Hands-On Exercise, Step 2: Understanding the outcomes

Thinking about the data-generating process

First, let us think about the process that relates mortality to weather. Weather fluctations can have impacts on all scales, but generally when we are thinking of heat waves killing people, it is because of direct exposure. The main data-generating process is local.

It is also non-linear. Both cold and hot weather kills people, relative to deaths at moderate (pleasant) temperatures. We can model this with a quadratic relationship. We need to choose some baseline temperature for comparison purposes. For our example, we will use 20 C. The dose-response function will describe excess mortality, relative to a day with an average temperature of 20 C.

We also need to weight our pixel data. We want the dose-response function to be representative of a random individual, not a random region-year data point, so we will weight gridcells by population.

Finally, the mortality data we will use is annual, while the weather data is daily. We still want to estimate a daily dose-response function, so we will say that take sums over all days of both the weather and outcome data. The sum over daily death data is annual death data, which is what we have.

Then, we want to transform the weather data by creating two predictor variables, for the linear and quadratic terms relative to 20 C.

\[X_{1, i, y} = \sum_{t \in \text{Year}(y)} \sum_{p \in \Theta(i)} \psi_{p} (T_{p i t} - 20)\]
\[X_{2, i, y} = \sum_{t \in \text{Year}(y)} \sum_{p \in \Theta(i)} \psi_{p} (T_{p i t}^2 - 20^2)\]

where \(\psi_{p}\) is the population in gridcell \(p\).

Download the population data

We can use the gridded population data from Gridded Population of the World, since the weather data is not very high resolution. Download it from https://sedac.ciesin.columbia.edu/data/set/gpw-v3-population-count.

This is global data, so it will be useful to clip it to the US and aggregate it to the scale of the weather. We also need it in NetCDF format, for the aggregation step. Again, this code assumes that it is being run from a directory code, sister to the data directory.

library(raster)
rr <- raster("../data/pcount/usap90ag.bil")

rr2 <- aggregate(rr, fact=24, fun=sum)
rr3 <- crop(rr2, extent(-126, -65, 23, 51))

writeRaster(rr3, "../data/pcount/usap90ag.nc4",
 overwrite=TRUE, format="CDF", varname="Population", varunit="people",
 xname="lon", yname="lat")
#!pip install rasterio # will work in Jupyter Notebook
import xarray as xr
rr = xr.open_rasterio("../data/pcount/usap90ag.bil")
rr = rr.sel(band=1, drop=True)

# Crop to US bounding box
xmin = -126
xmax = -65
ymin = 23
ymax = 51

sel_lon = (rr.x >= xmin) & (rr.x <= xmax)
sel_lat = (rr.y >= ymin) & (rr.y <= ymax)
rr2 = rr[sel_lat, sel_lon]

# Aggregate to 1-degree cells
rr3 = rr2.coarsen(x=24, y=24).sum()

rr3 = rr3.rename(x='lon', y='lat')
rr3.to_dataset(name="Population").to_netcdf("../data/pcount/usap90ag.nc4")

Downloading the mortality data

The Compressed Mortality File (CMF) provides comprehensive, county-scale mortality data for the United States. The data through 1988 is publically available, so we will use this for our analysis.

  1. Go to the CMF information page, https://www.cdc.gov/nchs/data_access/cmf.htm.

  2. Under “Data Availability”, find the mortality and population files for 1979 - 1988, and download these.

  3. Unzip these files, and place the resulting text files, Mort7988.txt and Pop7988.txt into the data/cmf folder.

These files report data as fixed-width ASCII text, meaning that spans of characters on each line represent columns of the data.

In the mortality data file, Mort7988.txt, here are the elements of interest: Characters 1 - 5 provide the FIPS code (FIPS is a 5 digit code uniquely identifying each county in the US). Characters 6 - 9 report the year of death. The next few columns give the race, age, and cause of death, but we will combine results across all of these. Characters 20 - 23 report the number of deaths that correspond to that county, year, race, age, and cause.

In the population data file, Pop7988.txt, the lines start with FIPS codes and years, like the mortality data. But then the age groups are all listed on the line: starting with character 19, the population in each of 12 age groups is reported with 8 characters per age group number (so, the first age group, 1 - 4 year-olds, is characters 19 - 26; then 5 - 9 year-olds is reported in characters 27 - 34; and so on).

Preparing the mortality data

Here we sum across all races and ages and merge the mortality and population data.

library(dplyr)

df.mort <- read.fwf("../data/cmf/Mort7988.txt",
   c(5, 4, 10, 4), col.names=c('fips', 'year', 'ignore', 'deaths'))

df2.mort <- df.mort %>% group_by(fips, year) %>% summarize(deaths=sum(deaths))

df.pop <- read.fwf("../data/cmf/Pop7988.txt",
   c(5, 4, 9, rep(8, 12), 25, 1), col.names=c('fips', 'year',
   'ignore', paste0('pop', 1:12), 'county', 'type'))

df2.pop <- df.pop %>% group_by(fips, year) %>% summarize(pop=sum(pop1 +
    pop2 + pop3 + pop4 + pop5 + pop6 + pop7 + pop8 + pop9 + pop10 +
    pop11 + pop12), type=type[1])

df3 <- df2.pop %>% left_join(df2.mort, by=c('fips', 'year'))
df3$deaths[is.na(df3$deaths)] <- 0

df4 <- subset(df3, type == 3)

write.csv(df4[, -which(names(df4) == 'type')], "../data/cmf/merged.csv", row.names=F)
import pandas as pd
df_mort = pd.read_csv("../data/cmf/Mort7988.txt", names = ['input'])

# parse input
df_mort2 = pd.DataFrame(df_mort.input.apply(
    lambda x: [
        x[slice(*slc)] for slc in [(0,5), (5,9), (20,len(x))]]).tolist(),
	columns=['fips', 'year', 'deaths'])

df_mort3 = df_mort2.apply(pd.to_numeric, errors='coerce')

df_mort4 = df_mort3.groupby(['fips', 'year']).sum()
df_mort4.head()

fips, year

deaths

(1001, 1979)

225

(1001, 1980)

221

(1001, 1981)

221

(1001, 1982)

223

(1001, 1983)

267

df_pop = pd.read_csv("../data/cmf/Pop7988.txt", names = ['input'])

slices = [(0, 5), (5, 9), (9,18)] + \
         [(n, n+8) for n in range(18, 114, 8)] + \
         [(114, 139), (139, 140)]

# parse input
df_pop2 = pd.DataFrame(df_pop.input.apply(
    lambda x: [
        x[slice(*slc)] for slc in slices]).tolist(),
	columns=['fips', 'year', 'ignore'] + ["pop" + str(i) for i in range(1,13)] + ['county', 'type'])

cols = ['fips', 'year'] + ["pop" + str(i) for i in range(1,13)] + ['type']
df_pop3 = df_pop2[cols].apply(pd.to_numeric, errors='coerce')
df_pop4 = df_pop3[df_pop3.type == 3]

df_pop5 = df_pop4.groupby(['fips', 'year', 'type']).sum()
df_pop5['pop'] = df_pop5.pop1 + df_pop5.pop2 + df_pop5.pop3 + df_pop5.pop4 + df_pop5.pop5 + df_pop5.pop6 + df_pop5.pop7 + df_pop5.pop8 + df_pop5.pop9 + df_pop5.pop10 + df_pop5.pop11 + df_pop5.pop12

df_pop5.head()

fips, year, type

pop1

pop2

pop3

pop4

pop5

pop6

pop7

pop8

pop9

pop10

pop11

pop12

pop

(1001, 1979, 3)

2022

2982

3248

3491

2640

4414

4211

3310

2457

1813

779

178

31545

(1001, 1980, 3)

2021

2952

3184

3495

2663

4463

4293

3373

2487

1848

795

181

31755

(1001, 1981, 3)

2037

2776

3132

3320

2664

4646

4210

3330

2516

1829

824

192

31476

(1001, 1982, 3)

2042

2707

3098

3190

2651

4714

4343

3327

2565

1835

856

201

31529

(1001, 1983, 3)

2044

2670

3054

3063

2625

4815

4408

3325

2613

1833

882

215

31547

df = df_pop5.merge(df_mort4, how='left', on=['fips', 'year'])
df.to_csv("../data/cmf/merged.csv", header=True)

The final dataset (merged.csv) should look like:

fips, year

pop1

pop2

pop3

pop4

pop5

pop6

pop7

pop8

pop9

pop10

pop11

pop12

pop

deaths

(1001, 1979)

2022

2982

3248

3491

2640

4414

4211

3310

2457

1813

779

178

31545

225

(1001, 1980)

2021

2952

3184

3495

2663

4463

4293

3373

2487

1848

795

181

31755

221

(1001, 1981)

2037

2776

3132

3320

2664

4646

4210

3330

2516

1829

824

192

31476

221

(1001, 1982)

2042

2707

3098

3190

2651

4714

4343

3327

2565

1835

856

201

31529

223

(1001, 1983)

2044

2670

3054

3063

2625

4815

4408

3325

2613

1833

882

215

31547

267