epi-gala
Most demos in R; can be executed on your own Google Colab account
Science Score: 67.0%
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○Scientific vocabulary similarity
Low similarity (8.3%) to scientific vocabulary
Last synced: 6 months ago
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Repository
Most demos in R; can be executed on your own Google Colab account
Basic Info
- Host: GitHub
- Owner: lisatwyw
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://lisatwyw.github.io/epi-gala/
- Size: 3.86 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Created over 3 years ago
· Last pushed almost 2 years ago
Metadata Files
Readme
License
Citation
README.md
Epi-Gala
Great references
- Jekel's: Epidemiology, Biostatistics, Preventive Medicine, and Public Health, 5th Edition
- Epidemiology: Beyond the Basics, 4th Edition
- Dr. Martin Bland's "An Introduction to Medical Statistics"
- "Data from: The reproducibility of research and the misinterpretation of p-values", Colquhoun (DRYAD 2017)
- "Applied Survival Analysis using R"
- Epidemics: Models and Data Using R Links to an external site
- "Maximum Likelihood, Profile Likelihood, and Penalized Likelihood: A Primer", Cole et al. J of Epidemiology 2013
- Basic Models for Disease Occurrence in Epidemiology, Flanders et al. 1995
Topics
Click on white arrow to view a table of key terms, related chapter readings (above list), demo notebooks, and supplemental readings.
Epi tooklits
| Topic | Relevant chapters | Supp. readings | Colab demos | Key terms / R functions | | -- | -- |-- | -- |-- | | Describing trends & variations in data | Jekel:9 | ["Too many digits"](https://adc.bmj.com/content/100/7/608) | | ```mean()```, ```sd()```, ```median()```, ```IQR()```; ```stem()```; ```hist()```| || | Bivariate regression & correlation | Bland:11; Jekel:11 | | [Bivariate regression vs correlation](https://github.com/lisatwyw/epi-galla/blob/main/1st_bivariate_regression.ipynb) | ```data.frame```; ```t()```; ```matrix()```| | Sample size; Type I & II errors | Jekel:12 | | || | Linear regression | Bland:15 (multiple regression) | | [Simulate funnel plot, LR recapped](https://github.com/lisatwyw/epi-galla/blob/main/LR_recap.ipynb) | | | GLM | Jekel:13 | | Logistic regression | Bland:15.10 | [Harris’ primer](https://fmch.bmj.com/content/fmch/9/Suppl_1/e001290.full.pdf) | |- VIF
- logit
Study designs
| Topic | Relevant chapters | Supp. readings | Colab demos | Key terms / R functions | | -- | -- |-- | -- |-- | | Experimental | Bland:2; Jekel:4,12-13 | [Series #11: Data Analysis of Epidemiological Studies](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853157/pdf/Dtsch_Arztebl_Int-107-0187.pdf) | | Review on applications of- poisson regression
- logistic regresssion
- relative risk (vs difference), prevalence, cumulative incidence estimate
- effect modifications
Advanced topics
| Topic | Relevant chapters | Supp. readings | Colab demos | Key terms | | -- | -- |-- | -- |-- | | Replication | | [Harris et al. "Reproducibility of 6 Published Studies in Public Health Services and Systems Research"](https://journals.lww.com/jphmp/Abstract/2019/03000/Examining_the_Reproducibility_of_6_Published.6.aspx) | | Reproducibility | [Szklo:9](http://proxy.lib.sfu.ca/login?url=https://search.ebscohost.com/login.aspx?direct=true&db=nlebk&AN=1229435&site=ehost-live&ebv=EB&ppid=pp_411) | [Coding style guide](https://google.github.io/styleguide/Rguide.html); [Writing functions to prevent errors](https://bookdown.org/medepi/phds/programming-and-r-functions.html#writing-r-functions) | [```for```loop](https://colab.research.google.com/drive/1YFrdQoDtLMLczXt0PHXKwHEFDa8Ee4rV?authuser=1#scrollTo=2_for_loop_quick_dive) | | Maximum likelihood | Bland:22.7 | | Likelihood; AIC; BIC; ```source()``` | | Predictive models | | | [LDA/ Bone mineral density](https://github.com/lisatwyw/epi-galla/blob/main/LDA_predictions_BoneMineralDensity.ipynb) | |R: importing function definitions
### ncvTest ``` source('https://raw.githubusercontent.com/cran/car/master/R/durbinWatsonTest.R'); durbinWatsonTest( fit2 ) source('https://raw.githubusercontent.com/cran/AICcmodavg/master/R/useBIC.R'); message( 'BIC of fit1: ', useBIC( fit1 ) ) source('https://raw.githubusercontent.com/cran/car/master/R/ncvTest.R' ); ncvTest( fit2) ``` ### ```epi.2by2``` ``` source('https://raw.githubusercontent.com/cran/epiR/master/R/epi.2by2.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zexact.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zincrate.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zRRwald.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zRRtaylor.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zRRscore.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zORwald.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zORscore.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zlimit.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zORml.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zARwald.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zARscore.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zz2stat.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zlimit.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zMHRD.Sato.R') source('https://raw.githubusercontent.com/cran/epiR/master/R/zMHRD.GR.R') epi.2by2( c(13,2163,5,3349) ) ``` ### ```riskratio.wald``` ``` if (0 & (!exists('riskratio')) ) { install.packages("epitools") library( epitools ) } else { source( 'https://raw.githubusercontent.com/cran/epitools/master/R/ormidp.test.R' ) source( 'https://raw.githubusercontent.com/cran/epitools/master/R/tab2by2.test.R' ) source( 'https://raw.githubusercontent.com/cran/epitools/master/R/table.margins.R' ) source( 'https://raw.githubusercontent.com/cran/epitools/master/R/riskratio.wald.R' ) source( 'https://raw.githubusercontent.com/cran/epitools/master/R/epitable.R' ) riskratio.wald( matrix( c(11,23,11,22), 2) ) } ```Owner
- Login: lisatwyw
- Kind: user
- Website: about.me/lisa.tang
- Repositories: 6
- Profile: https://github.com/lisatwyw
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: TANG
given-names: "Lisa Y.W."
orcid: https://orcid.org/0000-0003-2545-8440
title: "epi-gala"
version: 2.0.4
identifiers:
- type: doi
value: https://zenodo.org/records/11247684