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2024-11-20

There are updates to six MetrumRG-developed packages:

  • mpn.scorecard: Collects various measures of quality and risk-of-use for an R package and formats them into a "scorecard" report for assessment.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • pmparams: Package for generating clear, well-formatted parameter tables to report NONMEM model results.

  • pmplots: Create exploratory and diagnostic plots commonly used in pharmacometrics in a highly efficient manner.

  • pmtables: Summarize data sets and create publication-quality tables for inclusion in 'tex' documents.

  • review: Package for managing QC review logs in subversion.

Notable new packages:

  • ECOSolveR: R interface to the Embedded COnic Solver (ECOS), an efficient and robust C library for convex problems.

  • extraDistr: Density, distribution function, quantile function and random generation for a number of univariate and multivariate distributions.

  • IRkernel: Native R Kernel for the Jupyter Notebook.

  • logr: Contains functions to help create log files.

  • pbdZMQ: This package provides high-level R wrapper functions to easily utilize ZeroMQ, a well-known library for high-performance asynchronous messaging.

  • reformulas: Machinery for processing random effect formulas

  • Rmpfr: Arithmetic for arbitrary precision floating point numbers, including transcendental functions.

  • scs: Solves convex cone programs via operator splitting.

  • tidycmprsk: This package wraps the cmprsk package and exports functions for univariate cumulative incidence estimates and competing risk regression.

The packages rxode2et, rxode2parse, and rxode2random have been removed because their functionality has been absorbed into the rxode2 package.

2024-09-23

There are updates to eight MetrumRG-developed packages:

  • bbr: R package for making calls to bbi for running NONMEM and other models. Also manages model metadata, workflow, and run logs.

  • bbr.bayes: Extends bbr for Bayesian modeling. It adds support for running Stan models via the CmdStanR interface and for running NONMEM models with Bayesian estimation methods via bbi.

  • mpn.scorecard: Collects various measures of quality and risk-of-use for an R package and formats them into a "scorecard" report for assessment.

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgmisc: Miscellaneous helpers for getting work done on MetrumRG projects.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • pmplots: Create exploratory and diagnostic plots commonly used in pharmacometrics in a highly efficient manner.

  • pmtables: Summarize data sets and create publication-quality tables for inclusion in 'tex' documents.

Notable new packages:

  • cards: Construct CDISC (Clinical Data Interchange Standards Consortium) compliant Analysis Results Data objects.

  • duckplyr: A drop-in replacement for dplyr, powered by DuckDB for performance.

  • formatters: Framework for rendering complex tables to ASCII, and a set of formatters for transforming values or sets of values into ASCII-ready display strings.

  • ggsurvfit: Ease the creation of time-to-event (i.e. survival) endpoint figures.

  • gridpattern: Provides grid grobs that fill in a user-defined area with various patterns.

  • linpk: Generate concentration-time profiles from linear pharmacokinetic (PK) systems.

  • mmrm: Mixed models for repeated measures (MMRM) are a popular choice for analyzing longitudinal continuous outcomes in randomized clinical trials and beyond.

  • nanoparquet: Self-sufficient reader and writer for flat Parquet files.

  • rtables: Provides a framework for declaring complex multi-level tabulations and then applying them to data.

  • tabulapdf: Bindings for the Tabula Java library, which can extract tables from PDF files.

  • tern: Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.

  • tidytlg: Generate tables, listings, and graphs (TLG) using tidyverse.

The package maptools has been removed. It has been archived on CRAN at the request of the maintainer with the note to "consider using 'sf' or 'terra' instead".

2024-06-12

There are updates to nine MetrumRG-developed packages:

  • mpn.scorecard: Collects various measures of quality and risk-of-use for an R package and formats them into a "scorecard" report for assessment.

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgmisc: Miscellaneous helpers for getting work done on MetrumRG projects.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • pmparams: Package for generating clear, well-formatted parameter tables to report NONMEM model results.

  • pmplots: Create exploratory and diagnostic plots commonly used in pharmacometrics in a highly efficient manner.

  • pmtables: Summarize data sets and create publication-quality tables for inclusion in 'tex' documents.

  • review: Package for managing QC review logs in subversion.

  • yspec: Package for documenting analysis data sets and utilizing data attributes in a modeling and simulation workflow.

Notable new packages:

  • box: A modern module system for R.

  • bsicons: Easily use Bootstrap icons inside Shiny apps and R Markdown documents.

  • collapsibleTree: Interactive tree diagrams created using D3.js.

  • rhino: A framework that supports creating and extending enterprise Shiny applications using best practices.

  • webshot2: Takes screenshots of web pages, including Shiny applications and R Markdown documents.

The package ggstance has been removed because it is superseded by ggplot2 3.3.0 and incompatible with ggplot2 3.5.0 and later.

2024-03-01

This is the first snapshot targeting the upcoming Metworx blueprint release. It aims to be compatible with R 4.2 and 4.3, the two most recent R versions on the upcoming Metworx blueprint. Note, however, that the majority of the packages on this snapshot remain compatible with earlier R versions.

There are updates to eight MetrumRG-developed packages:

  • bbr: R package for making calls to bbi for running NONMEM and

other models. Also manages model metadata, workflow, and run logs.

  • bbr.bayes: Extends bbr for Bayesian modeling. It adds support for running Stan models via the CmdStanR interface and for running NONMEM models with Bayesian estimation methods via bbi.

  • lastdose: Efficient calculation of time after last dose and last dose amount for analysis data sets.

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • mpn.scorecard: Collects various measures of quality and risk-of-use for an R package and formats them into a "scorecard" report for assessment.

  • nmrec: Package for reading records from a NONMEM control stream, parsing and modifying records of interest, and writing the result.

  • pmplots: Create exploratory and diagnostic plots commonly used in pharmacometrics in a highly efficient manner.

Notable new packages:

  • ggh4x: A ggplot2 extension that does a variety of little helpful things.

  • markovchain: Functions and S4 methods to create and manage discrete time Markov chains more easily.

  • rstanemax: Perform sigmoidal Emax model fit using Stan in a formula notation, without writing Stan model code.

The lixoftConnectors package has been removed in favor of the recommended approach of installing the lixoftConnectors package that is bundled with each Monolix installation. Tailored instructions for Metworx are available at https://kb.metworx.com/Users/Tutorials/Monolix/lixoftConnectors/.

The following packages have been removed due to longstanding unaddressed R CMD check issues: RNMGraphics, RNMImport, dummies, mnlogit, tabulizer, and tnam.

2023-12-05

There are updates to four MetrumRG-developed packages:

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • lastdose: Efficient calculation of time after last dose and last dose amount for analysis data sets.

  • review: Functions for managing logs of reviews of subversioned files.

New packages:

  • ggstats: Provides new statistics, new geometries and new positions for ggplot2 and a suite of functions to facilitate the creation of statistical plots.

  • r2rtf: Create production-ready Rich Text Format (RTF) table and figure with flexible format.

2023-10-19

There are updates to three MetrumRG-developed packages:

  • mpn.scorecard: Collects various measures of quality and risk-of-use for an R package and formats them into a "scorecard" report for assessment.

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • review: Functions for managing logs of reviews of subversioned files.

One new package:

  • NMsim: A complete and seamless NONMEM simulation interface from within R.

2023-09-19

Four new MetrumRG-developed packages have been added:

  • bbr.bayes: Extends the bbr package for Bayesian modeling. Initial support has been added for Stan models (powered by cmdstanr). Upcoming releases will extend Stan support and add support for NONMEM Bayes models.

  • mpn.scorecard: Collects various measures of quality and risk-of-use for an R package and formats them into a "scorecard" report for assessment. Leans heavily on the metrics developed by R Validation Hub's riskmetric package.

  • nmrec: Package for reading records from a NONMEM control stream, parsing and modifying records of interest, and writing the result.

  • pmparams: Package for generating clear, well-formatted parameter tables to report NONMEM model results.

There are updates to five MetrumRG-developed packages:

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgmisc: Miscellaneous helpers for getting work done on MetrumRG projects.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • pmforest: Create forest plots.

  • review: Functions for managing logs of reviews of subversioned files (http://subversion.apache.org/).

Other notable new packages:

  • pharmaversesdtm: A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages.

  • riskmetric: Facilities for assessing R packages against a number of metrics to help quantify their robustness.

  • shinyvalidate: Improves the user experience of Shiny apps by helping to provide feedback when required inputs are missing, or input values are not valid.

2023-08-24

There are updates to seven MetrumRG-developed packages:

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrggsave: Package for annotating plots with the name of the generating R script and the name of the output file.

  • mrgmisc: Miscellaneous helpers for getting work done on MetrumRG projects.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • pmplots: Create exploratory and diagnostic plots commonly used in pharmacometrics in a highly efficient manner.

  • pmtables: Summarize data sets and create publication-quality tables for inclusion in 'tex' documents.

  • yspec: Package for documenting analysis data sets and utilizing data attributes in a modeling and simulation workflow.

Three new packages:

  • common: Functions for solving commonly encountered problems while programming in R.

  • fmtr: Functions that can be used to apply formats to data frames or vector.

  • reporter: Package for creating regulatory-style statistical reports.

The package qapply has been removed because it is no longer actively developed or maintained. Consider using future.batchtools instead.

2023-06-29

There are updates to three MetrumRG-developed packages:

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgmisc: Miscellaneous helpers for getting work done on MetrumRG projects.

  • review: Package for managing QC review logs in subversion.

Two new packages:

  • rpsftm: Rank preserving structural failure time models.

  • nonmem2rx: Tool for converting NONMEM models to rxode2 models.

2023-05-14

There are updates to three MetrumRG-developed packages:

  • bbr: R package for making calls to bbi for running NONMEM and other models. Also manages model metadata, workflow, and run logs.

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • review: Package for managing QC review logs in subversion.

Other notable new packages:

  • rintrojs: Package that makes it easy to include step-by-step introductions and clickable hints in a Shiny application.

  • shinytest2: Automated unit testing of Shiny applications through a headless Chromium browser.

The package mrggt has been removed because it is no longer actively developed and was superseded by pmtables (available on MPN since the 2020-08-15 snapshot).

2023-03-13

A new MetrumRG-developed package has been added:

  • simpar: Create parameters for simulation with uncertainty.

There are updates to six MetrumRG-developed packages

  • bbr: R package for making calls to bbi for running NONMEM and other models. Also manages model metadata, workflow, and run logs.

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrggsave: Package for annotating plots with the name of the generating R script and the name of the output file.

  • mrgmisc: Miscellaneous helpers for getting work done on MetrumRG projects.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • review: Package for managing QC review logs in subversion.

Other notable new packages:

  • ggbreak: An implementation of scale functions for setting axis breaks of a 'gg' plot.

  • ggfun: Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).

  • PFIM: Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix

2023-01-25

Updates to three MetrumRG-developed packages:

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • pmplots: Create exploratory and diagnostic plots commonly used in pharmacometrics also in a highly efficient manner.

Two new packages:

  • ggfortify: Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis.

  • ggnewscale: Use multiple fill and color scales in ggplot2.

2022-12-21

Updates to six MetrumRG-developed packages:

  • bbr: R package for making calls to bbi for running NONMEM and other models. Also manages model metadata, workflow, and run logs.

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgmisc: Miscellaneous helpers for getting work done on MetrumRG projects.

  • mrgvalprep: Preprocessing for mrgvalidate.

  • pmforest: Create forest plots.

  • pmtables: Summarize data sets and create publication-quality tables for inclusion in 'tex' documents.

Notable new packages:

  • consort: Package to make it easy to create CONSORT diagrams for the transparent reporting of participant allocation in randomized, controlled clinical trials.

  • NMcalc: Essentials for PK/PD (pharmacokinetics/pharmacodynamics) such as area under the curve, (geometric) coefficient of variation, and other calculations that are not part of base R.

  • quarto: R interface to quarto-cli.

  • shinyFiles: Functionality for client-side navigation of the server side file system in shiny apps.

  • RxODE, nlmixr, and xpose.nlmixr have been replaced by their successors, rxode2 and nlmixr2 along with their suites of underlying dependencies.

    • babelmixr2: Run other estimation and simulation software via the nlmixr2 interface including PKNCA, NONMEM, and Monolix.

    • nlmixr2: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics.

    • nlmixr2data: Datasets for nlmixr2 and rxode2.

    • nlmixr2est: nlmixr2 core estimation routines.

    • nlmixr2extra: Tools to help with common pharmacometric tasks with nlmixr2 models like bootstrapping and covariate selection.

    • nlmixr2lib: This is a model library for nlmixr2.

    • nlmixr2plot: Plotting support for nlmixr2.

    • rxode2: Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models.

    • rxode2et: Event table and support functions needed for rxode2.

    • rxode2ll: Provides the log-likelihoods with gradients from Stan needed for generalized log-likelihood estimation in nlmixr2.

    • rxode2parse: Provides the parsing needed for rxode2.

    • rxode2random: Provides the random number generation (in parallel) needed for rxode2 and nlmixr2.

2022-10-20

Two new MetrumRG-developed packages:

  • mrgda: Run various tests on an NMTRAN dataset to validate it prior to modeling.

  • mrgmisc: Miscellaneous helpers for getting work done on MetrumRG projects. This package was constructed with select functions from two older packages PKPDmisc and metrumrg.

Notable new packages:

  • NMproject: Industrialisation of 'NONMEM' via fully and rapidly reusable model development 'workflows' entirely within 'RStudio'.

  • templater: A framework for safe, parallel processing of templated reports, allowing the same .Rmd template to be used, with different inputs, to create many reports.

Compatibility note:

  • The emmeans package was updated to version 1.8.0 in the 2022-08-31 snapshot. Unfortunately, emmeans 1.8.0 requires R 4.1 or later, while the aim is for MPN packages to be compatible with R 4.0 or later. In this snapshot, emmeans has been restored to version 1.7.4-1 to retain compatibility with R 4.0.

2022-08-31

Updates to three MetrumRG-developed packages:

  • bbr: R package for making calls to bbi for running NONMEM and other models. Also manages model metadata, workflow, and run logs.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • pmtables: Summarize data sets and create publication-quality tables for inclusion in TeX documents.

Notable new packages:

  • gnm: Functions to specify and fit generalized nonlinear models.

  • PropCIs: Computes two-sample confidence intervals for single, paired and independent proportions.

  • tracee: Simple but crucial functionality related to creation of reproducible and traceable output (plots) back to code.

  • assertr: Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly.

  • clinPK: Calculates equations commonly used in clinical pharmacokinetics and clinical pharmacology.

  • RhpcBLASctl: Control the number of threads on BLAS.

  • Rsmlx: Provides methods for model building and model evaluation of mixed effects models using Monolix.

2022-06-15

While there have not been any MetrumRG tool upgrades since the last release, this release includes updates to 116 packages, along with the addition of writexl, which is a package that wraps the libxlsxwriter library to create files in Microsoft Excel xlsx format.

2022-05-16

Updates to five MetrumRG-developed packages:

  • mrgsolve: mrgsolve is an R package for simulation from hierarchical, ordinary differential equation (ODE) based models typically employed in drug development.

  • pmtables: pmtables is designed to create summary tables commonly used in pharmacometrics in a highly efficient manner.

  • pmplots: pmplots creates exploratory and diagnostic plots commonly used in pharmacometrics also in a highly efficient manner.

  • yspec: yspec documents analysis data sets and utilizes data attributes in a modeling and simulation workflow. (Very helpful in leveraging the efficiency of pmtables,pmplots, & pmforest)

  • lastdose: lastdose is a package that calculates the time since and amount of the last dose for a NM-TRAN (NonMem TRANslator) data set.

2022-03-21

Two new MetrumRG-developed packages:

  • paquet: paquet helps create and manage large amounts of data that are generated through simulations or processes like Bayesian modeling. It is particularly useful for processes that use parallel computing to generate a large amount of data in chunks or "packets." Simulations done with mrgsolve are an example of this, and were one of the primary motivations for developing this package.

  • pmforest: package for producing forest plots: graphical summaries of covariate effects or covariate-dependent predictions in a pharmacometric model. It is designed to integrate well with other MetrumRG-developed packages like mrgsolve and bbr.

Updates to three MetrumRG-developed packages:

  • bbr: R package for making calls to bbi for running NONMEM and other models. Also manages model metadata, workflow, and run logs.

  • mrgsolve: Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

  • pmtables: Summarize data sets and create publication-quality tables for inclusion in TeX documents.

  • pmplots: pmplots creates exploratory and diagnostic plots commonly used in pharmacometrics also in a highly efficient manner.

  • yspec: yspec documents analysis data sets and utilizes data attributes in a modeling and simulation workflow. (Very helpful in leveraging the efficiency of pmtables,pmplots, & pmforest)

Notable new packages:

  • admiral: A toolbox for programming Clinical Analysis Data Model data sets, which are a mandatory part of any New Drug or Biologics License Application submitted to the FDA.

  • boxr: R interface for accessing box.com.

  • campsis: PK/PD simulation platform based on RxODE and mrgsolve.

  • RBesT: Tools to support Bayesian evidence synthesis.