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Today's Topics:
1. Re: R-sig-teaching Digest, Vol 102, Issue 3 (Christopher W. Ryan)
----------------------------------------------------------------------
Message: 1
Date: Wed, 1 Aug 2018 14:01:42 -0400
From: "Christopher W. Ryan" <cryan at binghamton.edu>
To: r-sig-teaching at r-project.org
Subject: Re: [R-sig-teaching] R-sig-teaching Digest, Vol 102, Issue 3
Message-ID: <3ab4ea10-57c8-6f21-f2fb-fb26d170ce41 at binghamton.edu>
Content-Type: text/plain; charset="utf-8"
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 at 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 at binghamton.edu>
To: R-sig-teaching <r-sig-teaching at r-project.org>
Subject: [R-sig-teaching] source for rhodococcus nosocomial outbreak
data
Message-ID: <737cc7a5-234c-067b-0f6d-03c50bc1e16c at 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 at reed.edu>
To: "Christopher W. Ryan" <cryan at binghamton.edu>
Cc: R-sig-teaching <r-sig-teaching at r-project.org>
Subject: Re: [R-sig-teaching] source for rhodococcus nosocomial
outbreak data
Message-ID:
<CA+3jU8E3ffxwPePEHpdwKLLYyDn6feKXoX55KWMMZmquPRyLEA at 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 at 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
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R-sig-teaching at r-project.org mailing list
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[[alternative HTML version deleted]]
------------------------------
Message: 3
Date: Fri, 20 Jul 2018 13:09:12 -0400
From: "Christopher W. Ryan" <cryan at binghamton.edu>
To: R-sig-teaching <r-sig-teaching at r-project.org>
Subject: Re: [R-sig-teaching] source for rhodococcus nosocomial
outbreak data
Message-ID: <7b5fad86-2909-a44a-8c2e-4433549cc6f3 at 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 at binghamton.edu <mailto:cryan at 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
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