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  • RxODE, nlmixr, and xpose.nlmixr have been replaced by their successors, rxode2 and nlmixr2 along with their suites of underlying dependencies.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