diff --git a/CITATION.cff b/CITATION.cff index 3163d175..20b9a6b7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -8,7 +8,7 @@ message: 'To cite package "multinma" in publications use:' type: software license: GPL-3.0-only title: 'multinma: Bayesian Network Meta-Analysis of Individual and Aggregate Data' -version: 0.5.1.9000 +version: 0.6.0 doi: 10.5281/zenodo.3904454 abstract: Network meta-analysis and network meta-regression models for aggregate data, individual patient data, and mixtures of both individual and aggregate data using @@ -28,7 +28,7 @@ preferred-citation: email: david.phillippo@bristol.ac.uk orcid: https://orcid.org/0000-0003-2672-7841 year: '2023' - notes: R package version 0.5.1.9000 + notes: R package version 0.6.0 url: https://dmphillippo.github.io/multinma/ doi: 10.5281/zenodo.3904454 repository: https://CRAN.R-project.org/package=multinma @@ -80,7 +80,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing version: '>= 3.4.0' @@ -92,7 +92,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing - type: software @@ -103,7 +103,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing - type: software @@ -114,9 +114,20 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing +- type: software + title: survival + abstract: 'survival: Survival Analysis' + notes: Imports + url: https://github.com/therneau/survival + repository: https://CRAN.R-project.org/package=survival + authors: + - family-names: Therneau + given-names: Terry M + email: therneau.terry@mayo.edu + year: '2024' - type: software title: Rcpp abstract: 'Rcpp: Seamless R and C++ Integration' @@ -142,7 +153,7 @@ references: given-names: Douglas - family-names: Chambers given-names: John - year: '2023' + year: '2024' version: '>= 0.12.0' - type: software title: RcppParallel @@ -164,7 +175,7 @@ references: - family-names: Geelnard given-names: Marcus - name: Intel - year: '2023' + year: '2024' version: '>= 5.0.1' - type: software title: rstan @@ -182,11 +193,18 @@ references: - family-names: Goodrich given-names: Ben email: benjamin.goodrich@columbia.edu + - family-names: Johnson + given-names: Andrew + email: andrew.johnson@arjohnsonau.com - family-names: Weber given-names: Sebastian email: sdw.post@waebers.de - year: '2023' - version: '>= 2.19.2' + - family-names: Badr + given-names: Hamada S. + email: badr@jhu.edu + orcid: https://orcid.org/0000-0002-9808-2344 + year: '2024' + version: '>= 2.26.0' - type: software title: rstantools abstract: 'rstantools: Tools for Developing R Packages Interfacing with ''Stan''' @@ -205,7 +223,7 @@ references: email: mlysy@uwaterloo.ca - family-names: Johnson given-names: Andrew - year: '2023' + year: '2024' version: '>= 2.0.0' - type: software title: Rdpack @@ -217,7 +235,7 @@ references: - family-names: Boshnakov given-names: Georgi N. email: georgi.boshnakov@manchester.ac.uk - year: '2023' + year: '2024' version: '>= 0.7' - type: software title: tibble @@ -233,7 +251,7 @@ references: - family-names: Wickham given-names: Hadley email: hadley@rstudio.com - year: '2023' + year: '2024' version: '>= 2.1.3' - type: software title: dplyr @@ -258,7 +276,7 @@ references: given-names: Davis email: davis@posit.co orcid: https://orcid.org/0000-0003-4777-038X - year: '2023' + year: '2024' version: '>= 1.0.0' - type: software title: rlang @@ -273,7 +291,7 @@ references: - family-names: Wickham given-names: Hadley email: hadley@posit.co - year: '2023' + year: '2024' - type: software title: purrr abstract: 'purrr: Functional Programming Tools' @@ -288,7 +306,7 @@ references: - family-names: Henry given-names: Lionel email: lionel@rstudio.com - year: '2023' + year: '2024' - type: software title: forcats abstract: 'forcats: Tools for Working with Categorical Variables (Factors)' @@ -299,7 +317,7 @@ references: - family-names: Wickham given-names: Hadley email: hadley@rstudio.com - year: '2023' + year: '2024' - type: software title: glue abstract: 'glue: Interpreted String Literals' @@ -314,29 +332,28 @@ references: given-names: Jennifer email: jenny@rstudio.com orcid: https://orcid.org/0000-0002-6983-2759 - year: '2023' + year: '2024' - type: software title: randtoolbox abstract: 'randtoolbox: Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests' notes: Imports - url: https://r-forge.r-project.org/projects/rmetrics/ repository: https://CRAN.R-project.org/package=randtoolbox authors: - family-names: Chalabi - given-names: R code by Yohan + given-names: R port by Yohan - family-names: Dutang given-names: Christophe - family-names: Savicky given-names: Petr - - family-names: Torus - given-names: Diethelm Wuertz; C code of - - name: Halton - - family-names: Dutang - given-names: Sobol sequences by Christophe - - family-names: Saito. - given-names: Mutsuo - year: '2023' + - family-names: Matsumoto + given-names: Diethelm Wuertz with some underlying C codes of the SFMT algorithm + from M. + - family-names: Saito + given-names: M. + - family-names: Knuth. + given-names: the Knuth-TAOCP RNG from D. + year: '2024' - type: software title: copula abstract: 'copula: Multivariate Dependence with Copulas' @@ -360,7 +377,7 @@ references: given-names: Jun email: jun.yan@uconn.edu orcid: https://orcid.org/0000-0003-4401-7296 - year: '2023' + year: '2024' - type: software title: tidyr abstract: 'tidyr: Tidy Messy Data' @@ -376,7 +393,7 @@ references: email: davis@posit.co - family-names: Girlich given-names: Maximilian - year: '2023' + year: '2024' version: '>= 1.0.0' - type: software title: stringr @@ -388,7 +405,7 @@ references: - family-names: Wickham given-names: Hadley email: hadley@rstudio.com - year: '2023' + year: '2024' - type: software title: Matrix abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods' @@ -406,7 +423,7 @@ references: - family-names: Jagan given-names: Mikael orcid: https://orcid.org/0000-0002-3542-2938 - year: '2023' + year: '2024' - type: software title: igraph abstract: 'igraph: Network Analysis and Visualization' @@ -433,7 +450,7 @@ references: - family-names: Müller given-names: Kirill email: kirill@cynkra.com - year: '2023' + year: '2024' - type: software title: ggraph abstract: 'ggraph: An Implementation of Grammar of Graphics for Graphs and Networks' @@ -445,7 +462,7 @@ references: given-names: Thomas Lin email: thomasp85@gmail.com orcid: https://orcid.org/0000-0002-5147-4711 - year: '2023' + year: '2024' - type: software title: ggplot2 abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics' @@ -480,7 +497,7 @@ references: - family-names: Dunnington given-names: Dewey orcid: https://orcid.org/0000-0002-9415-4582 - year: '2023' + year: '2024' version: '>= 3.3.0' - type: software title: ggdist @@ -492,7 +509,7 @@ references: - family-names: Kay given-names: Matthew email: mjskay@northwestern.edu - year: '2023' + year: '2024' version: '>= 2.1.1' - type: software title: truncdist @@ -506,7 +523,7 @@ references: - family-names: Nadarajah given-names: Saralees email: saralees.nadarajah@manchester.ac.uk - year: '2023' + year: '2024' - type: software title: bayesplot abstract: 'bayesplot: Plotting for Bayesian Models' @@ -519,7 +536,7 @@ references: email: jsg2201@columbia.edu - family-names: Mahr given-names: Tristan - year: '2023' + year: '2024' - type: software title: BH abstract: 'BH: Boost C++ Header Files' @@ -533,7 +550,7 @@ references: given-names: John W. - family-names: Kane given-names: Michael J. - year: '2023' + year: '2024' version: '>= 1.66.0' - type: software title: RcppEigen @@ -551,29 +568,8 @@ references: given-names: Romain - family-names: Eigen given-names: Yixuan Qiu; the authors of Eigen for the included version of - year: '2023' + year: '2024' version: '>= 0.3.3.3.0' -- type: software - title: rstan - abstract: 'rstan: R Interface to Stan' - notes: Imports - url: https://mc-stan.org/rstan/ - repository: https://CRAN.R-project.org/package=rstan - authors: - - family-names: Guo - given-names: Jiqiang - email: guojq28@gmail.com - - family-names: Gabry - given-names: Jonah - email: jsg2201@columbia.edu - - family-names: Goodrich - given-names: Ben - email: benjamin.goodrich@columbia.edu - - family-names: Weber - given-names: Sebastian - email: sdw.post@waebers.de - year: '2023' - version: '>= 2.18.1' - type: software title: StanHeaders abstract: 'StanHeaders: C++ Header Files for Stan' @@ -626,8 +622,12 @@ references: given-names: Michael - family-names: Gao given-names: Yuanjun - year: '2023' - version: '>= 2.18.0' + - family-names: Badr + given-names: Hamada S. + email: badr@jhu.edu + orcid: https://orcid.org/0000-0002-9808-2344 + year: '2024' + version: '>= 2.26.0' - type: software title: testthat abstract: 'testthat: Unit Testing for R' @@ -638,7 +638,7 @@ references: - family-names: Wickham given-names: Hadley email: hadley@posit.co - year: '2023' + year: '2024' version: '>= 2.1.0' - type: software title: withr @@ -663,7 +663,7 @@ references: email: hadley@rstudio.com - family-names: Chang given-names: Winston - year: '2023' + year: '2024' - type: software title: knitr abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R' @@ -675,7 +675,7 @@ references: given-names: Yihui email: xie@yihui.name orcid: https://orcid.org/0000-0003-0645-5666 - year: '2023' + year: '2024' - type: software title: rmarkdown abstract: 'rmarkdown: Dynamic Documents for R' @@ -718,7 +718,7 @@ references: given-names: Richard email: rich@posit.co orcid: https://orcid.org/0000-0003-3925-190X - year: '2023' + year: '2024' - type: software title: parallel abstract: 'R: A Language and Environment for Statistical Computing' @@ -727,7 +727,7 @@ references: - name: R Core Team location: name: Vienna, Austria - year: '2023' + year: '2024' institution: name: R Foundation for Statistical Computing - type: software @@ -740,7 +740,7 @@ references: - family-names: Bengtsson given-names: Henrik email: henrikb@braju.com - year: '2023' + year: '2024' - type: software title: rprojroot abstract: 'rprojroot: Finding Files in Project Subdirectories' @@ -752,7 +752,7 @@ references: given-names: Kirill email: krlmlr+r@mailbox.org orcid: https://orcid.org/0000-0002-1416-3412 - year: '2023' + year: '2024' - type: software title: loo abstract: 'loo: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models' @@ -776,7 +776,7 @@ references: given-names: Topi - family-names: Gelman given-names: Andrew - year: '2023' + year: '2024' version: '>= 2.0.0' - type: software title: logitnorm @@ -786,7 +786,7 @@ references: authors: - family-names: Wutzler given-names: Thomas - year: '2023' + year: '2024' - type: software title: crayon abstract: 'crayon: Colored Terminal Output' @@ -797,7 +797,7 @@ references: - family-names: Csárdi given-names: Gábor email: csardi.gabor@gmail.com - year: '2023' + year: '2024' - type: software title: tidygraph abstract: 'tidygraph: A Tidy API for Graph Manipulation' @@ -809,7 +809,7 @@ references: given-names: Thomas Lin email: thomasp85@gmail.com orcid: https://orcid.org/0000-0002-5147-4711 - year: '2023' + year: '2024' - type: software title: pkgdown abstract: 'pkgdown: Make Static HTML Documentation for a Package' @@ -827,4 +827,48 @@ references: - family-names: Salmon given-names: Maëlle orcid: https://orcid.org/0000-0002-2815-0399 - year: '2023' + year: '2024' +- type: software + title: splines2 + abstract: 'splines2: Regression Spline Functions and Classes' + notes: Suggests + url: https://wwenjie.org/splines2 + repository: https://CRAN.R-project.org/package=splines2 + authors: + - family-names: Wang + given-names: Wenjie + email: wang@wwenjie.org + orcid: https://orcid.org/0000-0003-0363-3180 + - family-names: Yan + given-names: Jun + orcid: https://orcid.org/0000-0003-4401-7296 + year: '2024' + version: '>= 0.5.0' +- type: software + title: flexsurv + abstract: 'flexsurv: Flexible Parametric Survival and Multi-State Models' + notes: Suggests + url: https://github.com/chjackson/flexsurv-dev + repository: https://CRAN.R-project.org/package=flexsurv + authors: + - family-names: Jackson + given-names: Christopher + email: chris.jackson@mrc-bsu.cam.ac.uk + year: '2024' +- type: software + title: rstpm2 + abstract: 'rstpm2: Smooth Survival Models, Including Generalized Survival Models' + notes: Suggests + url: https://github.com/mclements/rstpm2 + repository: https://CRAN.R-project.org/package=rstpm2 + authors: + - family-names: Clements + given-names: Mark + email: mark.clements@ki.se + - family-names: Liu + given-names: Xing-Rong + email: xingrong.liu@ki.se + - family-names: Christoffersen + given-names: Benjamin + email: benjamin.christoffersen@ki.se + year: '2024' diff --git a/DESCRIPTION b/DESCRIPTION index aa59507d..0a0c2eeb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: multinma Title: Bayesian Network Meta-Analysis of Individual and Aggregate Data -Version: 0.5.1.9007 +Version: 0.6.0 Authors@R: person(given = c("David", "M."), family = "Phillippo", diff --git a/NEWS.md b/NEWS.md index 528f0ffe..1e80270b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# multinma 0.5.1.9000 +# multinma 0.6.0 ## Feature: Survival/time-to-event models are now supported diff --git a/README.md b/README.md index 1659236e..096b55d9 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,7 @@ papers: The `multinma` package can be cited as follows: > Phillippo, D. M. (2024). *multinma: Bayesian Network Meta-Analysis of -> Individual and Aggregate Data*. R package version 0.5.1.9007, doi: +> Individual and Aggregate Data*. R package version 0.6.0, doi: > [10.5281/zenodo.3904454](https://doi.org/10.5281/zenodo.3904454). When fitting ML-NMR models, please cite the methods paper: diff --git a/cran-comments.md b/cran-comments.md index e06bcb8e..78942958 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,11 +1,12 @@ -This update fixes runtime errors in donttest examples (caused by latest -StanHeaders), as per email from CRAN. +This release ensures compatibility with the forthcoming update to rstan and +StanHeaders, as well as providing extensive new features, improvements, and +fixes. ## Test environments -* local R installation (Windows 10), R 4.3.0 +* local R installation (Windows 10), R 4.3.2 * win-builder (release, devel) -* Ubuntu 22.04.2 on GitHub Actions (release, devel, oldrel) -* Mac OS 12.6.5 on GitHub Actions (release) +* Ubuntu 22.04.3 on GitHub Actions (release, devel, oldrel) +* Mac OS 12.7.2 on GitHub Actions (release) * Windows Server 2022 10.0.20348 on GitHub Actions (release) ## R CMD check results @@ -13,15 +14,16 @@ StanHeaders), as per email from CRAN. 0 errors | 0 warnings | 3 notes * checking package dependencies ... NOTE - Imports includes 22 non-default packages. + Imports includes 23 non-default packages. -* checking installed package size ... - installed size is 12.3Mb +* checking installed package size ... NOTE + installed size is 18.2Mb sub-directories of 1Mb or more: - doc 4.0Mb - libs 6.9Mb + R 1.6Mb + doc 4.3Mb + libs 11.6Mb -The docs directory contains 12 html vignettes demonstrating full analyses using +The docs directory contains 13 html vignettes demonstrating full analyses using the package. * checking for GNU extensions in Makefiles ... NOTE