Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Use pharmaverseadam data in safety templates - part 1 #153

Open
wants to merge 6 commits into
base: main
Choose a base branch
from
Open

Use pharmaverseadam data in safety templates - part 1 #153

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
4580168
Use pharmaverseadam
edelarua Oct 15, 2024
331e0ff
Update tests
edelarua Oct 15, 2024
e48da56
Merge branch 'main' into 133_pv_safety_pt_1@main
edelarua Oct 15, 2024
4d87b9f
Update exl01
edelarua Oct 15, 2024
c3ab96b
adcm_raw no longer used
edelarua Oct 15, 2024
07cfa77
CMENRTPT will be added to adcm in pharmaverseadam
edelarua Oct 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ Depends:
rtables (>= 0.6.8),
tern (>= 0.9.5)
Imports:
pharmaverseadam (>= 0.2.0),
pharmaverseadam (>= 1.0.0),
random.cdisc.data (>= 0.3.15.9001)
Suggests:
broom,
Expand Down
110 changes: 55 additions & 55 deletions tests/testthat/_snaps/listing_cml01.md
View file
Open in desktop

Large diffs are not rendered by default.

75 changes: 54 additions & 21 deletions tests/testthat/_snaps/listing_cml02a_gl.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,25 +5,58 @@
Output
Listing of Concomitant Medication Class Level 2, Preferred Name, and Investigator-Specified Terms

———————————————————————————————————————————————————————————————————
Investigator-Specified
ATC Class Level 2 WHODrug Preferred Name Treatment Term
———————————————————————————————————————————————————————————————————
ATCCLAS2 A medname A_1/3 A_1/3
medname A_2/3 A_2/3
medname A_3/3 A_3/3
ATCCLAS2 A p2 medname A_3/3 A_3/3
ATCCLAS2 B medname B_1/4 B_1/4
medname B_2/4 B_2/4
medname B_3/4 B_3/4
medname B_4/4 B_4/4
ATCCLAS2 B p2 medname B_1/4 B_1/4
medname B_2/4 B_2/4
ATCCLAS2 B p3 medname B_1/4 B_1/4
medname B_2/4 B_2/4
ATCCLAS2 C medname C_1/2 C_1/2
medname C_2/2 C_2/2
ATCCLAS2 C p2 medname C_1/2 C_1/2
medname C_2/2 C_2/2
ATCCLAS2 C p3 medname C_2/2 C_2/2
——————————————————————————————————————————————————————————————————————————————
Investigator-Specified
ATC Class Level 2 WHODrug Preferred Name Treatment Term
——————————————————————————————————————————————————————————————————————————————
ATCCLAS2_1 ALGELDRATE MAALOX
CALCIUM CALCIUM
CALCIUM CARBONATE CALTRATE
CIMETIDINE TAGAMET
LOPERAMIDE HYDROCHLORIDE IMODIUM
METFORMIN HYDROCHLORIDE GLUCOPHAGE
NIZATIDINE AXID
SIMETICONE GAS-X
ATCCLAS2_2 LEUPRORELIN ACETATE LUPRON
ATCCLAS2_3 FERROUS SULFATE FERROUS SULFATE
ATCCLAS2_4 AMLODIPINE NORVASC
DIGOXIN LANOXIN
DILTIAZEM HYDROCHLORIDE CARDIZEM
DOXAZOSIN MESILATE CARDURA
FELODIPINE PLENDIL
FLUVASTATIN LESCOL
FUROSEMIDE LASIX
LOSARTAN POTASSIUM COZAAR
NIFEDIPINE ADALAT
ATCCLAS2_5 CLOBETASOL PROPIONATE TEMOVATE
ATCCLAS2_6 ESTROGENS CONJUGATED PREMARIN
ATCCLAS2_7 ACETYLSALICYLIC ACID ASPIRIN
ALPRAZOLAM XANAX
DONEPEZIL HYDROCHLORIDE ARICEPT
HALOPERIDOL HALDOL
PAROXETINE HYDROCHLORIDE PAXIL
SUMATRIPTAN IMITREX
ATCCLAS2_8 BUDESONIDE RHINOCORT
GUAIFENESIN GUAIFENESIN
IPRATROPIUM BROMIDE ATROVENT
NAPROXEN SODIUM ALEVE
SALBUTAMOL SULFATE PROVENTIL
VENTOLIN
ATCCLAS2_9 HYDROCORTISONE HYDROCORTISONE
ATCCLAS2_10 UNCODED ACCUPRIL
ACETAMINOPHEN
ACUPRIL
ADVIL
AEROBID
ALBUTEROL
ALLEGRA
ALOE VERA
ALOES
ALPHAGAN
ALTACE
AMOXICILLIN
AMPICILLIN
ANACIN
ANTI-OXIDANT
ANTIHISTAMINES FOR SYSTEMIC USE

75 changes: 54 additions & 21 deletions tests/testthat/_snaps/listing_cml02b_gl.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,25 +5,58 @@
Output
Listing of Concomitant Medication Class, Preferred Name, and Investigator-Specified Terms

———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Investigator-Specified
ATC Class Level 1 ATC Class Level 2 ATC Class Level 3 ATC Class Level 4 WHODrug Preferred Name Treatment Term
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
ATCCLAS1 A ATCCLAS2 A ATCCLAS3 A ATCCLAS4 A medname A_1/3 A_1/3
medname A_2/3 A_2/3
medname A_3/3 A_3/3
ATCCLAS1 A p2 ATCCLAS2 A p2 ATCCLAS3 A p2 ATCCLAS4 A p2 medname A_3/3 A_3/3
ATCCLAS1 B ATCCLAS2 B ATCCLAS3 B ATCCLAS4 B medname B_1/4 B_1/4
medname B_2/4 B_2/4
medname B_3/4 B_3/4
medname B_4/4 B_4/4
ATCCLAS1 B p2 ATCCLAS2 B p2 ATCCLAS3 B p2 ATCCLAS4 B p2 medname B_1/4 B_1/4
medname B_2/4 B_2/4
ATCCLAS1 B p3 ATCCLAS2 B p3 ATCCLAS3 B p3 ATCCLAS4 B p3 medname B_1/4 B_1/4
medname B_2/4 B_2/4
ATCCLAS1 C ATCCLAS2 C ATCCLAS3 C ATCCLAS4 C medname C_1/2 C_1/2
medname C_2/2 C_2/2
ATCCLAS1 C p2 ATCCLAS2 C p2 ATCCLAS3 C p2 ATCCLAS4 C p2 medname C_1/2 C_1/2
medname C_2/2 C_2/2
ATCCLAS1 C p3 ATCCLAS2 C p3 ATCCLAS3 C p3 ATCCLAS4 C p3 medname C_2/2 C_2/2
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Investigator-Specified
ATC Class Level 1 ATC Class Level 2 ATC Class Level 3 ATC Class Level 4 WHODrug Preferred Name Treatment Term
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
ATCCLAS1_1 ATCCLAS2_1 ATCCLAS3_1 ATCCLAS4_1 ALGELDRATE MAALOX
CALCIUM CALCIUM
CALCIUM CARBONATE CALTRATE
CIMETIDINE TAGAMET
LOPERAMIDE HYDROCHLORIDE IMODIUM
METFORMIN HYDROCHLORIDE GLUCOPHAGE
NIZATIDINE AXID
SIMETICONE GAS-X
ATCCLAS1_2 ATCCLAS2_2 ATCCLAS3_2 ATCCLAS4_2 LEUPRORELIN ACETATE LUPRON
ATCCLAS1_3 ATCCLAS2_3 ATCCLAS3_3 ATCCLAS4_3 FERROUS SULFATE FERROUS SULFATE
ATCCLAS1_4 ATCCLAS2_4 ATCCLAS3_4 ATCCLAS4_4 AMLODIPINE NORVASC
DIGOXIN LANOXIN
DILTIAZEM HYDROCHLORIDE CARDIZEM
DOXAZOSIN MESILATE CARDURA
FELODIPINE PLENDIL
FLUVASTATIN LESCOL
FUROSEMIDE LASIX
LOSARTAN POTASSIUM COZAAR
NIFEDIPINE ADALAT
ATCCLAS1_5 ATCCLAS2_5 ATCCLAS3_5 ATCCLAS4_5 CLOBETASOL PROPIONATE TEMOVATE
ATCCLAS1_6 ATCCLAS2_6 ATCCLAS3_6 ATCCLAS4_6 ESTROGENS CONJUGATED PREMARIN
ATCCLAS1_7 ATCCLAS2_7 ATCCLAS3_7 ATCCLAS4_7 ACETYLSALICYLIC ACID ASPIRIN
ALPRAZOLAM XANAX
DONEPEZIL HYDROCHLORIDE ARICEPT
HALOPERIDOL HALDOL
PAROXETINE HYDROCHLORIDE PAXIL
SUMATRIPTAN IMITREX
ATCCLAS1_8 ATCCLAS2_8 ATCCLAS3_8 ATCCLAS4_8 BUDESONIDE RHINOCORT
GUAIFENESIN GUAIFENESIN
IPRATROPIUM BROMIDE ATROVENT
NAPROXEN SODIUM ALEVE
SALBUTAMOL SULFATE PROVENTIL
VENTOLIN
ATCCLAS1_9 ATCCLAS2_9 ATCCLAS3_9 ATCCLAS4_9 HYDROCORTISONE HYDROCORTISONE
ATCCLAS1_10 ATCCLAS2_10 ATCCLAS3_10 ATCCLAS4_10 UNCODED ACCUPRIL
ACETAMINOPHEN
ACUPRIL
ADVIL
AEROBID
ALBUTEROL
ALLEGRA
ALOE VERA
ALOES
ALPHAGAN
ALTACE
AMOXICILLIN
AMPICILLIN
ANACIN
ANTI-OXIDANT
ANTIHISTAMINES FOR SYSTEMIC USE

Loading
Loading