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Bring clean up and fixes to dev #19

Merged
merged 64 commits into from
Aug 8, 2023
Merged

Bring clean up and fixes to dev #19

merged 64 commits into from
Aug 8, 2023

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davidsantiagoquevedo
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pratikunterwegs and others added 30 commits July 5, 2023 10:41
@pratikunterwegs
Initial styler run on R files
a707fee
@pratikunterwegs
Styler run on vignette
3816b92
@pratikunterwegs
Styler run on regenerated documentation
d404c67
@pratikunterwegs
Correct spellings and update WORDLIST
a87e176
@actions-user
Automatic readme update
996c620
@pratikunterwegs
Remove empty file visualisation.R
ec07d64
@pratikunterwegs
Add author ORCIDs, URL, BugReports to DESCRIPTION
751ccff
@pratikunterwegs
Add author ORCID
a7dc44d
@pratikunterwegs
Update title and description in DESCRIPTION
9dd9336
@pratikunterwegs
Add R dependency >= 3.5.0 for serialised data
239ce45
@pratikunterwegs
Update WORDLIST and pkg doc Rd with study authors
ed0886d
@pratikunterwegs
Edit Readme to allow automated packagename and GH repo
11776c8
@pratikunterwegs
Add contributing guide
7893f43
@actions-user
Automatic readme update
8d15476
@pratikunterwegs
Add general reference to Readme & vignette, add CSL refs file
02d2a5f
@actions-user
Automatic readme update
ffb809f
@pratikunterwegs
Update WORDLIST for Readme updates
974fa7f
@pratikunterwegs
Add {qtl} to Suggests to avoid GHA R CMD check Note
e3de11f
@pratikunterwegs
Update WORDLIST with word in paper title
65536cd
@pratikunterwegs
Update LICENSE files with correct year and pkg name
b2ab24f
@pratikunterwegs
Add input checking get_age_group
9c77115
@pratikunterwegs
Minor formatting edits get_age_group()
df84f34
@pratikunterwegs
Update documentation get_age_groups()
12200e8
@pratikunterwegs
Add testthat.R file
77fc46d
@pratikunterwegs
Add tests for get_age_groups()
fe87ab2
@pratikunterwegs
Add {checkmate} to Imports
627c992
@pratikunterwegs
Update documentation get_age_group()
85047ce
@pratikunterwegs
Ignore scratch file for development
7eaa6be
@pratikunterwegs
Add input checking for set_status()
9653755
@pratikunterwegs
Update documentation for set_status()
88d6a4d
pratikunterwegs and others added 29 commits July 7, 2023 15:38
@pratikunterwegs
Nolint surv object for coxph, avoid warning from coxph
9e97ecc
@pratikunterwegs
Add snapshot test for get_immunization_date()
bfc6675
@pratikunterwegs
Add input checking for get_immunization_date()
86065ec
@pratikunterwegs
Simplify calculations in get_immunization_date(), rm dependencies
fd24683
@pratikunterwegs
Run examples for get_immunization_date(), update Rd documentation, fo…
340c3bb 
…rmat test file
@pratikunterwegs
Remove {rlang} from Imports
23ed0bc
@pratikunterwegs
Add tests for immunization_date()
a8291df
@pratikunterwegs
Make coh_eff_noconf return p-val as a numeric
42385e7
@pratikunterwegs
Input checking, inherit params for fn coh_test_noconf()
3982603
@pratikunterwegs
Add tests, update documentation for cohort effectiveness fns
e271ac3
@pratikunterwegs
Add tests for time_to_event()
44e1307
@pratikunterwegs
Add input checking for time_to_event()
46f9bdb
@pratikunterwegs
Clean up code time_to_event()
21ba6ae
@pratikunterwegs
Handle case of full immunity after cohort end
c445e20
@pratikunterwegs
Handle case of death before full immunity
5a0e416
@pratikunterwegs
Cleanup of option from cohort start date
08aee4a
@pratikunterwegs
Minor formatting and run examples in time_to_event()
fd135ca
@pratikunterwegs
Update tests for time to event
7c9e57f
@pratikunterwegs
Update documentation time_to_event()
e4d5440
@pratikunterwegs
Correct comments in tests for immunisation_date
34c53b5
@pratikunterwegs
Add tests for immunization_dose()
2b81a3c
@pratikunterwegs
Add input checking, shorten fn get_immunization_dose()
2a249b6
@pratikunterwegs
Add tests for immunizing_vaccine - fn broken
a83376c
@pratikunterwegs
Add snapshot test for immunizing_vaccine()
8f71cfd
@pratikunterwegs
Simplify immunization_vaccine() fn
294c698
@pratikunterwegs
Update documentation immunization_vaccine()
9329811
@pratikunterwegs
Remove {dplyr} and {data.table} dependencies
f2712ff
@davidsantiagoquevedo
Merge branch 'main' into dev-fixes-pratik
36552ff
@davidsantiagoquevedo
Merge pull request #13 from epiverse-trace/dev-fixes-pratik
60a4efa 
Package cleanup
@davidsantiagoquevedo davidsantiagoquevedo merged commit fe068b3 into dev Aug 8, 2023
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3 participants
@davidsantiagoquevedo @pratikunterwegs @actions-user