A review (sorry in Japanese) on the calculation of odds ratios with confidence intervals using several packages in R is given by Prof. Okumura, Mie Univ.
https://oku.edu.mie-u.ac.jp/~okumura/stat/2by2.html x <- matrix(c(6, 3, 4, 5), 2) # using vcd library(vcd) res <- oddsratio(x) exp(confint(res)) summary(res) # Note: summary(oddsratio(x, log=FALSE)) gives inappropriate p-value. # using fmsb library(fmsb) oddsratio(x, p.calc.by.independence=FALSE) Best, Minato Nakazawa On Mon, 6 Jul 2020 15:01:34 +0200 Luigi Marongiu <marongiu.lu...@gmail.com> wrote: > Hello, > Is it possible to calculate with a single function the odd ratios? > Now I can use this implement: > ``` > or <- (De/He)/(Dn/Hn) # Disease exposed, Healthy non-exposed > logo <- log(or) > x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn))) > lower_ci = exp(logo - 1.96*x) > upper_ci = exp(logo + 1.96*x) > cat("OR:", round(or, 3), "(", round(lower_ci, 3), "-", round(upper_ci, 3), > ")", > spe = "") > ``` > for instance, > ``` > De <-6 > Dn <-3 > He <-4 > Hn <-5 > or <- (De/He)/(Dn/Hn) > logo <- log(or) > x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn))) > lower_ci = exp(logo - 1.96*x) > upper_ci = exp(logo + 1.96*x) > cat("OR:", round(or, 3), "(", round(lower_ci, 3), "-", round(upper_ci, 3), > ")", > spe = "") > > OR: 2.5 ( 0.37 - 16.889 ) > ``` > Is there a simple function from some package that can also add a > p-value to this test? Or how can I calculate the p-value on my own? > -- > Best regards, > Luigi > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Minato Nakazawa <minato-nakaz...@umin.net> Professor, Division of Global Health, Department of Public Health, Kobe University Graduate School of Health Sciences [web] http://minato.sip21c.org/ [phone] +81-78-796-4551 [mobile e-mail] minatonakaz...@gmail.com ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
