Analytic data sets

Catalog

The following data is available at: /n/dominici_nsaph_l3/Lab/projects/analytic/

MedPar (Admissions)

admissions_by_year

data_source	MedPar
fasse_location	admissions_by_year
rce_location	~/shared_space/ci3_health_data/medicare/gen_admission/ 1999_2016/targeted_conditions/cache_data/admissions_by_year/
date_created	Feb 20 2020
size	22 GB
files

   ├── admissions_1999.fst
   ├── admissions_2000.fst
   ├── ...
   └── admissions_2016.fst

header

QID                      : chr  
AGE                      : int  
SEX                      : int  
RACE                     : int  
SSA_STATE_CD             : int  
SSA_CNTY_CD              : int  
PROV_NUM                 : int  
ADM_SOURCE               : chr  
ADM_TYPE                 : int  
ADATE                    : chr  
DDATE                    : chr  
BENE_DOD                 : chr  
DODFLAG                  : chr  
ICU_DAY                  : int  
CCI_DAY                  : int  
ICU                      : int  
CCI                      : int  
DIAG1                    : chr  
DIAG2                    : chr  
DIAG3                    : chr  
DIAG4                    : chr  
DIAG5                    : chr  
DIAG6                    : chr  
DIAG7                    : chr  
DIAG8                    : chr  
DIAG9                    : chr  
DIAG10                   : logi 
diag11                   : logi 
diag12                   : logi 
diag13                   : logi 
diag14                   : logi 
diag15                   : logi 
diag16                   : logi 
diag17                   : logi 
diag18                   : logi 
diag19                   : logi 
diag20                   : logi 
diag21                   : logi 
diag22                   : logi 
diag23                   : logi 
diag24                   : logi 
diag25                   : logi 
YEAR                     : int  
LOS                      : int  
Parkinson_pdx            : int  
Parkinson_pdx2dx_10      : int  
Parkinson_pdx2dx_25      : int  
Alzheimer_pdx            : int  
Alzheimer_pdx2dx_10      : int  
Alzheimer_pdx2dx_25      : int  
Dementia_pdx             : int  
Dementia_pdx2dx_10       : int  
Dementia_pdx2dx_25       : int  
CHF_pdx                  : int  
CHF_pdx2dx_10            : int  
CHF_pdx2dx_25            : int  
AMI_pdx                  : int  
AMI_pdx2dx_10            : int  
AMI_pdx2dx_25            : int  
COPD_pdx                 : int  
COPD_pdx2dx_10           : int  
COPD_pdx2dx_25           : int  
DM_pdx                   : int  
DM_pdx2dx_10             : int  
DM_pdx2dx_25             : int  
Stroke_pdx               : int  
Stroke_pdx2dx_10         : int  
Stroke_pdx2dx_25         : int  
CVD_pdx                  : int  
CVD_pdx2dx_10            : int  
CVD_pdx2dx_25            : int  
CSD_pdx                  : int  
CSD_pdx2dx_10            : int  
CSD_pdx2dx_25            : int  
Ischemic_stroke_pdx      : int  
Ischemic_stroke_pdx2dx_10: int  
Ischemic_stroke_pdx2dx_25: int  
Hemo_Stroke_pdx          : int  
Hemo_Stroke_pdx2dx_10    : int  
Hemo_Stroke_pdx2dx_25    : int  
zipcode_R                : int  
Race_gp                  : chr  
Sex_gp                   : chr  
age_gp                   : chr  
Dual                     : int  

MBSF (Denominator)

denom

data_source	MBSF
fasse_location	denom
size	7.4 GB
files

   ├── qid_data_2009.fst
   ├── qid_data_2010.fst
   ├── ...
   ├── qid_data_2016.fst
   ├── qid_entry_exit.fst
   └── year_zip_confounders.fst

header (qid_data_yyyy)

qid   : chr  
year  : int  
zip   : int  
sex   : int  
age   : int  
dual  : chr  
dead  : logi 
hmo_mo: chr  
fips  : int  
race  : chr  
sexM  : num  

header (year_zip_confounders)

zip               : num  
year              : int  
mean_bmi          : num  
smoke_rate        : num  
hispanic          : num  
pct_blk           : num  
medhouseholdincome: num  
medianhousevalue  : num  
poverty           : num  
education         : num  
popdensity        : num  
pct_owner_occ     : num  
summer_tmmx       : num  
winter_tmmx       : num  
summer_rmax       : num  
winter_rmax       : num  
city              : chr  
statecode         : chr  
latitude          : num  
longitude         : num  

min_year: 2000
max_year: 2016

Annual Exposure per Medicare Beneficiary

qid_yr_exposures

rce_location	~/shared_space/ci3_analysis/dmork/Data/DLM_ADRD
fasse_location	qid_yr_exposures
dataset_author	Daniel Mork
date_created	April 2022
size	139 GB
description	Annual exposure measurements (columns, 2000-2016) for each Medicare benficiary (rows) tied to their zip code of residence in a given year. Exposures (xxx in file name) include: no2, ozone, pm2.5, pm2.5components, pr (precipitation), rmax (max humidity), tmmx (max temperature), zip (zip code of residence).
files

    ├── qid_yr_no2.fst
    ├── qid_yr_ozone.fst
    ├── qid_yr_pm25comp_br.fst
    ├── qid_yr_pm25comp_ca.fst
    ├── qid_yr_pm25comp_cu.fst
    ├── qid_yr_pm25comp_ec.fst
    ├── qid_yr_pm25comp_fe.fst
    ├── qid_yr_pm25comp_k.fst
    ├── qid_yr_pm25comp_nh4.fst
    ├── qid_yr_pm25comp_ni.fst
    ├── qid_yr_pm25comp_no3.fst
    ├── qid_yr_pm25comp_oc.fst
    ├── qid_yr_pm25comp_pb.fst
    ├── qid_yr_pm25comp_si.fst
    ├── qid_yr_pm25comp_so4.fst
    ├── qid_yr_pm25comp_v.fst
    ├── qid_yr_pm25comp_z.fst
    ├── qid_yr_pm25.fst
    ├── qid_yr_pr.fst
    ├── qid_yr_rmax.fst
    ├── qid_yr_tmmx.fst
    └── qid_yr_zip.fst

header (qid_yr_xxx.fst):

qid : chr  
2000: num  
2001: num  
2002: num  
2003: num  
2004: num  
2005: num  
2006: num  
2007: num  
2008: num  
2009: num  
2010: num  
2011: num  
2012: num  
2013: num  
2014: num  
2015: num  
2016: num

MBSF (Enrollment file, denominator)

denom_by_year

data_source	MBSF, census (interpolated), BRFSS (interpolated), PM2.5 exposure, seasonal temperature
rce_location	~/shared_space/ci3_health_data/medicare/mortality/ 1999_2016/wu/cache_data/merged_by_year_v2
fasse_location	denom_by_year
git_repository	github.com/NSAPH/National-Causal-Analysis
dataset_author	Ben Sabath, Xiao Wu
spatial_resolution	zipcode
temporal_coverage	1999-2016
processing_description	Recommended for use. Available in both .fst and .csv formats on FASSE.
date_created	Apr 2021
size	7.4 GB
files

   ├── confounder_exposure_merged_nodups_health_1999.fst
   ├── ...
   └── confounder_exposure_merged_nodups_health_2016.fst

header

zip                         : int  
year                        : int  
qid                         : chr  
dodflag                     : chr  
bene_dod                    : chr  
sex                         : int  
race                        : int  
age                         : int  
hmo_mo                      : chr  
hmoind                      : chr  
statecode                   : chr  
latitude                    : num  
longitude                   : num  
dual                        : chr  
death                       : int  
dead                        : logi 
entry_age                   : int  
entry_year                  : int  
entry_age_break             : int  
followup_year               : num  
followup_year_plus_one      : num  
pm25_ensemble               : num  
pm25_no_interp              : num  
pm25_nn                     : num  
ozone                       : num  
ozone_no_interp             : num  
zcta                        : int  
poverty                     : num  
popdensity                  : num  
medianhousevalue            : num  
pct_blk                     : num  
medhouseholdincome          : num  
pct_owner_occ               : num  
hispanic                    : num  
education                   : num  
population                  : num  
zcta_no_interp              : int  
poverty_no_interp           : num  
popdensity_no_interp        : num  
medianhousevalue_no_interp  : num  
pct_blk_no_interp           : num  
medhouseholdincome_no_interp: num  
pct_owner_occ_no_interp     : num  
hispanic_no_interp          : num  
education_no_interp         : num  
population_no_interp        : int  
smoke_rate                  : num  
mean_bmi                    : num  
smoke_rate_no_interp        : num  
mean_bmi_no_interp          : num  
amb_visit_pct               : num  
a1c_exm_pct                 : num  
amb_visit_pct_no_interp     : num  
a1c_exm_pct_no_interp       : num  
tmmx                        : num  
rmax                        : num  
pr                          : num  
cluster_cat                 : chr  
fips_no_interp              : int  
fips                        : int  
summer_tmmx                 : num  
summer_rmax                 : num  
winter_tmmx                 : num  
winter_rmax                 : num  

AD/ADRD Hospitalization

hospitalization

data_source	MedPar derived
rce_location	~/shared_space/ci3_analysis/dmork/Data/DLM_ADRD
fasse_location	hospitalization
dataset_author	Daniel Mork
description	The first recorded hospitalization for each individual broken down by primary/secondary/any billing code (ICD).
size	1.2 GB
files

   ├── First_hosp_AD_any.fst
   ├── First_hosp_AD_primary.fst
   ├── First_hosp_ADRD_any.fst
   ├── First_hosp_ADRD_primary.fst
   ├── First_hosp_ADRD_secondary.fst
   └── First_hosp_AD_secondary.fst

header

QID  : Factor 
ADATE: Date
year : num  

Medicare Entry Age

medicare_entry_age

data_source	MBSF derived
rce_location	/nfs/nsaph_ci3/scratch/jan2021_whanhee_cache/entry_age/
fasse_location	medicare_entry_age
size	2.3 GB
date_created	Jan 26, 2021
dataset_author	Ben Sabath, Whenhee Lee
spatial_resolution	zipcode
git_repository	NSAPH/data_requests
files

   └── medicare_entry_age.csv

Years in Medicare

years_in_medicare

data_source	MBSF derived
rce_location	/nfs/nsaph_ci3/scratch/jan2021_whanhee_cache/follow_up/
fasse_location	years_in_medicare
description	Number of years a beneficiary has been in Medicare (or in other words, the number of years since one has entered Medicare). Allows for grouping on how long beneficiaries have been in Medicare.
size	8.8 GB
date_created	Jan 26, 2021
temporal_coverage	1999-2016
dataset_author	Ben Sabath, Whanhee Lee
spatial_resolution	zipcode
git_repository	NSAPH/data_requests
files

   ├── follow_up_year_2000.fst
   ├── ...
   └── follow_up_year_2016.fst

Temperature Humidity Precipitation

temperature_seasonal_zipcode

rce_location	/nfs/nsaph_ci3/ci3_confounders/data_for_analysis/earth_engine/ temperature/temperature_seasonal_zipcode_combined.csv
fasse_location	temperature_seasonal_zipcode
dataset_author	Xiao Wu, Ben Sabath
date_created	Jul 23, 2020
data_source	Google Earth Engine provides a single interface for interacting with a number of geospatial data sources. The sources used and links to their documentation are: GRIDMET, NLDAS, MODIS MOD10A1.006, GLDAS, NOAA CDR PATMOSX, NOAA NCEP Climate Forecast System V2
spatial_coverage	contiguous US
spatial_resolution	zipcode
temporal_coverage	1999-2019
temporal_resolution	annually
description	This dataset contains information on temperature, relative humidity, and total precipitation data. The data is available as raster files on Google earth engine. The temporal and spatial resolutions varied by data source, but all were available at a daily resolution or more frequently. Where the time resolution of the rasters is more than daily, daily averages for each raster were calculated. Next, using Google earth engine’s spatial averaging algorithms and a set of polygons representing the areas of interest, the daily value for each polygon was calculated. The polygons used were the ones described in the preceding section. The results of this calculation were then downloaded as a csv file to the RCE. At this point, there is one file for each year. Following this, annual averages are calculated for each location, and these are combined in to a single file. The daily values are also combined in to a single file. For the combined_zips files (which combine the zip code polygon based measures with the the point based estimates to address zip codes without area) there is an additional step. Values for zip codes not in the polygon based measure are taken from the point based measures to address the ~7000 zip codes without area that are missing from the polygon shape file.
git_repository	NSAPH/data_documentation
meterological	Temperature (K) - variable name: tmmx (Source: GRIDMET); Relative Humidity - variable name: rmax (Source: GRIDMET)
size	65 MB
header	ZIP,year,summer_tmmx,summer_rmax,winter_tmmx,winter_rmax
files

   └── temperature_seasonal_zipcode_combined.csv

Pollution-Census-Temperature covariates

merged_covariates_pm_census_temp

data_source	US Census/ACS, Business Analyst Data Set, BRFSS
rce_location	/nfs/nsaph_ci3/ci3_health_data/medicare/ mortality/1999_2016/wu/output_data /merged_covariates.csv
fasse_location	merged_covariates_pm_census_temp
dataset_author	Xiao Wu, Ben Sabath
date_created	May 29, 2019
spatial_coverage	contiguous US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
publication	https://www.science.org/doi/10.1126/sciadv.aba5692
git_repository	nejm_confounder_summary/nejm_confounder and rce_data_list/confounder_data
size	296 MB
header	zip, year, pm25_ensemble, pm25_no_interp, pm25_nn, ozone, ozone_no_interp, zcta, poverty, popdensity, medianhousevalue, pct_blk, medhouseholdincome, pct_owner_occ, hispanic, education, population, zcta_no_interp, poverty_no_interp, popdensity_no_interp, medianhousevalue_no_interp, pct_blk_no_interp, medhouseholdincome_no_interp, pct_owner_occ_no_interp, hispanic_no_interp, education_no_interp, population_no_interp, smoke_rate, mean_bmi, smoke_rate_no_interp, mean_bmi_no_interp, amb_visit_pct, a1c_exm_pct, amb_visit_pct_no_interp, a1c_exm_pct_no_interp, tmmx, rmax, pr, cluster_cat, fips, fips_no_interp
files

   └── merged_covariates.csv

Population-Weighted Daily County-Level Heat Metrics

county_heat_metrics

data_source	ERA5-Land gridded data
fasse_location	heatvars_county_2000-2020
dataset_author	Keith Spangler
date_created	June 17, 2022
spatial_coverage	contiguous US
spatial_resolution	county
temporal_coverage	2000-2020
temporal_resolution	daily
publication	https://pubmed.ncbi.nlm.nih.gov/35715416/
size	1.03 GB
header	"StCoFIPS", "Date", "Tmin_C", "Tmax_C", "Tmean_C", "TDmin_C", "TDmax_C", "TDmean_C", "NETmin_C", "NETmax_C", "NETmean_C", "HImin_C", "HImax_C", "HImean_C", "HXmin_C", "HXmax_C", "HXmean_C", "WBGTmin_C", "WBGTmax_C", "WBGTmean_C", "UTCImin_C", "UTCImax_C", "UTCImean_C", "Flag_T", "Flag_TD", "Flag_NET", "Flag_HI", "Flag_HX", "Flag_WBGT", "Flag_UTCI"
files

   └── Heatvars_County_2000-2020_v1.2.Rds

Medicaid - Respiratory Hospitalizations in Children

medicaid_children_99-12

data_source	Medicaid
rce_location	/nfs/nsaph_ci3/ci3_health_data/medicaid/respiratory /1999_2012/youth_resp_hosps_jlee/data
fasse_location	medicaid_children_99-12
dataset_author	Jenny Lee
date_created	2021
spatial_coverage	contiguous US
spatial_resolution	zipcode
temporal_coverage	1999-2012
temporal_resolution	annually
description	The data prepared for this project consists of the Medicaid Fee For Service population, with unrestricted Medicaid benefits, under the age of 20 from 1999-2012. This data also includes all hospitalizations for that population, with indicators included regarding whether or not they were associated with a set of respiratory hospitalizations. See the schema for the hospitalization data below for details on specific indicators.
git_repository	NSAPH/data_requests
exposures	Xiao Wu’s CausalGPS PM2.5 data
size	14 GB
files

├── denom
│   ├── denom_under_20_1999.fst
│   ├── ...
│   └── denom_under_20_2012.fst
└── hosps
    ├── under_20_admissions_1999.fst
    ├── ...
    └── under_20_admissions_2012.fst

Exposure-census-BRFFS confounders

confounders

data_source	US Census, BRFSS
rce_location	/nfs/nsaph_ci3/scratch/jan2021_whanhee_cache/cache_dir/ merged_exposure_confounders/
fasse_location	confounders
dataset_author	Ben Sabath, Whanhee Lee
date_created	Apr 23, 2021
spatial_coverage	contiguous US
spatial_resolution	zipcode, zcta
temporal_coverage	2000-2016
temporal_resolution	annually
git_repository	data_requests
size	247 MB
header	ZIP, year, zcta, poverty, popdensity, medianhousevalue, pct_blk, medhouseholdincome, pct_owner_occ, hispanic, education, population, pct_asian, pct_native, pct_white, smoke_rate, mean_bmi, pm25.current_year, ozone.current_year, no2.current_year, ozone_summer.current_year, pm25.one_year_lag, ozone.one_year_lag, no2.one_year_lag, ozone_summer.one_year_lag
files

   ├── merged_confounders_2000.csv
   ├── ...
   └── merged_confounders_2016.csv

ADRD Hospitalization Records

adrd_hospitalization

dataset_author	Shuxin Dong
date_created	Jan 27, 2022
data_source	MedPar (admissions)
spatial_coverage	US
spatial_resolution	zipcode (unaggregated)
temporal_coverage	2000-2016
temporal_resolution	daily (with admission date)
description	extract the ADRD hospitalizations based on the Chronic Condition Warehouse
rce_location	~/shared_space/ci3_analysis/ data_ADRDhospitalization/ ADRDhospitalization_CCWlist/
fasse_location	adrd_hospitalization
size	1.9 GB
git_repository	ShuxinD/ADRDdata
other	The Chronic Condition Warehouse list for ADRD: https://www2.ccwdata.org/web/guest/condition-categories
files

   ├── ADRD_2000.fst
   ├── ...
   └── ADRD_2016.fst

header

QID           : chr 
ADATE         : Date
DDATE         : Date
zipcode_R     : int 
DIAG1         : chr 
DIAG2         : chr 
DIAG3         : chr 
DIAG4         : chr 
DIAG5         : chr 
DIAG6         : chr 
DIAG7         : chr 
DIAG8         : chr 
DIAG9         : chr 
DIAG10        : chr 
AGE           : int 
Sex_gp        : chr 
Race_gp       : chr 
SSA_STATE_CD  : int 
SSA_CNTY_CD   : int 
PROV_NUM      : int 
ADM_SOURCE    : chr 
ADM_TYPE      : int 
Dual          : int 
year          : num 
AD_primary    : logi
AD_any        : logi
AD_secondary  : logi
ADRD_primary  : logi
ADRD_any      : logi
ADRD_secondary: logi

Medpar File 2000-2016 Clean

medpar_hospital_clean_0619

dataset_author	Mahdieh Danesh Yazdi
date_created	May 2019
data_source	MedPar (admissions)
spatial_coverage	US
size	1.8 GB
spatial_resolution	zipcode, city
temporal_coverage	2000-2016
temporal_resolution	admissions date
processing_description	The data was limited to the years 2000-2016 (1999 was dropped). Demographic data was removed (use demographic data from denominator file). Duplicated admission records were removed. For multiple admissions on the same day, the longer length of stay was kept and those without missing diagnositic codes. Subset data to keep only first two diagnostic codes. A diabetes varible was created (would review ICD codes used clinically prior to use).
rce_location	~/shared_space/ci3_mdaneshyazdi/Medpar_Data/ data/medpar_hospital_clean_0619.rds
fasse_location	medpar_hospital_clean_0619
files

   └── medpar_hospital_clean_0619.rds

Denominator File 2000-2016 Clean

denominator_clean_0619

dataset_author	Mahdieh Danesh Yazdi
date_created	May 2019
data_source	MBSF (denominator)
spatial_coverage	US
size	3.8 GB
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
processing_description	The data was limited to the years 2000-2016 (1999 was dropped). Rows with empty or missing QID values were dropped. Those whose sex changed through follow up were dropped. Those whose race changed through follow up were assigned “Other/Unknown” category. Those who had multiple dates of death in different years were dropped. For those with multiple dates of death in the same year, earlier date of death was assigned. If duplicate rows existed, one with date of death and one without, the row with non-missing date of death was kept. Multiple QID-year rows with differing values of other variables were removed. Observations with invalid zip codes were removed. Warning: There may be excess deaths on the last day of the month due to CMS processing. Sometimes when the exact date of death is unknown, it is assigned to the last day of the month.
rce_location	~/shared_space/ci3_mdaneshyazdi/Denominator_Data/ data/denominator_clean_0619.rds
fasse_location	denominator_clean_0619
files

   └── denominator_clean_0619.rds

Denominator Clean Merged with Exposure and Covariate Data

merged_denominator_clean_0619_exp_conf

dataset_author	Mahdieh Danesh Yazdi
date_created	February 2020
data_source	MedPar (admissions), MBSF (denominator)
spatial_coverage	US
size	30 GB (fst) and 4.4 GB (rds)
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
description	The clean denominator file merged with annual PM2.5, NO2, O3 levels from 1-km exposure models generated by Qian Di and Weeberb Requia aggregatetd to zip code level by Yaguang Wei. Also merged with covariate data from the Census, ACS, BRFSS, and Dartmouth Health Atlas created by Ben Sabath. Missing values were filled in using interpolated/extrapolated values from Liuhua Shi. (Negative values were set to 0 and values greater than 100% were set to 100%). Other missing values were dropped. The exposure values and covariate data may need to updated depending on study being done.
rce_location	~/shared_space/ci3_mdaneshyazdi/ Merged_Data/data/denominator.rds and ~/shared_space/ci3_mdaneshyazdi/ Merged Data/denominator.fst
fasse_location	merged_denominator_clean_0619_exp_conf
files

   ├── denominator.rds
   └── denominator.fst

Hospital Admissions Merged with Denominator, Exposure, and Covariates

national_exp_0621

dataset_author	Mahdieh Danesh Yazdi
date_created	Jun 2021
data_source	MedPar (admissions), MBSF (denominator)
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
description	The clean denominator file merged with the clean hospital admissions data, limited to FFS patients, and then merged with annual PM2.5, NO2, O3 levels and Warm-season O3 levels from 1-km exposure models generated by Qian Di and Weeberb Requia aggregatetd to zip code level by Yaguang Wei. Also merged with covariate data from the Census, ACS, BRFSS, and Dartmouth Health Atlas created by Ben Sabath. Missing values were filled in using interpolated/extrapolated values from Liuhua Shi. (Negative values were set to 0 and values greater than 100% were set to 100%). Other missing values were dropped. The exposure values and covariate data may need to updated depending on study being done. Individuals may have multiple admissions per year.
size	32 GB
rce_location	~/shared_space/ci3_mdaneshyazdi/ Merged_Data/data/national_exp_0621.fst
fasse_location	national_exp_0621
files

   └── national_exp_0621.fst

Aggregated 2010-2016 Medicare Mortality Data with PM2.5 Exposure and ZIP code level variables

aggregate_medicare_data_2010to2016

description	This data contain (annually aggregated) exposure to PM2.5 data, demographic data from census and mortality data + individual level characteristics for the entire Medicare population in 1999-2016. See Xiao’s paper for processing description.
dataset_author	Xiao Wu, Ben Sabath
date_created	2020
data_source	Medicaid, Exposure Data, Census Data
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2010-2016
temporal_resolution	Annually
publication	https://www.science.org/doi/10.1126/sciadv.aba5692
rce_location	~shared_space/ci3_analysis/causal_rule_ensemble /aggregate_medicare_data_2010to2016.fst
fasse_location	aggregate_medicare_data_2010to2016
git_repository	wxwx1993/National_Causal
files

   └── aggregate_medicare_data_2010to2016.fst

Nationwide Medicare Strata

erc_strata

dataset_author	Kevin Josey
date_created	Aug 5 2022
data_source	Medicare File from Xiao et al.’s Science Advances paper (see denom_by_year)
spatial_coverage	contiguous US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annual
description	Data were divided and aggregated into custom strata, then subsetted depending on several individual factors. I further merged these data tables with neighborhood level covariates.
rce_location	~/shared_space/ci3_analysis/josey_erc_strata/Data
fasse_location	erc_strata
git_repository	kevjosey/erc-strata
size	6.9 GB
files

├── aggregate_data_qd.RData
├── aggregate_data_rm.RData
├── national_merged2016_qd.RData
├── national_merged2016_rm.RData
├── qd
│   ├── 0_all_qd.RData
│   ├── 0_asian_qd.RData
│   ├── 0_black_qd.RData
│   ├── 0_hispanic_qd.RData
│   ├── 0_white_qd.RData
│   ├── 1_all_qd.RData
│   ├── 1_asian_qd.RData
│   ├── 1_black_qd.RData
│   ├── 1_hispanic_qd.RData
│   ├── 1_white_qd.RData
│   ├── 2_all_qd.RData
│   ├── 2_asian_qd.RData
│   ├── 2_black_qd.RData
│   ├── 2_hispanic_qd.RData
│   └── 2_white_qd.RData
└── rm
    ├── 0_all_rm.RData
    ├── 0_asian_rm.RData
    ├── 0_black_rm.RData
    ├── 0_hispanic_rm.RData
    ├── 0_white_rm.RData
    ├── 1_all_rm.RData
    ├── 1_asian_rm.RData
    ├── 1_black_rm.RData
    ├── 1_hispanic_rm.RData
    ├── 1_white_rm.RData
    ├── 2_all_rm.RData
    ├── 2_asian_rm.RData
    ├── 2_black_rm.RData
    ├── 2_hispanic_rm.RData
    └── 2_white_rm.RData

CVD Medicaid

cvd_medicaid

dataset_author	Ben Sabath
date_created	January 28, 2020
data_source	Medicaid
spatial_coverage	US (continental)
spatial_resolution	zipcode
temporal_coverage	2002-2012
temporal_resolution	daily
size	86 GB
git_repository	dec2019_medicaid_platform_cvd
rce_location	~/shared_space/ci3_health_data /medicaid/cvd/2010_2011/desouza-2
fasse_location	cvd_medicaid
publication	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7896354/
files

├── [2.3G]  cvd.csv
├── [2.1G]  cvd.sas7bdat
├── [6.3K]  CVD-specific data dictionary-07-12-2018.docx
├── [6.8K]  data_dictionary.md
├── [ 70G]  merged_cvd_data.csv
├── [ 18K]  merge.out
│   ├── [5.7K]  log.txt
│   ├── [  77]  r_error.0
│   └── [ 12K]  r_out.0
├── [1.7K]  merge.R
├── [ 906]  readme
└── [ 899]  r.submit

Aggregated CVD cohort Medicare

aggregated_cvd_cohort_medicare

dataset_author	Jochem Klompmaker
date_created	April 2022
data_source	MedPar (admissions), MBSF (denominator)
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
description	Denominator file linked with hospitalization data and merged with confounders and exposures (NO2, PM2.5, ozone, temperature, humidity). Person records were aggregated by zip code, year and individual demographics
rce_location	~/shared_space/ci3_health_data/medicare/gen_admission /1999_2016/Klompmaker/merged_data/cvd2/
fasse_location	aggregated_cvd_cohort_medicare
size	38 GB
files

├── [4.2G]  aggregate_CVD_65yrs.fst
├── [3.8G]  aggregate_CVD_75yrs.fst
├── [3.1G]  aggregate_CVD_85yrs.fst
├── [6.5G]  aggregate_CVD.fst
├── [4.8G]  aggregate_death_CVD.fst
├── [4.6G]  aggregate__excl_1yrhosp_CVD.fst
├── [4.3G]  aggregate_excl_1yrhosp_RES.fst
├── [1.2M]  cc_zipyear_all.fst
├── [1.2M]  cc_zipyear_confounder.fst
├── [941K]  cc_zipyear_cvd.fst
├── [347M]  CVD_count.fst
├── [354M]  CVD_death_count.fst
├── [439M]  time_count.fst
└── [439M]  time_death_count.fst

Aggregated CHD cohort Medicare

aggregated_chd_cohort_medicare

dataset_author	Jochem Klompmaker
date_created	April 2022
data_source	MedPar (admissions), MBSF (denominator)
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
description	Denominator file linked with hospitalization data and merged with confounders and exposures (NO2, PM2.5, ozone, temperature, humidity). Person records were aggregated by zip code, year and individual demographics
rce_location	~/shared_space/ci3_health_data/medicare /gen_admission /1999_2016/Klompmaker/merged_data/chd2/
fasse_location	aggregated_chd_cohort_medicare
size	35 GB
files

├── [4.1G]  aggregate_CHD_65yrs.fst
├── [3.8G]  aggregate_CHD_75yrs.fst
├── [3.2G]  aggregate_CHD_85yrs.fst
├── [ 14G]  aggregate_CHD.fst
├── [4.3G]  aggregate_excl_1yrhosp_CHD.fst
├── [1.2M]  cc_zipyear_chd.fst
├── [ 92M]  CHD_count.fst
└── [116M]  time_count.fst

Aggregated CBV cohort Medicare

aggregated_cbv_cohort_medicare

dataset_author	Jochem Klompmaker
date_created	April 2022
data_source	MedPar (admissions), MBSF (denominator)
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
description	Denominator file linked with hospitalization data and merged with confounders and exposures (NO2, PM2.5, ozone, temperature, humidity). Person records were aggregated by zip code, year and individual demographics
rce_location	~/shared_space/ci3_health_data/medicare/gen_admission /1999_2016/Klompmaker/merged_data/cbv2/
fasse_location	aggregated_cbv_cohort_medicare
size	35 GB
files

├── [4.1G]  aggregate_CBV_65yrs.fst
├── [3.8G]  aggregate_CBV_75yrs.fst
├── [3.2G]  aggregate_CBV_85yrs.fst
├── [ 14G]  aggregate_CBV.fst
├── [4.4G]  aggregate__excl_1yrhosp_CBV.fst
├── [ 93M]  CBV_count.fst
├── [1.2M]  cc_zipyear_cbv.fst
└── [117M]  time_count.fst

Aggregated ADRD cohort Medicare

aggregated_adrd_cohort_medicare

dataset_author	Jochem Klompmaker
date_created	February 2022
data_source	MedPar (admissions), MBSF (denominator)
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
description	Denominator file linked with hospitalization data and merged with confounders and exposures (NDVI, blue space, park cover, NO2, PM2.5, ozone, temperature, humidity). Person records were aggregated by zip code, year and individual demographics
rce_location	~/shared_space/ci3_health_data/medicare/gen_admission /1999_2016/Klompmaker/merged_data/alz2/
fasse_location	aggregated_adrd_cohort_medicare
size	28 GB
files

├── [3.6G]  aggregate_ALZ_65yrs.fst
├── [3.4G]  aggregate_ALZ_75yrs.fst
├── [2.8G]  aggregate_ALZ_85yrs.fst
├── [4.5G]  aggregate_ALZ.fst
├── [4.4G]  aggregate_death_ALZ.fst
├── [3.8G]  aggregate_excl_1yrhosp_ALZ.fst
├── [358M]  ALZ_count.fst
├── [387M]  ALZ_death_count.fst
├── [471M]  time_count.fst
└── [472M]  time_death_count.fst

Aggregated PD cohort Medicare

aggregated_pd_cohort_medicare

dataset_author	Jochem Klompmaker
date_created	February 2022
data_source	MedPar (admissions), MBSF (denominator)
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
description	Denominator file linked with hospitalization data and merged with confounders and exposures (NDVI, blue space, park cover, NO2, PM2.5, ozone, temperature, humidity). Person records were aggregated by zip code, year and individual demographics.
rce_location	~/shared_space/ci3_health_data/medicare /gen_admission/1999_2016 /Klompmaker/merged_data/par2/
fasse_location	aggregated_pd_cohort_medicare
size	29 GB
files

├── [4.4G]  aggregate_death_PAR.fst
├── [4.4G]  aggregate_excl_1yrhosp_PAR.fst
├── [3.7G]  aggregate_PAR_65yrs.fst
├── [3.4G]  aggregate_PAR_75yrs.fst
├── [2.9G]  aggregate_PAR_85yrs.fst
├── [4.6G]  aggregate_PAR.fst
├── [ 94M]  PAR_count.fst
├── [405M]  PAR_death_count.fst
├── [222M]  time_count.fst
└── [486M]  time_death_count.fst

Daily County Level Heatwave Associated Hospitalizations

daily_county_level_heatwave_assosciated_hospitalizations

dataset_author	Ben Sabath
date_created	July 10, 2020
size	7.7 GB
data_source	MedPar (admissions), MBSF (denominator), Medicaid MAX
spatial_coverage	US
spatial_resolution	county
temporal_coverage	2006-2016, 1999-2016
temporal_resolution	daily
description	FIPS code, race, sex, age, and dual eligibility were determined for each case based on the information in the patient summary file for that individual in the year of their admission. The denominator for each observation is calculated monthly and contains all individuals who are eligible for Fee for Service (FFS) hospitalization coverage and have not died prior to that month. The CCS codes included were 2, 50, 55, 114, 157, 159, and 244. ICD processing done using the ICD package(Wasey 2018). The author of this package asks that it be cited in papers using data that was created using the package.
rce_location	~/shared_space/ci3_health_data/medicare/heat_related
fasse_location	daily_county_level_heatwave_assosciated_hospitalizations
publication	https://arxiv.org/abs/2102.10478
git_repository	wxwx1993/TS_Stochastic
files

├── 1999_2016
│   └── county_ccs_hosps
│       ├── cache_dir
│       │   ├── daily_counts
│       │   │   ├── daily_counts_by_ccs_1999.fst
│       │   │   ├── ...
│       │   │   └── daily_counts_by_ccs_2016.fst
│       │   └── denom
│       │       ├── ffs_patient_summary_by_county_1999.fst
│       │       ├── ...
│       │       └── ffs_patient_summary_by_county_2016.fst
│       ├── data
│       │   ├── daily_ccs_heatwave_counts_by_fips_1999.fst
│       │   ├── ...
│       │   └── daily_ccs_heatwave_counts_by_fips_2016.fst
│       └── data_daily_hosp_mort
│           ├── daily_only_ccs_heatwave_hosp_mort_counts_by_fips_1999.fst
│           ├── ...
│           └── daily_only_ccs_heatwave_hosp_mort_counts_by_fips_2016.fst
└── 2006_2016
    └── county_ccs_hosps
        ├── cache_dir
        │   ├── daily_counts
        │   │   ├── daily_counts_by_ccs_2006.fst
        │   │   ├── ...
        │   │   └── daily_counts_by_ccs_2016.fst
        │   └── denom
        │       ├── ffs_patient_summary_by_county_2006.fst
        │       ├── ...
        │       └── ffs_patient_summary_by_county_2016.fst
        ├── data
        │   ├── daily_ccs_heatwave_counts_by_fips_2006.fst
        │   ├── ...
        │   ├── daily_ccs_heatwave_counts_by_fips_2016.fst
        │   ├── Daily_Heat_CCS_2006-2016_with_Temperature_by_WFO.Rda
        │   ├── Daily_Heat_CCS_2006-2016_with_Temperature_by_WFO_v0.Rda
        │   ├── Daily_Heat_CCS_2006-2016_with_Temperature_ERA5Land.Rda
        │   ├── Daily_Heat_CCS_2006-2016_with_Temperature.Rda
        │   └── Daily_Heat_CCS_2006-2016_with_Temperature_v0.Rda
        ├── readme.md
        └── schema.yml

Hospitalizations for kidney disease and comorbidities

medicare_for_kidney_diseases

dataset_author	Ana Trisovic
date_created	July 10, 2022
data_source	MedPar (admissions), MBSF (denominator), confounders
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	annually
git_repository	mbsf-medpar-aki-first-hospitalization
description	Special modifications for the kidney diseases for numerators and denominators (people at risk) for the analysis by Whanhee Lee.
rce_location	~/shared_space/ci3_analysis/whanhee_revisions
fasse_location	medicare_for_kidney_diseases
size	31 GB
header	year, sex, race, zip, dual, follow_up, entry_age_group, aki_primary_secondary_first_hosp, aki_primary_secondary_first_hosp_denom, ckdhosp_prior_aki, ckdhosp_prior_aki_denom, diabeteshosp_prior_aki, diabeteshosp_prior_aki_denom, diabetes_primary_aki_secondary_first_hosp, diabetes_primary_aki_secondary_first_hosp_denom, csd_primary_aki_secondary_first_hosp, csd_primary_aki_secondary_first_hosp_denom, ihd_primary_aki_secondary_first_hosp, ihd_primary_aki_secondary_first_hosp_denom, pneumonia_primary_aki_secondary_first_hosp, pneumonia_primary_aki_secondary_first_hosp_denom, hf_primary_aki_secondary_first_hosp, hf_primary_aki_secondary_first_hosp_denom, ami_primary_aki_secondary_first_hosp, ami_primary_aki_secondary_first_hosp_denom, cerd_primary_aki_secondary_first_hosp, cerd_primary_aki_secondary_first_hosp_denom, uti_primary_aki_secondary_first_hosp, uti_primary_aki_secondary_first_hosp_denom, zcta, poverty, popdensity, medianhousevalue, pct_blk, medhouseholdincome, pct_owner_occ, hispanic, education, population, pct_asian, pct_native, pct_white, smoke_rate, mean_bmi, pm25.current_year, ozone.current_year, no2.current_year, ozone_summer.current_year, pm25.one_year_lag, ozone.one_year_lag, no2.one_year_lag, ozone_summer.one_year_lag
files

└── [ 27G]  final.csv

IHD medicare hospitalizations (2005)

ihd_medicare_hosp_2005

dataset_name	IHD medicare hospitalizations (2005)
dataset_author	Cory Zigler
date_created	Oct 4 2018
data_source	MedPar (admissions)
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2005
temporal_resolution	annually
size	234 MB
rce_location	~/shared_space/ci3_analysis/ zigler_lab/projects/ BipartiteInterference_GPS/ BipartiteInterference_GPS/ Data
fasse_location	ihd_medicare_hosp_2005
files

├── [4.8K]  00Tree.html
├── [348K]  AnnualFacilityData.Rda
├── [773K]  AnnualUnitData.Rda
├── [ 12K]  Create Analysis Data.R
├── [6.4K]  Create HyADS Adjacency Matrix.R
├── [9.3K]  Create Power Plant Data.R
├── [5.8K]  Create Zip Code Data.R
├── [ 10M]  data_nomed.Rda
├── [ 31K]  facilities_for_analysis.Rda
├── [ 53M]  HyADSmat.Rda
├── [108M]  HyADSmat_replaced20191212.Rda
├── [3.1M]  MonthlyFacilityData.Rda
├── [9.7M]  MonthlyUnitData.Rda
├── [ 11M]  out.zip_pp.rda
├── [ 114]  Readme
├── [5.6M]  ZipcodeData.Rda
└── [ 89K]  zips_included.rda

Daily Florida Hospitalization Counts by Zip

daily-florida-hosp-counts-zip

dataset_author	Ben Sabath, Kate Burrows
date_created	February 07 2020
data_source	MedPar (admissions), MBSF (denominator)
spatial_coverage	Florida
spatial_resolution	zipcode
temporal_coverage	1999-2016
temporal_resolution	daily
processing_description	Denominator file linked with hospitalization data. This is the raw unprocessed data.
size	2.1 GB
rce_location	~/shared_space/ci3_health_data /medicare/gen_admission /1999_2016/burrows/cache_data
fasse_location	daily-florida-hosp-counts-zip
files

├── [308K]  Burrows_DataRequest_September2019.pdf
├── [ 19M]  death_count
│   ├── [1.0M]  death_count_1999.fst
│   ├── [1.0M]  ...
│   └── [1.2M]  death_count_2016.fst
├── [104M]  hosp_count
│   ├── [5.5M]  hosp_count_1999.fst
│   ├── [5.6M]  ...
│   └── [5.2M]  hosp_count_2016.fst
├── [1.6G]  merged_data
│   ├── [ 86M]  daily_zips_1999.fst
│   ├── [106M]  ...
│   └── [106M]  daily_zips_2016.fst
└── [7.2M]  zip_denom
    ├── [382K]  zip_denom_1999.fst
    ├── [440K]  ...
    └── [450K]  zip_denom_2016.fst

Coal PM2.5 Source Impacts

coal_exposure_pm25

dataset_author	Lucas Henneman
date_created	Sep 14, 2022
data_source	HyADS exposure modeling
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	1999-2020
temporal_resolution	annually
rce_location	/nfs/home/H/henneman /shared_space/ci3_nsaph/ LucasH/disperseR/ main/output/ zips_model.lm.cv_single_poly
fasse_location	coal_exposure_pm25
GitHub repository/directory on how the data was processed	lhenneman/coal_unit_PM25
exposures	This was created with the HyADS model using emissions from EPA’s CAMD database.
meterological	NOAA/NCAR reanalysis data.
size	6.3 GB
files

├── [300M]  zips_pm25_byunit_1999.fst
├── [291M]  ...
├── [134M]  zips_pm25_byunit_2020.fst
├── [599K]  zips_pm25_total_1999.fst
├── [599K]  ...
└── [599K]  zips_pm25_total_2020.fst

Aggregated 2000-2016 Medicare Mortality Data with PM2.5 Exposure by ZIP code

aggregated_2000-2016_medicare_mortality_pm25_zip

dataset_author	Xiao Wu, Ben Sabath
date_created	2020
data_source	Medicaid, Exposure Data, Census Data
spatial_coverage	US
spatial_resolution	zipcode
temporal_coverage	2000-2016
temporal_resolution	Annually
processing_description	See Xiao’s paper for processing description.
rce_location	~/shared_space/ci3_mic6949/ input_data/aggregate_data.RDS
fasse_location	aggregated_2000-2016_medicare_mortality_pm25_zip
publication	Xiao’s paper
git_repository	National_Causal
size	166 MB
files

└── [166M]  aggregate_data.RDS

Warning

The space of FASSE is limited, so do not copy analytic data to your own folder! Create symlinks to the data in your data folder. Symbolic links (or symlinks) are special files that point to files or directories in other locations on your system. You will be able to use data with symlinks as normal.

Create the symlink in your data folder in the following way:

cd data
ln -s /n/dominici_nsaph_l3/Lab/projects/analytic/fasse_location .

Note

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Data questions

1. What data sources (MedPar, MBSF, other) were used to create this data file? How many different data sources went into it?

2. What, if any, processing was done to the data sources? Were there any selections (cuts) done, data quality checks and aggregations?

3. Was this data used in any publication (add a link)?

4. Is there any git repository (or subfolder) related to it? (add git location)?

5. What is the RCE source location?

6. When was the data created and by who?

7. What is the spatial, temporal resolution?