How do I import a file into r with extension .DUSMCPUB? - r

Question

I’m trying to import the Mortality Multiple Cause Files from the National Center for Health Statistics, located at this link:
https://www.cdc.gov/nchs/data_access/vitalstatsonline.htm#Downloadable
link to image of where to find file on NCHS website
The files have an extension .DUSMCPUB (e.g., the file for 2020 is called "VS20MORT.DUSMCPUB_r20220105”). How do I import such a file? I’m not familiar with the extension.
I have tried to import with the following code, but it causes my R program to terminate. Can you please provide me with a suggestion on how to import these types of files?
VS20MORT <- read_delim("VS20MORT.DUSMCPUB_r20220105")

Answer 1

Thanks #Mel G for sharing this approach. When I tried to run it, I realized that the mortality file includes a few new variables as of 2020 (namely decedent’s occupation and industry). Here’s a slight variation that includes the new variables.
# Install and load necessary packages
# install.packages("sqldf") # Used to read in DUSMCPUB file
# install.packages("dplyr") # Used for tidy data management
library(sqldf)
library(dplyr)
#Increase memory limit to make space for large file
# memory.limit()
memory.limit(size=20000)
# Create dataframe containing variables for column width, name, and end position
columns <- data.frame(widths=c(19,1,40,2,1,1,2,2,1,4,1,2,2,2,2,1,1,1,16,4,1,1,1,
1,34,1,1,4,3,1,3,3,2,1,2,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,36,2,1,5,5,5,5,5,5,5,5,5,5,5,5,5,
5,5,5,5,5,5,5,1,2,1,1,1,1,33,3,1,1,2,315,4,2,4,2))
columns$names <- c("blank1", # tape locations 1-19
"Resident_Status_US", # tape location 20
"blank2",
"Education_1989",
"Education_2003",
"Education_flag",
"Month_of_Death",
"blank3",
"Sex",
"DetailAge",
"Age_Substitution_Flag",
"Age_Recode_52",
"Age_Recode_27",
"Age_Recode_12",
"Infant_Age_Recode_22",
"Place_of_Death_and_Status",
"Marital_Status",
"Day_of_Week_of_Death",
"blank4",
"Current_Data_Year",
"Injury_at_Work",
"Manner_of_Death",
"Method_of_Disposition",
"Autopsy",
"blank5",
"Activity_Code",
"Place_of_Injury",
"ICD_Code_10",
"Cause_Recode_358",
"blank6",
"Cause_Recode_113",
"Infant_Cause_Recode_130",
"Cause_Recode_39",
"blank7",
"Number_Entity_Axis_Conditions",
"Condition_1EA", "Condition_2EA", "Condition_3EA", "Condition_4EA", "Condition_5EA",
"Condition_6EA", "Condition_7EA", "Condition_8EA", "Condition_9EA", "Condition_10EA",
"Condition_11EA", "Condition_12EA", "Condition_13EA", "Condition_14EA", "Condition_15EA",
"Condition_16EA", "Condition_17EA", "Condition_18EA", "Condition_19EA", "Condition_20EA",
"blank8",
"Number_Record_Axis_Conditions",
"blank9",
"Condition_1RA", "Condition_2RA", "Condition_3RA", "Condition_4RA", "Condition_5RA",
"Condition_6RA", "Condition_7RA", "Condition_8RA", "Condition_9RA", "Condition_10RA",
"Condition_11RA", "Condition_12RA", "Condition_13RA", "Condition_14RA", "Condition_15RA",
"Condition_16RA", "Condition_17RA", "Condition_18RA", "Condition_19RA", "Condition_20RA",
"blank10",
"Race",
"Bridged_Race_Flag",
"Race_Imputation_Flag",
"Race_Recode_3",
"Race_Recode_5",
"blank11",
"Hispanic_Origin",
"blank12",
"Hispanic_Origin_9_Race_Recode",
"Race_Recode_40",
"blank13",
"CensusOcc",
"Occ_26",
"CensusInd",
"Ind_23")
# Read in file using parameters from 'columns' dataframe
mort2020<- read.fwf("VS20MORT.DUSMCPUB_r20220105", widths=columns$widths, stringsAsFactors=F)
# Attach column names to variables
colnames(mort2020) <- columns$names
# Remove blank variables
mort2020x <- mort2020 %>% dplyr::select(-starts_with("blank"))
Alternatively, it looks like the files are published for most years in a CSV format here: https://www.nber.org/research/data/mortality-data-vital-statistics-nchs-multiple-cause-death-data. 2020 isn’t up yet, but for other years, it can be much faster to read a CSV into R than to use read.fwf.

Answer 2

The data is in the form of a fixed-width file. The user's guide to the data from the National Center for Health Statistics contains the appropriate widths. The answer I present is a modified answer from another forum, posted by #Hack-R.
https://opendata.stackexchange.com/questions/18375/how-can-one-interpret-the-nvss-mortality-multiple-cause-of-death-data-sets
map <- data.frame(widths=c(19, 1,40,2,1,1,2,2,1,1,1,1,1,1,2,2,2,2,1,1,1,16,4,1,1,1,1,34,1,1,4,
3,1,3,3,2,1,2,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
36,2,1,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,1,2,1,1,1,1,33,3,
1,1))
#Set column names
map$cn <- c("blank", # cols 1-19
"res_status", #20
"blank2", # 21-60
"ed_v89",#61-62
"ed_v03",#63
"ed_flag", #64
"death_month", #65-66
"blank3",
"sex",
"age_years",
"age_months",
"age_3",
"age_4",
"age_sub_flag",
"age_recode_52",
"age_recode_27",
"age_recode_12",
"infant_age_recode_22",
"place_of_death",
"marital_status",
"death_day",
"blank4",
"current_year",
"work_injury",
"death_manner",
"disposition",
"autopsy",
"blank5",
"activity_code",
"place_injured",
"icd_cause_of_death",
"cause_recode358",
"blank6",
"cause_recode113",
"infant_cause_recode130",
"cause_recode39",
"blank7",
"num_entity_axis",
"cond1","cond2","cond3","cond4","cond5","cond6","cond7","cond8","cond9","cond10",
"cond11","cond12","cond13","cond14","cond15","cond16","cond17","cond18","cond19",
"cond20",
"blank7",
"num_rec_axis_cond",
"blank8",
"acond1", "acond2", "acond3", "acond4", "acond5", "acond6", "acond7",
"acond8", "acond9", "acond10", "acond11", "acond12", "acond13", "acond14",
"acond15", "acond16", "acond17", "acond18", "acond19", "acond20",
"blank9",
"race",
"bridged_race_flag",
"race_imp_flag",
"race_recode3",
"race_recode5",
"blank10",
"hisp",
"blank11",
"hisp_recode")
#Import the file
mort2020 <- read_fwf("./data/original/VS20MORT.DUSMCPUB_r20220105", fwf_widths(map$widths, map$cn))