diff --git a/DESCRIPTION b/DESCRIPTION index 34bc702..d4ead43 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,7 @@ Description: Tool-set to support Bayesian evidence synthesis. This and Schmidli et al. (2014) explain details on the methodology. Version: 1.7-4 -Date: 2024-11-20 +Date: 2024-11-21 Authors@R: c(person("Novartis", "Pharma AG", role = "cph") ,person("Sebastian", "Weber", email="sebastian.weber@novartis.com", role=c("aut", "cre")) ,person("Beat", "Neuenschwander", email="beat.neuenschwander@novartis.com", role="ctb") diff --git a/NAMESPACE b/NAMESPACE index 377f92c..103bfa0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -76,6 +76,7 @@ S3method(print,betaBinomialMix) S3method(print,betaMix) S3method(print,decision1S) S3method(print,decision2S) +S3method(print,dlink) S3method(print,gMAP) S3method(print,gMAPpred) S3method(print,gMAPsummary) diff --git a/NEWS.md b/NEWS.md index b5fc06c..bcc1ea5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# RBesT 1.7-4 - November 20th, 2024 +# RBesT 1.7-4 - November 21st, 2024 ## Enhancements @@ -7,7 +7,7 @@ * Slight speed increase for Stan model by more efficient construction of likelihood. Also reducing object size of `gMAP` objects by avoiding to store redundant variables. -* Upgraded testhat edition to version 3. +* Upgraded `testthat` edition to version 3. ## Bugfixes diff --git a/R/RBesT-package.R b/R/RBesT-package.R index d128d85..14cc304 100644 --- a/R/RBesT-package.R +++ b/R/RBesT-package.R @@ -38,6 +38,7 @@ #' \tab \code{rel.tol=.Machine$double.eps^0.25,} \tab \cr #' \tab \code{abs.tol=.Machine$double.eps^0.25,} \tab \cr #' \tab \code{subdivisions=1E3)} \tab \cr +#' \code{RBesT.integrate_prob_eps} \tab \code{1E-6} \tab probability mass left out from tails if integration needs to be restricted in range \cr #' } #' #' @section Version History: diff --git a/R/sysdata.rda b/R/sysdata.rda index b219798..2064e02 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data/AS.rda b/data/AS.rda index 290f944..97965a4 100644 Binary files a/data/AS.rda and b/data/AS.rda differ diff --git a/data/colitis.rda b/data/colitis.rda index 7af25b0..937189f 100644 Binary files a/data/colitis.rda and b/data/colitis.rda differ diff --git a/data/crohn.rda b/data/crohn.rda index 746c481..de50e5d 100644 Binary files a/data/crohn.rda and b/data/crohn.rda differ diff --git a/data/transplant.rda b/data/transplant.rda index 3ca48e6..0c5c615 100644 Binary files a/data/transplant.rda and b/data/transplant.rda differ diff --git a/man/RBesT-package.Rd b/man/RBesT-package.Rd index e321ebc..e2802a1 100644 --- a/man/RBesT-package.Rd +++ b/man/RBesT-package.Rd @@ -45,6 +45,7 @@ Option \tab Default \tab Description \cr \tab \code{rel.tol=.Machine$double.eps^0.25,} \tab \cr \tab \code{abs.tol=.Machine$double.eps^0.25,} \tab \cr \tab \code{subdivisions=1E3)} \tab \cr +\code{RBesT.integrate_prob_eps} \tab \code{1E-6} \tab probability mass left out from tails if integration needs to be restricted in range \cr } } diff --git a/man/ess.Rd b/man/ess.Rd index e277ae9..717c6ee 100644 --- a/man/ess.Rd +++ b/man/ess.Rd @@ -120,14 +120,12 @@ round(sum(ab_matched)) ess(bmix, method="morita") # Predictive consistency of elir -\donttest{ n_forward <- 1E2 bmixPred <- preddist(bmix, n=n_forward) pred_samp <- rmix(bmixPred, 1E3) pred_ess <- sapply(pred_samp, function(r) ess(postmix(bmix, r=r, n=n_forward), "elir") ) ess(bmix, "elir") mean(pred_ess) - n_forward -} # Normal mixture example nmix <- mixnorm(rob=c(0.5, 0, 2), inf=c(0.5, 3, 4), sigma=10) diff --git a/man/integrate_density_log.Rd b/man/integrate_density_log.Rd index 1989106..a1682ac 100644 --- a/man/integrate_density_log.Rd +++ b/man/integrate_density_log.Rd @@ -14,7 +14,7 @@ integrate_density_log( mix, Lplower = -Inf, Lpupper = Inf, - eps = 1e-09 + eps = getOption("RBesT.integrate_prob_eps", 1e-06) ) } \arguments{ diff --git a/man/mixbeta.Rd b/man/mixbeta.Rd index 8f2f6a5..e930df4 100644 --- a/man/mixbeta.Rd +++ b/man/mixbeta.Rd @@ -86,11 +86,11 @@ print(bm4) } \seealso{ Other mixdist: +\code{\link{mix}}, \code{\link{mixcombine}()}, \code{\link{mixgamma}()}, \code{\link{mixmvnorm}()}, \code{\link{mixnorm}()}, -\code{\link{mixplot}}, -\code{\link{mix}} +\code{\link{mixplot}} } \concept{mixdist} diff --git a/man/mixcombine.Rd b/man/mixcombine.Rd index 4925797..eb43676 100644 --- a/man/mixcombine.Rd +++ b/man/mixcombine.Rd @@ -35,17 +35,16 @@ bm <- mixbeta(inf=c(0.5, 10, 100), inf2=c(0.5, 30, 80)) # robustified with mixcombine, i.e. a 10\% uninformative part added unif <- mixbeta(rob=c(1,1,1)) mixcombine(bm, unif, weight=c(9, 1)) - } \seealso{ \code{\link{robustify}} Other mixdist: +\code{\link{mix}}, \code{\link{mixbeta}()}, \code{\link{mixgamma}()}, \code{\link{mixmvnorm}()}, \code{\link{mixnorm}()}, -\code{\link{mixplot}}, -\code{\link{mix}} +\code{\link{mixplot}} } \concept{mixdist} diff --git a/man/mixgamma.Rd b/man/mixgamma.Rd index e1d97cb..8d0950b 100644 --- a/man/mixgamma.Rd +++ b/man/mixgamma.Rd @@ -104,11 +104,11 @@ gfmix <- mixgamma(rob1=c(0.15, mn2gamma(2, 1)), rob2=c(0.15, ms2gamma(2, 5)), in } \seealso{ Other mixdist: +\code{\link{mix}}, \code{\link{mixbeta}()}, \code{\link{mixcombine}()}, \code{\link{mixmvnorm}()}, \code{\link{mixnorm}()}, -\code{\link{mixplot}}, -\code{\link{mix}} +\code{\link{mixplot}} } \concept{mixdist} diff --git a/man/mixmvnorm.Rd b/man/mixmvnorm.Rd index 3c352d1..d97dc2a 100644 --- a/man/mixmvnorm.Rd +++ b/man/mixmvnorm.Rd @@ -81,11 +81,11 @@ colMeans(mixSamp1) } \seealso{ Other mixdist: +\code{\link{mix}}, \code{\link{mixbeta}()}, \code{\link{mixcombine}()}, \code{\link{mixgamma}()}, \code{\link{mixnorm}()}, -\code{\link{mixplot}}, -\code{\link{mix}} +\code{\link{mixplot}} } \concept{mixdist} diff --git a/man/mixnorm.Rd b/man/mixnorm.Rd index cac7eb3..e28033e 100644 --- a/man/mixnorm.Rd +++ b/man/mixnorm.Rd @@ -107,11 +107,11 @@ ess(nm) } \seealso{ Other mixdist: +\code{\link{mix}}, \code{\link{mixbeta}()}, \code{\link{mixcombine}()}, \code{\link{mixgamma}()}, \code{\link{mixmvnorm}()}, -\code{\link{mixplot}}, -\code{\link{mix}} +\code{\link{mixplot}} } \concept{mixdist} diff --git a/man/mixplot.Rd b/man/mixplot.Rd index 7fe703c..8bd5706 100644 --- a/man/mixplot.Rd +++ b/man/mixplot.Rd @@ -25,7 +25,7 @@ density in addition to the density.} \item{size}{controls the linesize in plots.} -\item{...}{extra arguments passed on to the \code{\link[ggplot2]{qplot}} call.} +\item{...}{extra arguments passed on to the plotted function.} } \value{ A \code{\link[ggplot2]{ggplot}} object is returned. @@ -92,11 +92,11 @@ pl + ggtitle("Normal 2-Component Mixture") } \seealso{ Other mixdist: +\code{\link{mix}}, \code{\link{mixbeta}()}, \code{\link{mixcombine}()}, \code{\link{mixgamma}()}, \code{\link{mixmvnorm}()}, -\code{\link{mixnorm}()}, -\code{\link{mix}} +\code{\link{mixnorm}()} } \concept{mixdist} diff --git a/man/oc1S.Rd b/man/oc1S.Rd index c1797da..9884172 100644 --- a/man/oc1S.Rd +++ b/man/oc1S.Rd @@ -143,8 +143,8 @@ designC2_nL(theta_eval) } \seealso{ Other design1S: -\code{\link{decision1S_boundary}()}, \code{\link{decision1S}()}, +\code{\link{decision1S_boundary}()}, \code{\link{pos1S}()} } \concept{design1S} diff --git a/man/oc2S.Rd b/man/oc2S.Rd index a817d1f..7ff428b 100644 --- a/man/oc2S.Rd +++ b/man/oc2S.Rd @@ -152,8 +152,8 @@ Robust meta-analytic-predictive priors in clinical trials with historical contro } \seealso{ Other design2S: -\code{\link{decision2S_boundary}()}, \code{\link{decision2S}()}, +\code{\link{decision2S_boundary}()}, \code{\link{pos2S}()} } \concept{design2S} diff --git a/man/plot.gMAP.Rd b/man/plot.gMAP.Rd index 538f1c4..ffa83f0 100644 --- a/man/plot.gMAP.Rd +++ b/man/plot.gMAP.Rd @@ -14,7 +14,7 @@ \item{...}{Ignored.} } \value{ -The function returns a list of \code{\link{ggplot}} +The function returns a list of \code{\link[ggplot2:ggplot]{ggplot}} objects. } \description{ diff --git a/man/pos1S.Rd b/man/pos1S.Rd index fb18882..63d9aa9 100644 --- a/man/pos1S.Rd +++ b/man/pos1S.Rd @@ -121,8 +121,8 @@ pos_ia(post_ia) } \seealso{ Other design1S: -\code{\link{decision1S_boundary}()}, \code{\link{decision1S}()}, +\code{\link{decision1S_boundary}()}, \code{\link{oc1S}()} } \concept{design1S} diff --git a/man/pos2S.Rd b/man/pos2S.Rd index 4e3f026..4486039 100644 --- a/man/pos2S.Rd +++ b/man/pos2S.Rd @@ -155,8 +155,8 @@ pos_final(postP_interim, postT_interim) } \seealso{ Other design2S: -\code{\link{decision2S_boundary}()}, \code{\link{decision2S}()}, +\code{\link{decision2S_boundary}()}, \code{\link{oc2S}()} } \concept{design2S} diff --git a/man/predict.gMAP.Rd b/man/predict.gMAP.Rd index 2c46d1a..c87e32d 100644 --- a/man/predict.gMAP.Rd +++ b/man/predict.gMAP.Rd @@ -89,7 +89,6 @@ summary(pred_cov) # obtain a prediction for new data with specific covariates pred_new <- predict(map, data.frame(country="CH", study=12)) pred_new - ## Recover user set sampling defaults options(.user_mc_options) diff --git a/tools/make-ds.R b/tools/make-ds.R index 200cf30..66911bd 100644 --- a/tools/make-ds.R +++ b/tools/make-ds.R @@ -43,7 +43,7 @@ make_internal_ds <- function() { calibration_meta["MD5"] <- vals["MD5"] pkg_create_date <- Sys.time() - pkg_sha <- "a0c573a" + pkg_sha <- "ff4fcab" if (gsub("\\$", "", pkg_sha) == "Format:%h") { pkg_sha <- system("git rev-parse --short HEAD", intern=TRUE)