Binary files /tmp/tmp8bmwfbvt/v0orRkJLEo/abc-2.1/build/vignette.rds and /tmp/tmp8bmwfbvt/VXKq2m7IDJ/abc-2.2.1/build/vignette.rds differ diff -Nru abc-2.1/CHANGES abc-2.2.1/CHANGES --- abc-2.1/CHANGES 2015-04-23 15:14:01.000000000 +0000 +++ abc-2.2.1/CHANGES 2022-05-17 20:46:27.000000000 +0000 @@ -1,77 +1,83 @@ -Changes in abc 2.1 -============================ - ---------- - o Remove a bug in the cv4abc function. It is now possible to use the argument hcorr in this function. - o Remove the line - desc <- packageDescription("GWRM") - in the CITATION file - -Changes in abc 2.0 -============================ - ---------- - o Include goodness-of-fit functions (gfit, plot.gfit, summary.gfit, is.gfit and gfitpca) written by Louisiane Lemaire. - - -Changes in abc 1.8 -============================ - ---------- - o The problem in the abc function that arises when using kernel="gaussian" is fixed - o Checking dependencies in R code ... NOTE - ‘library’ or ‘require’ call to ‘nnet’ which was already attached by Depends. - Please remove these calls from your code. - require(nnet) removed from postpr.R - o Changes in the details of the summary.cv4abc.Rd function - o Compression of the data with the resaveRdaFiles function (package tools ) - - -Changes in abc 1.7 -============================ - ---------- - o In the getmode function of the abc.R file - d$x[which(d$y == max(d$y))] replaced by d$x[which(d$y == max(d$y))][1] - o In the cv4postpr function - The line - subres <- withCallingHandlers( postpr(target = mytarget, index = myindex, sumstat = mysumstat, tol=mytol, - subset = mysubset, method = method, kernel = kernel), warning = namesWarningFilter) - has been changed and there is no call to withCallingHandlers anymore - - -Changes in abc 1.6 -============================ - ---------- - o Add 2 times (mnlogistic and neural net) - ss<-data.frame(ss) - colnames(ss)<-statnames - in postpr so that mnlogistic and neural net work when there is only one sum stat - o Michael Blum is the unique maintainer conforming to the new CRAN policy - - o Michael Blum is the unique maintainer conforming to the new CRAN policy - - -Changes in abc 1.5 -============================ - ---------- - o Add the reference to the MEE paper in the CITATION file and in the vignette - try and enjoy - >if(nchar(system.file(package="abc"))) citation("abc") - o Add the AIC and BIC computation in the abc function. - They are used to select a subset of informative statistics. - It is the AIC/BIC of the local linear regression that is returned. - -Changes in abc 2.1 -============================ - ---------- - o Thanks to the work of Louisiane Lemaire, two new functions, gfit - and gfitpca, were added to the package along with a plot and summary - S3 method for gfit to perform a goodness of fit. gfit tests if the - model preferred with postpr provides a good fit to the data - - o A separate data package (abc.data) was developped to store the - package's three data sets +Changes in abc 2.2.1 +============================ +--------- + o Remove the file build/vignette.rds + o Do not run some examples in Rd file to avoid generating files + +Changes in abc 2.2 +============================ +--------- + o Remove a bug in the hist function when unadj=TRUE + +Changes in abc 2.1 +============================ + +--------- + o Remove a bug in the cv4abc function. It is now possible to use the argument hcorr in this function. + o Remove the line + desc <- packageDescription("GWRM") + in the CITATION file + o Thanks to the work of Louisiane Lemaire, two new functions, gfit + and gfitpca, were added to the package along with a plot and summary + S3 method for gfit to perform a goodness of fit. gfit tests if the + model preferred with postpr provides a good fit to the data + o A separate data package (abc.data) was developped to store the + package's three data sets + + +Changes in abc 2.0 +============================ + +--------- + o Include goodness-of-fit functions (gfit, plot.gfit, summary.gfit, is.gfit and gfitpca) written by Louisiane Lemaire. + + +Changes in abc 1.8 +============================ + +--------- + o The problem in the abc function that arises when using kernel="gaussian" is fixed + o Checking dependencies in R code ... NOTE + ‘library’ or ‘require’ call to ‘nnet’ which was already attached by Depends. + Please remove these calls from your code. + require(nnet) removed from postpr.R + o Changes in the details of the summary.cv4abc.Rd function + o Compression of the data with the resaveRdaFiles function (package tools ) + + +Changes in abc 1.7 +============================ + +--------- + o In the getmode function of the abc.R file + d$x[which(d$y == max(d$y))] replaced by d$x[which(d$y == max(d$y))][1] + o In the cv4postpr function + The line + subres <- withCallingHandlers( postpr(target = mytarget, index = myindex, sumstat = mysumstat, tol=mytol, + subset = mysubset, method = method, kernel = kernel), warning = namesWarningFilter) + has been changed and there is no call to withCallingHandlers anymore + + +Changes in abc 1.6 +============================ + +--------- + o Add 2 times (mnlogistic and neural net) + ss<-data.frame(ss) + colnames(ss)<-statnames + in postpr so that mnlogistic and neural net work when there is only one sum stat + o Michael Blum is the unique maintainer conforming to the new CRAN policy + + o Michael Blum is the unique maintainer conforming to the new CRAN policy + + +Changes in abc 1.5 +============================ + +--------- + o Add the reference to the MEE paper in the CITATION file and in the vignette + try and enjoy + >if(nchar(system.file(package="abc"))) citation("abc") + o Add the AIC and BIC computation in the abc function. + They are used to select a subset of informative statistics. + It is the AIC/BIC of the local linear regression that is returned. diff -Nru abc-2.1/debian/changelog abc-2.2.1/debian/changelog --- abc-2.1/debian/changelog 2022-05-27 13:44:12.000000000 +0000 +++ abc-2.2.1/debian/changelog 2022-05-27 13:41:56.000000000 +0000 @@ -1,16 +1,23 @@ -abc (2.1-1cran2.2004.0) focal; urgency=medium +abc (2.2.1-1cran1.2004.0) focal; urgency=medium - * Compilation for Ubuntu 20.04 LTS + * Compilation for Ubuntu 20.04.4 LTS * Build for c2d4u for R 4.0.0 plus * Focal only build amd64 packages for Launchpad - -- Michael Rutter Thu, 07 May 2020 06:18:44 +0000 + -- Michael Rutter Fri, 27 May 2022 13:41:56 +0000 + +abc (2.2.1-1cran1) testing; urgency=low + + * cran2deb svn: 362M with DB version 1. + + -- cran2deb4ubuntu Wed, 25 May 2022 09:35:04 -0400 + abc (2.1-1cran2) testing; urgency=low * cran2deb svn: 362M with DB version 1. - -- cran2deb4ubuntu Sun, 23 Oct 2016 02:17:36 -0400 + -- cran2deb4ubuntu Sun, 23 Oct 2016 02:17:42 -0400 abc (2.1-1cran1) testing; urgency=low diff -Nru abc-2.1/debian/compat abc-2.2.1/debian/compat --- abc-2.1/debian/compat 2022-05-27 13:44:12.000000000 +0000 +++ abc-2.2.1/debian/compat 2022-05-25 13:35:04.000000000 +0000 @@ -1 +1 @@ -7 \ No newline at end of file +9 \ No newline at end of file diff -Nru abc-2.1/debian/control abc-2.2.1/debian/control --- abc-2.1/debian/control 2022-05-27 13:44:12.000000000 +0000 +++ abc-2.2.1/debian/control 2022-05-27 13:41:56.000000000 +0000 @@ -5,7 +5,7 @@ Build-Depends: r-base-dev, r-cran-abc.data, r-cran-nnet, r-cran-quantreg, r-cran-mass, r-cran-locfit, xvfb, xauth, xfonts-base, r-base-core, debhelper (>> 4.1.0), cdbs -Standards-Version: 3.9.1 +Standards-Version: 4.1.4 Package: r-cran-abc Architecture: all @@ -22,4 +22,4 @@ Author: Csillery Katalin [aut], Lemaire Louisiane [aut], Francois Olivier [aut], Blum Michael [aut, cre] . - Maintainer: Blum Michael + Maintainer: Blum Michael diff -Nru abc-2.1/debian/copyright abc-2.2.1/debian/copyright --- abc-2.1/debian/copyright 2022-05-27 13:44:12.000000000 +0000 +++ abc-2.2.1/debian/copyright 2022-05-25 13:35:04.000000000 +0000 @@ -2,12 +2,12 @@ automatically using cran2deb4ubuntu by cran2deb4ubuntu . -The original GNU R package is Copyright (C) 2016 Csillery Katalin +The original GNU R package is Copyright (C) 2022 Csillery Katalin [aut], Lemaire Louisiane [aut], Francois Olivier [aut], Blum Michael [aut, cre] and possibly others. The original GNU R package is maintained by Blum Michael - and was obtained from: + and was obtained from: http://cran.r-project.org/src/contrib diff -Nru abc-2.1/debian/source/format abc-2.2.1/debian/source/format --- abc-2.1/debian/source/format 1970-01-01 00:00:00.000000000 +0000 +++ abc-2.2.1/debian/source/format 2022-05-25 13:35:04.000000000 +0000 @@ -0,0 +1 @@ +3.0 (quilt) \ No newline at end of file diff -Nru abc-2.1/DESCRIPTION abc-2.2.1/DESCRIPTION --- abc-2.1/DESCRIPTION 2015-05-05 09:34:14.000000000 +0000 +++ abc-2.2.1/DESCRIPTION 2022-05-19 07:20:02.000000000 +0000 @@ -1,14 +1,14 @@ Package: abc Type: Package Title: Tools for Approximate Bayesian Computation (ABC) -Version: 2.1 -Date: 2015-05-04 +Version: 2.2.1 +Date: 2022-05-17 Authors@R: c( person("Csillery", "Katalin", role = "aut", email="kati.csillery@gmail.com"), person("Lemaire", "Louisiane", role = "aut"), person("Francois", "Olivier", role = "aut"), person("Blum", "Michael", - email = "michael.blum@imag.fr", role = c("aut", "cre"))) + email = "michael.blum.temp@gmail.com", role = c("aut", "cre"))) Depends: R (>= 2.10), abc.data, nnet, quantreg, MASS, locfit Description: Implements several ABC algorithms for performing parameter estimation, model selection, and goodness-of-fit. @@ -18,10 +18,10 @@ Repository: CRAN License: GPL (>= 3) NeedsCompilation: no -Packaged: 2015-05-05 08:35:25 UTC; mblum +Packaged: 2022-05-18 18:46:30 UTC; mblum Author: Csillery Katalin [aut], Lemaire Louisiane [aut], Francois Olivier [aut], Blum Michael [aut, cre] -Maintainer: Blum Michael -Date/Publication: 2015-05-05 11:34:14 +Maintainer: Blum Michael +Date/Publication: 2022-05-19 07:20:02 UTC diff -Nru abc-2.1/inst/CITATION abc-2.2.1/inst/CITATION --- abc-2.1/inst/CITATION 2015-04-09 07:42:18.000000000 +0000 +++ abc-2.2.1/inst/CITATION 2019-05-10 12:44:06.000000000 +0000 @@ -10,5 +10,5 @@ as.person("Michael G. B. Blum")), year = 2012, journal = "Methods in Ecology and Evolution", - DOI = "http://dx.doi.org/10.1111/j.2041-210X.2011.00179.x", + DOI = "10.1111/j.2041-210X.2011.00179.x", textVersion = "Csillery, K., Francois, O. and Blum, M. G. B. (2012), abc: an R package for approximate Bayesian computation (ABC). Methods in Ecology and Evolution 3: 475-479. doi: 10.1111/j.2041-210X.2011.00179.x") \ No newline at end of file Binary files /tmp/tmp8bmwfbvt/v0orRkJLEo/abc-2.1/inst/doc/abcvignette.pdf and /tmp/tmp8bmwfbvt/VXKq2m7IDJ/abc-2.2.1/inst/doc/abcvignette.pdf differ diff -Nru abc-2.1/man/abc.Rd abc-2.2.1/man/abc.Rd --- abc-2.1/man/abc.Rd 2015-04-23 15:18:11.000000000 +0000 +++ abc-2.2.1/man/abc.Rd 2022-05-17 20:42:33.000000000 +0000 @@ -261,9 +261,10 @@ expression(sigma^2))) ## or send histograms to a pdf file +\dontrun{ hist(linhc, file="linhc", breaks=30, caption=c(expression(mu), expression(sigma^2))) - +} ## diagnostic plots: compare the 2 'abc' objects: "loclinear", ## "loclinear" with correction for heteroscedasticity ## diff -Nru abc-2.1/man/cv4abc.Rd abc-2.2.1/man/cv4abc.Rd --- abc-2.1/man/cv4abc.Rd 2015-04-23 15:18:21.000000000 +0000 +++ abc-2.2.1/man/cv4abc.Rd 2022-05-17 20:40:37.000000000 +0000 @@ -162,8 +162,10 @@ plot(cv.rej, log=c("", "xy"), caption=c(expression(mu), expression(sigma^2))) ## or printing results directly to a postscript file... +\dontrun{ plot(cv.lin, log=c("xy", "xy"), caption=c(expression(mu), expression(sigma^2)), file="CVrej", postscript=TRUE) +} ## using the summary method to calculate the prediction error summary(cv.lin) diff -Nru abc-2.1/MD5 abc-2.2.1/MD5 --- abc-2.1/MD5 2015-05-05 09:34:14.000000000 +0000 +++ abc-2.2.1/MD5 2022-05-19 07:20:02.000000000 +0000 @@ -1,21 +1,22 @@ -1e680ef5d0eda41bd7cb8dbe9e1e4c81 *CHANGES -20aecbfadd9cc802f67ed98f0d842759 *DESCRIPTION -3271211869587af54863478756e438f4 *NAMESPACE -4cb3c26e41b8650ad1888c99f9ccd47b *R/abc.R +adeba25bedccff842e6a98c08c3496ec *CHANGES +145ab2b6a7d3f8809059673da399e3a1 *DESCRIPTION +46a5ec038326de6028ef5c278d34f11f *NAMESPACE +c297e75bb2f6ec2eea4d1ea336d630ea *R/abc.R a4875d0d61238d65f12ab84a7977d9a7 *R/cv4abc.R -174f2145c65613b9d91c3fb7f46c09da *R/cv4postpr.R +aa21f063cfb5a2a8d5790910ddcc5b13 *R/cv4postpr.R 101ef3d2883a34eee66bc4da36458e05 *R/expected.deviance.R 6c9bc20a33f0548fd7d4051dd662b7c5 *R/gfit.R c160ec2476d167bbd0af0fb0941e6039 *R/gfitpca.R acc48726d9098fdd2e33d0b747cc6cf0 *R/misc.R c7907c8fb3df495d7a40bcd1816b52ac *R/postpr.R -af465a32ddcb5bc4b5dee6499eda454e *build/vignette.rds -33c0e91d95b3e258a2621c710f3637f6 *inst/CITATION +b8d52f397ee1c343fa431f8903731efb *README.md +f4385b1361e3eb38ac977bdaf7b5dea6 *build/vignette.rds +f7b02d963f155ee45aa54393cd3aa7eb *inst/CITATION b7877d321663ff9c9e7cf668cf169bda *inst/doc/abcvignette.R 39ba12e087a7b42bda99bc124e3b35f0 *inst/doc/abcvignette.Rnw -61867e5b0c02b896d2adee1adbd5e992 *inst/doc/abcvignette.pdf -0b80e7b3e0bd4ede950f12b494cd182c *man/abc.Rd -c9c18f83498b53f56108a3d60b1a9751 *man/cv4abc.Rd +44b84b6ba84a4d5c66eea43433055026 *inst/doc/abcvignette.pdf +b169c0eda43e3b00d4bd813f2882b3d4 *man/abc.Rd +fed3a9e3dcfb1e58f7d8b1560bf294a8 *man/cv4abc.Rd b144497efa15fd6d9339d31797d70e1e *man/cv4postpr.Rd ab09d7d3191670c03890d5d4e1ebc7c5 *man/expected.deviance.Rd 677341f78b733a318a7049f50516ade4 *man/gfit.Rd diff -Nru abc-2.1/NAMESPACE abc-2.2.1/NAMESPACE --- abc-2.1/NAMESPACE 2015-04-19 06:45:11.000000000 +0000 +++ abc-2.2.1/NAMESPACE 2022-05-18 07:39:06.000000000 +0000 @@ -4,8 +4,16 @@ importFrom(MASS,lm.ridge) importFrom(quantreg,rq) importFrom(locfit,locfit) +importFrom("grDevices", "as.graphicsAnnot", "dev.off", "devAskNewPage", + "deviceIsInteractive", "heat.colors", "pdf") +importFrom("graphics", "abline", "barplot", "hist", "legend", "lines", + "mtext", "par", "segments", "title") +importFrom("stats", "as.formula", "coef", "density", "fitted", "lsfit", + "mad", "median", "na.omit", "prcomp", "predict", "qqline", + "qqnorm", "quantile", "runif", "var", "weighted.mean") + import(abc.data) - + # abc S3methods S3method(print, abc) S3method(summary, abc) diff -Nru abc-2.1/R/abc.R abc-2.2.1/R/abc.R --- abc-2.1/R/abc.R 2015-04-09 07:30:07.000000000 +0000 +++ abc-2.2.1/R/abc.R 2019-04-09 07:30:14.000000000 +0000 @@ -599,8 +599,7 @@ if(abc.out$method == "rejection") res <- abc.out$unadj.values else if (unadj){ - rej <- abc.out$unadj.values - res <- abc.out$adj.values + res <- abc.out$unadj.values } else res <- abc.out$adj.values diff -Nru abc-2.1/R/cv4postpr.R abc-2.2.1/R/cv4postpr.R --- abc-2.1/R/cv4postpr.R 2013-06-06 14:18:32.000000000 +0000 +++ abc-2.2.1/R/cv4postpr.R 2019-05-10 11:56:31.000000000 +0000 @@ -111,7 +111,7 @@ myindex <- index[-mysamp] mysumstat <- sumstat[-mysamp,] mysubset <- subset[-mysamp] - subres <- postpr(target = mytarget, index = myindex, sumstat = mysumstat, tol=mytol,subset = mysubset, method = method, kernel = kernel) + subres <- postpr(target = mytarget, index = myindex, sumstat = mysumstat, tol=mytol,subset = mysubset, method = method, kernel = kernel,...) if(subres$method=="rejection") res[i,] <- summary.postpr(subres, print = F, ...)$Prob if(subres$method=="mnlogistic") res[i, ] <- summary.postpr(subres, print = F, ...)$mnlogistic$Prob diff -Nru abc-2.1/README.md abc-2.2.1/README.md --- abc-2.1/README.md 1970-01-01 00:00:00.000000000 +0000 +++ abc-2.2.1/README.md 2019-04-09 07:26:18.000000000 +0000 @@ -0,0 +1,2 @@ +# abc +R package for Approximate Bayesian Computation