[R-sig-teaching] R-sig-teaching Digest, Vol 102, Issue 3
Christopher W. Ryan
cry@n @ending from bingh@mton@edu
Wed Aug 1 20:01:42 CEST 2018
Thanks for the advice, Jose. I discovered that the latest version of
EpiInfo does not seem to contain the data for this particular tutorial,
but version 3.5.4 does, so I downloaded and installed it. I was able
easily to extract the rhodoccus data to a plain text file.
Here is a link to a nice collection of plain text data files for use
with R. Not all are medical/epidemiological in nature, but I think I can
make use of several:
http://vincentarelbundock.github.io/Rdatasets/datasets.html
I'll be teaching the intro epi course for a new MPH degree program at
Binghamton University in Binghamton, NY, US. I've taught family medicine
for about 25 years; this will be my first experience with formal
teaching of MPH students. Roughly speaking, I plan to use about 90
minutes of each 3-hour weekly class session for the usual, general,
principles of epidemiology. I'll use about 45 minutes for a "computer
lab" of sorts with R, for practical application of the principles. And
about 45 minutes for a substantive discussion of the epidemiology of an
important health problem, communicable or non-communicable.
I hope the early introduction of R will seque well into their intro
stats course that I'll teach second semester.
Tentaively, these are the R-related concepts I hope to practice with them:
Overview of R
Installation of R
Saving your R code: why and how
R as a calculator. Rate standardization.
Data structures, types and levels of measurement
Dates and times
Tables
Analysis of tabular data
Introduction to good graphics
More analysis of tabular data
More on good graphics
Data discipline
Data sharing
Installing and using packages
Getting data into R from "the wild"
Data wrangling in the tidyverse
Getting things out of R
Epidemic curves
More on good graphics
Brief foray into maps and spatial epidemiology
We'll see how it all works out! I'd love to hear from others their
thoughts or experiences using R in teaching intro epidemiology.
--Chris
Jose Arturo Farfan wrote:
> Hi Chris,
>
> My sugestion is to download the epi info version3..5.4 from
>
> https://www.cdc.gov/epiinfo/support/downloads/prevversions.html
>
> Install that version, and get the data files, and also the old
> tutorials are going to be installled.
>
> I am very interested in your epidemiology class using R. I am trying
> to do something similar, but I teach statistisc and epidemiology to
> doctors doing the speciality in psychiatry. I have been having
> problems founding databases to present examples to them.
>
> I will appreciate if you can share some information about the approach
> you are doing using R.
>
> Bes wishes and blesings
> Jose A. Farfan-Ale
>
>
>
>
>
> 2018-07-21 5:00 GMT-05:00 <r-sig-teaching-request using r-project.org>:
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>> Today's Topics:
>>
>> 1. source for rhodococcus nosocomial outbreak data
>> (Christopher W. Ryan)
>> 2. Re: source for rhodococcus nosocomial outbreak data (Albyn Jones)
>> 3. Re: source for rhodococcus nosocomial outbreak data
>> (Christopher W. Ryan)
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 20 Jul 2018 11:13:46 -0400
>> From: "Christopher W. Ryan" <cryan using binghamton.edu>
>> To: R-sig-teaching <r-sig-teaching using r-project.org>
>> Subject: [R-sig-teaching] source for rhodococcus nosocomial outbreak
>> data
>> Message-ID: <737cc7a5-234c-067b-0f6d-03c50bc1e16c using binghamton.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Many moons ago, the US CDC came out with DoEpi, which was computer-based
>> instruction in outbreak investigation, using the CDC's Epi Info software.
>>
>> I recall two instructionally useful cases in DoEpi: the Oswego church
>> supper outbreak (a classic!) and a nosocomial outbreak of
>> post-sternotomy sternal osteomyelitis with Rhodococcus.
>>
>> I'd like to use these cases in an intro epidemiology class in a new MPH
>> program, but with R. I no longer have my old DoEpi files. I found the
>> Oswego church supper data in the R epitools package. Does anyone know if
>> the rhodococcus dataset is available somewhere?
>>
>> Thanks.
>>
>> --Chris Ryan
>> SUNY Upstate Medical University
>> and
>> Binghamton University
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 20 Jul 2018 09:46:44 -0700
>> From: Albyn Jones <jones using reed.edu>
>> To: "Christopher W. Ryan" <cryan using binghamton.edu>
>> Cc: R-sig-teaching <r-sig-teaching using r-project.org>
>> Subject: Re: [R-sig-teaching] source for rhodococcus nosocomial
>> outbreak data
>> Message-ID:
>> <CA+3jU8E3ffxwPePEHpdwKLLYyDn6feKXoX55KWMMZmquPRyLEA using mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Google points me to
>>
>> New England Journal of Medicine
>> <https://www.researchgate.net/journal/0028-4793_New_England_Journal_of_Medicine>
>> 324(2):104-9 · February 1991.
>>
>> and
>>
>> https://www.nejm.org/doi/full/10.1056/NEJM199101103240206
>>
>> On Fri, Jul 20, 2018 at 8:13 AM, Christopher W. Ryan <cryan using binghamton.edu>
>> wrote:
>>
>>> Many moons ago, the US CDC came out with DoEpi, which was computer-based
>>> instruction in outbreak investigation, using the CDC's Epi Info software.
>>>
>>> I recall two instructionally useful cases in DoEpi: the Oswego church
>>> supper outbreak (a classic!) and a nosocomial outbreak of
>>> post-sternotomy sternal osteomyelitis with Rhodococcus.
>>>
>>> I'd like to use these cases in an intro epidemiology class in a new MPH
>>> program, but with R. I no longer have my old DoEpi files. I found the
>>> Oswego church supper data in the R epitools package. Does anyone know if
>>> the rhodococcus dataset is available somewhere?
>>>
>>> Thanks.
>>>
>>> --Chris Ryan
>>> SUNY Upstate Medical University
>>> and
>>> Binghamton University
>>>
>>> _______________________________________________
>>> R-sig-teaching using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-teaching
>>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 20 Jul 2018 13:09:12 -0400
>> From: "Christopher W. Ryan" <cryan using binghamton.edu>
>> To: R-sig-teaching <r-sig-teaching using r-project.org>
>> Subject: Re: [R-sig-teaching] source for rhodococcus nosocomial
>> outbreak data
>> Message-ID: <7b5fad86-2909-a44a-8c2e-4433549cc6f3 using binghamton.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Thanks. I'm looking for raw anonymous data, e.g. a csv file of a line
>> listing.
>>
>> --Chris
>>
>> Albyn Jones wrote:
>>> Google points me to
>>>
>>> New England Journal of Medicine
>>> <https://www.researchgate.net/journal/0028-4793_New_England_Journal_of_Medicine>
>>> 324(2):104-9 · February 1991.
>>>
>>> and
>>>
>>> https://www.nejm.org/doi/full/10.1056/NEJM199101103240206
>>>
>>> On Fri, Jul 20, 2018 at 8:13 AM, Christopher W. Ryan
>>> <cryan using binghamton.edu <mailto:cryan using binghamton.edu>> wrote:
>>>
>>> Many moons ago, the US CDC came out with DoEpi, which was computer-based
>>> instruction in outbreak investigation, using the CDC's Epi Info
>>> software.
>>>
>>> I recall two instructionally useful cases in DoEpi: the Oswego church
>>> supper outbreak (a classic!) and a nosocomial outbreak of
>>> post-sternotomy sternal osteomyelitis with Rhodococcus.
>>>
>>> I'd like to use these cases in an intro epidemiology class in a new MPH
>>> program, but with R. I no longer have my old DoEpi files. I found the
>>> Oswego church supper data in the R epitools package. Does anyone know if
>>> the rhodococcus dataset is available somewhere?
>>>
>>> Thanks.
>>>
>>> --Chris Ryan
>>> SUNY Upstate Medical University
>>> and
>>> Binghamton University
>>>
>>> _______________________________________________
>>> R-sig-teaching using r-project.org <mailto:R-sig-teaching using r-project.org>
>>> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-teaching
>>> <https://stat.ethz.ch/mailman/listinfo/r-sig-teaching>
>>>
>>>
>>
>>
>>
>>
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>> End of R-sig-teaching Digest, Vol 102, Issue 3
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