simulations-class.R          +1       0  +1.25%
R/Simulations-methods.R        +7      +6  +0.02%
R/Simulations-validity.R      +75     +75  +100.00%
TOTAL                        +112     +99  -0.48%

Results for commit: 9cdeabe

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

…into 656_additional_stat

* Refactor setSeed and getResultList (#676) Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * 675: Add `DesignGrouped` (#677) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Fixes first cohort logic for grouped design simulation (#684) * Remove references to is.bool and is.scalar (#686) * Remove references to is.bool and is.scalar * [skip actions] Restyle files * Responding to review comments * Removing lintr moan * Updating documentation --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Remove plot.gtable and print.gtable (#697) * Remove plot.gtable and print.gtable * Fix _pkgdown.yaml * 690 remove safeinteger and iswholenumber 1 (#693) * Remove safeInteger and is.wholenumber * Fixing false test failures * [skip actions] Restyle files --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Remove noOverlap (#695) * remove %~% (#689) * remove %~% * Fixing NAMESPACE * 699 remove multiplot (#700) * Remove multiplot * Correct typo * Correcting typo in argument to assert_integerish * New commit for additional statistics (#663) * New commit for additional statistics * [skip actions] Restyle files * Update: additional statstics added to other designs bug correction suggetions by Clara * bug corrected * Update: Additional_stats * update: additional_stats * updaze: error_corrections (additional_stats) * update: additional_statistics * Dynamic: Additional_statistical_summary * Additional statistical summary function update * additional statistical summary changes * Update: Additional Statistical Summary * small change: additional stat summary * Suggested changes: additional_statistics and validation * [skip actions] Restyle files * Simulation refectoring * Simulation small update * [skip actions] Restyle files * small update * incorrectly named file:delete * removing documentation errors * update yaml file --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Clara <clara.beck@bayer.com> Co-authored-by: Oliver Boix <95433070+0liver0815@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> * Refactor myBarplot (#703) * Refactor myBarplot * [skip actions] Restyle files * Responding to lintr complaints * Rsponding to review comments --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> --------- Co-authored-by: Oliver Boix <95433070+0liver0815@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Prerana Chandratre <82475780+Prerana17@users.noreply.github.com> Co-authored-by: Clara <clara.beck@bayer.com>

New commit for additional statistics

02e6855

Prerana17 requested a review from danielinteractive as a code owner August 16, 2023 13:19

Merge 02e6855 into 23982de

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Prerana17 and others added 2 commits August 17, 2023 13:50

Update: additional statstics added to other designs bug correction su…

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…ggetions by Clara

bug corrected

ebfd762

Prerana17 added 4 commits August 18, 2023 11:54

Update: Additional_stats

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update: additional_stats

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updaze: error_corrections (additional_stats)

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update: additional_statistics

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danielinteractive linked an issue Aug 29, 2023 that may be closed by this pull request

Add additional statistics to the analysis of simulation output #656

Closed

Dynamic: Additional_statistical_summary

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Prerana17 added 2 commits August 31, 2023 12:27

Additional statistical summary function update

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additional statistical summary changes

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Prerana17 added 2 commits September 1, 2023 12:30

Update: Additional Statistical Summary

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small change: additional stat summary

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Merge branch 'main' into 656_additional_stat

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Prerana17 and others added 9 commits September 14, 2023 16:48

Suggested changes: additional_statistics and validation

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Merge bea2537 into 1762da7

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Merge branch 'main' into 656_additional_stat

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Simulation small update

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Merge branch 'main' into 656_additional_stat

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Prerana17 and others added 8 commits October 9, 2023 12:52

small update

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Merge branch '656_additional_stat' of https://github.com/Roche/crmPack …

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incorrectly named file:delete

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Merge branch 'main' into 656_additional_stat

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Merge branch 'main' into 656_additional_stat

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Merge branch 'main' into 656_additional_stat

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Prerana17 merged commit 14d4d52 into main Oct 11, 2023
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Prerana17 deleted the 656_additional_stat branch October 11, 2023 08:35

Puzzled-Face mentioned this pull request Oct 16, 2023

Implement the LogisticLogNormalOrdinal class (#708) #709

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New commit for additional statistics #663

New commit for additional statistics #663

Prerana17 commented Aug 16, 2023 •

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		# Create a function for additional statistical summary.

		additional_stats <- lapply(derive, function(f) f(target_dose_samples))

	additional_stats <- lapply(derive, function(f) f(target_dose_samples))
	additional_stats <- lapply(derive, f, target_dose_samples)

New commit for additional statistics #663

New commit for additional statistics #663

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