Hi all, Please help on this. We will be teaching epidemiology using opensource software. What are R built-in functions or functions in available packages that are capable of doing these: a) Logistic regression (glm?) b) Conditional logistic regression c) Logistic regression with random effects d) Beta-binomial regression e) Poisson regression f) Weibull regression (eha?) g) Exponential regression h) Cox proportional hazards regression (survival?, eha?) i) Cox regression with time repeated covariables j) Kaplan-Meier Analysis and Plots (survival?) k) Post-fit analysis with plots, delta-betas, hazard functions l) meta analysis (rmeta?) Thanks in advance for your help. ------------------ Francis D. Dimzon Assistant Professor, Computer Science University of the Philippines in the Visayas Miag-ao, Iloilo, Philippines
Yes I found that: I already integrated menus using the functions at http://www.medepi.org/epitools/rfunctions/index.html in Rcmdr. The work of Tomas Aragon (http://www.medepi.org/rdocs/index.html) is still in progress. My objective actually is to provide in R those functions available in non-opensource epidemiology software (epiinfo for example, no linux version available) Pease help. Nick Drew writes:> You might try: > http://www.medepi.org/epitools/rfunctions/index.html#A> and > > http://www.medepi.org/rdocs/index.html > > -----Original Message----- > From: r-help-bounces at stat.math.ethz.ch > [mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of Francis Dimzon > Sent: Monday, May 03, 2004 5:47 PM > To: r-help > Subject: [R] Epidemiology Tools > > > Hi all, > > Please help on this. We will be teaching epidemiology using opensource > software. What are R built-in functions or functions in available packages > that are capable of doing these: > > a) Logistic regression (glm?) > b) Conditional logistic regression > c) Logistic regression with random effects > d) Beta-binomial regression > e) Poisson regression > f) Weibull regression (eha?) > g) Exponential regression > h) Cox proportional hazards regression (survival?, eha?) > i) Cox regression with time repeated covariables > j) Kaplan-Meier Analysis and Plots (survival?) > k) Post-fit analysis with plots, delta-betas, hazard functions > l) meta analysis (rmeta?) > > Thanks in advance for your help. > > > ------------------ > Francis D. Dimzon > Assistant Professor, Computer Science > University of the Philippines in the Visayas > Miag-ao, Iloilo, Philippines > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > >Francis D. Dimzon Assistant Professor, Computer Science University of the Philippines in the Visayas Miag-ao, Iloilo, Philippines
On Mon, 3 May 2004, Francis Dimzon wrote:> Hi all, > > Please help on this. We will be teaching epidemiology using opensource > software. What are R built-in functions or functions in available packages > that are capable of doing these: > > a) Logistic regression (glm?)glm> b) Conditional logistic regressionclogit (survival package)> c) Logistic regression with random effectsIt depends what you mean. Random intercept models are in the glmmML package, approximate maximum likelihood for more complicated models (PQL) is available in MASS and nlme packages. Doug Bates is making progress on more accurate approximations, but I'm not sure where he's got to. Personally, I teach marginal models (GEE estimates) before random effects effects models to epidemiologists. GEE is in the gee and geepack packages. (I realise this is a minority view, but it is based on experience).> d) Beta-binomial regressionDon't know. I'd use a logistic regression model with sandwich variances (eg gee or glm with robcov from the Design package). I don't see any real advantage of beta-binomial regression.> e) Poisson regressionglm> f) Weibull regressionsurvreg in the survival package> g) Exponential regressionFor censored data, survreg, for uncensored data, glm> h) Cox proportional hazards regressioncoxph in survival> i) Cox regression with time repeated covariablescoxph in survival> j) Kaplan-Meier Analysis and Plotssurvfit and survdiff (for left-truncated data you need to use coxph).> k) Post-fit analysis with plots, delta-betas, hazard functionsJust about every model has delta-betas. For the Cox model look at the help page help(residuals.coxph). Tests and graphical diagnostics for the proportional hazards assumption are in cox.zph. survfit() gives fitted survival curves Hazard rate functions are estimated by the muhaz package.> l) meta analysisrmeta (which is also useful for Mantel-Haenszel-type analyses of stratified 2x2 tables, and for drawing forest plots even outside meta-analyses). -thomas