{ "_id": "6a16c7b4acfb0bcc41d88d37", "Package": "MBNMAtime", "Type": "Package", "Title": "Run Time-Course Model-Based Network Meta-Analysis (MBNMA) Models", "Version": "0.2.6", "Language": "en-GB", "Date": "2025-01-28", "Authors@R": "c(person(\"Hugo\", \"Pedder\", \nemail = \"hugopedder@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7813-3749\")))", "Maintainer": "Hugo Pedder ", "Description": "Fits Bayesian time-course models for model-based network\nmeta-analysis (MBNMA) that allows inclusion of multiple\ntime-points from studies. Repeated measures over time are\naccounted for within studies by applying different time-course\nfunctions, following the method of Pedder et al. (2019)\n. The method allows synthesis of studies\nwith multiple follow-up measurements that can account for\ntime-course for a single or multiple treatment comparisons.\nSeveral general time-course functions are provided; others may\nbe added by the user. Various characteristics can be flexibly\nadded to the models, such as correlation between time points\nand shared class effects. The consistency of direct and\nindirect evidence in the network can be assessed using\nunrelated mean effects models and/or by node-splitting.", "License": "GPL-3", "SystemRequirements": "JAGS (>= 4.3.0) (http://mcmc-jags.sourceforge.net)", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr, rmarkdown", "RdMacros": "Rdpack", "URL": "https://hugaped.github.io/MBNMAtime/", "Config/pak/sysreqs": "libglpk-dev jags libicu-dev libpng-dev libxml2-dev", "Repository": "https://hugaped.r-universe.dev", "Date/Publication": "2025-02-06 19:05:41 UTC", "RemoteUrl": "https://github.com/hugaped/mbnmatime", "RemoteRef": "HEAD", "RemoteSha": "603ac46124fddaf83e10efa8a7953aa54eeb468f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 10:26:43 UTC", "User": "root" }, "Author": "Hugo Pedder [aut, cre] (ORCID: )", "MD5sum": "63fa6e10ede94be1a7362049273ead30", "_user": "hugaped", "_type": "src", "_file": 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[ "get.model.vals" ] }, { "page": "get.prior", "title": "Get current priors from JAGS model code", "topics": [ "get.prior" ] }, { "page": "get.relative", "title": "Calculates relative effects/mean differences at a particular time-point", "topics": [ "get.relative" ] }, { "page": "getjagsdata", "title": "Prepares data for JAGS", "topics": [ "getjagsdata" ] }, { "page": "getnmadata", "title": "Prepares NMA data for JAGS", "topics": [ "getnmadata" ] }, { "page": "goutSUA_CFB", "title": "Studies of treatments for reducing serum uric acid in patients with gout", "topics": [ "goutSUA_CFB" ] }, { "page": "goutSUA_CFBcomb", "title": "Studies of combined treatments for reducing serum uric acid in patients with gout", "topics": [ "goutSUA_CFBcomb" ] }, { "page": "hyalarthritis", "title": "Studies comparing hyaluronan (HA)–based viscosupplements for osteoarthritis", "topics": [ "hyalarthritis" ] }, { "page": "inconsistency.loops", "title": "Identify comparisons in loops that fulfil criteria for 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node-splitting on a MBNMA time-course network", "topics": [ "mb.nodesplit", "plot.nodesplit" ] }, { "page": "predict.mbnma", "title": "Predict effects over time in a given population based on MBNMA time-course models", "topics": [ "predict.mbnma" ] }, { "page": "print.mb.network", "title": "Print mb.network information to the console", "topics": [ "print.mb.network" ] }, { "page": "print.mb.predict", "title": "Print summary information from an mb.predict object", "topics": [ "print.mb.predict" ] }, { "page": "print.mb.rank", "title": "Prints a summary of rankings for each parameter", "topics": [ "print.mb.rank" ] }, { "page": "print.nodesplit", "title": "Prints basic results from a node-split to the console", "topics": [ "print.nodesplit" ] }, { "page": "print.relative.array", "title": "Print posterior medians (95% credible intervals) for table of relative effects/mean differences between treatments/classes", "topics": [ "print.relative.array" ] }, { "page": "radian.rescale", "title": 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"remove.loops", "title": "Removes any loops from MBNMA model JAGS code that do not contain any expressions", "topics": [ "remove.loops" ] }, { "page": "replace.prior", "title": "Replace original priors in an MBNMA model with new priors", "topics": [ "replace.prior" ] }, { "page": "summary.mb.network", "title": "Print summary mb.network information to the console", "topics": [ "summary.mb.network" ] }, { "page": "summary.mb.predict", "title": "Prints summary of mb.predict object", "topics": [ "summary.mb.predict" ] }, { "page": "summary.mbnma", "title": "Print summary MBNMA results to the console", "topics": [ "summary.mbnma" ] }, { "page": "summary.nodesplit", "title": "Takes node-split results and produces summary data frame", "topics": [ "summary.nodesplit" ] }, { "page": "temax", "title": "Emax time-course function", "topics": [ "temax" ] }, { "page": "tfpoly", "title": "Fractional polynomial time-course function", "topics": [ "tfpoly" ] }, { "page": "timeplot", "title": "Plot raw responses over time by treatment or class", "topics": [ "timeplot" ] }, { "page": "titp", "title": "Integrated Two-Component Prediction (ITP) function", "topics": [ "titp" ] }, { "page": "tloglin", "title": "Log-linear (exponential) time-course function", "topics": [ "tloglin" ] }, { "page": "tpoly", "title": "Polynomial time-course function", "topics": [ "tpoly" ] }, { "page": "tspline", "title": "Spline time-course functions", "topics": [ "tspline" ] }, { "page": "tuser", "title": "User-defined time-course function", "topics": [ "tuser" ] }, { "page": "write.beta", "title": "Adds sections of JAGS code for an MBNMA model that correspond to beta parameters", "topics": [ "write.beta" ] }, { "page": "write.check", "title": "Checks validity of arguments for mb.write", "topics": [ "write.check" ] }, { "page": "write.cor", "title": "Adds correlation between time-course relative effects", "topics": [ "write.cor" ] }, { "page": "write.likelihood", "title": "Adds sections of JAGS code for an MBNMA model that correspond to the likelihood", "topics": [ "write.likelihood" ] }, { "page": "write.model", "title": "Write the basic JAGS model code for MBNMA to which other lines of model code can be added", "topics": [ "write.model" ] }, { "page": "write.ref.synth", "title": "Write MBNMA time-course models JAGS code for synthesis of studies investigating reference treatment", "topics": [ "write.ref.synth" ] }, { "page": "write.timecourse", "title": "Adds sections of JAGS code for an MBNMA model that correspond to alpha parameters", "topics": [ "write.timecourse" ] } ], "_readme": "https://github.com/hugaped/mbnmatime/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "boot", "checkmate", "cli", "coda", "cpp11", "crayon", "distributional", "dplyr", "evaluate", "farver", "generics", "ggdist", "ggplot2", "glue", "gridExtra", "gtable", "highr", "igraph", "isoband", "knitr", "labeling", "lattice", "lifecycle", "lspline", "magrittr", "Matrix", "numDeriv", "pillar", "pkgconfig", 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It is a program for analysis of\nBayesian hierarchical models using Markov Chain Monte Carlo (MCMC)\nsimulation not wholly unlike BUGS.\n\nJAGS was written with three aims in mind:\n* To have an engine for the BUGS language that runs on Unix\n* To be extensible, allowing users to write their own functions,\ndistributions and samplers.\n* To be a plaftorm for experimentation with ideas in Bayesian modelling\n\nThis package contains the 'jags' binary as well as the associated\nshared library modules loaded by the binary." }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "predictions-5.Rmd", "filename": "predictions-5.html", "title": "Calculating model predictions", "author": "Hugo Pedder", "engine": "knitr::rmarkdown", "headings": [ "Prediction", "E0 (time=0)", "Baseline (reference treatment) 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"title": "MBNMAtime: Package Overview", "author": "Hugo Pedder", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Workflow within the package", "Datasets Included in the Package", "Pain relief in osteoarthritis", "Alogliptin for lowering blood glucose concentration in type II diabetes", "Tiotropium, Aclidinium and Placebo for maintenance treatment of moderate to severe chronic obstructive pulmonary disease", "Body weight reduction in obesity patients", "Serum uric acid concentration in gout", "References" ], "created": "2023-08-08 15:57:12", "modified": "2023-08-08 15:57:12", "commits": 1 }, { "source": "outputs-4.Rmd", "filename": "outputs-4.html", "title": "Outputs: Relative effects, forest plots and rankings", "author": "Hugo Pedder", "engine": "knitr::rmarkdown", "headings": [ "Estimating relatived effects between treatments at a specified time-point", "Fitted values", "Forest plots", "rank(): Ranking", "References" ], "created": "2023-08-08 15:57:12", "modified": 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