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Type 'q()' to quit R. > # This file is copied and modified from runjags package > # Copyright (C) 2013 Matthew Denwood and Achmad Syahrul Choir > # > # This code allows the distributions provided by the neojags module > # to be tested from within R. > # > # This version of the module is compatible with JAGS version 3 and 4. > # Some necessary modifications are controlled using the INCLUDERSCALARDIST > # macro which is defined by makevars if JAGS version 3 is detected. > # Once JAGS version 3 becomes obsolete the redundant code will be > # removed from neojags. > # > # neojags is free software: you can redistribute it and/or modify > # it under the terms of the GNU General Public License as published by > # the Free Software Foundation, either version 3 of the License, or > # (at your option) any later version. > # > # neojags is distributed in the hope that it will be useful, > # but WITHOUT ANY WARRANTY; without even the implied warranty of > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the > # GNU General Public License for more details. > # > # You should have received a copy of the GNU General Public License > # along with runjags If not, see . > > > > library("neojags") > library("runjags") > runjags::runjags.options(nodata.warning=FALSE) > > # Checks that the neojags module distributions are correct. > > # Loading the dynlib requires rjags for Windows: > if(.Platform$OS.type != 'windows' || requireNamespace('rjags')){ + + loaded <- neojags:::dynloadmodule() + if(!loaded) + stop("The internal JAGS dynlib could not be loaded - if you installed this package from CRAN, please file a bug report to the package author") + + cat('Running module tests\n') + + # Required for nchain etc: + library("coda") + cat("The internal module tests were passed\n") + }else{ + cat("The internal module tests were skipped (not available on Windows)\n") + } Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double) Running module tests The internal module tests were passed Warning message: In swcat("Loading shared library from: ", slibpath, "\n", sep = "") : Loading shared library from: D:/temp/RtmpMrZ69q/RLIBS_c1503a2756a5/neojags/libs/x64/neojags.dll > > > # Require the rjags library to run the rest of the checks: > dotests <- TRUE > if(!require("rjags")){ + cat("The module checks were not performed as rjags is not installed\n") + dotests <- FALSE + } Loading required package: rjags Linked to JAGS 4.3.1 Loaded modules: basemod,bugs > > if(dotests){ + + # Try to load the module: + loaded <- load.neojagsmodule(fail=FALSE) + if(!loaded){ + warning("The module checks were not performed as the internal JAGS module could not be loaded") + dotests <- FALSE + } + + # Now check the JAGS implementations just to make sure the functions are found OK: + + m <- "model{ + + r0 ~ dmsnburr(0,1,1) + f0 ~ dmsnburr(0,1,1) + d0 <- dmsnburr(0.5,0,1,1) + p0 <- pmsnburr(0.5,0,1,1) + q0 <- qmsnburr(0.5,0,1,1) + + r1 ~ dmsnburr2a(0,1,1) + f1 ~ dmsnburr2a(0,1,1) + d1 <- dmsnburr2a(0.5,0,1,1) + p1 <- pmsnburr2a(0.5,0,1,1) + q1 <- qmsnburr2a(0.5,0,1,1) + + r2 ~ dgmsnburr(0,1,1,1) + f2 ~ dgmsnburr(0,1,1,1) + d2 <- dgmsnburr(0.5,0,1,1,1) + p2 <- pgmsnburr(0.5,0,1,1,1) + q2 <- qgmsnburr(0.5,0,1,1,1) + + r3 ~ dfskew.norm(0,1,1) + f3 ~ dfskew.norm(0,1,1) + d3 <- dfskew.norm(0.5,0,1,1) + p3 <- pfskew.norm(0.5,0,1,1) + q3 <- qfskew.norm(0.5,0,1,1) + + r4 ~ dfskew.t(0,1,10,1) + f4 ~ dfskew.t(0,1,10,1) + d4 <- dfskew.t(0.5,0,1,10,1) + p4 <- pfskew.t(0.5,0,1,10,1) + q4 <- qfskew.t(0.5,0,1,10,1) + + r5 ~ dlep(1,1,1) + f5 ~ dlep(1,1,1) + d5 <- dlep(0.5,1,1,1) + p5 <- plep(0.5,1,1,1) + q5 <- qlep(0.5,1,1,1) + + + r6 ~ djskew.ep(0,1,2,2) + f6 ~ djskew.ep(0,1,2,2) + d6 <- djskew.ep(0.5,0,1,2,2) + p6 <- pjskew.ep(0.5,0,1,2,2) + q6 <- qjskew.ep(0.5,0,1,2,2) + + + #monitor# r0,d0,p0,q0,r1,d1,p1,q1,r2,d2,p2,q2,r3,d3,p3,q3,r4,d4,p4,q4, r5,d5,p5,q5,r6,d6,p6,q6, + #data# f0, f1, f2, f3, f4, f5, f6 + + }" + + f0=f1=f2=f3=f4=f5=f6<- 2 + + r <- runjags::run.jags(m, n.chains=2, burnin=100, sample=100, method='rjags') + stopifnot(nchain(as.mcmc.list(r))==2) + + + # Now check that my p and q functions are symmetric: + + m <- "model{ + + qsn <- qnorm(sp, cont1, pos1) + psn <- pnorm(qsn, cont1, pos1) + + qsg <- qgamma(sp, pos1, pos2) + psg <- pgamma(qsg, pos1, pos2) + + qsl <- qlnorm(sp, cont1, pos2) + psl <- plnorm(qsl, cont1, pos2) + + qsp <- qmsnburr(sp, cont1, pos1, pos2) + psp <- pmsnburr(qsp, cont1, pos1, pos2) + + qsp1 <- qmsnburr2a(sp, cont1, pos1, pos2) + psp1 <- pmsnburr2a(qsp1, cont1, pos1, pos2) + + qsp2 <- qgmsnburr(sp, cont1, pos1, pos2, pos3) + psp2 <- pgmsnburr(qsp2, cont1, pos1, pos2, pos3) + + qsp3 <- qfskew.norm(sp, cont1, pos1, pos2) + psp3 <- pfskew.norm(qsp3, cont1, pos1, pos2) + + qsp4 <- qfskew.t(sp, cont1, pos1, pos2, pos3) + psp4 <- pfskew.t(qsp4, cont1, pos1, pos2, pos3) + + qsp5 <- qlep(sp, pos1, pos1, pos2) + psp5 <- plep(qsp5, pos1, pos1, pos2) + + + qsp6 <- qjskew.ep(sp, cont1, pos1, pos2,pos3) + psp6 <- pjskew.ep(qsp6, cont1, pos1, pos2,pos3) + + + #monitor# psn, psg, psl, psp, psp1, psp2, psp3, psp4, psp5, psp6 + + + #psp, + #data# sp, cont1, pos1, pos2, pos3 + + }" + + + sp <- 1:7/10 + set.seed(1) + cont1 <- runif(1,-10,10) + cont2 <- runif(1,-10,10) + pos1 <- rgamma(1,1,1) + pos2 <- rgamma(1,1,1) + pos3 <- rgamma(1,1,1) + + r <- run.jags(m, burnin=100, sample=10, n.chains=1, method='rjags', summarise=FALSE) + + sp <- rep(sp,10) + ps <- combine.mcmc(r,vars='ps')[1,] + stopifnot(length(sp)==length(ps)) + if(!isTRUE(all.equal(sp,ps))){ + # Reduce stringency of the test - roughly 10^7 different on linux: + problem <- abs(sp-ps) > max(10^-4, .Machine$double.eps^0.5) + if(any(problem)) stop(paste("Error with ps/sp check (which expected observed): ", paste(paste(names(ps)[which(problem)], " ", sp[problem], " ", ps[problem], "; ", sep=""), collapse=""), sep="")) + } + + cat("The neojags module tests were passed\n") + + }else{ + cat("The neojags module tests were skipped (rjags not installed)\n") + } Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double) module neojags loaded Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double) Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double) Compiling rjags model... Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double) Calling the simulation using the rjags method... Note: the model did not require adaptation Burning in the model for 100 iterations... Running the model for 100 iterations... Simulation complete Calculating summary statistics... Note: The monitored variables 'd0', 'p0', 'q0', 'd1', 'p1', 'q1', 'd2', 'p2', 'q2', 'd3', 'p3', 'q3', 'd4', 'p4', 'q4', 'd5', 'p5', 'q5', 'd6', 'p6' and 'q6' appear to be non-stochastic; they will not be included in the convergence diagnostic Calculating the Gelman-Rubin statistic for 28 variables.... Finished running the simulation Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double) Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double) Compiling rjags model... Warning in .make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version) : invalid non-character version specification 'x' (type: double) Calling the simulation using the rjags method... Note: the model did not require adaptation Burning in the model for 100 iterations... Running the model for 10 iterations... Simulation complete Finished running the simulation The neojags module tests were passed Warning message: No initial values were provided - JAGS will use the same initial values for all chains > > cat("All module checks passed\n") All module checks passed > > > proc.time() user system elapsed 0.60 0.07 4.51 Error in dyn.unload(slibpath) : shared object 'D:/RCompile/CRANincoming/R-devel/lib/neojags/libs/x64/neojags.dll' was not loaded In addition: Warning message: In swcat("Unloading shared library from: ", slibpath, "\n", sep = "") : Unloading shared library from: D:/RCompile/CRANincoming/R-devel/lib/neojags/libs/x64/neojags.dll Warning message: In dynunloadmodule() : The internal dynlib could not be unloaded