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Capr Issue #99: Potential improvements to Capr #105

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e6ad3c1
Merge pull request #78 from OHDSI/develop
mdlavallee92 Sep 7, 2023
e44ec1c
Merge pull request #84 from OHDSI/develop
mdlavallee92 Sep 12, 2023
b05984f
Renaming weekly R check yaml for consistency with rest of HADES
Oct 9, 2023
c25f736
Merge pull request #94 from OHDSI/develop
mdlavallee92 May 16, 2024
e163e80
copy files from PHEMS repo
guuswilmink Jul 4, 2024
bb1ce28
Function for checking standard concepts; add descendant record counts…
guuswilmink Jul 5, 2024
66775fa
knitted script
guuswilmink Jul 5, 2024
e3e47f4
Update main code
guuswilmink Jul 5, 2024
372ef31
update concept sets
guuswilmink Jul 5, 2024
feca1e2
update cohort json
guuswilmink Jul 5, 2024
899a33e
update renv
guuswilmink Jul 5, 2024
f699167
update concept sets
guuswilmink Jul 9, 2024
700b2c3
update json save
guuswilmink Jul 9, 2024
382aefd
add PHEMS OMOP mappings (Hyve suggestions)
guuswilmink Jul 9, 2024
7459994
Add check for standard concepts
guuswilmink Jul 9, 2024
6fcd12e
index=False update for standard concept check save file
guuswilmink Jul 9, 2024
7af95d3
replace python isStandard function with R
guuswilmink Jul 9, 2024
3dd9323
update standard concept tables
guuswilmink Jul 9, 2024
2ccad5b
update isStandard.R
guuswilmink Jul 9, 2024
95c026c
update main code
guuswilmink Jul 9, 2024
9641bbc
knitted html update
guuswilmink Jul 9, 2024
731a1d9
update cohort jsons
guuswilmink Jul 9, 2024
88a08f2
Merge pull request #1 from thehyve/copy-PHEMS-repo-to-Capr-fork
guuswilmink Jul 10, 2024
6b12243
update gitignore
guuswilmink Jul 10, 2024
32f9d96
rename R project
guuswilmink Jul 10, 2024
b686131
add config
guuswilmink Jul 10, 2024
b5c0945
update variable mapping tables and standard concept check result tables
guuswilmink Jul 12, 2024
1fa06c2
update .gitignore
guuswilmink Jul 12, 2024
b4af833
update renv
guuswilmink Jul 12, 2024
9269137
add config files
guuswilmink Jul 12, 2024
fcafc8d
update function to use SQL queries
guuswilmink Jul 12, 2024
e39ca44
update function to use SQL queries
guuswilmink Jul 12, 2024
a7c491a
update main code
guuswilmink Jul 12, 2024
73d5989
update mismatched concepts
guuswilmink Jul 12, 2024
daa56e9
Added UC1 tables 5.15 - 5.19 & UC3 tables to conceptSets.R, and added…
LP-Glueck Jul 12, 2024
d2dc72b
update gitignore
guuswilmink Jul 12, 2024
c1398bc
remove json files
guuswilmink Jul 12, 2024
a762265
update concept sets for shared vars, uc1 vars, uc2 vars
guuswilmink Jul 12, 2024
0867c6f
sync R script
guuswilmink Jul 12, 2024
9e58988
update cohort definition
guuswilmink Jul 12, 2024
4847572
update standard_config-sample.yml
guuswilmink Jul 15, 2024
4fd9a44
remove unnecessary file
guuswilmink Jul 15, 2024
4946c35
update standard concept check
guuswilmink Jul 15, 2024
3c3ed54
Add standard concept checker for across concept setS
guuswilmink Jul 15, 2024
8466f8b
docstring for conceptSets.R
guuswilmink Jul 15, 2024
07a3794
update with docstring
guuswilmink Jul 15, 2024
00116e5
update main code
guuswilmink Jul 15, 2024
18a6637
restore
guuswilmink Jul 15, 2024
e2b1e89
update reduce no. SQL queries to 1 for efficiency
guuswilmink Jul 16, 2024
3ce3c8b
remove renv; only keep lockfile
guuswilmink Jul 16, 2024
b6f2c32
update lockfile
guuswilmink Jul 16, 2024
0d03b91
remove unnecessary file
guuswilmink Jul 16, 2024
8fcf546
migrate files
guuswilmink Jul 16, 2024
f05f39c
update .gitignore
guuswilmink Jul 16, 2024
1767466
use Capr.Rproj
guuswilmink Jul 16, 2024
b8ec494
update R profile
guuswilmink Jul 16, 2024
ccda61b
remove outdated html
guuswilmink Jul 16, 2024
071b6b4
.Renviron to configure rJava installation
guuswilmink Jul 17, 2024
239853e
update .Rproj
guuswilmink Jul 17, 2024
2b366a5
update renv lock
guuswilmink Jul 17, 2024
f056636
renamed .Rproj
guuswilmink Jul 17, 2024
5aafcc8
update DESCRIPTION
guuswilmink Jul 17, 2024
b0bdffb
update script
guuswilmink Jul 17, 2024
fbfa18f
renv library updates and install configurations
guuswilmink Jul 17, 2024
aeec12f
update readme
guuswilmink Jul 18, 2024
7deeb04
Addressing PR comments
LP-Glueck Jul 18, 2024
b544f50
update config
guuswilmink Jul 18, 2024
7ed8727
update config
guuswilmink Jul 18, 2024
a079563
Updated drug concepts for concepts sets and variable list
LP-Glueck Jul 18, 2024
5c092a1
move files
guuswilmink Jul 19, 2024
75c3dbe
small code updates
guuswilmink Jul 19, 2024
e22a7da
update config samples
guuswilmink Jul 19, 2024
c48e148
update docs
guuswilmink Jul 19, 2024
52028f3
update environment
guuswilmink Jul 19, 2024
ed6f01d
Update 5.22_vital_signs.csv
guuswilmink Jul 19, 2024
6e7a968
update concept set and extdata
guuswilmink Jul 19, 2024
5afa369
Update 5.14_cardiac_complications.csv
guuswilmink Jul 19, 2024
b471c82
remove empty lines
guuswilmink Jul 19, 2024
948050d
update README
guuswilmink Jul 19, 2024
6e1bd5b
update README
guuswilmink Jul 19, 2024
c854918
small fixes and additional documentation
guuswilmink Jul 19, 2024
495d8b8
update .gitignore
guuswilmink Jul 19, 2024
58aaaae
Update conceptSets.R
LP-Glueck Jul 19, 2024
13e2334
remove json files
guuswilmink Jul 19, 2024
0463e30
Merge pull request #5 from thehyve/Capr-uc3-updates
LP-Glueck Jul 19, 2024
bdfb571
minor updates
guuswilmink Jul 19, 2024
726ecaa
update gitignore
guuswilmink Jul 19, 2024
09abdc0
update gitignore
guuswilmink Jul 19, 2024
3b9368d
update gitignore
guuswilmink Jul 19, 2024
0f55d9c
merge main into branch
guuswilmink Jul 19, 2024
1c5af40
update conceptSets.R
guuswilmink Jul 19, 2024
87eafac
Merge pull request #4 from thehyve/conceptSets-shared_uc1_uc2
guuswilmink Jul 19, 2024
d3e531b
Merge branch 'main' into feature
guuswilmink Jul 19, 2024
a55ab9f
update cohort definition
guuswilmink Jul 19, 2024
1e907d1
remove project folder
guuswilmink Jul 19, 2024
b5c1e37
Merge pull request #2 from thehyve/feature
guuswilmink Jul 19, 2024
9e66480
re-knit script up to date
guuswilmink Jul 19, 2024
13869db
Update README.md
guuswilmink Jul 19, 2024
053335f
Update README.md
guuswilmink Jul 19, 2024
7cc352b
Update README.md
guuswilmink Jul 19, 2024
b8a105a
Update README.md
guuswilmink Jul 19, 2024
173d727
remove unnecessary files
guuswilmink Aug 5, 2024
1fee523
Merge pull request #1 from thehyve/feature
guuswilmink Aug 5, 2024
3703c6a
remove unnecessary files
guuswilmink Aug 5, 2024
6a81914
Merge pull request #2 from thehyve/feature
guuswilmink Aug 5, 2024
56d1a81
remove unnecessary files
guuswilmink Aug 5, 2024
cf411f1
Merge pull request #3 from thehyve/feature
guuswilmink Aug 5, 2024
8e90a4d
minor fix and update for counts save path
guuswilmink Aug 5, 2024
6f218bf
update for save option
guuswilmink Aug 5, 2024
401cba4
Merge pull request #7 from thehyve/csv_save
guuswilmink Aug 5, 2024
b2c1aa3
add links object
guuswilmink Aug 6, 2024
e5c8182
Merge pull request #4 from thehyve/feature
guuswilmink Aug 7, 2024
e47d532
update comments countOccurrences
guuswilmink Aug 8, 2024
9ada37a
better countOccurrences example
guuswilmink Aug 8, 2024
860f88f
update tables
guuswilmink Aug 8, 2024
ee48fd6
typo fix
guuswilmink Aug 8, 2024
d3c4350
clean-up
guuswilmink Aug 8, 2024
3378587
markdown pdf
guuswilmink Aug 8, 2024
e72ea42
update knitted R script
guuswilmink Aug 8, 2024
706d0dc
Merge pull request #8 from thehyve/small_updates
guuswilmink Aug 9, 2024
66cc3fe
implement feedback
guuswilmink Aug 12, 2024
cbcadea
add files temporarily for fork sync
guuswilmink Aug 12, 2024
7bb20fe
delete temp files
guuswilmink Aug 12, 2024
4b7c81b
temporarily add files for fork sync
guuswilmink Aug 12, 2024
5ef2a5f
Merge branch 'main' into fork_sync-remove_temp_files
guuswilmink Aug 12, 2024
8a884d8
delete temp files
guuswilmink Aug 12, 2024
f53ece6
Merge pull request #5 from thehyve/fork_sync-remove_temp_files
guuswilmink Aug 12, 2024
b7ab55d
merge main branch
guuswilmink Aug 12, 2024
0181391
update functions
guuswilmink Aug 13, 2024
4dc7b78
add test conceptsets
guuswilmink Aug 13, 2024
b83f758
add tests
guuswilmink Aug 13, 2024
783cb3c
update gitignore
guuswilmink Aug 19, 2024
db78c43
small updates
guuswilmink Aug 19, 2024
3d95df6
add standardness check for checking in DB
guuswilmink Aug 19, 2024
f957d07
small fixes
guuswilmink Aug 19, 2024
be4ea8a
add test for DB standardness check
guuswilmink Aug 19, 2024
245c832
update gitignore
guuswilmink Aug 23, 2024
5beeca5
update functions
guuswilmink Aug 23, 2024
8fc6f44
update unit tests
guuswilmink Aug 23, 2024
23b78a4
Merge pull request #6 from thehyve/feature
guuswilmink Aug 23, 2024
0805878
gitignore .Rprofile
guuswilmink Aug 23, 2024
1258254
Merge pull request #7 from thehyve/feature
guuswilmink Aug 23, 2024
c6d754b
restore .Rproj
guuswilmink Aug 23, 2024
1b9d83c
change line endings
guuswilmink Aug 23, 2024
7ebed42
Merge branch 'main' of https://github.com/thehyve/Capr-Enhancements
guuswilmink Aug 23, 2024
5f0bac6
update docs
guuswilmink Aug 23, 2024
8e71e36
clean up fork
guuswilmink Aug 23, 2024
c6abec2
clean-up fork
guuswilmink Aug 23, 2024
f14c3ef
line endings
guuswilmink Aug 23, 2024
c1c38fa
remove library references
guuswilmink Aug 23, 2024
1d62deb
dplyr package references fix
guuswilmink Aug 26, 2024
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guuswilmink committed Jul 15, 2024
commit 18a66371d2d785d7e5e63c6b01068cc2fcdfa4a0
14 changes: 14 additions & 0 deletions project/R/table_linked_to_concept_field.R
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
# Link table names to respective concept_id field
links <- list(
condition_occurrence = "condition_concept_id",
death = "cause_concept_id",
device_exposure = "device_concept_id",
drug_exposure = "drug_concept_id",
measurement = "measurement_concept_id",
observation = "observation_concept_id",
procedure_occurrence = "procedure_concept_id",
specimen = "specimen_concept_id",
visit_occurrence = "visit_concept_id"
)

cat("Sourced links object")