search for: epitool

At work after updating to R 2.5 I get an error using epitab from package epitools, when at home (R 2.4) I get no error. Could someone help me? Thanks Pietro Bulian Servizio di Onco-Ematologia Clinico-Sperimentale I.R.C.C.S. Centro di Riferimento Oncologico Via Franco Gallini 2 33081 Aviano (PN) - Italy phone: +39 0434 659 412 fax: +39 0434 659 409 e-mail: pbulian at cro.it...

Here is a working snippet. library(epitools) mat <- matrix(c(10,15,60,25,98, 12,10,70,28,14, 9,11,68,10,12 ,8,13,20,11,58) ,ncol=2) colnames(mat) <- c("treatmentA","treatmentB") row.names(mat) <- paste("Cond",rep(1:10,1)) dimnames(mat) <- list("Condition" = row.names(mat), "instrumen...

Here is a working snippet. library(epitools) mat <- matrix(c(10,15,60,25,98, 12,10,70,28,14, 9,11,68,10,12 ,8,13,20,11,58) ,ncol=2) colnames(mat) <- c("treatmentA","treatmentB") row.names(mat) <- paste("Cond",rep(1:10,1)) dimnames(mat) <- list("Condition" = row.names(mat), "instrumen...

Here is a working snippet. library(epitools) mat <- matrix(c(10,15,60,25,98, 12,10,70,28,14, 9,11,68,10,12 ,8,13,20,11,58) ,ncol=2) colnames(mat) <- c("treatmentA","treatmentB") row.names(mat) <- paste("Cond",rep(1:10,1)) dimnames(mat) <- list("Condition" = row.names(mat), "instrumen...

...lternative hypothesis: true odds ratio is not equal to 1 95 percent confidence interval: 1.694792 Inf sample estimates: odds ratio Inf === end example === but in epidemiology authors often prefer to present risk ratios. Using the facility on CRAN to search the site I find packages epitools and Epi which both offer confidence intervals for the risk ratio === Epi example === > library(Epi) > twoby2(outcome[c(2,1),c(2,1)]) 2 by 2 table analysis: ------------------------------------------------------ Outcome : Col 1 Comparing : Row 1 vs. Row 2 Col 1 Col 2 P(Col 1)...

...the odds ratio in fisher.test? # Nicholas Horton, nhorton at smith.edu Fri Jan 22 08:29:07 EST 2010 x1 = c(rep(0, 244), rep(1, 209)) x2 = c(rep(0, 177), rep(1, 67), rep(0, 169), rep(1, 40)) or1 = sum(x1==1&x2==1)*sum(x1==0&x2==0)/ (sum(x1==1&x2==0)*sum(x1==0&x2==1)) library(epitools) or2 = oddsratio.wald(x1, x2)$measure[2,1] or3 = fisher.test(x1, x2)$estimate # or1=or2 = 0.625276, but or3=0.6259267! I'm running R 2.10.1 under Mac OS X 10.6.2. Nick Nicholas Horton Department of Mathematics and Statistics, Smith College Clark Science Center, Northampton, MA 01063-000...

Hello, I am looking for a function which allows to calculate the confidence interval for a standard mortality ratio. I do have vectors with the number of observed and expected death. Has anybody a hint where to look? Best, Stefan

Hi, I was wondering if there was some sort of package or function that calculated asymmetric confidence intervals for small proportions. I thought of both the epicalc and epitools package, but I am hoping to find something where you can just plug in a standard error and point estimate and it will output the upper and lower CI bounds. Thanks! Sarah

I would like to compare the incidence rates of three groups. They are supposed to have different risks so I would like to test whether there is a increasing trend in the incidence rates. Does R or any packages provide a trend test for incidence rates? I checked epiR and epitools. It seems they do not have this function. Thank you for the help. -- View this message in context: http://r.789695.n4.nabble.com/trend-in-incidence-rate-tp4634591.html Sent from the R help mailing list archive at Nabble.com.

Hi, I'm new to R, and I'm STATA user before, could you help me where I can get document about comparison command between STATA and R. Thank you very much, Best regards, -iip-

...SNEW.txt file says that 2.0.5a contains a fix for a DOS wildcard bug, so I'm wondering if that fix fixed one thing and broke another. I did search the archive of this list, and was surprised to find no mention of this problem. Does anyone have any ideas? TIA... - Fred Viles <mailto:fv@epitools.com>

Hi, I asked this question before, which was hidden in a bunch of questions. I repharse it here and hope I can get some help this time: I have 2 contingency tables which have the same group variable Y. I want to compare the strength of association between X1/Y and X2/Y. I am not sure if comparing p-values IS the way even though the probability of seeing such "weird" observation under H0

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

Hi Cristian, I don't know about a R routine for exact CIs, but I found a function called "ageadjust" using a gamma distribution approximation some time ago -take a look at http://medepi.org/epitools/rfunctions/index.html. That Webpage seems a bit outdated now, but the calculations given in the ageadjust functions should still work, I think. Maybe this helps; regards Heinrich. > -----Urspr?ngliche Nachricht----- > Von: cristian at biometria.univr.it [mailto:cristian at biometria.univr...

Hi, I am trying to output an dataframe from R to Excel file. Can anyone tell me how to do it? Thanks a lot. Eg. R dataframe: A B C 1 2 1 3 4 2 . . . [[alternative HTML version deleted]]

Hi friends, I have a doubt reg the application of odds ratio. When evaluating a diagnostic test, what odds ratio I should apply? When I use.. *>oddsratio (X)** * the OR I get is not ad/bc. Thank you. Regards, Dr Manoj Aravind, PG Resident, Dept of Community Medicine, Osmania Medical College, Hyderabad, India. [[alternative HTML version deleted]]

mantelhaen.test() gives the exact conditional p-value (for independence) and confidence intervals (CIs)for the common odds ratio for a stratified 2x2 table. The epitools package by Tomas Aragon (available via CRAN) contains functions which use fisher.test() to calculate mid-p exact p-values and CIs for the CMLE odds ratio for a single 2x2 table. The mid-p p-value for independence for a stratified 2x2 table is easy to calculate using mantelhaen.test(), but can anyo...

Stata users can rely on the very neat Episens package for sensitivity analysis. Briefly, it allows one to specify a diagnostic tool's sensitivity and specificity and take those into account when estimating a risk ratio, for instance. A full description of the package is available at <http://www.stata-journal.com/sjpdf.html?articlenum=st0138>

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really so broad field that I belive one person

...s, gray * tim.colors in package fields contains palette similar to Matlab's jet palette (see examples for simpler implementation) * rich.colors in package gplots contains two palettes of continuous colors. * Functions brewer.pal from RColorBrewer package and colorbrewer.palette from epitools package contain tools for generating palettes * rgb and hsv creates palette from RGB or HSV 3-vectors. Maybe one of those will work for you. Jarek -----Original Message----- From: r-help-bounces at stat.math.ethz.ch [mailto:r-help-bounces at stat.math.ethz.ch] Sent: Saturday, January 07, 2...