diff -Nru r-cran-epibasix-1.3/debian/changelog r-cran-epibasix-1.5/debian/changelog --- r-cran-epibasix-1.3/debian/changelog 2018-05-31 09:43:45.000000000 +0000 +++ r-cran-epibasix-1.5/debian/changelog 2018-12-05 10:03:43.000000000 +0000 @@ -1,3 +1,12 @@ +r-cran-epibasix (1.5-1) unstable; urgency=medium + + * New upstream version + * Standards-Version: 4.2.1 + * Secure URI in copyright format + * Remove trailing whitespace in debian/changelog + + -- Andreas Tille Wed, 05 Dec 2018 11:03:43 +0100 + r-cran-epibasix (1.3-4) unstable; urgency=medium * Rebuild for R 3.5 transition @@ -36,7 +45,7 @@ * New upstream release * Normalised Debian copyright file with config-model-edit. - * Does not depend on r-cran-foreign nor r-cran-sp. + * Does not depend on r-cran-foreign nor r-cran-sp. * Normalised debian/control with config-model-edit. * Normalised VCS URLs following Lintian's standard. * Acquire R:Depends directly from r-base-dev. @@ -65,7 +74,7 @@ (debian/control, no changes needed). * Depend on a version equal or superior than the R upstream release that was used to build this package, using a R:Depends substvar - (debian/control, debian/rules). + (debian/control, debian/rules). * Added a note to explain how to test this package (debian/README.Debian). * Indicate a more generic URL in debian/copyright, to reduce redundancy with debian/watch. diff -Nru r-cran-epibasix-1.3/debian/control r-cran-epibasix-1.5/debian/control --- r-cran-epibasix-1.3/debian/control 2018-05-31 09:43:45.000000000 +0000 +++ r-cran-epibasix-1.5/debian/control 2018-12-05 10:03:43.000000000 +0000 @@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 11~), dh-r, r-base-dev -Standards-Version: 4.1.4 +Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-cran-epibasix Vcs-Git: https://salsa.debian.org/r-pkg-team/r-cran-epibasix.git Homepage: https://cran.r-project.org/package=epibasix diff -Nru r-cran-epibasix-1.3/debian/copyright r-cran-epibasix-1.5/debian/copyright --- r-cran-epibasix-1.3/debian/copyright 2018-05-31 09:43:45.000000000 +0000 +++ r-cran-epibasix-1.5/debian/copyright 2018-12-05 10:03:43.000000000 +0000 @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: epibasix Upstream-Contact: Michael A Rotondi Source: https://cran.r-project.org/package=epibasix diff -Nru r-cran-epibasix-1.3/DESCRIPTION r-cran-epibasix-1.5/DESCRIPTION --- r-cran-epibasix-1.3/DESCRIPTION 2012-11-15 21:51:56.000000000 +0000 +++ r-cran-epibasix-1.5/DESCRIPTION 2018-11-19 23:20:03.000000000 +0000 @@ -1,22 +1,20 @@ Package: epibasix -Version: 1.3 -Date: 2012-11-15 +Version: 1.5 +Date: 2018-11-19 Title: Elementary Epidemiological Functions for Epidemiology and Biostatistics Author: Michael A Rotondi Maintainer: Michael A Rotondi Depends: R (>= 2.01) -Description: This package contains elementary tools for analysis of +Description: Contains elementary tools for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement (kappa, sensitivity/specificity). Appropriate print and summary statements are also written to - facilitate interpretation wherever possible. Source code is - commented throughout to facilitate modification. The target - audience includes advanced undergraduate and graduate students - in epidemiology or biostatistics courses, and clinical - researchers. + facilitate interpretation wherever possible. Source code is commented throughout to facilitate modification. The target audience includes advanced undergraduate and graduate students + in epidemiology or biostatistics courses, and clinical researchers. License: GPL (>= 2) -Packaged: 2012-11-15 21:31:52 UTC; mrotondi +NeedsCompilation: no +Packaged: 2018-11-19 21:25:51 UTC; mrotondi Repository: CRAN -Date/Publication: 2012-11-15 21:51:56 +Date/Publication: 2018-11-19 23:20:03 UTC diff -Nru r-cran-epibasix-1.3/man/corXY.Rd r-cran-epibasix-1.5/man/corXY.Rd --- r-cran-epibasix-1.3/man/corXY.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/corXY.Rd 2015-02-02 17:06:26.000000000 +0000 @@ -40,7 +40,7 @@ Koepsell TD and Weiss NS. Epidemiologic Methods. Oxford University Press: New York, 2003. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \examples{ \dontrun{Suppose we want to test whether two randomly generated normal vectors are uncorrelated} diff -Nru r-cran-epibasix-1.3/man/diffDetect.Rd r-cran-epibasix-1.5/man/diffDetect.Rd --- r-cran-epibasix-1.3/man/diffDetect.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/diffDetect.Rd 2015-02-02 17:06:42.000000000 +0000 @@ -42,7 +42,7 @@ Matthews JNS. Introduction to Randomized Controlled Clinical Trials (2nd Ed.) Chapman & Hall: New York, 2006. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \examples{ \dontrun{Suppose, for financial considerations we can only enroll 100 people in a blood diff -Nru r-cran-epibasix-1.3/man/epi2x2.Rd r-cran-epibasix-1.5/man/epi2x2.Rd --- r-cran-epibasix-1.3/man/epi2x2.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/epi2x2.Rd 2015-02-02 17:06:52.000000000 +0000 @@ -55,7 +55,7 @@ Szklo M and Nieto FJ. Epidemiology: Beyond the Basics, Jones and Bartlett: Boston, 2007. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \seealso{\code{\link{mcNemar}}} diff -Nru r-cran-epibasix-1.3/man/epiKappa.Rd r-cran-epibasix-1.5/man/epiKappa.Rd --- r-cran-epibasix-1.3/man/epiKappa.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/epiKappa.Rd 2015-02-02 17:07:04.000000000 +0000 @@ -47,7 +47,7 @@ Fleiss J. Statistical Methods for Rates and Proportions, 2nd ed. New York: John Wiley and Sons; 1981. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \seealso{\code{\link{sensSpec}}} diff -Nru r-cran-epibasix-1.3/man/epiTTest.Rd r-cran-epibasix-1.5/man/epiTTest.Rd --- r-cran-epibasix-1.3/man/epiTTest.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/epiTTest.Rd 2015-02-02 17:07:16.000000000 +0000 @@ -54,7 +54,7 @@ } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \examples{ X <- rnorm(100,10,1); diff -Nru r-cran-epibasix-1.3/man/mcNemar.Rd r-cran-epibasix-1.5/man/mcNemar.Rd --- r-cran-epibasix-1.3/man/mcNemar.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/mcNemar.Rd 2015-02-02 17:07:26.000000000 +0000 @@ -42,7 +42,7 @@ Szklo M and Nieto FJ. Epidemiology: Beyond the Basics, Jones and Bartlett: Boston, 2007. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \seealso{\code{\link{epi2x2}}} diff -Nru r-cran-epibasix-1.3/man/n4means.Rd r-cran-epibasix-1.5/man/n4means.Rd --- r-cran-epibasix-1.3/man/n4means.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/n4means.Rd 2015-02-02 17:07:38.000000000 +0000 @@ -47,7 +47,7 @@ Matthews JNS. Introduction to Randomized Controlled Clinical Trials (2nd Ed.) Chapman & Hall: New York, 2006. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \seealso{\code{\link{n4props}}} diff -Nru r-cran-epibasix-1.3/man/n4props.Rd r-cran-epibasix-1.5/man/n4props.Rd --- r-cran-epibasix-1.3/man/n4props.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/n4props.Rd 2018-11-19 20:47:24.000000000 +0000 @@ -48,12 +48,14 @@ Matthews JNS. Introduction to Randomized Controlled Clinical Trials (2nd Ed.) Chapman & Hall: New York, 2006. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \seealso{\code{\link{n4means}}} \examples{ -\dontrun{Suppose a new drug is thought to reduce heart attack mortality from 0.10 to 0.03. Calculate the required number of subjects that must be enrolled in a study to detect this difference with alpha = 0.05 and power = 0.80.} +\dontrun{Suppose a new drug is thought to reduce heart attack mortality from +0.10 to 0.03. Calculate the required number of subjects that must be enrolled +in a study to detect this difference with alpha = 0.05 and power = 0.80.} n4props(0.03, 0.10, AR=1, alpha=0.05, power=0.80); } diff -Nru r-cran-epibasix-1.3/man/sensSpec.Rd r-cran-epibasix-1.5/man/sensSpec.Rd --- r-cran-epibasix-1.3/man/sensSpec.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/sensSpec.Rd 2015-02-02 17:08:02.000000000 +0000 @@ -58,7 +58,7 @@ of the Epi package, which employs a logit transformation. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \seealso{\code{\link{kappa}}} diff -Nru r-cran-epibasix-1.3/man/univar.Rd r-cran-epibasix-1.5/man/univar.Rd --- r-cran-epibasix-1.3/man/univar.Rd 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/man/univar.Rd 2015-02-02 17:08:10.000000000 +0000 @@ -50,7 +50,7 @@ \references{ Casella G and Berger RL. Statistical Inference (2nd Ed.) Duxbury: New York, 2002. } -\author{Michael Rotondi, \email{mrotondi@uwo.ca}} +\author{Michael Rotondi, \email{mrotondi@yorku.ca}} \examples{ x <- rexp(100); diff -Nru r-cran-epibasix-1.3/MD5 r-cran-epibasix-1.5/MD5 --- r-cran-epibasix-1.3/MD5 2012-11-15 21:51:56.000000000 +0000 +++ r-cran-epibasix-1.5/MD5 2018-11-19 23:20:03.000000000 +0000 @@ -1,8 +1,8 @@ -6a2bd65876f6d1cee5e695e7209705be *DESCRIPTION -8a2499f5cf3c09cb547c794179e8ff4e *NAMESPACE +c35df699adf1bf268ecf9b36ea65fba5 *DESCRIPTION +6a5469a1d7d606b18d75fd4dd1beeb0d *NAMESPACE 623240ba2b1e1dc854889ff434ebed5d *R/corXY.R 09b25c367148357f56f10447eb04f36e *R/diffDetect.R -f0df9439d5f273b679a357f9b0902d52 *R/epi2x2.R +df0f1a480cdf5f41465e1a80b30b4e39 *R/epi2x2.R 2d83d2ba460de7e69752c68a40f55bdd *R/epiKappa.R b91e4626369af06cbd56790316d605ec *R/epiTTest.R d535bdddaf7c8e477d35171697c14bff *R/mcNemar.R @@ -10,13 +10,13 @@ defdc6e3cf1eb5706395639192ffc8d2 *R/n4props.R 62105be3bf35ce5f4c976366efebbf91 *R/sensSpec.R b2699b9f5fb0018e49ea99582b904e9d *R/univar.R -ad74925aa871185e068a95aac7549f78 *man/corXY.Rd -75543ec0e19a26038a5aed3e0e7e34f6 *man/diffDetect.Rd -741aab3a7d1e766aaccd9e17683d7d64 *man/epi2x2.Rd -ea8fa1cfbd4951fdbc40d2d034265afc *man/epiKappa.Rd -5bd532f28f4865ecfdec89193ac4e243 *man/epiTTest.Rd -e112bd7654749eebf1db0e54a1028662 *man/mcNemar.Rd -92dc0d6c7ad68fc42bf2b19e8784e5eb *man/n4means.Rd -6e9fabf7bd1dd04b122114d114cfcaaf *man/n4props.Rd -79cfcd417f514d5b7b362d184d8a8af6 *man/sensSpec.Rd -3edfce08392d3cc6851c0bf0f955092d *man/univar.Rd +db3f043bd2560b9527262678d271b574 *man/corXY.Rd +9a3b4119807127fafb355274ff1466cd *man/diffDetect.Rd +34d95e7219ceabca84a23d7e3f6d6cdd *man/epi2x2.Rd +5461499641446bdecc2740f082a3bfde *man/epiKappa.Rd +f3da9ada10eed7b6b95bfcea78fa57e5 *man/epiTTest.Rd +08b07df4fd8a46d601a0f0c6cd0ae530 *man/mcNemar.Rd +b3e7da0ed26c6bfa00f0b4901edb848d *man/n4means.Rd +3a4a305b26809613fdfbd8ebbe7c63ef *man/n4props.Rd +013a46124af28f7e6175d668fc1e0dab *man/sensSpec.Rd +7543f8cd44940aa23bb258b42e1eb17b *man/univar.Rd diff -Nru r-cran-epibasix-1.3/NAMESPACE r-cran-epibasix-1.5/NAMESPACE --- r-cran-epibasix-1.3/NAMESPACE 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/NAMESPACE 2018-11-19 21:10:34.000000000 +0000 @@ -1,3 +1,29 @@ # Exports all functions not beginning with a period. exportPattern("^[^\\.]") +#Import other helper functions +importFrom("stats", "cor", "fisher.test", "median", "pchisq", "pnorm", + "pt", "qnorm", "qt", "sd", "shapiro.test", "var") + +#Register S3 +S3method(print, corXY) +S3method(print, diffDetect) +S3method(print, epi2x2) +S3method(print, epiKappa) +S3method(print, epiTTest) +S3method(print, mcNemar) +S3method(print, n4means) +S3method(print, n4props) +S3method(print, sensSpec) +S3method(print, univar) + +S3method(summary, corXY) +S3method(summary, diffDetect) +S3method(summary, epi2x2) +S3method(summary, epiKappa) +S3method(summary, epiTTest) +S3method(summary, mcNemar) +S3method(summary, n4means) +S3method(summary, n4props) +S3method(summary, sensSpec) +S3method(summary, univar) \ No newline at end of file diff -Nru r-cran-epibasix-1.3/R/epi2x2.R r-cran-epibasix-1.5/R/epi2x2.R --- r-cran-epibasix-1.3/R/epi2x2.R 2012-11-15 21:31:52.000000000 +0000 +++ r-cran-epibasix-1.5/R/epi2x2.R 2018-11-19 21:12:54.000000000 +0000 @@ -67,7 +67,7 @@ cat("Input Matrix: \n") print(x$X) cat("\n", "Pearson Chi-Squared Statistic (Includes Yates' Continuity Correction): ", round(x$Sy, digits=x$digits), "\n", sep="") -cat("Associated p.value for H0: There is an association between exposure and outcome vs. HA: No association : ", round(x$Sy.p.value, digits=x$digits), "\n", sep="") +cat("Associated p.value for H0: There is no association between exposure and outcome vs. HA: There is an association : ", round(x$Sy.p.value, digits=x$digits), "\n", sep="") cat("p.value using Fisher's Exact Test: ", round(x$Fisher.p.value, digits=x$digits), "\n \n", sep=""); cat("Estimate of Odds Ratio: ", round(x$OR, digits=x$digits), "\n", sep="") @@ -81,7 +81,7 @@ cat("Input Matrix: \n") print(object$X) cat("\n", "Pearson Chi-Squared Statistic (Includes Yates' Continuity Correction): ", round(object$Sy, digits=object$digits), "\n", sep="") -cat("Associated p.value for H0: There is an association between exposure and outcome vs. HA: No association : ", round(object$Sy.p.value, digits=object$digits), "\n", sep="") +cat("Associated p.value for H0: There is no association between exposure and outcome vs. HA: There is an association : ", round(object$Sy.p.value, digits=object$digits), "\n", sep="") cat("p.value using Fisher's Exact Test (1 DF) : ", round(object$Fisher.p.value, digits=object$digits), "\n \n", sep=""); cat("Estimate of Odds Ratio: ", round(object$OR, digits=object$digits), "\n", sep="")