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

CDCWonder_NNDSS_InfectiousAnnual_changes #1101

Closed
wants to merge 7 commits into from
Closed

CDCWonder_NNDSS_InfectiousAnnual_changes #1101

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
e725549
script modification of nndss
SudhishaK Oct 30, 2024
b404545
script modification of nndss
SudhishaK Oct 30, 2024
32e8401
script modification of nndss
SudhishaK Nov 4, 2024
9ac606b
CDCWonder_NNDSS_InfectiousAnnual_changes
SudhishaK Nov 4, 2024
e66fb25
CDCWonder_NNDSS_InfectiousAnnual_changes
SudhishaK Nov 4, 2024
ffee172
CDCWonder_NNDSS_InfectiousAnnual_changes
SudhishaK Dec 23, 2024
fbefa5f
CDCWonder_NNDSS_InfectiousAnnual_changes
SudhishaK Dec 23, 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
3,974 changes: 3,974 additions & 0 deletions scripts/us_cdc/nndss_annual_tables/annual_tables_disease_mapping.csv
View file
Open in desktop

Large diffs are not rendered by default.

275 changes: 275 additions & 0 deletions scripts/us_cdc/nndss_annual_tables/config.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,275 @@
_PV_MAP = {
'confirmed': {
'medicalStatus': 'dcs:ConfirmedCase'
},
'probable': {
'medicalStatus': 'dcs:ProbableCase'
},
'deaths': {
'medicalStatus': 'dcs:PatientDeceased'
},
'pediatric mortality': {
'medicalStatus': 'dcs:PediatricMortality'
},
'all serotypes': {
'serotype': 'dcs:AllSerotypes'
},
'serotype b': {
'serotype': 'dcs:SerotypeB'
},
'unknown serotype': {
'serotype': 'dcs:UnknownSerotype'
},
'non-b serotype': {
'serotype': 'dcs:NonSerotypeB'
},
'other serogroups': {
'serogroup': 'dcs:OtherSerogroups'
},
'nontypeable': {
'serogroup': 'dcs:OtherSerogroups'
},
'unknown serogroup': {
'serogroup': 'dcs:UnknownSerogroups'
},
'all groups': {
'serogroup': 'dcs:AllSerogroups'
},
'all serogroups': {
'serogroup': 'dcs:AllSerogroups'
},
'serogroups acwy': {
'serogroup': 'dcs:ACWYSerogroup'
},
'serogroup b': {
'serogroup': 'dcs:SerogroupB'
},
'group a': {
'serogroup': 'dcs:SerogroupA'
},
'perinatal infection': {
'medicalCondition': 'dcs:PerinatalInfection'
},
'acute': {
'medicalCondition': 'dcs:AcuteCondition'
},
'chronic': {
'medicalCondition': 'dcs:ChronicCondition'
},
'imported': {
'medicalStatus': 'dcs:ImportedCase'
},
'indigenous': {
'medicalStatus': 'dcs:IndigenousCase'
},
'clinical': {
'medicalStatus': 'dcs:ClinicalCase'
},
'neuroinvasive': {
'medicalCondition': 'dcs:NeuroinvasiveDisease'
},
'non-neuroinvasive': {
'medicalCondition': 'dcs:NonNeuroinvasiveDisease'
},
'congenital': {
'medicalCondition': 'dcs:CongenitalDisease'
},
'non-congenital': {
'medicalCondition': 'dcs:NonCongenitalDisease'
},
'drug resistant': {
'medicalCondition': 'dcs:DrugResistantDisease'
},
'nondrug resistant': {
'medicalCondition': 'dcs:NonDrugResistantDisease'
},
'invasive disease': {
'medicalCondition': 'dcs:InvasiveDisease'
},
'post-diarrheal': {
'medicalCondition': 'dcs:PostDiarrheal'
},
'<1 yr': {
'age': '[- 1 Years]'
},
'1-4 yrs': {
'age': '[1 4 Years]'
},
'5-14 yrs': {
'age': '[5 14 Years]'
},
'15-24 yrs': {
'age': '[15 24 Years]'
},
'25-39 yrs': {
'age': '[25 39 Years]'
},
'40-64 yrs': {
'age': '[40 64 Years]'
},
'≥65 yrs': {
'age': '[65 - Years]'
},
'age <5 years': {
'age': '[- 5 Years]'
},
'age not stated': {
'age': 'dcs:USC_AgeNotStated'
},
'male': {
'gender': 'dcs:Male'
},
'female': {
'gender': 'dcs:Female'
},
'sex not stated': {
'gender': 'dcs:CDC_GenderUnknownOrNotStated'
},
'american indian or alaska native': {
'race': 'dcs:AmericanIndianAndAlaskaNativeAlone'
},
'american indian or alaska native': {
'race': 'dcs:AmericanIndianAndAlaskaNativeAlone'
},
'asian or pacific islander': {
'race': 'dcs:AsianOrPacificIslander'
},
'asian or pacific islander': {
'race': 'dcs:AsianOrPacificIslander'
},
'black or african american': {
'race': 'dcs:BlackOrAfricanAmericanAlone'
},
'black': {
'race': 'dcs:Black'
},
'white': {
'race': 'dcs:White'
},
'other race': {
'race': 'dcs:CDC_OtherRace'
},
'other or multi-race ¶': {
'race': 'dcs:CDC_OtherRace'
},
'race not stated': {
'race': 'dcs:CDC_RaceUnknownOrNotStated'
},
'hispanic': {
'ethnicity': 'dcs:HispanicOrLatino'
},
'hispanic or latino': {
'ethnicity': 'dcs:HispanicOrLatino'
},
'non-hispanic/latino': {
'ethnicity': 'dcs:NotHispanicOrLatino'
},
'non-hispanic': {
'ethnicity': 'dcs:NotHispanicOrLatino'
},
'ethnicity not stated': {
'ethnicity': 'dcs:CDC_EthnicityUnknownOrNotStated'
},
'confirmed': {
'medicalStatus': 'dcs:ConfirmedCase'
},
'probable': {
'medicalStatus': 'dcs:ProbableCase'
},
'pediatric mortality': {
'medicalStatus': 'dcs:PediatricMortality'
},
'deaths': {
'medicalStatus': 'dcs:PatientDeceased'
},
'age <5': {
'age': '[- 5 Years]'
},
'age < 5': {
'age': '[- 5 Years]'
},
'age <5 years': {
'age': '[- 5 Years]'
},
'age < 5 years': {
'age': '[- 5 Years]'
},
'all serotypes': {
'serotype': 'dcs:AllSerotypes'
},
'serotype b': {
'serotype': 'dcs:SerotypeB'
},
'unknown serotype': {
'serotype': 'dcs:UnknownSerotype'
},
'non-b serotype': {
'serotype': 'dcs:NonSerotypeB'
},
'other serogroups': {
'serogroup': 'dcs:OtherSerogroups'
},
'nontypeable': {
'serogroup': 'dcs:OtherSerogroups'
},
'unknown serogroup': {
'serogroup': 'dcs:UnknownSerogroups'
},
'all groups': {
'serogroup': 'dcs:AllSerogroups'
},
'all serogroups': {
'serogroup': 'dcs:AllSerogroups'
},
'serogroups acwy': {
'serogroup': 'dcs:ACWYSerogroup'
},
'serogroup b': {
'serogroup': 'dcs:SerogroupB'
},
'group a': {
'serogroup': 'dcs:SerogroupA'
},
'perinatal infection': {
'medicalCondition': 'dcs:PerinatalInfection'
},
'acute': {
'medicalCondition': 'dcs:AcuteCondition'
},
'chronic': {
'medicalCondition': 'dcs:ChronicCondition'
},
'imported': {
'medicalStatus': 'dcs:ImportedCase'
},
'indigenous': {
'medicalStatus': 'dcs:IndigenousCase'
},
'clinical': {
'medicalStatus': 'dcs:ClinicalCase'
},
'neuroinvasive': {
'medicalCondition': 'dcs:NeuroinvasiveDisease'
},
'non-neuroinvasive': {
'medicalCondition': 'dcs:NonNeuroinvasiveDisease'
},
'congenital': {
'medicalCondition': 'dcs:CongenitalDisease'
},
'non-congenital': {
'medicalCondition': 'dcs:NonCongenitalDisease'
},
'drug resistant': {
'medicalCondition': 'dcs:DrugResistantDisease'
},
'nondrug resistant': {
'medicalCondition': 'dcs:NonDrugResistantDisease'
},
'invasive disease': {
'medicalCondition': 'dcs:InvasiveDisease'
},
'post-diarrheal': {
'medicalCondition': 'dcs:PostDiarrheal'
}
}
Loading
Loading