Showing 66 of total 66 results (show query)
billdenney
PKNCA:Perform Pharmacokinetic Non-Compartmental Analysis
Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.
Maintained by Bill Denney. Last updated 16 days ago.
ncanoncompartmental-analysispharmacokinetics
18.9 match 73 stars 12.61 score 214 scripts 4 dependents
cran
nlme:Linear and Nonlinear Mixed Effects Models
Fit and compare Gaussian linear and nonlinear mixed-effects models.
Maintained by R Core Team. Last updated 2 months ago.
18.0 match 6 stars 13.00 score 13k scripts 8.7k dependents
insightrx
PKPDsim:Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations
Simulate dose regimens for pharmacokinetic-pharmacodynamic (PK-PD) models described by differential equation (DE) systems. Simulation using ADVAN-style analytical equations is also supported (Abuhelwa et al. (2015) <doi:10.1016/j.vascn.2015.03.004>).
Maintained by Ron Keizer. Last updated 19 days ago.
odepharmacodynamicspharmacokineticspharmacometricscpp
13.5 match 36 stars 9.47 score 100 scripts
syneoshealth
puzzle:Assembling Data Sets for Non-Linear Mixed Effects Modeling
To Simplify the time consuming and error prone task of assembling complex data sets for non-linear mixed effects modeling. Users are able to select from different absorption processes such as zero and first order, or a combination of both. Furthermore, data sets containing data from several entities, responses, and covariates can be simultaneously assembled.
Maintained by Mario Gonzalez Sales. Last updated 5 years ago.
28.7 match 3 stars 3.65 score 9 scripts
kestrel99
pmxTools:Pharmacometric and Pharmacokinetic Toolkit
Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero- and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008) <http://lixoft.com/wp-content/uploads/2016/03/PKPDlibrary.pdf>); parametric simulation from NONMEM-generated parameter estimates and other output; and parsing, tabulating and plotting results generated by Perl-speaks-NONMEM (PsN).
Maintained by Justin Wilkins. Last updated 7 months ago.
nonmempharmacokineticssimulation
15.0 match 30 stars 6.40 score 84 scripts
andrewhooker
PopED:Population (and Individual) Optimal Experimental Design
Optimal experimental designs for both population and individual studies based on nonlinear mixed-effect models. Often this is based on a computation of the Fisher Information Matrix. This package was developed for pharmacometric problems, and examples and predefined models are available for these types of systems. The methods are described in Nyberg et al. (2012) <doi:10.1016/j.cmpb.2012.05.005>, and Foracchia et al. (2004) <doi:10.1016/S0169-2607(03)00073-7>.
Maintained by Andrew C. Hooker. Last updated 5 months ago.
nlmeoptimal-designpharmacodynamicspharmacokineticspharmacometricspkpdpopulationpopulation-model
10.0 match 33 stars 9.58 score 300 scripts 1 dependentsinsightrx
clinPK:Clinical Pharmacokinetics Toolkit
Provides equations commonly used in clinical pharmacokinetics and clinical pharmacology, such as equations for dose individualization, compartmental pharmacokinetics, drug exposure, anthropomorphic calculations, clinical chemistry, and conversion of common clinical parameters. Where possible and relevant, it provides multiple published and peer-reviewed equations within the respective R function.
Maintained by Ron Keizer. Last updated 2 months ago.
clinical-researchpharmacokinetics
14.1 match 30 stars 6.72 score 55 scripts
nanhung
pksensi:Global Sensitivity Analysis in Physiologically Based Kinetic Modeling
Applying the global sensitivity analysis workflow to investigate the parameter uncertainty and sensitivity in physiologically based kinetic (PK) models, especially the physiologically based pharmacokinetic/toxicokinetic model with multivariate outputs. The package also provides some functions to check the convergence and sensitivity of model parameters. The workflow was first mentioned in Hsieh et al., (2018) <doi:10.3389/fphar.2018.00588>, then further refined (Hsieh et al., 2020 <doi:10.1016/j.softx.2020.100609>).
Maintained by Nan-Hung Hsieh. Last updated 4 months ago.
gnu-mcsimpharmacokineticssensitivitysensitivity-analysis
14.5 match 5 stars 5.64 score 88 scripts
asancpt
caffsim:Simulation of Plasma Caffeine Concentrations by Using Population Pharmacokinetic Model
Simulate plasma caffeine concentrations using population pharmacokinetic model described in Lee, Kim, Perera, McLachlan and Bae (2015) <doi:10.1007/s00431-015-2581-x> and the package was published <doi:10.12793/tcp.2017.25.3.141>.
Maintained by Sungpil Han. Last updated 5 years ago.
caffeinemedicinemonte-carlo-simulationpharmacokineticspharmacometricstoxicology
18.5 match 9 stars 3.77 score 13 scripts
pharmaverse
pharmaversesdtm:SDTM Test Data for the 'Pharmaverse' Family of Packages
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. SDTM dataset specifications are described in the CDISC SDTM implementation guide, accessible by creating a free account on <https://www.cdisc.org/>.
Maintained by Edoardo Mancini. Last updated 2 days ago.
9.0 match 15 stars 7.40 score 143 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 5 days ago.
bayesianmodel-informed-precision-dosingpharmacokineticsprecision-medicinetherapeutic-drug-monitoring
13.7 match 12 stars 4.68 score 9 scripts
stevencarlislewalker
MEMSS:Data Sets from Mixed-Effects Models in S
Data sets and sample analyses from Pinheiro and Bates, "Mixed-effects Models in S and S-PLUS" (Springer, 2000).
Maintained by Steve Walker. Last updated 6 years ago.
22.5 match 2.62 score 102 scripts
higgi13425
medicaldata:Data Package for Medical Datasets
Provides access to well-documented medical datasets for teaching. Featuring several from the Teaching of Statistics in the Health Sciences website <https://www.causeweb.org/tshs/category/dataset/>, a few reconstructed datasets of historical significance in medical research, some reformatted and extended from existing R packages, and some data donations.
Maintained by Peter Higgins. Last updated 2 years ago.
7.2 match 48 stars 7.43 score 317 scripts
ecomets
npde:Normalised Prediction Distribution Errors for Nonlinear Mixed-Effect Models
Provides routines to compute normalised prediction distribution errors, a metric designed to evaluate non-linear mixed effect models such as those used in pharmacokinetics and pharmacodynamics.
Maintained by Emmanuelle Comets. Last updated 1 years ago.
11.8 match 3.70 score 119 scripts 7 dependents
metrumresearchgroup
mrgsolve:Simulate from ODE-Based Models
Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.
Maintained by Kyle T Baron. Last updated 1 months ago.
3.9 match 138 stars 10.90 score 1.2k scripts 3 dependents
certara-jcraig
Certara.RsNLME:Pharmacometric Modeling
Facilitate Pharmacokinetic (PK) and Pharmacodynamic (PD) modeling and simulation with powerful tools for Nonlinear Mixed-Effects (NLME) modeling. The package provides access to the same advanced Maximum Likelihood algorithms used by the NLME-Engine in the Phoenix platform. These tools support a range of analyses, from parametric methods to individual and pooled data analysis <https://www.certara.com/app/uploads/2020/06/BR_PhoenixNLME-v4.pdf>. Execution is supported both locally or on remote machines.
Maintained by James Craig. Last updated 4 months ago.
13.9 match 3.01 score 34 scripts 2 dependents
accelstab
AccelStab:Accelerated Stability Kinetic Modelling
Estimate the Šesták–Berggren kinetic model (degradation model) from experimental data. A A closed-form (analytic) solution to the degradation model is implemented as a non-linear fit, allowing for the extrapolation of the degradation of a drug product - both in time and temperature. Parametric bootstrap, with kinetic parameters drawn from the multivariate t-distribution, and analytical formulae (the delta method) are available options to calculate the confidence and prediction intervals. The results (modelling, extrapolations and statistical intervals) can be visualised with multiple plots. The examples illustrate the accelerated stability modelling in drugs and vaccines development.
Maintained by Ben Wells. Last updated 5 months ago.
arrheniuskineticsmodellingnon-linear-modelpharmaceuticalspharmacokineticssestak-berggrenstabilitystatisticstemperaturetemperature-excursionvaccine
10.0 match 1 stars 3.48 score 2 scripts
insightsengineering
random.cdisc.data:Create Random ADaM Datasets
A set of functions to create random Analysis Data Model (ADaM) datasets and cached dataset. ADaM dataset specifications are described by the Clinical Data Interchange Standards Consortium (CDISC) Analysis Data Model Team.
Maintained by Joe Zhu. Last updated 5 months ago.
3.8 match 33 stars 8.60 score 52 scripts
smouksassi
ggquickeda:Quickly Explore Your Data Using 'ggplot2' and 'table1' Summary Tables
Quickly and easily perform exploratory data analysis by uploading your data as a 'csv' file. Start generating insights using 'ggplot2' plots and 'table1' tables with descriptive stats, all using an easy-to-use point and click 'Shiny' interface.
Maintained by Samer Mouksassi. Last updated 7 days ago.
3.8 match 73 stars 8.31 score 27 scripts
bms63
admiral.test:Test Data for the 'admiral' Package
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) derivations inside the 'admiral' package.
Maintained by Ben Straub. Last updated 2 years ago.
8.0 match 3.19 score 310 scriptsinsightsengineering
tern:Create Common TLGs Used in Clinical Trials
Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.
Maintained by Joe Zhu. Last updated 2 months ago.
clinical-trialsgraphslistingsnestoutputstables
1.8 match 79 stars 12.62 score 186 scripts 9 dependents
jarretrt
tci:Target Controlled Infusion (TCI)
Implementation of target-controlled infusion algorithms for compartmental pharmacokinetic and pharmacokinetic-pharmacodynamic models. Jacobs (1990) <doi:10.1109/10.43622>; Marsh et al. (1991) <doi:10.1093/bja/67.1.41>; Shafer and Gregg (1993) <doi:10.1007/BF01070999>; Schnider et al. (1998) <doi:10.1097/00000542-199805000-00006>; Abuhelwa, Foster, and Upton (2015) <doi:10.1016/j.vascn.2015.03.004>; Eleveld et al. (2018) <doi:10.1016/j.bja.2018.01.018>.
Maintained by Ryan Jarrett. Last updated 2 years ago.
6.2 match 6 stars 3.48 score 8 scripts
swihart
rmutil:Utilities for Nonlinear Regression and Repeated Measurements Models
A toolkit of functions for nonlinear regression and repeated measurements not to be used by itself but called by other Lindsey packages such as 'gnlm', 'stable', 'growth', 'repeated', and 'event' (available at <https://www.commanster.eu/rcode.html>).
Maintained by Bruce Swihart. Last updated 2 years ago.
2.0 match 1 stars 8.35 score 358 scripts 70 dependents
benjaminrich
linpk:Generate Concentration-Time Profiles from Linear PK Systems
Generate concentration-time profiles from linear pharmacokinetic (PK) systems, possibly with first-order absorption or zero-order infusion, possibly with one or more peripheral compartments, and possibly under steady-state conditions. Single or multiple doses may be specified. Secondary (derived) PK parameters (e.g. Cmax, Ctrough, AUC, Tmax, half-life, etc.) are computed.
Maintained by Benjamin Rich. Last updated 11 months ago.
3.4 match 10 stars 4.90 score 16 scripts
omarashkar
PKbioanalysis:Pharmacokinetic Bioanalysis Experiments Design and Exploration
Automate pharmacokinetic/pharmacodynamic bioanalytical procedures based on best practices and regulatory recommendations. The package impose regulatory constrains and sanity checking for common bioanalytical procedures. Additionally, 'PKbioanalysis' provides a relational infrastructure for plate management and injection sequence.
Maintained by Omar Elashkar. Last updated 5 months ago.
3.5 match 4.40 score 4 scripts
stephen-amori
apmx:Automated Population Pharmacokinetic Dataset Assembly
Automated methods to assemble population PK (pharmacokinetic) and PKPD (pharmacodynamic) datasets for analysis in 'NONMEM' (non-linear mixed effects modeling) by Bauer (2019) <doi:10.1002/psp4.12404>. The package includes functions to build datasets from SDTM (study data tabulation module) <https://www.cdisc.org/standards/foundational/sdtm>, ADaM (analysis dataset module) <https://www.cdisc.org/standards/foundational/adam>, or other dataset formats. The package will combine population datasets, add covariates, and create documentation to support regulatory submission and internal communication.
Maintained by Stephen Amori. Last updated 1 years ago.
3.5 match 5 stars 4.40 score 10 scripts
huismanj
qpNCA:Noncompartmental Pharmacokinetic Analysis by qPharmetra
Computes noncompartmental pharmacokinetic parameters for drug concentration profiles. For each profile, data imputations and adjustments are made as necessary and basic parameters are estimated. Supports single dose, multi-dose, and multi-subject data. Supports steady-state calculations and various routes of drug administration. See ?qpNCA and vignettes. Methodology follows Rowland and Tozer (2011, ISBN:978-0-683-07404-8), Gabrielsson and Weiner (1997, ISBN:978-91-9765-100-4), and Gibaldi and Perrier (1982, ISBN:978-0824710422).
Maintained by Jan Huisman. Last updated 4 years ago.
3.6 match 3.83 score 34 scriptscran
NonCompart:Noncompartmental Analysis for Pharmacokinetic Data
Conduct a noncompartmental analysis with industrial strength. Some features are 1) Use of CDISC SDTM terms 2) Automatic or manual slope selection 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Maintained by Kyun-Seop Bae. Last updated 1 years ago.
5.5 match 1 stars 2.26 score 60 scripts 1 dependents
couthcommander
pkdata:Creates Pharmacokinetic/Pharmacodynamic (PK/PD) Data
Prepare pharmacokinetic/pharmacodynamic (PK/PD) data for PK/PD analyses. This package provides functions to standardize infusion and bolus dose raw data obtained from electronic health record (EHR) databases while linking it to drug level or concentration data.
Maintained by Cole Beck. Last updated 4 years ago.
3.4 match 2 stars 3.48 score 8 scripts 1 dependents
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 5 days ago.
monolixnonmempharmacometricscpp
1.9 match 9 stars 6.11 score 53 scriptscran
pkr:Pharmacokinetics in R
Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software. Some features are 1) CDISC SDTM terms 2) Automatic slope selection with the same criterion of WinNonlin(R) 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Maintained by Kyun-Seop Bae. Last updated 3 years ago.
6.5 match 1.52 score 33 scripts
tjaki
PK:Basic Non-Compartmental Pharmacokinetics
Estimation of pharmacokinetic parameters using non-compartmental theory.
Maintained by Thomas Jaki. Last updated 2 years ago.
3.7 match 2.59 score 13 scripts 1 dependentscran
scaRabee:Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models
A port of the Scarabee toolkit originally written as a Matlab-based application. scaRabee provides a framework for simulation and optimization of pharmacokinetic-pharmacodynamic models at the individual and population level. It is built on top of the neldermead package, which provides the direct search algorithm proposed by Nelder and Mead for model optimization.
Maintained by Sebastien Bihorel. Last updated 3 years ago.
3.5 match 2.70 score 3 scripts
openanalytics
inTextSummaryTable:Creation of in-Text Summary Table
Creation of tables of summary statistics or counts for clinical data (for 'TLFs'). These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report (Word format) or a 'topline' presentation (PowerPoint format), or as interactive table (with the 'DT' package) to an html document for clinical data review.
Maintained by Laure Cougnaud. Last updated 9 months ago.
1.5 match 1 stars 5.52 score 47 scriptscran
wnl:Minimization Tool for Pharmacokinetic-Pharmacodynamic Data Analysis
This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Maintained by Kyun-Seop Bae. Last updated 23 days ago.
5.2 match 1 stars 1.48 score 6 scripts
john-harrold
ubiquity:PKPD, PBPK, and Systems Pharmacology Modeling Tools
Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Maintained by John Harrold. Last updated 16 days ago.
0.8 match 13 stars 7.14 score 33 scriptscran
ncar:Noncompartmental Analysis for Pharmacokinetic Report
Conduct a noncompartmental analysis with industrial strength. Some features are 1) CDISC SDTM terms 2) Automatic or manual slope selection 3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method 4) Interval(partial) AUCs with 'linear' or 'log' interpolation method 5) Produce pdf, rtf, text report files. * Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Maintained by Kyun-Seop Bae. Last updated 1 years ago.
5.5 match 1 stars 1.00 score
oobianom
r2dictionary:A Mini-Dictionary for 'Shiny' and 'Rmarkdown' Documents
Despite the predominant use of R for data manipulation and various robust statistical calculations, in recent years, more people from various disciplines are beginning to use R for other purposes. A critical milestone that has enabled large influx of users in the R community is the development of the Tidyverse family of packages and Rmarkdown. With the latter, one can write all kinds of documents and produce output in formats such html and pdf very easily. In doing this seemlessly, further tools are needed for such users to easily and freely write in R for all kinds of purposes. The r2dictionary introduces a means for users to directly search for definitions of terms within the R environment.
Maintained by Obinna Obianom. Last updated 2 years ago.
1.3 match 2 stars 4.00 score 3 scriptscran
nmw:Understanding Nonlinear Mixed Effects Modeling for Population Pharmacokinetics
This shows how NONMEM(R) software works. NONMEM's classical estimation methods like 'First Order(FO) approximation', 'First Order Conditional Estimation(FOCE)', and 'Laplacian approximation' are explained.
Maintained by Kyun-Seop Bae. Last updated 2 years ago.
4.6 match 1 stars 1.00 score
dcnorris
DTAT:Dose Titration Algorithm Tuning
Dose Titration Algorithm Tuning (DTAT) is a methodologic framework allowing dose individualization to be conceived as a continuous learning process that begins in early-phase clinical trials and continues throughout drug development, on into clinical practice. This package includes code that researchers may use to reproduce or extend key results of the DTAT research programme, plus tools for trialists to design and simulate a '3+3/PC' dose-finding study. Please see Norris (2017a) <doi:10.12688/f1000research.10624.3> and Norris (2017c) <doi:10.1101/240846>.
Maintained by David C. Norris. Last updated 10 months ago.
1.5 match 2.90 score 20 scriptsnlmixr2
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 24 days ago.
0.5 match 50 stars 8.45 score 120 scripts 3 dependentsnlmixr2
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 25 days ago.
0.5 match 9 stars 8.26 score 26 scripts 9 dependents
iame-researchcenter
PFIM:Population Fisher Information Matrix
Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>, Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>, Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>, Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>, Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.
Maintained by Romain Leroux. Last updated 5 months ago.
1.5 match 2.78 score 9 scripts
nmautoverse
NMdata:Preparation, Checking and Post-Processing Data for PK/PD Modeling
Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Maintained by Philip Delff. Last updated 2 days ago.
0.5 match 17 stars 7.69 score 88 scripts 2 dependents
novartis
xgxr:Exploratory Graphics for Pharmacometrics
Supports a structured approach for exploring PKPD data <https://opensource.nibr.com/xgx/>. It also contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
Maintained by Andrew Stein. Last updated 1 years ago.
0.5 match 13 stars 7.76 score 105 scripts 5 dependents
calvagone
campsis:Generic PK/PD Simulation Platform CAMPSIS
A generic, easy-to-use and intuitive pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on R packages 'rxode2' and 'mrgsolve'. CAMPSIS provides an abstraction layer over the underlying processes of writing a PK/PD model, assembling a custom dataset and running a simulation. CAMPSIS has a strong dependency to the R package 'campsismod', which allows to read/write a model from/to files and adapt it further on the fly in the R environment. Package 'campsis' allows the user to assemble a dataset in an intuitive manner. Once the user’s dataset is ready, the package is in charge of preparing the simulation, calling 'rxode2' or 'mrgsolve' (at the user's choice) and returning the results, for the given model, dataset and desired simulation settings.
Maintained by Nicolas Luyckx. Last updated 1 months ago.
0.5 match 8 stars 7.52 score 93 scripts
ek-lee
nlmeVPC:Visual Model Checking for Nonlinear Mixed Effect Model
Various visual and numerical diagnosis methods for the nonlinear mixed effect model, including visual predictive checks, numerical predictive checks, and coverage plots (Karlsson and Holford, 2008, <https://www.page-meeting.org/?abstract=1434>).
Maintained by Eun-Kyung Lee. Last updated 2 years ago.
3.6 match 1.04 score 11 scripts
fuyongchao
pk.unit.trans:Achieve Numerical Conversion Between Units Commonly Used in Pharmacokinetics
Achieve internal conversions of mass units, molar units, and volume units commonly used in pharmacokinetics, as well as conversions between mass units and molar units.
Maintained by Fu Yongchao. Last updated 4 months ago.
3.4 match 1.00 scorecalvagone
campsismod:Generic Implementation of a PK/PD Model
A generic, easy-to-use and expandable implementation of a pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4 class system. This package allows the user to read/write a pharmacometric model from/to files and adapt it further on the fly in the R environment. For this purpose, this package provides an intuitive API to add, modify or delete equations, ordinary differential equations (ODE's), model parameters or compartment properties (like infusion duration or rate, bioavailability and initial values). Finally, this package also provides a useful export of the model for use with simulation packages 'rxode2' and 'mrgsolve'. This package is designed and intended to be used with package 'campsis', a PK/PD simulation platform built on top of 'rxode2' and 'mrgsolve'.
Maintained by Nicolas Luyckx. Last updated 1 months ago.
0.5 match 5 stars 6.64 score 42 scripts 1 dependentsnlmixr2
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 2 months ago.
0.5 match 6 stars 6.38 score 9 scriptsnlmixr2
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 27 days ago.
0.5 match 3 stars 5.80 score 11 scripts 5 dependentsnlmixr2
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 29 days ago.
0.5 match 2 stars 4.82 score 6 scripts 4 dependentsnlmixr2
nlmixr2data:Nonlinear Mixed Effects Models in Population PK/PD, Data
Datasets for 'nlmixr2' and 'rxode2'. 'nlmixr2' is used for fitting and comparing 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 years ago.
0.5 match 3 stars 4.73 score 6 scripts 10 dependents
felicienll
mapbayr:MAP-Bayesian Estimation of PK Parameters
Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in 'mrgsolve', typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format. The performance of the package was described by Le Louedec et al (2021) <doi:10.1002/psp4.12689>.
Maintained by Felicien Le Louedec. Last updated 2 years ago.
0.5 match 21 stars 4.55 score 34 scripts
kathrinmoellenhoff
SimDissolution:Modeling and Assessing Similarity of Drug Dissolutions Profiles
Implementation of a model-based bootstrap approach for testing whether two formulations are similar. The package provides a function for fitting a pharmacokinetic model to time-concentration data and comparing the results for all five candidate models regarding the Residual Sum of Squares (RSS). The candidate set contains a First order, Hixson-Crowell, Higuchi, Weibull and a logistic model. The assessment of similarity implemented in this package is performed regarding the maximum deviation of the profiles. See Moellenhoff et al. (2018) <doi:10.1002/sim.7689> for details.
Maintained by Kathrin Moellenhoff. Last updated 5 years ago.
2.3 match 1.00 score
rhoinc
CRANsearcher:RStudio Addin for Searching Packages in CRAN Database Based on Keywords
One of the strengths of R is its vast package ecosystem. Indeed, R packages extend from visualization to Bayesian inference and from spatial analyses to pharmacokinetics (<https://cran.r-project.org/web/views/>). There is probably not an area of quantitative research that isn't represented by at least one R package. At the time of this writing, there are more than 10,000 active CRAN packages. Because of this massive ecosystem, it is important to have tools to search and learn about packages related to your personal R needs. For this reason, we developed an RStudio addin capable of searching available CRAN packages directly within RStudio.
Maintained by Agustin Calatroni. Last updated 7 years ago.
0.5 match 34 stars 4.23 score 2 scripts
philipdelff
NMcalc:Basic Calculations for PK/PD Modeling
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. This is not a noncompartmental analysis (NCA) package.
Maintained by Philip Delff. Last updated 5 months ago.
0.5 match 3 stars 3.95 score 5 scripts 1 dependents
cran
ncappc:NCA Calculations and Population Model Diagnosis
A flexible tool that can perform (i) traditional non-compartmental analysis (NCA) and (ii) Simulation-based posterior predictive checks for population pharmacokinetic (PK) and/or pharmacodynamic (PKPD) models using NCA metrics.
Maintained by Andrew C. Hooker. Last updated 7 years ago.
0.5 match 2.70 score
vahidnassiri
BLOQ:Impute and Analyze Data with BLOQ Observations
It includes estimating the area under the concentrations versus time curve (AUC) and its standard error for data with Below the Limit of Quantification (BLOQ) observations. Two approaches are implemented: direct estimation using censored maximum likelihood, also by first imputing the BLOQ's using various methods, then compute AUC and its standard error using imputed data. Technical details can found in Barnett, Helen Yvette, Helena Geys, Tom Jacobs, and Thomas Jaki. "Methods for Non-Compartmental Pharmacokinetic Analysis With Observations Below the Limit of Quantification." Statistics in Biopharmaceutical Research (2020): 1-12. (available online: <https://www.tandfonline.com/doi/full/10.1080/19466315.2019.1701546>).
Maintained by Vahid Nassiri. Last updated 5 years ago.
0.5 match 1.11 score 13 scripts