Showing 89 of total 89 results (show query)
leifeld
btergm:Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood
Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs. The methods are described in Leifeld, Cranmer and Desmarais (2018), JStatSoft <doi:10.18637/jss.v083.i06>.
Maintained by Philip Leifeld. Last updated 12 months ago.
complex-networksdynamic-analysisergmestimationgoodness-of-fitinferencelongitudinal-datanetwork-analysispredictiontergm
13.5 match 17 stars 6.70 score 83 scripts 2 dependents
wviechtb
metadat:Meta-Analysis Datasets
A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.
Maintained by Wolfgang Viechtbauer. Last updated 3 days ago.
7.6 match 30 stars 10.54 score 65 scripts 93 dependents
pharmaverse
admiral:ADaM in R Asset Library
A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).
Maintained by Ben Straub. Last updated 7 hours ago.
cdiscclinical-trialsopen-source
5.6 match 238 stars 13.92 score 486 scripts 4 dependents
cran
iAdapt:Two-Stage Adaptive Dose-Finding Clinical Trial Design
Simulate and implement early phase two-stage adaptive dose-finding design for binary and quasi-continuous toxicity endpoints. See Chiuzan et al. (2018) for further reading <DOI:10.1080/19466315.2018.1462727>.
Maintained by Alyssa Vanderbeek. Last updated 4 years ago.
23.8 match 3.18 score 7 scripts
vivienjyin
phase1RMD:Repeated Measurement Design for Phase I Clinical Trial
Implements our Bayesian phase I repeated measurement design that accounts for multidimensional toxicity endpoints from multiple treatment cycles. The package also provides a novel design to account for both multidimensional toxicity endpoints and early-stage efficacy endpoints in the phase I design. For both designs, functions are provided to recommend the next dosage selection based on the data collected in the available patient cohorts and to simulate trial characteristics given design parameters. Yin, Jun, et al. (2017) <doi:10.1002/sim.7134>.
Maintained by Jun Yin. Last updated 4 years ago.
27.5 match 2.70 score 8 scripts
doi-usgs
toxEval:Exploring Biological Relevance of Environmental Chemistry Observations
Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.
Maintained by Laura DeCicco. Last updated 3 months ago.
10.0 match 21 stars 7.34 score 58 scripts
bioc
mixOmics:Omics Data Integration Project
Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.
Maintained by Eva Hamrud. Last updated 5 days ago.
immunooncologymicroarraysequencingmetabolomicsmetagenomicsproteomicsgenepredictionmultiplecomparisonclassificationregressionbioconductorgenomicsgenomics-datagenomics-visualizationmultivariate-analysismultivariate-statisticsomicsr-pkgr-project
5.3 match 182 stars 13.71 score 1.3k scripts 22 dependents
openpharma
crmPack:Object-Oriented Implementation of CRM Designs
Implements a wide range of model-based dose escalation designs, ranging from classical and modern continual reassessment methods (CRMs) based on dose-limiting toxicity endpoints to dual-endpoint designs taking into account a biomarker/efficacy outcome. The focus is on Bayesian inference, making it very easy to setup a new design with its own JAGS code. However, it is also possible to implement 3+3 designs for comparison or models with non-Bayesian estimation. The whole package is written in a modular form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules. Further details are presented in Sabanes Bove et al. (2019) <doi:10.18637/jss.v089.i10>.
Maintained by Daniel Sabanes Bove. Last updated 2 months ago.
9.2 match 21 stars 7.79 score 208 scripts
blakelanglais
ProAE:PRO-CTCAE Scoring, Analysis, and Graphical Tools
A collection of tools to facilitate standardized analysis and graphical procedures when using the National Cancer Institute’s Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE) and other PRO measurements.
Maintained by Blake Langlais. Last updated 5 months ago.
18.8 match 3.48 score 9 scripts
ichxw
mixtox:Dose Response Curve Fitting and Mixture Toxicity Assessment
Curve Fitting of monotonic(sigmoidal) & non-monotonic(J-shaped) dose-response data. Predicting mixture toxicity based on reference models such as 'concentration addition', 'independent action', and 'generalized concentration addition'.
Maintained by Xiangwei Zhu. Last updated 6 months ago.
15.8 match 3 stars 3.97 score 31 scripts
r-forge
QSARdata:Quantitative Structure Activity Relationship (QSAR) Data Sets
Molecular descriptors and outcomes for several public domain data sets
Maintained by Max Kuhn. Last updated 14 years ago.
21.6 match 2.83 score 68 scriptsr-forge
robustbase:Basic Robust Statistics
"Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Maintained by Martin Maechler. Last updated 4 months ago.
3.8 match 13.33 score 1.7k scripts 480 dependentscran
RFPM:Floating Percentile Model
Floating Percentile Model with additional functions for optimizing inputs and evaluating outputs and assumptions.
Maintained by Brian Church. Last updated 1 years ago.
23.7 match 2.00 score
aursiber
ssd4mosaic:Web Application for the SSD Module of the MOSAIC Platform
Web application using 'shiny' for the SSD (Species Sensitivity Distribution) module of the MOSAIC (MOdeling and StAtistical tools for ecotoxICology) platform. It estimates the Hazardous Concentration for x% of the species (HCx) from toxicity values that can be censored and provides various plotting options for a better understanding of the results. See our companion paper Kon Kam King et al. (2014) <doi:10.48550/arXiv.1311.5772>.
Maintained by Aurélie Siberchicot. Last updated 6 days ago.
17.8 match 2.60 score
brockk
trialr:Clinical Trial Designs in 'rstan'
A collection of clinical trial designs and methods, implemented in 'rstan' and R, including: the Continual Reassessment Method by O'Quigley et al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the two-parameter logistic method of Neuenschwander, Branson & Sponer (2008) <doi:10.1002/sim.3230>; and the Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and more. We provide functions to aid model-fitting and analysis. The 'rstan' implementations may also serve as a cookbook to anyone looking to extend or embellish these models. We hope that this package encourages the use of Bayesian methods in clinical trials. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a method you would like implemented, please get in touch.
Maintained by Kristian Brock. Last updated 1 years ago.
5.2 match 41 stars 8.55 score 106 scripts 3 dependents
rickhelmus
patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Maintained by Rick Helmus. Last updated 11 days ago.
mass-spectrometrynon-targetcppopenjdk
6.7 match 65 stars 6.22 score 43 scripts
niehs
amadeus:Accessing and Analyzing Large-Scale Environmental Data
Functions are designed to facilitate access to and utility with large scale, publicly available environmental data in R. The package contains functions for downloading raw data files from web URLs (download_data()), processing the raw data files into clean spatial objects (process_covariates()), and extracting values from the spatial data objects at point and polygon locations (calculate_covariates()). These functions call a series of source-specific functions which are tailored to each data sources/datasets particular URL structure, data format, and spatial/temporal resolution. The functions are tested, versioned, and open source and open access. For sum_edc() method details, see Messier, Akita, and Serre (2012) <doi:10.1021/es203152a>.
Maintained by Kyle Messier. Last updated 20 days ago.
5.6 match 8 stars 7.16 score 13 scripts
tidymodels
modeldata:Data Sets Useful for Modeling Examples
Data sets used for demonstrating or testing model-related packages are contained in this package.
Maintained by Max Kuhn. Last updated 5 months ago.
3.6 match 22 stars 10.66 score 2.2k scripts 17 dependents
ropensci
webchem:Chemical Information from the Web
Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
Maintained by Tamás Stirling. Last updated 3 months ago.
cas-numberchemical-informationchemspideridentifierropensciwebscraping
3.4 match 165 stars 10.31 score 173 scripts 10 dependents
julianfaraway
faraway:Datasets and Functions for Books by Julian Faraway
Books are "Linear Models with R" published 1st Ed. August 2004, 2nd Ed. July 2014, 3rd Ed. February 2025 by CRC press, ISBN 9781439887332, and "Extending the Linear Model with R" published by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN 9781584884248 and "Practical Regression and ANOVA in R" contributed documentation on CRAN (now very dated).
Maintained by Julian Faraway. Last updated 1 months ago.
3.8 match 29 stars 9.43 score 1.7k scripts 1 dependents
virgile-baudrot
morse:Modelling Reproduction and Survival Data in Ecotoxicology
Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of survival and reproduction Data. Among others, it facilitates Bayesian inference of the general unified threshold model of survival (GUTS). See our companion paper Baudrot and Charles (2021) <doi:10.21105/joss.03200>, as well as complementary details in Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464> and Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>.
Maintained by Virgile Baudrot. Last updated 6 months ago.
10.5 match 3.26 score 60 scriptscran
drc:Analysis of Dose-Response Curves
Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Maintained by Christian Ritz. Last updated 9 years ago.
4.0 match 8 stars 8.39 score 1.4k scripts 28 dependents
alanarnholt
BSDA:Basic Statistics and Data Analysis
Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.
Maintained by Alan T. Arnholt. Last updated 2 years ago.
3.4 match 7 stars 9.11 score 1.3k scripts 6 dependentscran
boot:Bootstrap Functions (Originally by Angelo Canty for S)
Functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Maintained by Alessandra R. Brazzale. Last updated 7 months ago.
3.8 match 2 stars 8.21 score 2.3k dependents
poissonconsulting
wqbench:Calculate Aquatic Life Benchmarks
Download recent versions of the US EPA ECOTOX database. Clean, standardize and classify data so values are comparable. Use a SSD or deterministic method to determine the critical toxicity value and assessment factors to compute the aquatic life water quality benchmark for a compound.
Maintained by Angeline Tillmanns. Last updated 2 months ago.
5.8 match 4.86 score 5 scripts 1 dependentsleifeld
xergm.common:Common Infrastructure for Extensions of Exponential Random Graph Models
Datasets and definitions of generic functions used in dependencies of the 'xergm' package.
Maintained by Philip Leifeld. Last updated 5 years ago.
13.5 match 2.01 score 34 scripts 1 dependents
tmungle
allMT:Acute Lymphoblastic Leukemia Maintenance Therapy Analysis
Evaluates acute lymphoblastic leukemia maintenance therapy practice at patient and cohort level.
Maintained by Tushar Mungle. Last updated 26 days ago.
7.0 match 3.70 score 2 scripts
bgoussen
BeeGUTS:General Unified Threshold Model of Survival for Bees using Bayesian Inference
Tools to calibrate, validate, and make predictions with the General Unified Threshold model of Survival adapted for Bee species. The model is presented in the publication from Baas, J., Goussen, B., Miles, M., Preuss, T.G., Roessing, I. (2022) <doi:10.1002/etc.5423> and Baas, J., Goussen, B., Taenzler, V., Roeben, V., Miles, M., Preuss, T.G., van den Berg, S., Roessink, I. (2024) <doi:10.1002/etc.5871>, and is based on the GUTS framework Jager, T., Albert, C., Preuss, T.G. and Ashauer, R. (2011) <doi:10.1021/es103092a>. The authors are grateful to Bayer A.G. for its financial support.
Maintained by Benoit Goussen. Last updated 5 months ago.
4.9 match 3 stars 4.95 score 6 scriptsr-forge
Sleuth3:Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.
Maintained by Berwin A Turlach. Last updated 1 years ago.
3.8 match 6.38 score 522 scripts
veseshan
clinfun:Clinical Trial Design and Data Analysis Functions
Utilities to make your clinical collaborations easier if not fun. It contains functions for designing studies such as Simon 2-stage and group sequential designs and for data analysis such as Jonckheere-Terpstra test and estimating survival quantiles.
Maintained by Venkatraman E. Seshan. Last updated 1 years ago.
2.9 match 5 stars 7.86 score 124 scripts 8 dependents
pepijn-devries
ECOTOXr:Download and Extract Data from US EPA's ECOTOX Database
The US EPA ECOTOX database is a freely available database with a treasure of aquatic and terrestrial ecotoxicological data. As the online search interface doesn't come with an API, this package provides the means to easily access and search the database in R. To this end, all raw tables are downloaded from the EPA website and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.
Maintained by Pepijn de Vries. Last updated 6 days ago.
3.5 match 10 stars 6.20 score 6 scriptsr-forge
Sleuth2:Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.
Maintained by Berwin A Turlach. Last updated 1 years ago.
3.8 match 5.70 score 191 scripts
open-aims
bayesnec:A Bayesian No-Effect- Concentration (NEC) Algorithm
Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).
Maintained by Rebecca Fisher. Last updated 7 months ago.
bayesian-inferenceconcentration-responseecotoxicologyno-effect-concentrationnon-linear-decaythreshold-derivationtoxicology
2.6 match 13 stars 8.15 score 360 scripts
usepa
tcpl:ToxCast Data Analysis Pipeline
The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Maintained by Jason Brown. Last updated 4 days ago.
1.7 match 36 stars 9.41 score 90 scripts
catstats
misspi:Missing Value Imputation in Parallel
A framework that boosts the imputation of 'missForest' by Stekhoven, D.J. and Bühlmann, P. (2012) <doi:10.1093/bioinformatics/btr597> by harnessing parallel processing and through the fast Gradient Boosted Decision Trees (GBDT) implementation 'LightGBM' by Ke, Guolin et al.(2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>. 'misspi' has the following main advantages: 1. Allows embrassingly parallel imputation on large scale data. 2. Accepts a variety of machine learning models as methods with friendly user portal. 3. Supports multiple initializations methods. 4. Supports early stopping that prohibits unnecessary iterations.
Maintained by Zhongli Jiang. Last updated 3 months ago.
4.5 match 1 stars 3.18 score
dnzmarcio
ewoc:Escalation with Overdose Control
An implementation of a variety of escalation with overdose control designs introduced by Babb, Rogatko and Zacks (1998) <doi:10.1002/(SICI)1097-0258(19980530)17:10%3C1103::AID-SIM793%3E3.0.CO;2-9>. It calculates the next dose as a clinical trial proceeds and performs simulations to obtain operating characteristics.
Maintained by Marcio A. Diniz. Last updated 3 years ago.
3.8 match 2 stars 3.30 score 20 scripts
luzhangstat
phase1PRMD:Personalized Repeated Measurement Design for Phase I Clinical Trials
Implements Bayesian phase I repeated measurement design that accounts for multidimensional toxicity endpoints and longitudinal efficacy measure from multiple treatment cycles. The package provides flags to fit a variety of model-based phase I design, including 1 stage models with or without individualized dose modification, 3-stage models with or without individualized dose modification, etc. Functions are provided to recommend dosage selection based on the data collected in the available patient cohorts and to simulate trial characteristics given design parameters. Yin, Jun, et al. (2017) <doi:10.1002/sim.7134>.
Maintained by Lu Zhang. Last updated 5 years ago.
4.5 match 2.74 score 11 scripts
jessicaweiss
swimplot:Tools for Creating Swimmers Plots using 'ggplot2'
Used for creating swimmers plots with functions to customize the bars, add points, add lines, add text, and add arrows.
Maintained by Jessica Weiss. Last updated 4 years ago.
3.1 match 2 stars 3.76 score 29 scripts
christinayap
dtpcrm:Dose Transition Pathways for Continual Reassessment Method
Provides the dose transition pathways (DTP) to project in advance the doses recommended by a model-based design for subsequent patients (stay, escalate, deescalate or stop early) using all the accumulated toxicity information; See Yap et al (2017) <doi: 10.1158/1078-0432.CCR-17-0582>. DTP can be used as a design and an operational tool and can be displayed as a table or flow diagram. The 'dtpcrm' package also provides the modified continual reassessment method (CRM) and time-to-event CRM (TITE-CRM) with added practical considerations to allow stopping early when there is sufficient evidence that the lowest dose is too toxic and/or there is a sufficient number of patients dosed at the maximum tolerated dose.
Maintained by Christina Yap. Last updated 6 years ago.
5.6 match 2.00 score 10 scripts
artemis-toumazi
dfmeta:Meta-Analysis of Phase I Dose-Finding Early Clinical Trials
Meta-analysis approaches for Phase I dose finding early phases clinical trials in order to better suit requirements in terms of maximum tolerated dose (MTD) and maximal dose regimen (MDR). This package has currently three different approaches: (a) an approach proposed by Zohar et al, 2011, <doi:10.1002/sim.4121> (denoted as ZKO), (b) the Variance Weighted pooling analysis (called VarWT) and (c) the Random Effects Model Based (REMB) algorithm, where user can input his/her own model based approach or use the existing random effect logistic regression model (named as glimem) through the 'dfmeta' package.
Maintained by Artemis Toumazi. Last updated 7 years ago.
6.3 match 1.70 score 8 scriptsbioc
Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Maintained by Nan Xiao. Last updated 5 months ago.
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences
1.2 match 37 stars 7.81 score 29 scripts
tjaki
PK:Basic Non-Compartmental Pharmacokinetics
Estimation of pharmacokinetic parameters using non-compartmental theory.
Maintained by Thomas Jaki. Last updated 2 years ago.
3.3 match 2.59 score 13 scripts 1 dependentscran
ecotoxicology:Methods for Ecotoxicology
Implementation of the EPA's Ecological Exposure Research Division (EERD) tools (discontinued in 1999) for Probit and Trimmed Spearman-Karber Analysis. Probit and Spearman-Karber methods from Finney's book "Probit analysis a statistical treatment of the sigmoid response curve" with options for most accurate results or identical results to the book. Probit and all the tables from Finney's book (code-generated, not copied) with the generating functions included. Control correction: Abbott, Schneider-Orelli, Henderson-Tilton, Sun-Shepard. Toxicity scales: Horsfall-Barratt, Archer, Gauhl-Stover, Fullerton-Olsen, etc.
Maintained by Jose Gama. Last updated 9 years ago.
3.9 match 3 stars 1.89 score 26 scripts
jakobraymaekers
cellWise:Analyzing Data with Cellwise Outliers
Tools for detecting cellwise outliers and robust methods to analyze data which may contain them. Contains the implementation of the algorithms described in Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access) Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access), Raymaekers and Rousseeuw (2021) <doi:10.1080/00401706.2019.1677270> (open access), Raymaekers and Rousseeuw (2021) <doi:10.1007/s10994-021-05960-5> (open access), Raymaekers and Rousseeuw (2021) <doi:10.52933/jdssv.v1i3.18> (open access), Raymaekers and Rousseeuw (2022) <arXiv:2207.13493> (open access) Rousseeuw (2022) <doi:10.1016/j.ecosta.2023.01.007> (open access). Examples can be found in the vignettes: "DDC_examples", "MacroPCA_examples", "wrap_examples", "transfo_examples", "DI_examples", "cellMCD_examples" , "Correspondence_analysis_examples", and "cellwise_weights_examples".
Maintained by Jakob Raymaekers. Last updated 1 years ago.
1.2 match 2 stars 6.06 score 54 scripts 16 dependents
andschar
standartox:Ecotoxicological Information from the Standartox Database
The <http://standartox.uni-landau.de> database offers cleaned, harmonized and aggregated ecotoxicological test data, which can be used for assessing effects and risks of chemical concentrations found in the environment.
Maintained by Andreas Scharmüller. Last updated 3 years ago.
1.9 match 14 stars 3.85 score 1 scripts
rahmasarina
NMTox:Dose-Response Relationship Analysis of Nanomaterial Toxicity
Perform an exploration and a preliminary analysis on the dose- response relationship of nanomaterial toxicity. Several functions are provided for data exploration, including functions for creating a subset of dataset, frequency tables and plots. Inference for order restricted dose- response data is performed by testing the significance of monotonic dose-response relationship, using Williams, Marcus, M, Modified M and Likelihood ratio tests. Several methods of multiplicity adjustment are also provided. Description of the methods can be found in <https://github.com/rahmasarina/dose-response-analysis/blob/main/Methodology.pdf>.
Maintained by Rahmasari Nur Azizah. Last updated 3 years ago.
7.2 match 1.00 score
prabhanjan-tattar
gpk:100 Data Sets for Statistics Education
Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India. With their permission, first letter of their names forms the name of this package, the package has been built by me and made available for the benefit of R users. This collection requires a rich class of models and can be a very useful building block for a beginner.
Maintained by Prabhanjan Tattar. Last updated 12 years ago.
4.0 match 1.69 score 49 scripts
baddstats
scuba:Diving Calculations and Decompression Models
Code for describing and manipulating scuba diving profiles (depth-time curves) and decompression models, for calculating the predictions of decompression models, for calculating maximum no-decompression time and decompression tables, and for performing mixed gas calculations.
Maintained by Adrian Baddeley. Last updated 2 years ago.
2.0 match 5 stars 3.32 score 42 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
1.6 match 9 stars 3.77 score 13 scripts
bcgov
ssdtools:Species Sensitivity Distributions
Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for different species as described by Posthuma et al.(2001) <isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to fit distributions such as the gamma, log-logistic, log-normal and log-normal log-normal mixture. Multiple distributions can be averaged using Akaike Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by bootstrapping.
Maintained by Joe Thorley. Last updated 25 days ago.
ecotoxicologyenvspecies-sensitivity-distributioncpp
0.5 match 31 stars 10.23 score 111 scripts 4 dependents
jingzhuzhuzhu
bfboinet:Backfill Bayesian Optimal Interval Design Using Efficacy and Toxicity
The backfill Bayesian optimal interval design using efficacy and toxicity outcomes for dose optimization (BF-BOIN-ET) design is a novel clinical trial design to allow patients to be backfilled at lower doses during a dose-finding trial while prioritizing the dose-escalation cohort to explore a higher dose. The advantages compared to the other designs in terms of the percentage of correct optimal dose (OD) selection, reducing the sample size, and shortening the duration of the trial, in various realistic setting.
Maintained by Jing Zhu. Last updated 1 months ago.
3.3 match 1.30 score
c1au6i0
extractox:Extract Tox Info from Various Databases
Extract toxicological and chemical information from databases maintained by scientific agencies and resources, including the Comparative Toxicogenomics Database <https://ctdbase.org/>, the Integrated Chemical Environment <https://ice.ntp.niehs.nih.gov/>, the Integrated Risk Information System <https://cfpub.epa.gov/ncea/iris/>, Provisional Peer-Reviewed Toxicity Values <https://www.epa.gov/pprtv/provisional-peer-reviewed-toxicity-values-pprtvs-assessments>, the CompTox Chemicals Dashboard Resource Hub <https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard-resource-hub>, PubChem <https://pubchem.ncbi.nlm.nih.gov/>, and others.
Maintained by Claudio Zanettini. Last updated 1 months ago.
0.8 match 3 stars 4.59 score 3 scriptscran
rmp:Rounded Mixture Package
Performs univariate probability mass function estimation via Bayesian nonparametric mixtures of rounded kernels as in Canale and Dunson (2011) <doi:10.1198/jasa.2011.tm10552>.
Maintained by Antonio Canale. Last updated 1 years ago.
3.5 match 1.00 score
heli-xu
findSVI:Calculate Social Vulnerability Index for Communities
Developed by CDC/ATSDR (Centers for Disease Control and Prevention/ Agency for Toxic Substances and Disease Registry), Social Vulnerability Index (SVI) serves as a tool to assess the resilience of communities by taking into account socioeconomic and demographic factors. Provided with year(s), region(s) and a geographic level of interest, 'findSVI' retrieves required variables from US census data and calculates SVI for communities in the specified area based on CDC/ATSDR SVI documentation. Reference for the calculation methods: Flanagan BE, Gregory EW, Hallisey EJ, Heitgerd JL, Lewis B (2011) <doi:10.2202/1547-7355.1792>.
Maintained by Heli Xu. Last updated 1 months ago.
0.5 match 12 stars 5.68 score 16 scripts
lsubioscomputing
titeIR:Isotonic Designs for Phase 1 Trials with Late-Onset Toxicities
Functions to design phase 1 trials using an isotonic regression based design incorporating time-to-event information. Simulation and design functions are available, which incorporate information about followup and DLTs, and apply isotonic regression to devise estimates of DLT probability.
Maintained by Lee McDaniel. Last updated 6 years ago.
2.8 match 1.00 score 2 scripts
cran
TEQR:Target Equivalence Range Design
The TEQR package contains software to calculate the operating characteristics for the TEQR and the ACT designs.The TEQR (toxicity equivalence range) design is a toxicity based cumulative cohort design with added safety rules. The ACT (Activity constrained for toxicity) design is also a cumulative cohort design with additional safety rules. The unique feature of this design is that dose is escalated based on lack of activity rather than on lack of toxicity and is de-escalated only if an unacceptable level of toxicity is experienced.
Maintained by M. Suzette Blanchard. Last updated 9 years ago.
2.8 match 1.00 score 7 scripts
farbfetzen
stressaddition:Modelling Tri-Phasic Concentration-Response Relationships
The stress addition approach is an alternative to the traditional concentration addition or effect addition models. It allows the modelling of tri-phasic concentration-response relationships either as single toxicant experiments, in combination with an environmental stressor or as mixtures of two toxicants. See Liess et al. (2019) <doi:10.1038/s41598-019-51645-4> and Liess et al. (2020) <doi:10.1186/s12302-020-00394-7>.
Maintained by Sebastian Henz. Last updated 4 years ago.
2.6 match 1 stars 1.00 score 1 scripts
zemmourc
UBCRM:Simulate and Conduct Dose-Escalation Phase I Studies
Two Phase I designs are implemented in the package: the classical 3+3 and the Continual Reassessment Method (<doi:10.2307/2531628>). Simulations tools are also available to estimate the operating characteristics of the methods with several user-dependent options.
Maintained by Christophe Zemmour. Last updated 11 months ago.
1.9 match 1.00 score 9 scripts
poissonconsulting
shinywqbench:R Shiny App to Calculates Aquatic Life Benchmarks
This package is the user interface to the wqbench R package and allows users to easily access standardized ecotoxicology data for thousands of chemicals. Either a SSD or deterministic method is used to determine the critical toxicity value and assessment factors to compute the aquatic life water quality benchmark for a compound.
Maintained by Angeline Tillmanns. Last updated 2 months ago.
0.5 match 2.95 score 2 scripts
wgost
tsdf:Two-/Three-Stage Designs for Phase 1&2 Clinical Trials
Calculate optimal Zhong's two-/three-stage Phase II designs (see Zhong (2012) <doi:10.1016/j.cct.2012.07.006>). Generate Target Toxicity decision table for Phase I dose-finding (two-/three-stage). This package also allows users to run dose-finding simulations based on customized decision table.
Maintained by Wenchuan Guo. Last updated 5 years ago.
0.5 match 2.78 score 12 scripts
mattreusswig
reasonabletools:Clean Water Quality Data for NPDES Reasonable Potential Analyses
Functions for cleaning and summarising water quality data for use in National Pollutant Discharge Elimination Service (NPDES) permit reasonable potential analyses and water quality-based effluent limitation calculations. Procedures are based on those contained in the "Technical Support Document for Water Quality-based Toxics Control", United States Environmental Protection Agency (1991).
Maintained by Matthew Reusswig. Last updated 4 years ago.
censored-datanpdesnpdes-permit-developmentreasonable-potential-analysiswater-quality
0.5 match 2.70 score 1 scriptscran
higlasso:Hierarchical Integrative Group LASSO
Environmental health studies are increasingly measuring multiple pollutants to characterize the joint health effects attributable to exposure mixtures. However, the underlying dose-response relationship between toxicants and health outcomes of interest may be highly nonlinear, with possible nonlinear interaction effects. Hierarchical integrative group least absolute shrinkage and selection operator (HiGLASSO), developed by Boss et al (2020) <arXiv:2003.12844>, is a general framework to identify noteworthy nonlinear main and interaction effects in the presence of group structures among a set of exposures.
Maintained by Alexander Rix. Last updated 5 years ago.
0.5 match 2.70 scorecran
SEARS:Seamless Dose Escalation/Expansion with Adaptive Randomization Scheme
A seamless design that combines phase I dose escalation based on toxicity with phase II dose expansion and dose comparison based on efficacy.
Maintained by Chia-Wei Hsu. Last updated 2 years ago.
0.5 match 2.00 score 2 scriptscran
pocrm:Dose Finding in Drug Combination Phase I Trials Using PO-CRM
Provides functions to implement and simulate the partial order continual reassessment method (PO-CRM) of Wages, Conaway and O'Quigley (2011) <doi:10.1177/1740774511408748> for use in Phase I trials of combinations of agents. Provides a function for generating a set of initial guesses (skeleton) for the toxicity probabilities at each combination that correspond to the set of possible orderings of the toxicity probabilities specified by the user.
Maintained by "Brewer, Ben (arb5mt)". Last updated 4 years ago.
0.8 match 1.20 score 16 scriptscran
HybridDesign:Hybrid Design for Phase I Dose-Finding Studies
The Hybrid design is a combination of model-assisted design (e.g., the modified Toxicity Probability Interval design) with dose-toxicity model-based design for phase I dose-finding studies. The hybrid design controls the overdosing toxicity well and leads to a recommended dose closer to the true maximum tolerated dose (MTD) due to its ability to calibrate for an intermediate dose. More details can be found in Liao et al. 2022 <doi:10.1002/ijc.34203>.
Maintained by Heng Zhou. Last updated 2 years ago.
0.9 match 1.00 score
jhjourdan
dfcomb:Phase I/II Adaptive Dose-Finding Design for Combination Studies
Phase I/II adaptive dose-finding design for combination studies where toxicity rates are supposed to increase with both agents.
Maintained by Jacques-Henri Jourdan. Last updated 6 months ago.
0.5 match 1 stars 1.00 score 4 scriptscran
gen2stage:Generalized Two-Stage Designs for Phase II Single-Arm Studies
One can find single-stage and two-stage designs for a phase II single-arm study with either efficacy or safety/toxicity endpoints as described in Kim and Wong (2019) <doi:10.29220/CSAM.2019.26.2.163>.
Maintained by Seongho Kim. Last updated 6 years ago.
0.5 match 1.00 scorecran
Phase12Compare:Simulates SPSO and Efftox Phase 12 Trials with Correlated Outcomes
Simulating and conducting four phase 12 clinical trials with correlated binary bivariate outcomes described. Uses the 'Efftox' (efficacy and toxicity tradeoff, <https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware/Index/2>) and SPSO (Semi-Parametric Stochastic Ordering) models with Utility and Desirability based objective functions for dose finding.
Maintained by Andrew G Chapple. Last updated 5 years ago.
0.5 match 1.00 scorecran
MinEDfind:A Bayesian Design for Minimum Effective Dosing-Finding Trial
The nonparametric two-stage Bayesian adaptive design is a novel phase II clinical trial design for finding the minimum effective dose (MinED). This design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. It is used to design single-agent trials.
Maintained by Chia-Wei Hsu. Last updated 5 years ago.
0.5 match 1.00 score