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Updates for 2019 including minor fixes. #1

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Updates for 2019 including minor fixes. #1

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45 changes: 32 additions & 13 deletions code.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,18 @@ library(dplyr)
library(magrittr)
library(haven)
#read aha file currently in use
aha_17 <- read_sas("/Volumes/George_Surgeon_Projects/standardized_medicare_data_using_R/input/aha_hosp_05_17.sas7bdat")
# Read in the previous version for checks
# aha_17 <- read_sas("/Volumes/DMH_Shared/George_Surgeon_Projects/standardized_medicare_data_using_R/input/archive/aha_hosp_05_17.sas7bdat")
aha_18_corrected = read.csv('/Volumes/DMH_Shared/George_Surgeon_Projects/standardized_medicare_data_using_R/input/aha_hosp_05_18_corrected.csv')
# aha_18 = read.csv('/Volumes/DMH_Shared/George_Surgeon_Projects/standardized_medicare_data_using_R/input/aha_hosp_05_18.csv')

#read aha file for new year
aha_18 <- read_sas("/Volumes/DMH_Shared/Resources/Provider/AHA_American_Hosp_Assoc_Survey/SAS_Data_Files/AHA2018/aha2018.sas7bdat")
# aha_18 <- read_sas("/Volumes/DMH_Shared/Resources/Provider/AHA_American_Hosp_Assoc_Survey/SAS_Data_Files/AHA2018/aha2018.sas7bdat")
aha_19 = read_sas('/Volumes/DMH_Shared/Resources/Provider/AHA_American_Hosp_Assoc_Survey/SAS_Data_Files/AHA2019/AS2019PUB.sas7bdat')
# aha_19 = read.csv('/Volumes/DMH_Shared/George_Surgeon_Projects/standardized_medicare_data_using_R/input/aha_hosp_05_19.csv')

#set year (should be the year processing)
current_year = 2018
current_year = 2019

#extract mapped variables, refer to variable map in data folder
aha_new <- aha_18 %>%
Expand All @@ -22,8 +27,8 @@ aha_new <- aha_18 %>%
MAPP2,
MAPP3,
MAPP5,
MAPP12,
MAPP13,
# MAPP12, # Retired in 2019. Check pg 5 of /Volumes/DMH_Shared/Resources/Provider/AHA_American_Hosp_Assoc_Survey/SAS_Data_Files/AHA2019 AnnualSurveyFY2019Doc.pdf
# MAPP13, # Retired in 2019. Check pg 5 of /Volumes/DMH_Shared/Resources/Provider/AHA_American_Hosp_Assoc_Survey/SAS_Data_Files/AHA2019 AnnualSurveyFY2019Doc.pdf
MAPP8,
MAPP19,
FTERN,
Expand Down Expand Up @@ -65,23 +70,27 @@ aha_new <- aha_18 %>%
year = current_year,
AHAID = ID,
provteach = ifelse(MAPP8 == 1,1,0),
provteach_all = ifelse((MAPP3 == 1 | MAPP5 == 1 | MAPP12 == 1 | MAPP13 == 1 | MAPP8== 1),1,0),
provteach_minor = ifelse((MAPP3 == 1 | MAPP5 == 1 | MAPP12 == 1 | MAPP13 == 1),1,0),
## Logic for pre 2019 data
# provteach_all = ifelse((MAPP3 == 1 | MAPP5 == 1 | MAPP12 == 1 | MAPP13 == 1 | MAPP8== 1),1,0),
# provteach_minor = ifelse((MAPP3 == 1 | MAPP5 == 1 | MAPP12 == 1 | MAPP13 == 1),1,0),
## Logic for post 2019 data
provteach_all = ifelse((MAPP3 == 1 | MAPP5 == 1 | MAPP8== 1),1,0),
provteach_minor = ifelse((MAPP3 == 1 | MAPP5 == 1 ),1,0),
rntopt = ifelse(ADJADC>0,(FTERN/ADJADC),NA),
RN_BED_ratio = ifelse(HOSPBD>0,round((FTERN/HOSPBD),.01),NA),
nurse_ratio2 = ifelse(IPDTOT>0,(FTERN/IPDTOT*1000),NA),
nurse_ratio = ifelse(IPDTOT>0,round((FTERN/IPDTOT),0.01),NA),
bedsize_cat = ifelse(HOSPBD >= 500, 4,
(ifelse(HOSPBD < 200, 1,
(ifelse((200 <= HOSPBD && HOSPBD <= 349),2,3))))),
(ifelse((200 <= HOSPBD & HOSPBD <= 349),2,3))))),
bedsize_cat2 = ifelse(HOSPBD >= 500, 3,
ifelse(HOSPBD < 250,1,2)),
beds_lt200 = ifelse((HOSPBD < 200),1,0),
beds_200_349 = ifelse((200 <= HOSPBD && HOSPBD <= 349),1,0),
beds_350_499 = ifelse((350 <= HOSPBD && HOSPBD <= 499),1,0),
beds_200_349 = ifelse((200 <= HOSPBD & HOSPBD <= 349),1,0),
beds_350_499 = ifelse((350 <= HOSPBD & HOSPBD <= 499),1,0),
beds_ge500 = ifelse((HOSPBD > 500),1,0),
beds_lt250 = ifelse((HOSPBD < 250),1,0),
beds_250_499 = ifelse((250 <= HOSPBD && HOSPBD <= 499),1,0),
beds_250_499 = ifelse((250 <= HOSPBD & HOSPBD <= 499),1,0),
region_ne = NA,
region_west = NA,
region_midwest = NA,
Expand Down Expand Up @@ -165,7 +174,17 @@ aha_new <- aha_18 %>%
trauma_level3,
trauma_level45)

# Diagnostic code check for hosp beds.
# aha_new %>% group_by(bedsize_cat) %>% count()
# aha_17 %>% group_by(bedsize_cat) %>% count()
# aha_18 %>% group_by(bedsize_cat) %>% count()
# aha_18_corrected %>% group_by(bedsize_cat) %>% count()
# aha_19 %>% group_by(bedsize_cat) %>% count()

#merge with old file to create updated file
aha_hosp_05_18 <- rbind(aha_17,aha_new)
# aha_hosp_05_18 <- rbind(aha_17,aha_new)
aha_hosp_05_19 <- rbind(aha_18_corrected, aha_new)

# write.csv(aha_hosp_05_18,"/Volumes/DMH_Shared/George_Surgeon_Projects/standardized_medicare_data_using_R/input/aha_hosp_05_18_corrected.csv", row.names = F)
write.csv(aha_hosp_05_19,"/Volumes/DMH_Shared/George_Surgeon_Projects/standardized_medicare_data_using_R/input/aha_hosp_05_19.csv", row.names = F)

write.csv(aha_hosp_05_18,"/Volumes/George_Surgeon_Projects/standardized_medicare_data_using_R/input/aha_hosp_05_18.csv")