HTTPS SSH

12/03/2018

Simple visualizations of near-current opioid data.

Near current? Yes, I am pulling data from the CDC's WONDER (Wide-ranging Online
Data for Epidemiologic Research), which contains Multiple Cause of Death files
to 2016. Although the Division of Vital Statistics has reported the 2017
figures (see https://www.cdc.gov/nchs/data_access/vitalstatsonline.htm), these
have not made it into WONDER yet.

viz*.R

The analysis is pretty straightforward in R's tidyverse.

  • The file prep only requires (1) filter to remove the data's embedded totals
    and (2) select to get the variables of interest
  • A single facet-wrapped plot. Note: I'm not using qplot; I want to get the
    full flexibility of ggplot.

But note! Gah, the tidyverse is still not quite there! Unlike pandas, which
can skip headers and footers, readr can only skip headers. And I found a
dsicussion on some tidyverse support board that said this would be forever so,
as one can reasonably hack it using some pipeline that involves read_lines and
filters; also it would be kinda messy to fix properly. Hmm. I think it is fair
to say that R != python.

NM counties

It is immediately obvious that NM has many counties with small populations.
These are the blank graphs in the faceted display: their populations are so low
that the data is suppressed. Of the 5 that have data, Rio Arriba stands out. It
has a mortality rate of 86.3 per 100,000 standard population in 2016. That is
crazily high: the national average is 19.8. Española is largest city in Rio
Arriba and it is famous for multi-generational opioid abuse.

It is going to be interesting to see what the 2017 figues are like. According to
the email I got back from the CDC yesterday, those will be released in WONDER
later this week.

MA counties

I'm mainly interested in this because of my upcoming call with the Community
Data Platform people on Nantucket. Nantucket is a small county and so its
results are suppressed. Barnstable (Cape Cod), Bristol (Taunton), and Plymouth
counties are bad: 50 and above

US states

If I want to avoid blanks in my plots, I probably need to look at states. I
cut-and-paste viz_state.R to get viz_US.R

Wow. Poor West Virginia. Though several other states show horribly steep curves
(OH, PA, NH, KY).

Next steps

Take a look at WV's counties. Or look at top-20 counties in US. Also, it might
be interesting to see whether these are particularly strong on fentanyl and
other synthetic opioids. (Actually given that fentanyl deaths are a comparaively
recent phenomenon, I might hold the latter till I have the 2017 figures.)

12/05/2018

Worst counties in US

I tweaked the US plot:

  • Use crude rate instead of age-adjusted rate. Crude rate is easier to explain,
    and the differences between the two rates is small.
  • Filter down to the 12 counties with the highest average death rate (measured
    over last 3 years)
  • Color by state
  • Size points by population

Latter shows that although NM and WV have the highest rates, the actual numbers
of people impacted are massive in OH and MD.

I shall put this on hold till I get the 2017 data.

Where is the data

Data does not belong in the git repository. It can be obtained at the link
above. I use the same ICD-10 codes to identify opioid deaths as are used in the
CDC's own reports (see Hedegaard et al "Drug Overdose Deaths in the United
States, 1999–2017"), specifically:

  • X40 (Accidental poisoning by and exposure to nonopioid analgesics, antipyretics and antirheumatics)

  • X41 (Accidental poisoning by and exposure to antiepileptic, sedative-hypnotic, antiparkinsonism and psychotropic drugs, not elsewhere classified)

  • X42 (Accidental poisoning by and exposure to narcotics and psychodysleptics [hallucinogens], not elsewhere classified)

  • X43 (Accidental poisoning by and exposure to other drugs acting on the autonomic nervous system)

  • X44 (Accidental poisoning by and exposure to other and unspecified drugs, medicaments and biological substances)

  • X60 (Intentional self-poisoning by and exposure to nonopioid analgesics, antipyretics and antirheumatics)

  • X61 (Intentional self-poisoning by and exposure to antiepileptic, sedative-hypnotic, antiparkinsonism and psychotropic drugs, not elsewhere classified)

  • X62 (Intentional self-poisoning by and exposure to narcotics and psychodysleptics [hallucinogens], not elsewhere classified)

  • X63 (Intentional self-poisoning by and exposure to other drugs acting on the autonomic nervous system)

  • X64 (Intentional self-poisoning by and exposure to other and unspecified drugs, medicaments and biological substances)

  • X85 (Assault by drugs, medicaments and biological substances)

  • Y10 (Poisoning by and exposure to nonopioid analgesics, antipyretics and antirheumatics, undetermined intent)

  • Y11 (Poisoning by and exposure to antiepileptic, sedative-hypnotic, antiparkinsonism and psychotropic drugs, not elsewhere classified, undetermined intent)

  • Y12 (Poisoning by and exposure to narcotics and psychodysleptics [hallucinogens], not elsewhere classified, undetermined intent)

  • Y13 (Poisoning by and exposure to other drugs acting on the autonomic nervous system, undetermined intent)

  • Y14 (Poisoning by and exposure to other and unspecified drugs, medicaments and biological substances, undetermined intent)

12/06/2018

Further tinkering

I have been reading Knaflic "Storytelling with Data", and that has led to some
tweaks to my plots. I can't go full SWD because at the moment I don't really
know what story I am telling. Perhaps it is something to do with issues
of rates vs absolute counts. This matters because I suspect that crisis response
does not scale in the same way that population scales. If county A has 10 times
the population of county B, I'm guessing (and it is a guess) that the number of
deaths at which local services in A get overloaded is not 10 times the threshold
in B but substantially less.

Anyway, some minor cleaning up on the plots

  • Make the titles bigger and clearer

  • Point sizes are a function of deaths (which is what the story is about) not
    population.

12/07/2018

2017 data from CDC

The CDC have put the 2017 data into WONDER. I pull the new data. In doing so I
discover that there is actually a radio button that automatically selects the
ICD-10 codes for opioid deaths. So no more need to remember X40-44 etc.

I rerun the "wrotsy counties" analysis. Rio Arriba slips to #2. Baltimore gets
worse. A county in WV has an astronomical rate of 160 per 100,000.

The folks at FRIAM had expressed an interest in this, so I compose a post on my
blog.

12/10/2018

I would like to create some choropleths but I am not up to speed on R's mapping
abilities. I spend the morning tinkering. I think I am ready to try in earnest,
but my project directory is getting messy. I think it is time for me to actually
use RStudio's project functionality. (That's my next task.)

12/11/2018

OK, so I have some reasonable choropleths. Matching the map data to the CDC was
a problem as the only common field is county name and its format is different
in the two sources. Converting one to the other proved difficult in the
tidyverse pipeline (I was bumping up against dplyr's "quosures") and so I end
up using sapply().

Got myself a neat map of MA. Barnstable is surprisingly bad. I thought it was
wealthy and problem free? By the way, this is the first time I noticed a big gap
between the age-adjusted rate (50 per 100k) and the crude rate (40 per 100k). Is
that a reflection of old/retiree communities?

Next: add some town names. Or put it on OpenMap.

12/13/2018

Next steps, revised

Yes, it would be interesting to get Open Map data, particularly as it can
localize the map nicely without adding too much visual noise. However I have a
couple of other things I want to look at too:

  • Wikipedia's page on chloropleths briefly mentioned a color scheme that is
    amenable to bivariate visualization. What? how is that possible? I need to
    investigate and trial. Perhaps look at an obesity dataset too? Ed (Angel) has
    already commented on a possible link (admittedly based on an n of 1).

  • sf or sp for geocomputation in R? Former is newer and (I think) is better
    integrated with the tidyverse; however some legacy packages require sp. I
    think I shall use sf and worry about legacy issues as they arise

  • leaflet for interactive maps?

  • And what about python? And what about putting some of these maps in
    dashboards?

First step: stick to R. Use sf (and tmap?) to create a lower-48 map of counties.
Switch between obesity (in the tmap demo) and opioids.

Second step: try datashader and plotly in python.

12/30/2018

Court Case: Rio Arriba vs Purdue et al

Tom Johnson brought this case to my attention. See NOTES.txt in the Medicare
D directory

12/31/2018

Martinez: "Continued Improvement in Drug Overdose Death Rankings"

So NM has fallen from #2 in 2014 to #17 in 2017 says DOH. Really? I think some
of those numbers might be cherry-picked. Let's go see.

OK, so I cannot duplicate the numbers using my 2017 data pull. It looks like my
assumption that the radio button that I thought selected the ICD-10 codes for
opioids (see 12/07 notes) doesn't. When I do it longhand (see 12/05) I get
numbers that correspond (i) with the CDC report and (ii) the raw rankings that
the press release quotes (though the latter does require me to omit DC from the
rankings).

However the claims a couple of paras on seem sketchy: how can NM get 4%
reduction in natural and semisynth, 9% reduction in heroin, and 6% reduction in
synth, when the overall AAR has only gone down from 25.2 to 24.8, i.e. 1.6%?
(Thiese are 2017 vs 2016). OK, I'm going to have to pull the raw numbers from
WONDER.

Later that day...

Gah! Getting the data to match is a problem! I am getting confused between
"underlying cause of death" (one only) and "multiple causes of death" (up to
20). Take a break, have a cuppa, and then lay out the exact WONDER queries
that enables me to duplicate the numbers in the CDC report (Data Brief 329).

Table 1: simple counts (e.g. 2017 deaths = 70,237)

- From section #6 "underlying cause of death" Select "UCD - ICD-10 Codes"
  X40-44, X60-64, X85, Y10-Y14
- Do not select anything under section #7 "multiple causes of death"

OK, while that is fresh in my mind I shall run this for state and produce

- "Multiple Cause of Death, 1999-2017, by state.txt"

Table 2: don't care.

Table 3: this is in two parts because of the double accounting problems!

- Start with the underlying COD selection as in table 1 and add multiple
  COD, specifically T40.0-40.4, T40.6
- Running without any additional grouping gives the results in the table's
  "any opioids" column
- Running with "multiple cause of death" grouping gives the breakdowns by
  heroin, synthetic, etc. **NOTE** double accounting means that the sum of
  these breakdowns exceeds the value in the "any opioids" column!

OK, I'm only going to run this query for NM. I'm not really interested in this
info for other states. The two files I get are

- "Multiple Cause of Death, 1999-2017, NM any opioid.txt"
- "Multiple Cause of Death, 1999-2017, NM by opioid.txt"

Table 4: don't care

OK, let's rerun my latest script, confirm_DOH.R.

Preliminary conclusions

The top-line claim "NM is getting better" is true. Yes NM is ranked #17. However
the breakdown into fentanyl, heroin etc is a little sketchy: these come from the
"multiple cause of death" fields (up to 20 of them) on a death certificate so
there's lots of double accounting. Unusually though, I'm getting fewer deaths
in aggregate on these fields. Which is odd, because NM is meant to be good at
filling these fields in (I saw some old CDC report that had the coverage rate at
~98%). So something is obviously adrift and I've not resolved what

I shall dig into this further after the New Year. It's going to be a chance to
play with RMarkdown too.

01/07/2019

Tableau

But first I want to tinker with Tableau Public. OK, re-pull the above data,
omitting the suppressed records. (Why? because Tableau Public has limits on the
number of records and I don't want to use up my limit on stuff that I will
immediately remove).

NOTE: I finally resolved the issue of getting 73,990 opioid deaths in 2017
instead of 70,237: when I choose the "drug-induced causes" button in WONDER I
must omit "all other drug induced causes". The latter pulls in some non-opioid
deaths in which I am not interested.

By the end of the day I've got a few plots: a table of death rate by year and
state and "bump" plots of states' ranks over time. Also maybe a "worst county"
plot, though I'm not sure this has saved to the public server (too big?). I've
also remembered why I can't stand Tableau. It's too hard to do some simple
stuff: rank in particular.

01/08/2019

Yeah Tableau Public has real issues with a large dataset. I actually have to
pull out the county data if I want the workbook to display online.

Back to R and proper programming.

RMarkdown

Much better! I have been able to write up my working on the Dept of Health
claims quite nicely. See confirm_DOH.Rmd.