Move time series preparation for cosinor analysis to new function #913

vincentvanhees · 2023-09-26T13:34:25Z

In preparation for work on Add optional cosinor analysis to part 6 #708 to include cosinor analysis in part 6 this PR moves code used for preparing the time series for cosinor analysis to its own function. This to help avoid duplication of code when also applying the analysis in part 6. No new unit tests because this should be covered by current unit test.
Added R2 as extra cosinor analysis outcome.
Minor effort to tidy up syntax in a few other functions such as g.part4.

Checklist before merging:

Existing tests still work (check by running the test suite, e.g. from RStudio).
Added tests (if you added functionality) or fixed existing test (if you fixed a bug).
Updated or expanded the documentation.
Updated release notes in inst/NEWS.Rd with a user-readable summary. Please, include references to relevant issues or PR discussions.
Added your name to the contributors lists in the DESCRIPTION and CITATION.cff files.

…R to a seperate function to ease re-using it in g.part5 #708

…works with both 5 second and 60second aggregated epochs

…alculated seperately for MM and WW window

…be applied, and adding division by 1000 because analyses expect g-units #708

…apply to the entire recording #708

…708

…R to a seperate function to ease re-using it in g.part5 #708

…works with both 5 second and 60second aggregated epochs

…alculated seperately for MM and WW window

…be applied, and adding division by 1000 because analyses expect g-units #708

…apply to the entire recording #708

…708

…issue708_cosinor_part5

… is to add them to part 5

codecov-commenter · 2023-10-05T13:21:25Z

Codecov Report

Merging #913 (75e6348) into master (d94ee28) will increase coverage by 0.03%.
The diff coverage is 89.13%.

❗ Current head 75e6348 differs from pull request most recent head 3db848b. Consider uploading reports for the commit 3db848b to get more accurate results

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@@            Coverage Diff             @@
##           master     #913      +/-   ##
==========================================
+ Coverage   78.12%   78.16%   +0.03%     
==========================================
  Files          92       93       +1     
  Lines       12308    12323      +15     
==========================================
+ Hits         9616     9632      +16     
+ Misses       2692     2691       -1

Files	Coverage Δ
R/cosinorAnalyses.R	`100.00% <100.00%> (ø)`
R/g.analyse.avday.R	`93.10% <100.00%> (+3.67%)`	⬆️
R/g.analyse.perfile.R	`84.23% <100.00%> (+0.18%)`	⬆️
R/g.report.part5.R	`85.24% <100.00%> (-0.04%)`	⬇️
R/g.report.part4.R	`83.58% <91.66%> (+0.16%)`	⬆️
R/g.part4.R	`80.41% <75.00%> (+0.17%)`	⬆️
R/applyCosinorAnalyses.R	`83.33% <83.33%> (ø)`

jhmigueles

I have already revised the changes and confirmed that all cosinor-related variables are exported in part 2. Tests are working and I don't see the need for new tests, maybe only for the calculation of the R2 if you think that is relevant.

Apart from that, only one minor comment, the documentation for cosinor in man/GGIR.Rd states that the argument is deprecated after version 1.5-24, but this is not correct, right? This argument is still used in GGIR to trigger the cosinor analyses.

vincentvanhees · 2023-10-11T07:40:00Z

Apart from that, only one minor comment, the documentation for cosinor in man/GGIR.Rd states that the argument is deprecated after version 1.5-24, b

Well spotted, I think I accidentally copied this line from the parameter above. Will fix it now.

…ation in GGIR.Rd, and move NEWS item to new 2.10-5 section #708

vincentvanhees added 30 commits December 13, 2022 15:48

moving the application of the cosinor anlyses inside g.analyse.avday.…

e0f5b0e

…R to a seperate function to ease re-using it in g.part5 #708

#708 implementing applyCosinorAnlayses in g.part5 and making sure it …

7eed109

…works with both 5 second and 60second aggregated epochs

adding cosinor variables to part 5 output

5ef3924

tidying up syntax

07ed472

add cosinor analyses to namespace

56af54a

adding mean and number of daytime sibs that last at least 15 minutes

a94cc01

adding R2

d3838ea

making sure that cosinor analyses in part5 only uses windows and is c…

5bcb882

…alculated seperately for MM and WW window

Merge branch 'master' into issue708_cosinor_part5

7840d95

remove parseGT3Xggir as function no longer used

fc45400

moving log transform outside ifelse statement as this always need to …

eee7aca

…be applied, and adding division by 1000 because analyses expect g-units #708

skip calculating weighted, WD and WE values for cosinor as estimates …

030a22a

…apply to the entire recording #708

fix misallignment in output columns caused by changes in this branch #…

caafd63

…708

moving the application of the cosinor anlyses inside g.analyse.avday.…

91b592d

…R to a seperate function to ease re-using it in g.part5 #708

#708 implementing applyCosinorAnlayses in g.part5 and making sure it …

64323bd

…works with both 5 second and 60second aggregated epochs

adding cosinor variables to part 5 output

003e561

tidying up syntax

a817df0

add cosinor analyses to namespace

6e6050c

adding mean and number of daytime sibs that last at least 15 minutes

32638bc

adding R2

3308d4e

making sure that cosinor analyses in part5 only uses windows and is c…

25cb509

…alculated seperately for MM and WW window

remove parseGT3Xggir as function no longer used

e18a5c1

moving log transform outside ifelse statement as this always need to …

be3f73a

…be applied, and adding division by 1000 because analyses expect g-units #708

skip calculating weighted, WD and WE values for cosinor as estimates …

3a5da8f

…apply to the entire recording #708

fix misallignment in output columns caused by changes in this branch #…

f5ea91c

…708

Merge branch 'issue708_cosinor_part5' of github.com:wadpac/GGIR into …

c2f059d

…issue708_cosinor_part5

comment out print statement

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merge master

6d1b163

merge master

12b739d

merge master

6c9b756

vincentvanhees added 18 commits June 6, 2023 18:21

Merge branch 'master' into issue708_cosinor_part5

ea816b2

Merge branch 'master' into issue708_cosinor_part5

c921992

merge master

53e0ef7

merge master

7645066

fix merge problem with previous commit

98f00f5

Merge branch 'master' into issue708_cosinor_part5

ea80e66

Merge branch 'master' into issue708_cosinor_part5

f52848b

Merge branch 'master' into issue708_cosinor_part5

1f3b0e3

Merge branch 'master' into issue708_cosinor_part5

7ed135f

undo indentation changes

7d47438

#708 omit addition of extra daytime sib variables to part 4, the plan…

f26e506

… is to add them to part 5

minor improvement to syntax

7150cd3

Merge branch 'master' into issue708_cosinor_part5

9bc321f

Merge branch 'issue708_cosinor_part5' into issue708_centralise_cosinor

be727fe

undo addition of cosinor to part 5 as this will be moved to part 6

8e5a4f6

remove cosinor from part5

16e8388

Update NEWS.md

9efe016

fix typo in documentation

90a3946

vincentvanhees marked this pull request as ready for review September 26, 2023 13:34

vincentvanhees requested a review from jhmigueles September 26, 2023 13:34

vincentvanhees added 2 commits September 27, 2023 11:14

Merge branch 'master' into issue708_centralise_cosinor

dd78d2f

Merge branch 'master' into issue708_centralise_cosinor

e419b26

jhmigueles reviewed Oct 10, 2023

View reviewed changes

vincentvanhees added 3 commits October 11, 2023 09:42

add unit test for cosinor R2, remove incorrect statement about deprec…

0fb6f92

…ation in GGIR.Rd, and move NEWS item to new 2.10-5 section #708

Merge branch 'master' into issue708_centralise_cosinor

3db848b

Merge branch 'master' into issue708_centralise_cosinor

f67cb4d

vincentvanhees merged commit 0e67881 into master Oct 11, 2023
8 checks passed

vincentvanhees deleted the issue708_centralise_cosinor branch October 12, 2023 15:24

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Move time series preparation for cosinor analysis to new function #913

Move time series preparation for cosinor analysis to new function #913

vincentvanhees commented Sep 26, 2023

codecov-commenter commented Oct 5, 2023 •

edited

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vincentvanhees commented Oct 11, 2023

Move time series preparation for cosinor analysis to new function #913

Move time series preparation for cosinor analysis to new function #913

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vincentvanhees commented Sep 26, 2023

codecov-commenter commented Oct 5, 2023 • edited Loading

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vincentvanhees commented Oct 11, 2023

codecov-commenter commented Oct 5, 2023 •

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