R-universe search: needs:stringfish

qsbase

qs:Quick Serialization of R Objects

Provides functions for quickly writing and reading any R object to and from disk.

Maintained by Travers Ching. Last updated 9 days ago.

compression data-storage encoding serialization libzstd lz4 cpp

417 stars 14.05 score 2.5k scripts 51 dependents

nlmixr2

rxode2:Facilities for Simulating from ODE-Based Models

Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.

Maintained by Matthew L. Fidler. Last updated 1 months ago.

fortran openblas cpp openmp

40 stars 11.24 score 220 scripts 13 dependents

tidyverse

multidplyr:A Multi-Process 'dplyr' Backend

Partition a data frame across multiple worker processes to provide simple multicore parallelism.

Maintained by Hadley Wickham. Last updated 8 months ago.

dplyr multiprocess

645 stars 10.82 score 460 scripts 5 dependents

predictiveecology

SpaDES.core:Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow. The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies. The suggested package 'NLMR' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Maintained by Eliot J B McIntire. Last updated 1 months ago.

discrete-events-simulations simulation-framework simulation-modeling

10 stars 10.61 score 142 scripts 6 dependents

predictiveecology

SpaDES:Develop and Run Spatially Explicit Discrete Event Simulation Models

Metapackage for implementing a variety of event-based models, with a focus on spatially explicit models. These include raster-based, event-based, and agent-based models. The core simulation components (provided by 'SpaDES.core') are built upon a discrete event simulation (DES; see Matloff (2011) ch 7.8.3 <https://nostarch.com/artofr.htm>) framework that facilitates modularity, and easily enables the user to include additional functionality by running user-built simulation modules (see also 'SpaDES.tools'). Included are numerous tools to visualize rasters and other maps (via 'quickPlot'), and caching methods for reproducible simulations (via 'reproducible'). Tools for running simulation experiments are provided by 'SpaDES.experiment'. Additional functionality is provided by the 'SpaDES.addins' and 'SpaDES.shiny' packages.

Maintained by Alex M Chubaty. Last updated 4 months ago.

simulation-framework simulation-toolkit spatially-explicit-models

55 stars 8.93 score 227 scripts

geco-bern

rsofun:The P-Model and BiomeE Modelling Framework

Implements the Simulating Optimal FUNctioning framework for site-scale simulations of ecosystem processes, including model calibration. It contains 'Fortran 90' modules for the P-model (Stocker et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH (Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>) and BiomeE (Weng et al. (2015) <doi:10.5194/bg-12-2655-2015>).

Maintained by Benjamin Stocker. Last updated 2 days ago.

dgvm growth modeling p-model simulation vegetation-dynamics fortran

27 stars 8.85 score 119 scripts

nlmixr2

nlmixr2:Nonlinear Mixed Effects Models in Population PK/PD

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).

Maintained by Matthew Fidler. Last updated 1 months ago.

52 stars 8.38 score 120 scripts 3 dependents

nlmixr2

nlmixr2est:Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).

Maintained by Matthew Fidler. Last updated 12 days ago.

openblas cpp openmp

9 stars 8.33 score 26 scripts 9 dependents

globalecologylab

poems:Pattern-Oriented Ensemble Modeling System

A framework of interoperable R6 classes (Chang, 2020, <https://CRAN.R-project.org/package=R6>) for building ensembles of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,2005, <doi:10.1126/science.1116681>). The package includes classes for encapsulating and generating model parameters, and managing the POM workflow. The workflow includes: model setup; generating model parameters via Latin hyper-cube sampling (Iman & Conover, 1980, <doi:10.1080/03610928008827996>); running multiple sampled model simulations; collating summary results; and validating and selecting an ensemble of models that best match known patterns. By default, model validation and selection utilizes an approximate Bayesian computation (ABC) approach (Beaumont et al., 2002, <doi:10.1093/genetics/162.4.2025>), although alternative user-defined functionality could be employed. The package includes a spatially explicit demographic population model simulation engine, which incorporates default functionality for density dependence, correlated environmental stochasticity, stage-based transitions, and distance-based dispersal. The user may customize the simulator by defining functionality for translocations, harvesting, mortality, and other processes, as well as defining the sequence order for the simulator processes. The framework could also be adapted for use with other model simulators by utilizing its extendable (inheritable) base classes.

Maintained by July Pilowsky. Last updated 1 months ago.

biogeography population-model process-based

10 stars 8.05 score 59 scripts 2 dependents

mrc-ide

naomi:Naomi Model for Subnational HIV Estimates

This package implements the Naomi model for subnational HIV estimates.

Maintained by Jeff Eaton. Last updated 19 days ago.

cpp

9 stars 7.74 score 54 scripts 2 dependents

qsbase

qs2:Efficient Serialization of R Objects

Streamlines and accelerates the process of saving and loading R objects, improving speed and compression compared to other methods. The package provides two compression formats: the 'qs2' format, which uses R serialization via the C API while optimizing compression and disk I/O, and the 'qdata' format, featuring custom serialization for slightly faster performance and better compression. Additionally, the 'qs2' format can be directly converted to the standard 'RDS' format, ensuring long-term compatibility with future versions of R.

Maintained by Travers Ching. Last updated 23 days ago.

compression data-storage serialization cpp

15 stars 7.57 score 25 scripts 2 dependents

ropensci

jagstargets:Targets for JAGS Pipelines

Bayesian data analysis usually incurs long runtimes and cumbersome custom code. A pipeline toolkit tailored to Bayesian statisticians, the 'jagstargets' R package is leverages 'targets' and 'R2jags' to ease this burden. 'jagstargets' makes it super easy to set up scalable JAGS pipelines that automatically parallelize the computation and skip expensive steps when the results are already up to date. Minimal custom code is required, and there is no need to manually configure branching, so usage is much easier than 'targets' alone. For the underlying methodology, please refer to the documentation of 'targets' <doi:10.21105/joss.02959> and 'JAGS' (Plummer 2003) <https://www.r-project.org/conferences/DSC-2003/Proceedings/Plummer.pdf>.

Maintained by William Michael Landau. Last updated 4 months ago.

bayesian high-performance-computing jags make r-targetopia reproducibility rjags statistics targets cpp

10 stars 6.95 score 32 scripts

ropensci

stantargets:Targets for Stan Workflows

Bayesian data analysis usually incurs long runtimes and cumbersome custom code. A pipeline toolkit tailored to Bayesian statisticians, the 'stantargets' R package leverages 'targets' and 'cmdstanr' to ease these burdens. 'stantargets' makes it super easy to set up scalable Stan pipelines that automatically parallelize the computation and skip expensive steps when the results are already up to date. Minimal custom code is required, and there is no need to manually configure branching, so usage is much easier than 'targets' alone. 'stantargets' can access all of 'cmdstanr''s major algorithms (MCMC, variational Bayes, and optimization) and it supports both single-fit workflows and multi-rep simulation studies. For the statistical methodology, please refer to 'Stan' documentation (Stan Development Team 2020) <https://mc-stan.org/>.

Maintained by William Michael Landau. Last updated 2 months ago.

bayesian high-performance-computing make r-targetopia reproducibility stan statistics targets

49 stars 6.85 score 180 scripts

cont-limno

LAGOSNE:Interface to the Lake Multi-Scaled Geospatial and Temporal Database

Client for programmatic access to the Lake Multi-scaled Geospatial and Temporal database <https://lagoslakes.org>, with functions for accessing lake water quality and ecological context data for the US.

Maintained by Jemma Stachelek. Last updated 2 years ago.

ecology geoscience limnology water-quality

15 stars 6.77 score 98 scripts

richardhooijmaijers

shinyMixR:Interactive 'shiny' Dashboard for 'nlmixr2'

An R shiny user interface for the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) package, designed to simplify the modeling process for users. Additionally, this package includes supplementary functions to further enhances the usage of 'nlmixr2'.

Maintained by Richard Hooijmaijers. Last updated 5 months ago.

11 stars 6.74 score 28 scripts

brunobrr

bdc:Biodiversity Data Cleaning

It brings together several aspects of biodiversity data-cleaning in one place. 'bdc' is organized in thematic modules related to different biodiversity dimensions, including 1) Merge datasets: standardization and integration of different datasets; 2) Pre-filter: flagging and removal of invalid or non-interpretable information, followed by data amendments; 3) Taxonomy: cleaning, parsing, and harmonization of scientific names from several taxonomic groups against taxonomic databases locally stored through the application of exact and partial matching algorithms; 4) Space: flagging of erroneous, suspect, and low-precision geographic coordinates; and 5) Time: flagging and, whenever possible, correction of inconsistent collection date. In addition, it contains features to visualize, document, and report data quality – which is essential for making data quality assessment transparent and reproducible. The reference for the methodology is Bruno et al. (2022) <doi:10.1111/2041-210X.13868>.

Maintained by Bruno Ribeiro. Last updated 3 months ago.

bdc biodiversity-data workflow

24 stars 6.66 score 53 scripts

nlmixr2

nonmem2rx:Converts 'NONMEM' Models to 'rxode2'

'NONMEM' has been a tool for running nonlinear mixed effects models since the 80s and is still used today (Bauer 2019 <doi:10.1002/psp4.12404>). This tool allows you to convert 'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax (Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2' syntax requires the residual specification to be included and it is not always translated. If available, the 'rxode2' model will read in the 'NONMEM' data and compare the simulation for the population model ('PRED') individual model ('IPRED') and residual model ('IWRES') to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rxode2' model. This is complementary to the 'babelmixr2' package that translates 'nlmixr2' models to 'NONMEM' and can convert the objects converted from 'nonmem2rx' to a full 'nlmixr2' fit.

Maintained by Matthew Fidler. Last updated 4 months ago.

nlmixr2 nonmem pharmacometrics rxode2 cpp

12 stars 6.46 score 23 scripts 1 dependents

nlmixr2

nlmixr2lib:A Model Library for 'nlmixr2'

A model library for 'nlmixr2'. The models include (and plan to include) pharmacokinetic, pharmacodynamic, and disease models used in pharmacometrics. Where applicable, references for each model are included in the meta-data for each individual model. The package also includes model composition and modification functions to make model updates easier.

Maintained by Bill Denney. Last updated 3 months ago.

6 stars 6.38 score 9 scripts

nlmixr2

babelmixr2:Use 'nlmixr2' to Interact with Open Source and Commercial Software

Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can get/install the 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When 'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up command line usage.

Maintained by Matthew Fidler. Last updated 19 days ago.

monolix nonmem pharmacometrics cpp

9 stars 6.11 score 53 scripts

warint

statcanR:Client for Statistics Canada's Open Economic Data

An easy connection with R to Statistics Canada's Web Data Service. Open economic data (formerly known as CANSIM tables, now identified by Product IDs (PID)) are accessible as a data frame, directly in the user's R environment. Warin, Le Duc (2019) <doi:10.6084/m9.figshare.10544735>.

Maintained by Thierry Warin. Last updated 9 months ago.

statistics-canada

20 stars 6.06 score 58 scripts

nlmixr2

nlmixr2extra:Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for support functions like preconditioned fits <doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate selection.

Maintained by Matthew Fidler. Last updated 1 months ago.

openblas cpp

3 stars 5.83 score 11 scripts 5 dependents

bioc

ChromSCape:Analysis of single-cell epigenomics datasets with a Shiny App

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

Maintained by Pacome Prompsy. Last updated 5 months ago.

shinyapps software singlecell chipseq atacseq methylseq classification clustering epigenetics principalcomponent annotation batcheffect multiplecomparison normalization pathways preprocessing qualitycontrol reportwriting visualization genesetenrichment differentialpeakcalling epigenomics shiny single-cell cpp

14 stars 5.83 score 16 scripts

mrc-ide

hintr:R API for calling naomi district level HIV model

R API for calling naomi district level HIV model.

Maintained by Robert Ashton. Last updated 18 days ago.

2 stars 5.80 score 2 scripts 1 dependents

nflverse

nflversedata:nflverse data storage functions

This repository holds automated data releases for nflverse projects and helper functions for managing the uploads.

Maintained by Tan Ho. Last updated 29 days ago.

214 stars 5.59 score

viralemergence

epizootic:Spatially Explicit Population Models of Disease Transmission in Wildlife

This extension of the pattern-oriented modeling framework of the 'poems' package provides a collection of modules and functions customized for modeling disease transmission on a population scale in a spatiotemporally explicit manner. This includes seasonal time steps, dispersal functions that track disease state of dispersers, results objects that store disease states, and a population simulator that includes disease dynamics.

Maintained by July Pilowsky. Last updated 6 months ago.

cpp

4 stars 5.45 score 5 scripts

globalecologylab

paleopop:Pattern-Oriented Modeling Framework for Coupled Niche-Population Paleo-Climatic Models

This extension of the poems pattern-oriented modeling (POM) framework provides a collection of modules and functions customized for paleontological time-scales, and optimized for single-generation transitions and large populations, across multiple generations.

Maintained by July Pilowsky. Last updated 3 months ago.

5 stars 5.22 score 11 scripts

urswilke

datadaptor:Modify Labelled Data Sets With Excel Files

An R package to modify labelled data sets with commands in Excel files. The commands in this package allow to create new variables, and modify the labels of the variables, as well as the variables themselves. The goal is to provide an easy & concise syntax, and to allow for fast systematic data entry using Excel for advanced users. The commands work on the variables inside the data.frame environment (like e.g. inside dplyr verbs), thus providing an approach that might ease the use for people without in-depth programming experience.

Maintained by Urs Wilke. Last updated 1 months ago.

5.13 score 1 dependents

bioc

cTRAP:Identification of candidate causal perturbations from differential gene expression data

Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.

Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.

differentialexpression geneexpression rnaseq transcriptomics pathways immunooncology genesetenrichment bioconductor bioinformatics cmap gene-expression l1000

5 stars 5.08 score 16 scripts

nlmixr2

nlmixr2plot:Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions

Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for 'ggplot2' plotting methods for 'nlmixr2' objects.

Maintained by Matthew Fidler. Last updated 1 months ago.

2 stars 4.93 score 6 scripts 4 dependents

xtimbeau

sourcoise:Source a Script and Cache

Provides a function that behaves nearly as base::source() but implements a caching mechanism on disk, project based. It allows to quasi source() R scripts that gather data but can fail or consume to much time to respond even if nothing new is expected. It comes with tools to check and execute on demand or when cache is invalid the script.

Maintained by Xavier Timbeau. Last updated 1 days ago.

1 stars 4.88 score

hugheylab

seeker:Simplified Fetching and Processing of Microarray and RNA-Seq Data

Wrapper around various existing tools and command-line interfaces, providing a standard interface, simple parallelization, and detailed logging. For microarray data, maps probe sets to standard gene IDs, building on 'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>, 'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>, Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>, and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>. For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>, performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>, quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197> and potentially 'refgenie' Stolarczyk et al. (2020) <doi:10.1093/gigascience/giz149>, aggregates the results using 'MultiQC' Ewels et al. (2016) <doi:10.1093/bioinformatics/btw354>, maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) <doi:10.1038/nprot.2009.97>, and summarizes transcript-level quantifications for gene-level analyses using 'tximport' Soneson et al. (2015) <doi:10.12688/f1000research.7563.2>.

Maintained by Jake Hughey. Last updated 7 months ago.

3 stars 4.78 score 1 scripts

nlmixr2

nlmixr2rpt:Templated Word and PowerPoint Reporting of 'nlmixr2' Fitting Results

This allows you to generate reporting workflows around 'nlmixr2' analyses with outputs in Word and PowerPoint. You can specify figures, tables and report structure in a user-definable 'YAML' file. Also you can use the internal functions to access the figures and tables to allow their including in other outputs (e.g. R Markdown).

Maintained by John Harrold. Last updated 6 months ago.

2 stars 4.75 score 14 scripts

levenc

posologyr:Individual Dose Optimization using Population Pharmacokinetics

Personalize drug regimens using individual pharmacokinetic (PK) and pharmacokinetic-pharmacodynamic (PK-PD) profiles. By combining therapeutic drug monitoring (TDM) data with a population model, 'posologyr' offers accurate posterior estimates and helps compute optimal individualized dosing regimens. The empirical Bayes estimates are computed following the method described by Kang et al. (2012) <doi:10.4196/kjpp.2012.16.2.97>.

Maintained by Cyril Leven. Last updated 19 days ago.

bayesian model-informed-precision-dosing pharmacokinetics precision-medicine therapeutic-drug-monitoring

12 stars 4.68 score 9 scripts

bklamer

depower:Power Analysis for Differential Expression Studies

Provides a convenient framework to simulate, test, power, and visualize data for differential expression studies with lognormal or negative binomial outcomes. Supported designs are two-sample comparisons of independent or dependent outcomes. Power may be summarized in the context of controlling the per-family error rate or family-wise error rate. Negative binomial methods are described in Yu, Fernandez, and Brock (2017) <doi:10.1186/s12859-017-1648-2> and Yu, Fernandez, and Brock (2020) <doi:10.1186/s12859-020-3541-7>.

Maintained by Brett Klamer. Last updated 1 months ago.

4.65 score 37 scripts

predictiveecology

fireSenseUtils:Utilities for Working With the 'fireSense' Group of 'SpaDES' Modules

Utilities for working with the 'fireSense' group of 'SpaDES' modules.

Maintained by Eliot J B McIntire. Last updated 1 months ago.

1 stars 4.51 score 2 scripts

urswilke

crosstabser:Generate Crosstabs of Labelled Data Sets with Excel Files

An R package to use commands in Excel files to generate crosstabs of labelled data sets (usually survey data). The crosstabs can be printed to the console, and serve as an input for an app to plot them interactively.

Maintained by Urs Wilke. Last updated 2 days ago.

4.50 score

hughparsonage

healthyAddress:Convert Addresses to Standard Inputs

Efficient tools for parsing and standardizing Australian addresses from textual data. It utilizes optimized algorithms to accurately identify and extract components of addresses, such as street names, types, and postcodes, especially for large batched data in contexts where sending addresses to internet services may be slow or inappropriate. The core functionality is built on fast string processing techniques to handle variations in address formats and abbreviations commonly found in Australian address data. Designed for data scientists, urban planners, and logistics analysts, the package facilitates the cleaning and normalization of address information, supporting better data integration and analysis in urban studies, geography, and related fields.

Maintained by Hugh Parsonage. Last updated 3 months ago.

openmp

6 stars 4.42 score 11 scripts

nlmixr2

monolix2rx:Converts 'Monolix' Models to 'rxode2'

'Monolix' is a tool for running mixed effects model using 'saem'. This tool allows you to convert 'Monolix' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) using the form compatible with 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>). If available, the 'rxode2' model will read in the 'Monolix' data and compare the simulation for the population model individual model and residual model to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rxode2' model. This is complementary to the 'babelmixr2' package that translates 'nlmixr2' models to 'Monolix' and can convert the objects converted from 'monolix2rx' to a full 'nlmixr2' fit. While not required, you can get/install the 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When 'lixoftConnectors' is available, 'Monolix' can be used to load its model library instead manually setting up text files (which only works with old versions of 'Monolix').

Maintained by Matthew Fidler. Last updated 4 months ago.

monolix nlmixr2 pharmacometrics rxode2 cpp

1 stars 4.40 score 14 scripts 1 dependents

philipberg

baldur:Bayesian Hierarchical Modeling for Label-Free Proteomics

Statistical decision in proteomics data using a hierarchical Bayesian model. There are two regression models for describing the mean-variance trend, a gamma regression or a latent gamma mixture regression. The regression model is then used as an Empirical Bayes estimator for the prior on the variance in a peptide. Further, it assumes that each measurement has an uncertainty (increased variance) associated with it that is also inferred. Finally, it tries to estimate the posterior distribution (by Hamiltonian Monte Carlo) for the differences in means for each peptide in the data. Once the posterior is inferred, it integrates the tails to estimate the probability of error from which a statistical decision can be made. See Berg and Popescu for details (<doi:10.1101/2023.05.11.540411>).

Maintained by Philip Berg. Last updated 8 months ago.

cpp

1 stars 4.00 score 8 scripts

fentouxungui

SeuratExplorer:An 'Shiny' App for Exploring scRNA-seq Data Processed in 'Seurat'

A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.

Maintained by Yongchao Zhang. Last updated 2 days ago.

3.95 score

predictiveecology

scfmutils:Tools and Utilities for Working With the SCFM Wildfire Simulation Model

The original fire model is described by Cumming et al. (1998), and more accessibly in Armstrong and Cumming (2003). It has recently been implemented as a collection of 'SpaDES' modules by Cumming, McIntire, Eddy, and Chubaty, available from <https://github.com/PredictiveEcology/scfm>.

Maintained by Alex M Chubaty. Last updated 9 days ago.

3.95 score

uzh-peg

microxanox:Oxic-Anoxic Regime Shifts in Microbial Communities

Model to simulate a three functional group system with four chemical substrates using a set of ordinary differential equations. Simulations can be run individually or over a parameter range, to find stable states. The model features multiple species per functional group, where the number is only limited by computational constraints. The R package is constructed in such a way, that the results contain the input parameter used, so that a saved results can be loaded again and thesimulation be repeated.

Maintained by Owen L. Petchey. Last updated 1 years ago.

3.85 score 35 scripts

pr2database

pr2database:PR2 database with shiny web interface

PR2 database See https://pr2-database.org

Maintained by Daniel Vaulot. Last updated 2 years ago.

18s-rrna database eukaryotes metabarcoding rrna taxonomy

80 stars 3.60 score 7 scripts

jfwambaugh

invivoPKfit:Fits Toxicokinetic Models to In Vivo PK Data Sets

Takes in vivo toxicokinetic concentration-time data and fits parameters of 1-compartment and 2-compartment models for each chemical. These methods are described in detail in "Informatics for Toxicokinetics" (submitted).

Maintained by John Wambaugh. Last updated 5 days ago.

3.48 score 4 scripts

kestrel99

xpose.nlmixr2:Graphical Diagnostics for Pharmacometric Models: Extension to 'nlmixr2'

Extension to 'xpose' to support 'nlmixr2'. Provides functions to import 'nlmixr2' fit data into an 'xpose' data object, allowing the use of 'xpose' for 'nlmixr2' model diagnostics.

Maintained by Justin Wilkins. Last updated 3 years ago.

3.38 score 40 scripts 1 dependents

predictiveecology

SpaDES.experiment:Simulation Experiments Within The SpaDES Ecosystem

Tools to do simulation experiments within the SpaDES ecosystem. This includes replication, parameter sweeps, scenario analysis, pattern oriented modeling, and simulation experiments. The package introduces a new object class, the simLists, which is an environment that contains many simList class objects. This package also includes tools to do post hoc analyses of such simLists objects.

Maintained by Eliot J B McIntire. Last updated 4 months ago.

simulation-experiments

1 stars 3.30 score 2 scripts

predictiveecology

SpaDES.addins:Development Tools for 'SpaDES' and 'SpaDES' Modules

Provides 'RStudio' addins for 'SpaDES' packages and 'SpaDES' module development. See '?SpaDES.addins' for an overview of the tools provided.

Maintained by Alex M Chubaty. Last updated 4 months ago.

1 stars 3.30 score

learnitr

learnitgrid:Manage Rubrics or Assessment Grids for GitHub Repositories

Create and manage semi-automatically rubrics to assess GitHub projects (R scripts, R Markdown or Quarto files). Create directed projects where students have to complete documents and submit them to GitHub (classroom) so that they are evaluated using the rubric (or assessment grid).

Maintained by Philippe Grosjean. Last updated 10 months ago.

learning project rubric

1 stars 3.00 score 7 scripts

jimbrig

jimstools:Tools for R

What the package does (one paragraph).

Maintained by Jimmy Briggs. Last updated 3 years ago.

functions personal utility

2 stars 3.00 score 2 scripts

cran

espadon:Easy Study of Patient DICOM Data in Oncology

Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.

Maintained by Cathy Fontbonne. Last updated 2 months ago.

cpp

2.85 score

nlmixr2

nlmixr2targets:Targets for 'nlmixr2' Pipelines

'nlmixr2' often has long runtimes. A pipeline toolkit tailored to 'nlmixr2' workflows leverages 'targets' and 'nlmixr2' to ease reproducible workflows. 'nlmixr2targets' ensures minimal rework in model development with 'nlmixr2' and 'targets' by simplifying and standardizing models and datasets.

Maintained by Bill Denney. Last updated 1 months ago.

2.70 score 6 scripts

geomarker-io

appc:Air Pollution Predictor Commons

Functions for geomarker assessment for s2 locations and dates. These are used to train and predict daily ambient air pollution concentrations across the contiguous US 2016 - 2022.

Maintained by Cole Brokamp. Last updated 3 months ago.

2.54 score 6 scripts

pr2database

metapr2:Eukaryotic 18S rRNA metabarcode database

Provides an interface to the metaPR2 database (current version = 1.0) which contains eukaryotic 18S rRNA metabarcodes. Many options for selecting samples are provided. Data can be displayed as maps, barplots, treemaps. Data can be searched and downloaded. See https://pr2-database.org for more information.

Maintained by Daniel Vaulot. Last updated 1 years ago.

18s-rrna metabarcoding shiny-apps

3 stars 2.18 score

mrc-ide