diff --git a/code.R b/code.R index 8750f2f..1440e9b 100644 --- a/code.R +++ b/code.R @@ -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 %>% @@ -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, @@ -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, @@ -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")