Description

This is a small PR addressing a potential issue where read_redcap may incorrectly guess a column type when a large amount of rows are empty or sparsely populated. This relates to default behavior documented in readr:

If you don’t explicit specify column types with the col_types argument, readr will attempt to guess them using some simple heuristics. By default, it will inspect 1000 values, evenly spaced from the first to the last row.

Proposed Changes

List changes below in bullet format:

Expose guess_max argument from REDCapR::redcap_read_oneshot() call via param in read_redcap
Update mocks with new Large Sparse REDCap
Add tests

Issue Addressed

Closes #141

`microbenchmark` Test Results

The test results from running microbenchmark across all creds in our utility/ folder didn't yield very consistent results:

Click me for comparison results - n of 1

Guess Max Inf | | Guess Max 1000 | | Difference | Database Type -- | -- | -- | -- | -- | -- max | neval | max | neval | | 1.2 | 1 | 1.71 | 1 | -0.51 | simple static (read-only) test project 2.24 | 1 | 2.11 | 1 | 0.13 | longitudinal (read-only) ARM test project 780.97 | 1 | 782.25 | 1 | -1.28 | simple write data 5.22 | 1 | 5.98 | 1 | -0.76 | Russian Characters 8.56 | 1 | 8.41 | 1 | 0.15 | super-wide --3,000 columns 864.01 | 1 | 1.21 | 1 | 862.8 | static (not longitudinal) survey test project 780.11 | 1 | 839.75 | 1 | -59.64 | Clinical Trial (Fake) --Read-only 786.01 | 1 | 1.04 | 1 | 784.97 | nonnumeric record_id 709.49 | 1 | 832.68 | 1 | -123.19 | DAG Read 742.39 | 1 | 1 | 1 | 741.39 | potentially problematic values 768.1 | 1 | 1.06 | 1 | 767.04 | Repeating Instruments 879.26 | 1 | 1.23 | 1 | 878.03 | simple write metadata 815.74 | 1 | 1.11 | 1 | 814.63 | DAG Write -admin 907.86 | 1 | 734.05 | 1 | 173.81 | DAG Write -group A 368.46 | 1 | 374.19 | 1 | -5.73 | super-wide --35,000 columns 762.27 | 1 | 819.12 | 1 | -56.85 | Repeating Instruments --Sparse 692.52 | 1 | 1.06 | 1 | 691.46 | Delete Single Arm 1.13 | 1 | 1.14 | 1 | -0.01 | Delete Multiple Arm 1.1 | 1 | 1.42 | 1 | -0.32 | longitudinal single arm 893.67 | 1 | 1.04 | 1 | 892.63 | decimal comma and dot 715.75 | 1 | 949.61 | 1 | -233.86 | decimal comma 760.67 | 1 | 943.93 | 1 | -183.26 | decimal dot 784.9 | 1 | 1.1 | 1 | 783.8 | Validation Types 783.78 | 1 | 1.14 | 1 | 782.64 | Blank for Gray Status 707.08 | 1 | 1.03 | 1 | 706.05 | Checkboxes 1 773.73 | 1 | 1.05 | 1 | 772.68 | Vignette: Longitudinal & Repeating Measures 2.61 | 1 | 2.7 | 1 | -0.09 | classic 3.43 | 1 | 3 | 1 | 0.43 | classic no repeat 3.51 | 1 | 4.27 | 1 | -0.76 | longitudinal 3 | 1 | 3.98 | 1 | -0.98 | longitudinal no arms 4.26 | 1 | 4.58 | 1 | -0.32 | longitudinal no repeat 5.27 | 1 | 7.98 | 1 | -2.71 | deep dive vignette 1.99 | 1 | 3.07 | 1 | -1.08 | repeat first instrument 3.36 | 1 | 4.69 | 1 | -1.33 | repeat event 2.18 | 1 | 3.81 | 1 | -1.63 | restricted access 8.11 | 1 | 8.97 | 1 | -0.86 | prodigy db 10.64 | 1 | 13.03 | 1 | -2.39 | cart comprehensive db 33.84 | 1 | 30.94 | 1 | 2.9 | bmt outcomes db 2.75 | 1 | 8.25 | 1 | -5.5 | large sparse db

Click me for comparison results - n of 5

Guess Max Inf | | Guess Max 500 | | Difference | Database Type -- | -- | -- | -- | -- | -- median | neval | median | neval | | 855.24 | 5 | 748.23 | 5 | 107.01 | simple static (read-only) test project 1.64 | 5 | 1.59 | 5 | 0.05 | longitudinal (read-only) ARM test project 746.76 | 5 | 775.16 | 5 | -28.4 | simple write data 3.24 | 5 | 3.28 | 5 | -0.04 | Russian Characters 6.8 | 5 | 7.91 | 5 | -1.11 | super-wide --3,000 columns 818.73 | 5 | 793.56 | 5 | 25.17 | static (not longitudinal) survey test project 722.27 | 5 | 732.26 | 5 | -9.99 | Clinical Trial (Fake) --Read-only 678.38 | 5 | 666.4 | 5 | 11.98 | nonnumeric record_id 685.29 | 5 | 702.38 | 5 | -17.09 | DAG Read 661.8 | 5 | 659.16 | 5 | 2.64 | potentially problematic values 726.56 | 5 | 721.93 | 5 | 4.63 | Repeating Instruments 743.85 | 5 | 743.27 | 5 | 0.58 | simple write metadata 656.47 | 5 | 691.02 | 5 | -34.55 | DAG Write -admin 687.78 | 5 | 715.43 | 5 | -27.65 | DAG Write -group A 392.27 | 5 | 392.53 | 5 | -0.26 | super-wide --35,000 columns 773.57 | 5 | 863.59 | 5 | -90.02 | Repeating Instruments --Sparse 732 | 5 | 677.43 | 5 | 54.57 | Delete Single Arm 1.07 | 5 | 1.08 | 5 | -0.01 | Delete Multiple Arm 1.07 | 5 | 1.09 | 5 | -0.02 | longitudinal single arm 704.46 | 5 | 690.17 | 5 | 14.29 | decimal comma and dot 685.99 | 5 | 806.9 | 5 | -120.91 | decimal comma 898.11 | 5 | 706.21 | 5 | 191.9 | decimal dot 825.59 | 5 | 784.48 | 5 | 41.11 | Validation Types 766.95 | 5 | 1137.18 | 5 | -370.23 | Blank for Gray Status 736.23 | 5 | 701.25 | 5 | 34.98 | Checkboxes 1 748.92 | 5 | 794.29 | 5 | -45.37 | Vignette: Longitudinal & Repeating Measures 2.86 | 5 | 2.55 | 5 | 0.31 | classic 2.43 | 5 | 2.27 | 5 | 0.16 | classic no repeat 3.39 | 5 | 3.6 | 5 | -0.21 | longitudinal 3.67 | 5 | 3.32 | 5 | 0.35 | longitudinal no arms 3.3 | 5 | 3.38 | 5 | -0.08 | longitudinal no repeat 4.65 | 5 | 4.82 | 5 | -0.17 | deep dive vignette 2.08 | 5 | 1.96 | 5 | 0.12 | repeat first instrument 3.37 | 5 | 3.34 | 5 | 0.03 | repeat event 2.08 | 5 | 2.54 | 5 | -0.46 | restricted access 2 | 5 | 2.21 | 5 | -0.21 | prodigy db 9.61 | 5 | 10.49 | 5 | -0.88 | cart comprehensive db 11.7 | 5 | 11.36 | 5 | 0.34 | bmt outcomes db 35.76 | 5 | 29.99 | 5 | 5.77 | large sparse db

Click me for comparison results - n of 10, using `.Machine$integer.max`

Machine Int Max | | | | | | | Difference | Database Type -- | -- | -- | -- | -- | -- | -- | -- | -- min | lq | mean | median | uq | max | neval | | 1.05 | 1.1 | 1.22 | 1.14 | 1.24 | 1.82 | 10 | -1291.78 | simple static (read-only) test project 2.21 | 2.24 | 2.42 | 2.28 | 2.34 | 3.64 | 10 | 2.01 | longitudinal (read-only) ARM test project 1.06 | 1.09 | 1.13 | 1.1 | 1.11 | 1.35 | 10 | -1083.12 | simple write data 2.91 | 3.08 | 3.52 | 3.48 | 3.72 | 4.82 | 10 | 1.1 | Russian Characters 5.75 | 5.94 | 6.32 | 6.07 | 6.5 | 7.43 | 10 | -3.66 | super-wide --3,000 columns 1.14 | 1.15 | 1.27 | 1.16 | 1.19 | 2.16 | 10 | -924.41 | static (not longitudinal) survey test project 1.09 | 1.1 | 1.13 | 1.13 | 1.15 | 1.2 | 10 | -805.76 | Clinical Trial (Fake) --Read-only 995.24 | 1006.76 | 1018.3 | 1014.4 | 1036.24 | 1042.6 | 10 | 370.35 | nonnumeric record_id 1.04 | 1.05 | 1.05 | 1.05 | 1.05 | 1.06 | 10 | -738.03 | DAG Read 993.61 | 998.68 | 1016.87 | 1006.58 | 1050.75 | 1056.32 | 10 | 348.67 | potentially problematic values 1.06 | 1.09 | 1.09 | 1.09 | 1.11 | 1.12 | 10 | -732.49 | Repeating Instruments 1.06 | 1.09 | 1.14 | 1.1 | 1.12 | 1.36 | 10 | -999.71 | simple write metadata 1.02 | 1.05 | 1.08 | 1.06 | 1.08 | 1.25 | 10 | -700.31 | DAG Write -admin 1 | 1.03 | 1.09 | 1.05 | 1.06 | 1.41 | 10 | -982.56 | DAG Write -group A 311.63 | 316.24 | 325.79 | 325.25 | 334.75 | 345.6 | 10 | -57.49 | super-wide --35,000 columns 1.02 | 1.04 | 1.06 | 1.05 | 1.08 | 1.13 | 10 | -1088.92 | Repeating Instruments --Sparse 956.78 | 995.96 | 1023.7 | 1008.13 | 1049.78 | 1127.14 | 10 | 136.95 | Delete Single Arm 1.79 | 1.8 | 1.87 | 1.81 | 1.84 | 2.22 | 10 | 1.1 | Delete Multiple Arm 1.74 | 1.75 | 1.84 | 1.78 | 1.82 | 2.39 | 10 | 1.01 | longitudinal single arm 1.01 | 1.04 | 1.04 | 1.05 | 1.05 | 1.06 | 10 | -712.8 | decimal comma and dot 983.67 | 1020.67 | 1056.7 | 1042.14 | 1117.88 | 1148.12 | 10 | 134.45 | decimal comma 968.38 | 995.09 | 1019.78 | 1000.14 | 1044.42 | 1148.79 | 10 | 399.11 | decimal dot 1.05 | 1.06 | 1.09 | 1.08 | 1.1 | 1.14 | 10 | -991.05 | Validation Types 1.11 | 1.11 | 1.14 | 1.12 | 1.15 | 1.29 | 10 | -1959.75 | Blank for Gray Status 1 | 1.04 | 1.04 | 1.05 | 1.06 | 1.09 | 10 | -1114.52 | Checkboxes 1 1.04 | 1.07 | 1.1 | 1.07 | 1.17 | 1.21 | 10 | -1047.2 | Vignette: Longitudinal & Repeating Measures 5.41 | 6.65 | 7.52 | 7.29 | 7.95 | 10.67 | 10 | 7.15 | classic 3.79 | 4.57 | 5.32 | 5.26 | 5.91 | 7.28 | 10 | 4.75 | classic no repeat 3.52 | 3.62 | 4.59 | 3.98 | 5.19 | 9.03 | 10 | 5.16 | longitudinal 3.5 | 3.75 | 3.92 | 3.87 | 4.03 | 4.47 | 10 | 0.97 | longitudinal no arms 3.3 | 3.76 | 3.83 | 3.85 | 3.89 | 4.2 | 10 | 0.4 | longitudinal no repeat 4.71 | 4.94 | 5.15 | 5.14 | 5.33 | 5.63 | 10 | 0.49 | deep dive vignette 2.04 | 2.06 | 2.2 | 2.1 | 2.35 | 2.49 | 10 | 0.28 | repeat first instrument 3.59 | 3.76 | 4.04 | 3.94 | 4.19 | 4.83 | 10 | 1.42 | repeat event 2.23 | 2.3 | 2.47 | 2.41 | 2.57 | 2.94 | 10 | 0.13 | restricted access 1.98 | 2.09 | 2.26 | 2.19 | 2.35 | 2.96 | 10 | 0.66 | prodigy db 8.18 | 8.5 | 8.75 | 8.77 | 8.97 | 9.15 | 10 | -5.67 | cart comprehensive db 10.65 | 10.72 | 11.31 | 10.93 | 11.61 | 13.05 | 10 | 0.76 | bmt outcomes db 28.8 | 29.15 | 30.29 | 30.37 | 30.65 | 33.99 | 10 | 3.15 | large sparse db

Some databases ran much slower while others ran much faster, but these large changes were all related to the OUHSC databases. The only pattern I can see is that this change sped up almost all of our test databases by a small amount (the last 13 rows) except for the BMT Outcomes database.

PR Checklist

Before submitting this PR, please check and verify below that the submission meets the below criteria:

[ ] New/revised functions have associated tests
[ ] New/revised functions that update downstream outputs have associated static testing files (.RDS) updated under inst/testdata/create_test_data.R
[ ] New tests that make API calls use httptest::with_mock_api and any new mocks were added to tests/testthat/fixtures/create_httptest_mocks.R
[ ] New/revised functions use appropriate naming conventions
[ ] New/revised functions don't repeat code
[ ] Code changes are less than 250 lines total
[ ] Issues linked to the PR using GitHub's list of keywords
[ ] The appropriate reviewer is assigned to the PR
[ ] The appropriate developers are assigned to the PR
[ ] Pre-release package version incremented using usethis::use_dev_version()

Code Review

This section to be used by the reviewer and developers during Code Review after PR submission

Code Review Checklist

[ ] I checked that new files follow naming conventions and are in the right place
[ ] I checked that documentation is complete, clear, and without typos
[ ] I added/edited comments to explain "why" not "how"
[ ] I checked that all new variable and function names follow naming conventions
[ ] I checked that new tests have been written for key business logic and/or bugs that this PR fixes
[ ] I checked that new tests address important edge cases

I love the benchmark table! I'd recommend you run tests at least 10 times (neval=10) to get more consistent results. S

From: Rich Hanna @.> Sent: Friday, March 31, 2023 12:11 PM To: CHOP-CGTInformatics/REDCapTidieR @.> Cc: Subscribed @.***> Subject: [External][CHOP-CGTInformatics/REDCapTidieR] Guess max coltypes (PR #144)

Description

This is a small PR addressing a potential issue where read_redcap may incorrectly guess a column type when a large amount of rows are empty or sparsely populated. This relates to default behavior documented in readrhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Freadr.tidyverse.org%2Farticles%2Fcolumn-types.html&data=05%7C01%7Ckadaukes%40chop.edu%7Cd3b1bf049ee543c9a54808db3202a5eb%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638158759175771356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NM2ToAN1dWLNFLKbTXnnvfycZQu4XB5xn7IVhwO4fvA%3D&reserved=0:

If you don’t explicit specify column types with the col_types argument, readr will attempt to guess them using some simple heuristics. By default, it will inspect 1000 values, evenly spaced from the first to the last row.

Proposed Changes

List changes below in bullet format:

Expose guess_max argument from REDCapR::redcap_read_oneshot() call via param in read_redcap
Update mocks with new Large Sparse REDCap
Add tests

Issue Addressed

Closes #141https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCHOP-CGTInformatics%2FREDCapTidieR%2Fissues%2F141&data=05%7C01%7Ckadaukes%40chop.edu%7Cd3b1bf049ee543c9a54808db3202a5eb%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638158759175927592%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=97IfIO2x1Heqm9lskKpt5kQpWG7V3EeakIMemYsI0ZY%3D&reserved=0

microbenchmark Test Results

The test results from running microbenchmark across all creds in our utility/ folder didn't yield very consistent results:

Click me for comparison results Guess Max Inf Guess Max 1000 Difference Database Type max neval max neval 1.2 1 1.71 1 -0.51 simple static (read-only) test project 2.24 1 2.11 1 0.13 longitudinal (read-only) ARM test project 780.97 1 782.25 1 -1.28 simple write data 5.22 1 5.98 1 -0.76 Russian Characters 8.56 1 8.41 1 0.15 super-wide --3,000 columns 864.01 1 1.21 1 862.8 static (not longitudinal) survey test project 780.11 1 839.75 1 -59.64 Clinical Trial (Fake) --Read-only 786.01 1 1.04 1 784.97 nonnumeric record_id 709.49 1 832.68 1 -123.19 DAG Read 742.39 1 1 1 741.39 potentially problematic values 768.1 1 1.06 1 767.04 Repeating Instruments 879.26 1 1.23 1 878.03 simple write metadata 815.74 1 1.11 1 814.63 DAG Write -admin 907.86 1 734.05 1 173.81 DAG Write -group A 368.46 1 374.19 1 -5.73 super-wide --35,000 columns 762.27 1 819.12 1 -56.85 Repeating Instruments --Sparse 692.52 1 1.06 1 691.46 Delete Single Arm 1.13 1 1.14 1 -0.01 Delete Multiple Arm 1.1 1 1.42 1 -0.32 longitudinal single arm 893.67 1 1.04 1 892.63 decimal comma and dot 715.75 1 949.61 1 -233.86 decimal comma 760.67 1 943.93 1 -183.26 decimal dot 784.9 1 1.1 1 783.8 Validation Types 783.78 1 1.14 1 782.64 Blank for Gray Status 707.08 1 1.03 1 706.05 Checkboxes 1 773.73 1 1.05 1 772.68 Vignette: Longitudinal & Repeating Measures 2.61 1 2.7 1 -0.09 classic 3.43 1 3 1 0.43 classic no repeat 3.51 1 4.27 1 -0.76 longitudinal 3 1 3.98 1 -0.98 longitudinal no arms 4.26 1 4.58 1 -0.32 longitudinal no repeat 5.27 1 7.98 1 -2.71 deep dive vignette 1.99 1 3.07 1 -1.08 repeat first instrument 3.36 1 4.69 1 -1.33 repeat event 2.18 1 3.81 1 -1.63 restricted access 8.11 1 8.97 1 -0.86 prodigy db 10.64 1 13.03 1 -2.39 cart comprehensive db 33.84 1 30.94 1 2.9 bmt outcomes db 2.75 1 8.25 1 -5.5 large sparse db

Some databases ran much slower while others ran much faster, but these large changes were all related to the OUHSC databases. The only pattern I can see is that this change sped up almost all of our test databases by a small amount (the last 13 rows) except for the BMT Outcomes database.

PR Checklist

Before submitting this PR, please check and verify below that the submission meets the below criteria:

New/revised functions have associated tests
New/revised functions that update downstream outputs have associated static testing files (.RDS) updated under inst/testdata/create_test_data.R
New tests that make API calls use httptest::with_mock_api and any new mocks were added to tests/testthat/fixtures/create_httptest_mocks.R
New/revised functions use appropriate naming conventions
New/revised functions don't repeat code
Code changes are less than 250 lines total
Issues linked to the PR using GitHub's list of keywordshttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.github.com%2Fen%2Fissues%2Ftracking-your-work-with-issues%2Flinking-a-pull-request-to-an-issue&data=05%7C01%7Ckadaukes%40chop.edu%7Cd3b1bf049ee543c9a54808db3202a5eb%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638158759175927592%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bKEdYfLWqKXnCAP1GGlRLXsY%2B1blg7rlvaj6kNTJcv0%3D&reserved=0
The appropriate reviewer is assigned to the PR
The appropriate developers are assigned to the PR
Pre-release package version incremented using usethis::use_dev_version()

Code Review

This section to be used by the reviewer and developers during Code Review after PR submission

Code Review Checklist

I checked that new files follow naming conventions and are in the right place
I checked that documentation is complete, clear, and without typos
I added/edited comments to explain "why" not "how"
I checked that all new variable and function names follow naming conventions
I checked that new tests have been written for key business logic and/or bugs that this PR fixes
I checked that new tests address important edge cases

You can view, comment on, or merge this pull request online at:

https://github.com/CHOP-CGTInformatics/REDCapTidieR/pull/144 https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCHOP-CGTInformatics%2FREDCapTidieR%2Fpull%2F144&data=05%7C01%7Ckadaukes%40chop.edu%7Cd3b1bf049ee543c9a54808db3202a5eb%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638158759175927592%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3vArJhIghCUtzsrYn5LbNHithxlBgReGxuIeZt9BHWw%3D&reserved=0

Commit Summary

File Changes

(39 fileshttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCHOP-CGTInformatics%2FREDCapTidieR%2Fpull%2F144%2Ffiles&data=05%7C01%7Ckadaukes%40chop.edu%7Cd3b1bf049ee543c9a54808db3202a5eb%7Ca611241607b041a59bb1d146b575c975%7C0%7C0%7C638158759175927592%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OhZk4Ngb8gsGvN2IyMO3SoQ7jKo8Fr3r7e1AvAMcaQI%3D&reserved=0)

Patch Links:

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CHOP-CGTInformatics / REDCapTidieR

Guess max coltypes #144

Description

Proposed Changes

Issue Addressed

`microbenchmark` Test Results

PR Checklist

Code Review

Code Review Checklist