Showing 200 of total 1369 results (show query)
ropensci
rredlist:'IUCN' Red List Client
'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
Maintained by William Gearty. Last updated 1 months ago.
iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize
60.3 match 53 stars 11.49 score 195 scripts 24 dependents
pharmar
riskmetric:Risk Metrics to Evaluating R Packages
Facilities for assessing R packages against a number of metrics to help quantify their robustness.
Maintained by Eli Miller. Last updated 9 days ago.
57.5 match 167 stars 8.89 score 43 scripts
equitable-equations
fqar:Floristic Quality Assessment Tools for R
Tools for downloading and analyzing floristic quality assessment data. See Freyman et al. (2015) <doi:10.1111/2041-210X.12491> for more information about floristic quality assessment and the associated database.
Maintained by Andrew Gard. Last updated 2 months ago.
43.9 match 5 stars 5.88 score 5 scripts
blue-matter
SAMtool:Stock Assessment Methods Toolkit
Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Maintained by Quang Huynh. Last updated 19 days ago.
38.1 match 3 stars 6.49 score 36 scripts 1 dependents
bioc
ShortRead:FASTQ input and manipulation
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
17.8 match 8 stars 12.08 score 1.8k scripts 49 dependents
mcguinlu
robvis:Visualize the Results of Risk-of-Bias (ROB) Assessments
Helps users in quickly visualizing risk-of-bias assessments performed as part of a systematic review. It allows users to create weighted bar-plots of the distribution of risk-of-bias judgments within each bias domain, in addition to traffic-light plots of the specific domain-level judgments for each study. The resulting figures are of publication quality and are formatted according the risk-of-bias assessment tool use to perform the assessments. Currently, the supported tools are ROB2.0 (for randomized controlled trials; Sterne et al (2019) <doi:10.1136/bmj.l4898>), ROBINS-I (for non-randomised studies of interventions; Sterne (2016) <doi:10.1136/bmj.i4919>), and Quality & Applicability of Diagnostic Accuracy Studies V2 (Whiting et al (2011) <doi:10.7326/0003-4819-155-8-201110180-00009>), and QUIPS (Hayden et al (2013) <doi:10.7326/0003-4819-158-4-201302190-00009>.
Maintained by Luke McGuinness. Last updated 2 years ago.
evidence-synthesisrisk-of-biassystematic-reviewsvisualisation
24.6 match 59 stars 7.99 score 67 scripts
fishr-core-team
FSA:Simple Fisheries Stock Assessment Methods
A variety of simple fish stock assessment methods.
Maintained by Derek H. Ogle. Last updated 2 months ago.
fishfisheriesfisheries-managementfisheries-stock-assessmentpopulation-dynamicsstock-assessment
17.8 match 68 stars 11.08 score 1.7k scripts 6 dependents
kosukeimai
MatchIt:Nonparametric Preprocessing for Parametric Causal Inference
Selects matched samples of the original treated and control groups with similar covariate distributions -- can be used to match exactly on covariates, to match on propensity scores, or perform a variety of other matching procedures. The package also implements a series of recommendations offered in Ho, Imai, King, and Stuart (2007) <DOI:10.1093/pan/mpl013>. (The 'gurobi' package, which is not on CRAN, is optional and comes with an installation of the Gurobi Optimizer, available at <https://www.gurobi.com>.)
Maintained by Noah Greifer. Last updated 1 days ago.
11.9 match 220 stars 15.03 score 2.4k scripts 21 dependents
pbs-assess
sdmTMB:Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Implements spatial and spatiotemporal GLMMs (Generalized Linear Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial Differential Equation) Gaussian Markov random field approximation to Gaussian random fields. One common application is for spatially explicit species distribution models (SDMs). See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.
Maintained by Sean C. Anderson. Last updated 1 days ago.
ecologyglmmspatial-analysisspecies-distribution-modellingtmbcpp
16.5 match 203 stars 10.71 score 848 scripts 1 dependents
pharmaverse
admiralonco:Oncology Extension Package for ADaM in 'R' Asset Library
Programming oncology specific 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>). The package is an extension package of the 'admiral' package.
Maintained by Stefan Bundfuss. Last updated 2 months ago.
20.2 match 32 stars 8.66 score 30 scripts
arni-magnusson
scape:Statistical Catch-at-Age Plotting Environment
Import, plot, and diagnose results from statistical catch-at-age models, used in fisheries stock assessment.
Maintained by Arni Magnusson. Last updated 5 months ago.
30.5 match 5.72 score 35 scripts
tidymodels
rsample:General Resampling Infrastructure
Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Maintained by Hannah Frick. Last updated 5 days ago.
10.4 match 341 stars 16.72 score 5.2k scripts 79 dependents
nmfs-ost
asar:Build NOAA Stock Assessment Report
Build a full or update stock assessment report for any stock assessment model. Parameterization allows the user to call a template based on their regional science center, species, area, ect.
Maintained by Samantha Schiano. Last updated 6 days ago.
latexquartostock-assessment-reports
21.6 match 21 stars 6.87 score 3 scriptsbioc
cogeqc:Systematic quality checks on comparative genomics analyses
cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.
Maintained by Fabrรญcio Almeida-Silva. Last updated 5 months ago.
softwaregenomeassemblycomparativegenomicsfunctionalgenomicsphylogeneticsqualitycontrolnetworkcomparative-genomicsevolutionary-genomics
24.2 match 10 stars 6.08 score 20 scriptsbioc
affycomp:Graphics Toolbox for Assessment of Affymetrix Expression Measures
The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.
Maintained by Robert D. Shear. Last updated 5 months ago.
onechannelmicroarraypreprocessing
23.0 match 5.92 score 14 scripts
tmsalab
edmdata:Data Sets for Psychometric Modeling
Collection of data sets from various assessments that can be used to evaluate psychometric models. These data sets have been analyzed in the following papers that introduced new methodology as part of the application section: Jimenez, A., Balamuta, J. J., & Culpepper, S. A. (2023) <doi:10.1111/bmsp.12307>, Culpepper, S. A., & Balamuta, J. J. (2021) <doi:10.1080/00273171.2021.1985949>, Yinghan Chen et al. (2021) <doi:10.1007/s11336-021-09750-9>, Yinyin Chen et al. (2020) <doi:10.1007/s11336-019-09693-2>, Culpepper, S. A. (2019a) <doi:10.1007/s11336-019-09683-4>, Culpepper, S. A. (2019b) <doi:10.1007/s11336-018-9643-8>, Culpepper, S. A., & Chen, Y. (2019) <doi:10.3102/1076998618791306>, Culpepper, S. A., & Balamuta, J. J. (2017) <doi:10.1007/s11336-015-9484-7>, and Culpepper, S. A. (2015) <doi:10.3102/1076998615595403>.
Maintained by James Joseph Balamuta. Last updated 6 months ago.
cognitive-diagnostic-modelsdataedm
29.7 match 5 stars 4.18 score 7 scripts 1 dependents
maelstrom-research
madshapR:Support Technical Processes Following 'Maelstrom Research' Standards
Functions to support rigorous processes in data cleaning, evaluation, and documentation across datasets from different studies based on Maelstrom Research guidelines. The package includes the core functions to evaluate and format the main inputs that define the process, diagnose errors, and summarize and evaluate datasets and their associated data dictionaries. The main outputs are clean datasets and associated metadata, and tabular and visual summary reports. As described in Maelstrom Research guidelines for rigorous retrospective data harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).
Maintained by Guillaume Fabre. Last updated 11 months ago.
22.9 match 2 stars 5.40 score 28 scripts 3 dependents
rapidsurveys
oldr:An Implementation of Rapid Assessment Method for Older People
An implementation of the Rapid Assessment Method for Older People or RAM-OP <https://www.helpage.org/resource/rapid-assessment-method-for-older-people-ramop-manual/>. It provides various functions that allow the user to design and plan the assessment and analyse the collected data. RAM-OP provides accurate and reliable estimates of the needs of older people.
Maintained by Ernest Guevarra. Last updated 1 months ago.
assessmentdata-analysisodkram-oprapid-assessment
24.2 match 2 stars 5.00 score 4 scripts
r4ss
r4ss:R Code for Stock Synthesis
A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.23.1, from December 2024). Support for 3.24 models is only through the core functions for reading output and plotting.
Maintained by Ian G. Taylor. Last updated 4 days ago.
fisheriesfisheries-stock-assessmentstock-synthesis
10.3 match 43 stars 11.38 score 1.0k scripts 2 dependents
guido-s
meta:General Package for Meta-Analysis
User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rรผcker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015): - common effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - three-level meta-analysis model; - generalised linear mixed model; - logistic regression with penalised likelihood for rare events; - Hartung-Knapp method for random effects model; - Kenward-Roger method for random effects model; - prediction interval; - statistical tests for funnel plot asymmetry; - trim-and-fill method to evaluate bias in meta-analysis; - meta-regression; - cumulative meta-analysis and leave-one-out meta-analysis; - import data from 'RevMan 5'; - produce forest plot summarising several (subgroup) meta-analyses.
Maintained by Guido Schwarzer. Last updated 25 days ago.
7.8 match 84 stars 14.84 score 2.3k scripts 29 dependents
tokami
TropFishR:Tropical Fisheries Analysis
A compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (<http://www.fao.org/documents/card/en/c/9bb12a06-2f05-5dcb-a6ca-2d6dd3080f65/>), as well as other more recent methods.
Maintained by Tobias K. Mildenberger. Last updated 5 months ago.
assessmentfao-manualfishfish-stocks
13.7 match 25 stars 8.12 score 149 scripts
smouksassi
coveffectsplot:Produce Forest Plots to Visualize Covariate Effects
Produce forest plots to visualize covariate effects using either the command line or an interactive 'Shiny' application.
Maintained by Samer Mouksassi. Last updated 1 months ago.
13.9 match 32 stars 7.86 score 40 scripts
fishr-core-team
FSAdata:Data to Support Fish Stock Assessment ('FSA') Package
The datasets to support the Fish Stock Assessment ('FSA') package.
Maintained by Derek Ogle. Last updated 2 years ago.
fishfisheriesfisheries-stock-assessmentfishr-websitestock-assessment
17.6 match 13 stars 5.75 score 285 scriptsbioc
msPurity:Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.
Maintained by Thomas N. Lawson. Last updated 5 months ago.
massspectrometrymetabolomicssoftwarebioconductor-packagedimsfragmentationlc-mslc-msmsmass-spectrometryprecursor-ion-purity
13.6 match 15 stars 7.03 score 44 scripts
flr
FLSAM:An Implementation of the State-Space Assessment Model for FLR
This package provides an FLR wrapper to the SAM state-space assessment model.
Maintained by N.T. Hintzen. Last updated 3 months ago.
21.0 match 4 stars 4.51 score 406 scripts
floschuberth
cSEM:Composite-Based Structural Equation Modeling
Estimate, assess, test, and study linear, nonlinear, hierarchical and multigroup structural equation models using composite-based approaches and procedures, including estimation techniques such as partial least squares path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc), generalized structured component analysis (GSCA), generalized structured component analysis with uniqueness terms (GSCAm), generalized canonical correlation analysis (GCCA), principal component analysis (PCA), factor score regression (FSR) using sum score, regression or Bartlett scores (including bias correction using Croonโs approach), as well as several tests and typical postestimation procedures (e.g., verify admissibility of the estimates, assess the model fit, test the model fit etc.).
Maintained by Florian Schuberth. Last updated 16 days ago.
9.7 match 28 stars 9.11 score 56 scripts 2 dependentsbioc
OLIN:Optimized local intensity-dependent normalisation of two-color microarrays
Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data
Maintained by Matthias Futschik. Last updated 5 months ago.
microarraytwochannelqualitycontrolpreprocessingvisualization
17.7 match 4.78 score 2 scripts 1 dependents
patriciamar
ShinyItemAnalysis:Test and Item Analysis via Shiny
Package including functions and interactive shiny application for the psychometric analysis of educational tests, psychological assessments, health-related and other types of multi-item measurements, or ratings from multiple raters.
Maintained by Patricia Martinkova. Last updated 1 months ago.
assessmentdifferential-item-functioningitem-analysisitem-response-theorypsychometricsshiny
10.5 match 44 stars 7.88 score 105 scripts 3 dependentsropensci
waywiser:Ergonomic Methods for Assessing Spatial Models
Assessing predictive models of spatial data can be challenging, both because these models are typically built for extrapolating outside the original region represented by training data and due to potential spatially structured errors, with "hot spots" of higher than expected error clustered geographically due to spatial structure in the underlying data. Methods are provided for assessing models fit to spatial data, including approaches for measuring the spatial structure of model errors, assessing model predictions at multiple spatial scales, and evaluating where predictions can be made safely. Methods are particularly useful for models fit using the 'tidymodels' framework. Methods include Moran's I ('Moran' (1950) <doi:10.2307/2332142>), Geary's C ('Geary' (1954) <doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995) <doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from 'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement metrics from 'Willmott' (1981) (<doi: 10.1080/02723646.1981.10642213>) and 'Willmott' 'et' 'al'. (2012) (<doi: 10.1002/joc.2419>), an implementation of the area of applicability methodology from 'Meyer' and 'Pebesma' (2021) (<doi:10.1111/2041-210X.13650>), and an implementation of multi-scale assessment as described in 'Riemann' 'et' 'al'. (2010) (<doi:10.1016/j.rse.2010.05.010>).
Maintained by Michael Mahoney. Last updated 12 days ago.
spatialspatial-analysistidymodelstidyverse
11.7 match 37 stars 6.87 score 19 scripts
centerforassessment
SGPdata:Exemplar Data Sets for Student Growth Percentiles (SGP) Analyses
Data sets utilized by the 'SGP' package as exemplars for users to conduct their own student growth percentiles (SGP) analyses.
Maintained by Damian W. Betebenner. Last updated 3 months ago.
sgpsgp-analysessgp-datastudent-growth-percentilesstudent-growth-projections
13.9 match 2 stars 5.75 score 36 scripts
trevorhastie
glmnet:Lasso and Elastic-Net Regularized Generalized Linear Models
Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression, Cox model, multiple-response Gaussian, and the grouped multinomial regression; see <doi:10.18637/jss.v033.i01> and <doi:10.18637/jss.v039.i05>. There are two new and important additions. The family argument can be a GLM family object, which opens the door to any programmed family (<doi:10.18637/jss.v106.i01>). This comes with a modest computational cost, so when the built-in families suffice, they should be used instead. The other novelty is the relax option, which refits each of the active sets in the path unpenalized. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers cited.
Maintained by Trevor Hastie. Last updated 2 years ago.
5.2 match 82 stars 15.15 score 22k scripts 736 dependents
bioc
AssessORF:Assess Gene Predictions Using Proteomics and Evolutionary Conservation
In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomic hits and evolutionarily conserved start codons as the forms of evidence.
Maintained by Deepank Korandla. Last updated 5 months ago.
comparativegenomicsgenepredictiongenomeannotationgeneticsproteomicsqualitycontrolvisualization
17.5 match 4.18 score 3 scripts
tbep-tech
tbeptools:Data and Indicators for the Tampa Bay Estuary Program
Several functions are provided for working with Tampa Bay Estuary Program data and indicators, including the water quality report card, tidal creek assessments, Tampa Bay Nekton Index, Tampa Bay Benthic Index, seagrass transect data, habitat report card, and fecal indicator bacteria. Additional functions are provided for miscellaneous tasks, such as reference library curation.
Maintained by Marcus Beck. Last updated 9 days ago.
data-analysistampa-baytbepwater-quality
9.2 match 10 stars 7.86 score 133 scriptscenterforassessment
SGP:Student Growth Percentiles & Percentile Growth Trajectories
An analytic framework for the calculation of norm- and criterion-referenced academic growth estimates using large scale, longitudinal education assessment data as developed in Betebenner (2009) <doi:10.1111/j.1745-3992.2009.00161.x>.
Maintained by Damian W. Betebenner. Last updated 2 months ago.
percentile-growth-projectionsquantile-regressionsgpsgp-analysesstudent-growth-percentilesstudent-growth-projections
7.5 match 20 stars 9.69 score 88 scriptsropensci
ramlegacy:Download and Read RAM Legacy Stock Assessment Database
Contains functions to download, cache and read in 'Excel' version of the RAM Legacy Stock Assessment Data Base, an online compilation of stock assessment results for commercially exploited marine populations from around the world. The database is named after Dr. Ransom A. Myers whose original stock-recruitment database, is no longer being updated. More information about the database can be found at <https://ramlegacy.org/>. Ricard, D., Minto, C., Jensen, O.P. and Baum, J.K. (2012) <doi:10.1111/j.1467-2979.2011.00435.x>.
Maintained by Kshitiz Gupta. Last updated 5 years ago.
fisheriesmarine-biologyramlegacyropenscistock-assessment
13.9 match 5 stars 5.11 score 26 scripts
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 2 days ago.
6.7 match 30 stars 10.54 score 65 scripts 93 dependents
stocnet
RSiena:Siena - Simulation Investigation for Empirical Network Analysis
The main purpose of this package is to perform simulation-based estimation of stochastic actor-oriented models for longitudinal network data collected as panel data. Dependent variables can be single or multivariate networks, which can be directed, non-directed, or two-mode; and associated actor variables. There are also functions for testing parameters and checking goodness of fit. An overview of these models is given in Snijders (2017), <doi:10.1146/annurev-statistics-060116-054035>.
Maintained by Tom A.B. Snijders. Last updated 1 months ago.
longitudinal-datarsienasocial-network-analysisstatistical-network-analysisstatisticscpp
7.0 match 107 stars 9.93 score 346 scripts 1 dependentsbioc
survcomp:Performance Assessment and Comparison for Survival Analysis
Assessment and Comparison for Performance of Risk Prediction (Survival) Models.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressiondifferentialexpressionvisualizationcpp
8.2 match 8.46 score 448 scripts 12 dependents
allenzhuaz
PPQplan:Process Performance Qualification (PPQ) Plans in Chemistry, Manufacturing and Controls (CMC) Statistical Analysis
Assessment for statistically-based PPQ sampling plan, including calculating the passing probability, optimizing the baseline and high performance cutoff points, visualizing the PPQ plan and power dynamically. The analytical idea is based on the simulation methods from the textbook Burdick, R. K., LeBlond, D. J., Pfahler, L. B., Quiroz, J., Sidor, L., Vukovinsky, K., & Zhang, L. (2017). Statistical Methods for CMC Applications. In Statistical Applications for Chemistry, Manufacturing and Controls (CMC) in the Pharmaceutical Industry (pp. 227-250). Springer, Cham.
Maintained by Yalin Zhu. Last updated 3 years ago.
biostatisticspharmaceuticalssampling-methods
16.2 match 1 stars 4.11 score 13 scriptsbioc
miRcomp:Tools to assess and compare miRNA expression estimatation methods
Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.
Maintained by Matthew N. McCall. Last updated 5 months ago.
softwareqpcrpreprocessingqualitycontrol
19.7 match 3.30 score 1 scripts
core-bioinformatics
ClustAssess:Tools for Assessing Clustering
A set of tools for evaluating clustering robustness using proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014) <doi:10.1038/srep06207>), as well as similarity across methods and method stability using element-centric clustering comparison (Gates et al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package enables stability-based parameter assessment for graph-based clustering pipelines typical in single-cell data analysis.
Maintained by Andi Munteanu. Last updated 1 months ago.
softwaresinglecellrnaseqatacseqnormalizationpreprocessingdimensionreductionvisualizationqualitycontrolclusteringclassificationannotationgeneexpressiondifferentialexpressionbioinformaticsgenomicsmachine-learningparameter-optimizationrobustnesssingle-cellunsupervised-learningcpp
11.1 match 23 stars 5.70 score 18 scriptsbioc
nullranges:Generation of null ranges via bootstrapping or covariate matching
Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.
Maintained by Michael Love. Last updated 5 months ago.
visualizationgenesetenrichmentfunctionalgenomicsepigeneticsgeneregulationgenetargetgenomeannotationannotationgenomewideassociationhistonemodificationchipseqatacseqdnaseseqrnaseqhiddenmarkovmodelbioconductorbootstrapgenomicsmatchingstatistics
7.7 match 27 stars 8.16 score 50 scripts 1 dependents
american-institutes-for-research
EdSurvey:Analysis of NCES Education Survey and Assessment Data
Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/en/about/directorates/directorate-for-education-and-skills.html>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education Study (CivEd).
Maintained by Paul Bailey. Last updated 15 days ago.
7.9 match 10 stars 7.86 score 139 scripts 1 dependents
geomorphr
geomorph:Geometric Morphometric Analyses of 2D and 3D Landmark Data
Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
Maintained by Dean Adams. Last updated 1 months ago.
5.2 match 76 stars 12.05 score 700 scripts 6 dependentsfishr-core-team
RFishBC:Back-Calculation of Fish Length
Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software (<https://fisheries.org/bookstore/all-titles/software/70317/>).
Maintained by Derek H. Ogle. Last updated 1 years ago.
fishfisheriesfisheries-managementfisheries-stock-assessmentpopulation-dynamicsstock-assessment
14.2 match 13 stars 4.26 score 28 scripts
ocbe-uio
BayesMallows:Bayesian Preference Learning with the Mallows Rank Model
An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>; Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>; Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Maintained by Oystein Sorensen. Last updated 1 months ago.
mallows-modelopenblascppopenmp
7.5 match 21 stars 7.91 score 36 scripts 1 dependents
easystats
performance:Assessment of Regression Models Performance
Utilities for computing measures to assess model quality, which are not directly provided by R's 'base' or 'stats' packages. These include e.g. measures like r-squared, intraclass correlation coefficient (Nakagawa, Johnson & Schielzeth (2017) <doi:10.1098/rsif.2017.0213>), root mean squared error or functions to check models for overdispersion, singularity or zero-inflation and more. Functions apply to a large variety of regression models, including generalized linear models, mixed effects models and Bayesian models. References: Lรผdecke et al. (2021) <doi:10.21105/joss.03139>.
Maintained by Daniel Lรผdecke. Last updated 18 days ago.
aiceasystatshacktoberfestloomachine-learningmixed-modelsmodelsperformancer2statistics
3.6 match 1.1k stars 16.17 score 4.3k scripts 47 dependents
asalavaty
influential:Identification and Classification of the Most Influential Nodes
Contains functions for the classification and ranking of top candidate features, reconstruction of networks from adjacency matrices and data frames, analysis of the topology of the network and calculation of centrality measures, and identification of the most influential nodes. Also, a function is provided for running SIRIR model, which is the combination of leave-one-out cross validation technique and the conventional SIR model, on a network to unsupervisedly rank the true influence of vertices. Additionally, some functions have been provided for the assessment of dependence and correlation of two network centrality measures as well as the conditional probability of deviation from their corresponding means in opposite direction. Fred Viole and David Nawrocki (2013, ISBN:1490523995). Csardi G, Nepusz T (2006). "The igraph software package for complex network research." InterJournal, Complex Systems, 1695. Adopted algorithms and sources are referenced in function document.
Maintained by Adrian Salavaty. Last updated 5 months ago.
centrality-measuresclassification-modelinfluence-rankingnetwork-analysispriaritization-model
9.0 match 27 stars 6.54 score 43 scripts 1 dependents
acorg
Racmacs:Antigenic Cartography Macros
A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.
Maintained by Sam Wilks. Last updated 9 months ago.
7.0 match 21 stars 8.06 score 362 scriptsbioc
Rmagpie:MicroArray Gene-expression-based Program In Error rate estimation
Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.
Maintained by Camille Maumet. Last updated 5 months ago.
17.1 match 3.30 score 1 scripts
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.
11.6 match 4.86 score 5 scripts 1 dependents
ices-tools-prod
icesSAG:Stock Assessment Graphs Database Web Services
R interface to access the web services of the ICES Stock Assessment Graphs database <https://sg.ices.dk>.
Maintained by Colin Millar. Last updated 5 months ago.
8.8 match 11 stars 6.24 score 131 scripts 2 dependents
tmatta
lsasim:Functions to Facilitate the Simulation of Large Scale Assessment Data
Provides functions to simulate data from large-scale educational assessments, including background questionnaire data and cognitive item responses that adhere to a multiple-matrix sampled design. The theoretical foundation can be found on Matta, T.H., Rutkowski, L., Rutkowski, D. et al. (2018) <doi:10.1186/s40536-018-0068-8>.
Maintained by Waldir Leoncio. Last updated 2 months ago.
8.5 match 6 stars 6.41 score 18 scripts
ggobi
GGally:Extension to 'ggplot2'
The R package 'ggplot2' is a plotting system based on the grammar of graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.
Maintained by Barret Schloerke. Last updated 10 months ago.
3.4 match 597 stars 16.15 score 17k scripts 154 dependents
fukayak
occumb:Site Occupancy Modeling for Environmental DNA Metabarcoding
Fits multispecies site occupancy models to environmental DNA metabarcoding data collected using spatially-replicated survey design. Model fitting results can be used to evaluate and compare the effectiveness of species detection to find an efficient survey design. Reference: Fukaya et al. (2022) <doi:10.1111/2041-210X.13732>.
Maintained by Keiichi Fukaya. Last updated 2 months ago.
10.1 match 2 stars 5.38 score 10 scripts
jranke
mkin:Kinetic Evaluation of Chemical Degradation Data
Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: 'Rtools') is installed, differential equation models are solved using automatically generated C functions. Non-constant errors can be taken into account using variance by variable or two-component error models <doi:10.3390/environments6120124>. Hierarchical degradation models can be fitted using nonlinear mixed-effects model packages as a back end <doi:10.3390/environments8080071>. Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Maintained by Johannes Ranke. Last updated 30 days ago.
degradationfocus-kineticskinetic-modelskineticsodeode-model
6.6 match 11 stars 8.18 score 78 scripts 1 dependentspharmaverse
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.
7.3 match 15 stars 7.40 score 143 scripts
ralmond
Proc4:Four Process Assessment Database and Dispatcher
Utilities for working with messages in the four four process architecture as json objects.
Maintained by Russell Almond. Last updated 1 years ago.
assessment-scoringevidence-centered-designmongodb-database
13.5 match 3.95 score 2 dependents
resplab
cumulcalib:Cumulative Calibration Assessment for Prediction Models
Tools for visualization of, and inference on, the calibration of prediction models on the cumulative domain. This provides a method for evaluating calibration of risk prediction models without having to group the data or use tuning parameters (e.g., loess bandwidth). This package implements the methodology described in Sadatsafavi and Patkau (2024) <doi:10.1002/sim.10138>. The core of the package is cumulcalib(), which takes in vectors of binary responses and predicted risks. The plot() and summary() methods are implemented for the results returned by cumulcalib().
Maintained by Mohsen Sadatsafavi. Last updated 9 months ago.
11.5 match 2 stars 4.60 score 8 scriptsbioc
EWCE:Expression Weighted Celltype Enrichment
Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.
Maintained by Alan Murphy. Last updated 30 days ago.
geneexpressiontranscriptiondifferentialexpressiongenesetenrichmentgeneticsmicroarraymrnamicroarrayonechannelrnaseqbiomedicalinformaticsproteomicsvisualizationfunctionalgenomicssinglecelldeconvolutionsingle-cellsingle-cell-rna-seqtranscriptomics
5.5 match 55 stars 9.28 score 99 scripts
r-forge
sandwich:Robust Covariance Matrix Estimators
Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. Details can be found in Zeileis et al. (2020) <doi:10.18637/jss.v095.i01>, Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.
Maintained by Achim Zeileis. Last updated 2 months ago.
3.4 match 14.92 score 11k scripts 887 dependents
adeverse
ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Maintained by Aurรฉlie Siberchicot. Last updated 12 days ago.
3.3 match 39 stars 14.96 score 2.2k scripts 256 dependentsbioc
Biostrings:Efficient manipulation of biological strings
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Maintained by Hervรฉ Pagรจs. Last updated 23 days ago.
sequencematchingalignmentsequencinggeneticsdataimportdatarepresentationinfrastructurebioconductor-packagecore-package
2.8 match 61 stars 17.83 score 8.6k scripts 1.2k dependents
brancaccioandrea
mycaas:My Computerized Adaptive Assessment
Implementation of adaptive assessment procedures based on Knowledge Space Theory (KST) and Formal Psychological Assessment (FPA) frameworks. An adaptive assessment is a type of evaluation that adjusts the difficulty and nature of subsequent questions based on the test-taker's responses to previous ones. The package contains functions to perform and simulate an adaptive assessment. Moreover, it is integrated with two 'Shiny' interfaces, making it both accessible and user-friendly. The package has been funded by the European Union - NextGenerationEU and by the Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.5, project โRAISE - Robotics and AI for Socio-economic Empowermentโ (ECS00000035).
Maintained by Andrea Brancaccio. Last updated 6 months ago.
21.4 match 2.30 scorebioc
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 3 days ago.
immunooncologymicroarraysequencingmetabolomicsmetagenomicsproteomicsgenepredictionmultiplecomparisonclassificationregressionbioconductorgenomicsgenomics-datagenomics-visualizationmultivariate-analysismultivariate-statisticsomicsr-pkgr-project
3.6 match 182 stars 13.71 score 1.3k scripts 22 dependents
calbertsen
multiStockassessment:Fitting Multiple State-Space Assessment Models
Fitting multiple SAM models.
Maintained by Christoffer Moesgaard Albertsen. Last updated 3 months ago.
fisheriesfisheries-stock-assessmentstock-assessmentstockassessmentcpp
17.1 match 5 stars 2.88 score 5 scripts
cefasrepres
EcoEnsemble:A General Framework for Combining Ecosystem Models
Fit and sample from the ensemble model described in Spence et al (2018): "A general framework for combining ecosystem models"<doi:10.1111/faf.12310>.
Maintained by Michael A. Spence. Last updated 1 months ago.
8.0 match 1 stars 6.07 score 19 scriptsbioc
tidytof:Analyze High-dimensional Cytometry Data Using Tidy Data Principles
This package implements an interactive, scientific analysis pipeline for high-dimensional cytometry data built using tidy data principles. It is specifically designed to play well with both the tidyverse and Bioconductor software ecosystems, with functionality for reading/writing data files, data cleaning, preprocessing, clustering, visualization, modeling, and other quality-of-life functions. tidytof implements a "grammar" of high-dimensional cytometry data analysis.
Maintained by Timothy Keyes. Last updated 5 months ago.
singlecellflowcytometrybioinformaticscytometrydata-sciencesingle-celltidyversecpp
6.7 match 19 stars 7.26 score 35 scriptsbioc
evaluomeR:Evaluation of Bioinformatics Metrics
Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.
Maintained by Josรฉ Antonio Bernabรฉ-Dรญaz. Last updated 5 months ago.
clusteringclassificationfeatureextractionassessmentclustering-evaluationevaluomeevaluomermetrics
10.0 match 4.82 score 33 scriptsbioc
MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Maintained by Laurent Gatto. Last updated 2 days ago.
immunooncologyinfrastructureproteomicsmassspectrometryqualitycontroldataimportbioconductorbioinformaticsmass-spectrometryproteomics-datavisualisationcpp
3.6 match 130 stars 12.81 score 772 scripts 36 dependents
uqwang
chest:Change-in-Estimate Approach to Assess Confounding Effects
Applies the change-in-effect estimate method to assess confounding effects in medical and epidemiological research (Greenland & Pearce (2016) <doi:10.1146/annurev-publhealth-031914-122559> ). It starts with a crude model including only the outcome and exposure variables. At each of the subsequent steps, one variable which creates the largest change among the remaining variables is selected. This process is repeated until all variables have been entered into the model (Wang Z. Stata Journal 2007; 7, Number 2, pp. 183โ196). Currently, the 'chest' package has functions for linear regression, logistic regression, negative binomial regression, Cox proportional hazards model and conditional logistic regression.
Maintained by Zhiqiang Wang. Last updated 2 years ago.
16.5 match 2.78 score 12 scripts
cran
datarobot:'DataRobot' Predictive Modeling API
For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Maintained by AJ Alon. Last updated 1 years ago.
13.2 match 2 stars 3.48 score
alexanderrobitzsch
CDM:Cognitive Diagnosis Modeling
Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. This package enables the estimation of the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>), the multiple group (polytomous) GDINA model (de la Torre, 2011, <doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009, <doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008, <doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992, <doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis (Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>). See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02> or Robitzsch and George (2019, <doi:10.1007/978-3-030-05584-4_26>) for further details on estimation and the package structure. For tutorials on how to use the CDM package see George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as Ravand and Robitzsch (2015).
Maintained by Alexander Robitzsch. Last updated 9 months ago.
cognitive-diagnostic-modelsitem-response-theorycpp
5.2 match 22 stars 8.76 score 138 scripts 28 dependents
spedygiorgio
markovchain:Easy Handling Discrete Time Markov Chains
Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>. Some functions for continuous times Markov chains depend on the suggested ctmcd package.
Maintained by Giorgio Alfredo Spedicato. Last updated 4 months ago.
ctmcdtmcmarkov-chainmarkov-modelr-programmingrcppopenblascpp
3.6 match 104 stars 12.78 score 712 scripts 4 dependentsr-forge
xtable:Export Tables to LaTeX or HTML
Coerce data to LaTeX and HTML tables.
Maintained by David Scott. Last updated 5 years ago.
3.4 match 13.25 score 26k scripts 2.3k dependents
inlabru-org
inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions
Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.
Maintained by Finn Lindgren. Last updated 3 days ago.
3.6 match 96 stars 12.62 score 832 scripts 6 dependents
fbartos
RoBMA:Robust Bayesian Meta-Analyses
A framework for estimating ensembles of meta-analytic and meta-regression models (assuming either presence or absence of the effect, heterogeneity, publication bias, and moderators). The RoBMA framework uses Bayesian model-averaging to combine the competing meta-analytic models into a model ensemble, weights the posterior parameter distributions based on posterior model probabilities and uses Bayes factors to test for the presence or absence of the individual components (e.g., effect vs. no effect; Bartoลก et al., 2022, <doi:10.1002/jrsm.1594>; Maier, Bartoลก & Wagenmakers, 2022, <doi:10.1037/met0000405>). Users can define a wide range of prior distributions for + the effect size, heterogeneity, publication bias (including selection models and PET-PEESE), and moderator components. The package provides convenient functions for summary, visualizations, and fit diagnostics.
Maintained by Frantiลกek Bartoลก. Last updated 1 months ago.
meta-analysismodel-averagingpublication-biasjagsopenblascpp
6.4 match 9 stars 6.97 score 53 scriptsbioc
SWATH2stats:Transform and Filter SWATH Data for Statistical Packages
This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.
Maintained by Peter Blattmann. Last updated 5 months ago.
proteomicsannotationexperimentaldesignpreprocessingmassspectrometryimmunooncology
6.9 match 1 stars 6.30 score 22 scriptsflr
FLBEIA:Bio-Economic Impact Assessment of Management Strategies using FLR
A simulation toolbox that describes a fishery system under a Management Strategy Estrategy approach. The objective of the model is to facilitate the Bio-Economic evaluation of Management strategies. It is multistock, multifleet and seasonal. The simulation is divided in 2 main blocks, the Operating Model (OM) and the Management Procedure (MP). In turn, each of these two blocks is divided in 3 components: the biological, the fleets and the covariables on the one hand, and the observation, the assessment and the advice on the other.
Maintained by FLBEIA Team. Last updated 5 days ago.
7.2 match 11 stars 5.97 score 156 scriptsflr
FLAssess:Generic Classes and Methods for Stock Assessment Models
A generic set of classes for stock assessment models are provided here. Individual assessment packages should extend the basic classes.
Maintained by Iago Mosqueira. Last updated 3 months ago.
9.0 match 4.77 score 324 scripts 3 dependents
dicook
nullabor:Tools for Graphical Inference
Tools for visual inference. Generate null data sets and null plots using permutation and simulation. Calculate distance metrics for a lineup, and examine the distributions of metrics.
Maintained by Di Cook. Last updated 1 months ago.
4.1 match 57 stars 10.38 score 370 scripts 2 dependents
e-sensing
sits:Satellite Image Time Series Analysis for Earth Observation Data Cubes
An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>. Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, Copernicus Data Space Environment (CDSE), Digital Earth Africa, Digital Earth Australia, NASA HLS using the Spatio-temporal Asset Catalog (STAC) protocol (<https://stacspec.org/>) and the 'gdalcubes' R package developed by Appel and Pebesma (2019) <doi:10.3390/data4030092>. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>. Includes methods to reduce training samples imbalance proposed by Chawla et al (2002) <doi:10.1613/jair.953>. Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks proposed by Pelletier et al (2019) <doi:10.3390/rs11050523>, and temporal attention encoders by Garnot and Landrieu (2020) <doi:10.48550/arXiv.2007.00586>. Supports GPU processing of deep learning models using torch <https://torch.mlverse.org/>. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference as described by Camara et al (2024) <doi:10.3390/rs16234572>, and methods for active learning and uncertainty assessment. Supports region-based time series analysis using package supercells <https://jakubnowosad.com/supercells/>. Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al (2014) <doi:10.1016/j.rse.2014.02.015>. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.
Maintained by Gilberto Camara. Last updated 1 months ago.
big-earth-datacbersearth-observationeo-datacubesgeospatialimage-time-seriesland-cover-classificationlandsatplanetary-computerr-spatialremote-sensingrspatialsatellite-image-time-seriessatellite-imagerysentinel-2stac-apistac-catalogcpp
4.4 match 494 stars 9.50 score 384 scriptsbioc
KnowSeq:KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis. KnowSeq expects to serve as an integrative tool that allows to process and extract relevant biomarkers, as well as to assess them through a Machine Learning approaches. Finally, the last objective of KnowSeq is the biological knowledge extraction from the biomarkers (Gene Ontology enrichment, Pathway listing and Visualization and Evidences related to the addressed disease). Although the package allows analyzing all the data manually, the main strenght of KnowSeq is the possibilty of carrying out an automatic and intelligent HTML report that collect all the involved steps in one document. It is important to highligh that the pipeline is totally modular and flexible, hence it can be started from whichever of the different steps. KnowSeq expects to serve as a novel tool to help to the experts in the field to acquire robust knowledge and conclusions for the data and diseases to study.
Maintained by Daniel Castillo-Secilla. Last updated 5 months ago.
geneexpressiondifferentialexpressiongenesetenrichmentdataimportclassificationfeatureextractionsequencingrnaseqbatcheffectnormalizationpreprocessingqualitycontrolgeneticstranscriptomicsmicroarrayalignmentpathwayssystemsbiologygoimmunooncology
12.6 match 3.30 score 5 scriptsropensci
epair:EPA Data Helper for R
Aid the user in making queries to the EPA API site found at https://aqs.epa.gov/aqsweb/documents/data_api. This package combines API calling methods from various web scraping packages with specific strings to retrieve data from the EPA API. It also contains easy to use loaded variables that help a user navigate services offered by the API and aid the user in determining the appropriate way to make a an API call.
Maintained by G.L. Orozco-Mulfinger. Last updated 3 years ago.
8.5 match 7 stars 4.89 score 11 scripts
aqlt
rjdqa:Quality Assessment for Seasonal Adjustment
Add-in to the 'RJDemetra' package on seasonal adjustments. It allows to produce dashboards to summarise models and quickly check the quality of the seasonal adjustment.
Maintained by Alain Quartier-la-Tente. Last updated 4 months ago.
jdemetraquality-assessmentopenjdk
10.6 match 2 stars 3.85 score 8 scripts
mncube
idmact:Interpreting Differences Between Mean ACT Scores
Interpreting the differences between mean scale scores across various forms of an assessment can be challenging. This difficulty arises from different mappings between raw scores and scale scores, complex mathematical relationships, adjustments based on judgmental procedures, and diverse equating functions applied to different assessment forms. An alternative method involves running simulations to explore the effect of incrementing raw scores on mean scale scores. The 'idmact' package provides an implementation of this approach based on the algorithm detailed in Schiel (1998) <https://www.act.org/content/dam/act/unsecured/documents/ACT_RR98-01.pdf> which was developed to help interpret differences between mean scale scores on the American College Testing (ACT) assessment. The function idmact_subj() within the package offers a framework for running simulations on subject-level scores. In contrast, the idmact_comp() function provides a framework for conducting simulations on composite scores.
Maintained by Mackson Ncube. Last updated 2 years ago.
assessmentmeasurementpsychometricsscale
10.9 match 3.70 score 4 scripts
sprfmo
FLjjm:Running the JJM Stock Assessment Model Inside the MSE FLR System
Runs the JJM stock assessment model for Chilean Jack Mackerel inside the MSE system of FLR's mse package.
Maintained by Iago Mosqueira. Last updated 9 days ago.
10.6 match 3.74 score 3 scripts
openplantpathology
hagis:Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity
Analysis of plant pathogen pathotype survey data. Functions provided calculate distribution of susceptibilities, distribution of complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes. This package is meant to be a direct replacement for Herrmann, Lรถwer and Schachtel's (1999) <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS', previously used for pathotype analysis.
Maintained by Adam H. Sparks. Last updated 10 days ago.
plant-pathologypathotypepathogen-surveyvirulence analysisdifferential setassessment scalepathotype-complexitiesplant-diseasepopulation-diversities
7.5 match 1 stars 5.26 score 8 scripts
duncanobrien
EWSmethods:Forecasting Tipping Points at the Community Level
Rolling and expanding window approaches to assessing abundance based early warning signals, non-equilibrium resilience measures, and machine learning. See Dakos et al. (2012) <doi:10.1371/journal.pone.0041010>, Deb et al. (2022) <doi:10.1098/rsos.211475>, Drake and Griffen (2010) <doi:10.1038/nature09389>, Ushio et al. (2018) <doi:10.1038/nature25504> and Weinans et al. (2021) <doi:10.1038/s41598-021-87839-y> for methodological details. Graphical presentation of the outputs are also provided for clear and publishable figures. Visit the 'EWSmethods' website for more information, and tutorials.
Maintained by Duncan OBrien. Last updated 7 months ago.
7.1 match 8 stars 5.51 score 20 scriptscran
randomizeR:Randomization for Clinical Trials
This tool enables the user to choose a randomization procedure based on sound scientific criteria. It comprises the generation of randomization sequences as well the assessment of randomization procedures based on carefully selected criteria. Furthermore, 'randomizeR' provides a function for the comparison of randomization procedures.
Maintained by Ralf-Dieter Hilgers. Last updated 1 years ago.
11.6 match 2 stars 3.38 score 1 dependentsices-tools-prod
fisheryO:Fisheries Overviews for ICES Advice
Functions that work with International Council for the Exploration of the Sea (ICES) web services and databases to collate, aggregate, and plot Fisheries Overview products.
Maintained by Scott Large. Last updated 7 years ago.
15.8 match 3 stars 2.45 score 19 scripts
lme4
lme4:Linear Mixed-Effects Models using 'Eigen' and S4
Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Maintained by Ben Bolker. Last updated 2 days ago.
1.9 match 647 stars 20.69 score 35k scripts 1.5k dependentsblue-matter
MSEtool:Management Strategy Evaluation Toolkit
Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Maintained by Adrian Hordyk. Last updated 25 days ago.
5.0 match 8 stars 7.69 score 163 scripts 3 dependents
jbryer
likert:Analysis and Visualization Likert Items
An approach to analyzing Likert response items, with an emphasis on visualizations. The stacked bar plot is the preferred method for presenting Likert results. Tabular results are also implemented along with density plots to assist researchers in determining whether Likert responses can be used quantitatively instead of qualitatively. See the likert(), summary.likert(), and plot.likert() functions to get started.
Maintained by Jason Bryer. Last updated 3 years ago.
3.8 match 310 stars 10.22 score 480 scripts 2 dependents
fishfollower
stockassessment:State-Space Assessment Model
Fitting SAM...
Maintained by Anders Nielsen. Last updated 13 days ago.
4.9 match 49 stars 7.76 score 324 scripts 2 dependents
athammad
pbox:Exploring Multivariate Spaces with Probability Boxes
Advanced statistical library offering a method to encapsulate and query the probability space of a dataset effortlessly using Probability Boxes (p-boxes). Its distinctive feature lies in the ease with which users can navigate and analyze marginal, joint, and conditional probabilities while taking into account the underlying correlation structure inherent in the data using copula theory and models. A comprehensive explanation is available in the paper "pbox: Exploring Multivariate Spaces with Probability Boxes" to be published in the Journal of Statistical Software.
Maintained by Ahmed T. Hammad. Last updated 8 months ago.
climate-changecopulaenvironmental-monitoringfinancial-analysisprobabilityrisk-assessmentrisk-managementstatistics
7.5 match 2 stars 5.04 score 4 scripts
oscarkjell
text:Analyses of Text using Transformers Models from HuggingFace, Natural Language Processing and Machine Learning
Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Maintained by Oscar Kjell. Last updated 3 days ago.
deep-learningmachine-learningnlptransformersopenjdk
2.9 match 146 stars 13.16 score 436 scripts 1 dependents
red-list-ecosystem
redlistr:Tools for the IUCN Red List of Ecosystems and Species
A toolbox created by members of the International Union for Conservation of Nature (IUCN) Red List of Ecosystems Committee for Scientific Standards. Primarily, it is a set of tools suitable for calculating the metrics required for making assessments of species and ecosystems against the IUCN Red List of Threatened Species and the IUCN Red List of Ecosystems categories and criteria. See the IUCN website for detailed guidelines, the criteria, publications and other information.
Maintained by Calvin Lee. Last updated 1 years ago.
5.9 match 32 stars 6.35 score 35 scripts
inseefr
JDCruncheR:Interface Between the 'JDemetra+' Cruncher and R, and Quality Report Generator
Tool for generating quality reports from cruncher outputs (and calculating series scores). The latest version of the cruncher can be downloaded here: <https://github.com/jdemetra/jwsacruncher/releases>.
Maintained by Tanguy Barthelemy. Last updated 19 days ago.
extensionjdemetrajwsacruncherquality-assessment
7.5 match 5 stars 4.92 score 16 scripts
tibshirani
samr:SAM: Significance Analysis of Microarrays
Significance Analysis of Microarrays for differential expression analysis, RNAseq data and related problems.
Maintained by Rob Tibshirani. Last updated 6 years ago.
7.4 match 3 stars 4.97 score 208 scripts 1 dependents
g-corbelli
reflectR:Automatic Scoring of the Cognitive Reflection Test
A tool for researchers and psychologists to automatically code open-ended responses to the Cognitive Reflection Test (CRT), a widely used class of tests in cognitive science and psychology for assessing an individual's propensity to override an incorrect gut response and engage in further reflection to find a correct answer. This package facilitates the standardization of Cognitive Reflection Test responses analysis across large datasets in cognitive psychology, decision-making, and related fields. By automating the coding process, it not only reduces manual effort but also aims to reduce the variability introduced by subjective interpretation of open-ended responses, contributing to a more consistent and reliable analysis. 'reflectR' supports automatic coding and machine scoring for the original English-language version of CRT (Frederick, 2005) <doi:10.1257/089533005775196732>, as well as for CRT4 and CRT7, 4- and 7-item versions, respectively (Toplak et al., 2014) <doi:10.1080/13546783.2013.844729>, for the CRT-long version built via Item Response Theory by Primi and colleagues (2016) <doi:10.1002/bdm.1883>, and for CRT-2 by Thomson & Oppenheimer (2016) <doi:10.1017/s1930297500007622>. Note: While 'reflectR' draws inspiration from the principles and scientific literature underlying the different versions of the Cognitive Reflection Test, it has been independently developed and does not hold any affiliation with any of the original authors. The development of this package benefited significantly from the kind insight and suggestion provided by Dr. Keela Thomson, whose contribution is gratefully acknowledged. Additional gratitude is extended to Dr. Paolo Giovanni Cicirelli, Prof. Marinella Paciello, Dr. Carmela Sportelli, and Prof. Francesca D'Errico, who not only contributed to the manual multi-rater coding of CRT-2 items but also profoundly influenced the understanding of the importance and practical relevance of cognitive reflection within personality, social, and cognitive psychology research. Acknowledgment is also due to the European project STERHEOTYPES (STudying European Racial Hoaxes and sterEOTYPES) for funding the data collection that produced the datasets initially used for manual multi-rater coding of CRT-2 items.
Maintained by Giuseppe Corbelli. Last updated 7 months ago.
assessmentcognitivecognitive-psychologycognitive-sciencecrtpsychological-sciencepsychological-testspsychologypsychometricsreflectionscoringtesting
10.5 match 1 stars 3.48 score
topepo
caret:Classification and Regression Training
Misc functions for training and plotting classification and regression models.
Maintained by Max Kuhn. Last updated 3 months ago.
1.9 match 1.6k stars 19.24 score 61k scripts 303 dependents
refunders
refund:Regression with Functional Data
Methods for regression for functional data, including function-on-scalar, scalar-on-function, and function-on-function regression. Some of the functions are applicable to image data.
Maintained by Julia Wrobel. Last updated 6 months ago.
3.5 match 41 stars 10.25 score 472 scripts 16 dependents
choi-phd
maat:Multiple Administrations Adaptive Testing
Provides an extension of the shadow-test approach to computerized adaptive testing (CAT) implemented in the 'TestDesign' package for the assessment framework involving multiple tests administered periodically throughout the year. This framework is referred to as the Multiple Administrations Adaptive Testing (MAAT) and supports multiple item pools vertically scaled and multiple phases (stages) of CAT within each test. Between phases and tests, transitioning from one item pool (and associated constraints) to another is allowed as deemed necessary to enhance the quality of measurement.
Maintained by Seung W. Choi. Last updated 9 months ago.
9.0 match 4.00 score 5 scripts
neuropsychology
psycho:Efficient and Publishing-Oriented Workflow for Psychological Science
The main goal of the psycho package is to provide tools for psychologists, neuropsychologists and neuroscientists, to facilitate and speed up the time spent on data analysis. It aims at supporting best practices and tools to format the output of statistical methods to directly paste them into a manuscript, ensuring statistical reporting standardization and conformity.
Maintained by Dominique Makowski. Last updated 4 years ago.
apaapa6bayesiancorrelationformatinterpretationmixed-modelsneurosciencepsychopsychologyrstanarmstatistics
3.3 match 149 stars 10.86 score 628 scripts 5 dependents
openintrostat
openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs
Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.
Maintained by Mine รetinkaya-Rundel. Last updated 2 months ago.
3.1 match 240 stars 11.39 score 6.0k scriptscran
soilassessment:Soil Health Assessment Models for Assessing Soil Conditions and Suitability
Soil health assessment builds information to improve decision in soil management. It facilitates assessment of soil conditions for crop suitability [such as those given by FAO <https://www.fao.org/land-water/databases-and-software/crop-information/en/>], groundwater recharge, fertility, erosion, salinization [<doi:10.1002/ldr.4211>], carbon sequestration, irrigation potential, and status of soil resources.
Maintained by Christian Thine Omuto. Last updated 2 months ago.
35.7 match 1 stars 1.00 score
epiforecasts
scoringutils:Utilities for Scoring and Assessing Predictions
Facilitate the evaluation of forecasts in a convenient framework based on data.table. It allows user to to check their forecasts and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The package mostly focuses on the evaluation of probabilistic forecasts and allows evaluating several different forecast types and input formats. Find more information about the package in the Vignettes as well as in the accompanying paper, <doi:10.48550/arXiv.2205.07090>.
Maintained by Nikos Bosse. Last updated 13 days ago.
forecast-evaluationforecasting
3.1 match 52 stars 11.37 score 326 scripts 7 dependentscran
epiR:Tools for the Analysis of Epidemiological Data
Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Maintained by Mark Stevenson. Last updated 2 months ago.
4.3 match 10 stars 8.18 score 10 dependentsbioc
tradeSeq:trajectory-based differential expression analysis for sequencing data
tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.
Maintained by Hector Roux de Bezieux. Last updated 5 months ago.
clusteringregressiontimecoursedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization
3.5 match 247 stars 10.06 score 440 scripts
mps9506
rATTAINS:Access EPA 'ATTAINS' Data
An R interface to United States Environmental Protection Agency (EPA) Assessment, Total Maximum Daily Load (TMDL) Tracking and Implementation System ('ATTAINS') data. 'ATTAINS' is the EPA database used to track information provided by states about water quality assessments conducted under federal Clean Water Act requirements. ATTAINS information and API information is available at <https://www.epa.gov/waterdata/attains>.
Maintained by Michael Schramm. Last updated 2 years ago.
7.7 match 8 stars 4.60 score 10 scriptsices-tools-prod
icesTAF:Functions to Support the ICES Transparent Assessment Framework
Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.
Maintained by Colin Millar. Last updated 2 years ago.
5.5 match 5 stars 6.37 score 1.1k scripts 1 dependents
zarquon42b
Morpho:Calculations and Visualisations Related to Geometric Morphometrics
A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.
Maintained by Stefan Schlager. Last updated 5 months ago.
3.4 match 51 stars 10.00 score 218 scripts 13 dependents
miracum
DQAstats:Core Functions for Data Quality Assessment
Perform data quality assessment ('DQA') of electronic health records ('EHR'). Publication: Kapsner et al. (2021) <doi:10.1055/s-0041-1733847>.
Maintained by Lorenz A. Kapsner. Last updated 13 days ago.
5.2 match 9 stars 6.55 score 4 scripts 1 dependents
kwb-r
kwb.fcr:Fertilizer chemical risk assessment
This risk assessment is based on the TGD on risk assessment by the European Comission. Possible Endpoints are soil organisms, groundwater organisms and human health via food consumption.Every variable can be entered as probability distribution to include uncertainties or site specific variations.
Maintained by Malte Zamzow. Last updated 1 years ago.
11.4 match 3.00 score 2 scripts
mahshaaban
pcr:Analyzing Real-Time Quantitative PCR Data
Calculates the amplification efficiency and curves from real-time quantitative PCR (Polymerase Chain Reaction) data. Estimates the relative expression from PCR data using the double delta CT and the standard curve methods Livak & Schmittgen (2001) <doi:10.1006/meth.2001.1262>. Tests for statistical significance using two-group tests and linear regression Yuan et al. (2006) <doi: 10.1186/1471-2105-7-85>.
Maintained by Mahmoud Ahmed. Last updated 8 months ago.
data-analysesmolecular-biologyqpcr
4.7 match 28 stars 7.25 score 63 scriptsbioc
uncoverappLib:Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.
Maintained by Emanuela Iovino. Last updated 5 months ago.
softwarevisualizationannotationcoverage
7.6 match 3 stars 4.48 score 4 scripts
plant-functional-trait-course
fluxible:Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Processes the raw data from closed loop flux chamber (or tent) setups into ecosystem gas fluxes usable for analysis. It goes from a data frame of gas concentration over time (which can contain several measurements) and a meta data file indicating which measurement was done when, to a data frame of ecosystem gas fluxes including quality diagnostics. Functions provided include different models (exponential as described in Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, quadratic and linear) to estimate the fluxes from the raw data, quality assessment, plotting for visual check and calculation of fluxes based on the setup specific parameters (chamber size, plot area, ...).
Maintained by Joseph Gaudard. Last updated 14 hours ago.
5.9 match 5.69 score 12 scriptsbioc
BASiCS:Bayesian Analysis of Single-Cell Sequencing data
Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.
Maintained by Catalina Vallejos. Last updated 5 months ago.
immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecelldifferentialexpressionbayesiancellbiologybioconductor-packagegene-expressionrcpprcpparmadilloscrna-seqsingle-cellopenblascppopenmp
3.3 match 83 stars 10.26 score 368 scripts 1 dependents
pacificcommunity
AMPLE:Shiny Apps to Support Capacity Building on Harvest Control Rules
Three Shiny apps are provided that introduce Harvest Control Rules (HCR) for fisheries management. 'Introduction to HCRs' provides a simple overview to how HCRs work. Users are able to select their own HCR and step through its performance, year by year. Biological variability and estimation uncertainty are introduced. 'Measuring performance' builds on the previous app and introduces the idea of using performance indicators to measure HCR performance. 'Comparing performance' allows multiple HCRs to be created and tested, and their performance compared so that the preferred HCR can be selected.
Maintained by Finlay Scott. Last updated 1 years ago.
6.0 match 5.56 score 24 scripts
cran
gss:General Smoothing Splines
A comprehensive package for structural multivariate function estimation using smoothing splines.
Maintained by Chong Gu. Last updated 5 months ago.
5.2 match 3 stars 6.40 score 137 dependentsg-corbelli
persval:Computing Personal Values Scores
Compute personal values scores from various questionnaires based on the theoretical constructs proposed by professor Shalom H. Schwartz. Designed for researchers and practitioners in psychology, sociology, and related fields, the package facilitates the quantification of different dimensions related to personal values from survey data. It incorporates the recommended statistical adjustment to enhance the accuracy and interpretation of the results. Note: The package 'persval' is independently developed based on the personal values theoretical framework, and is not directly endorsed by professor Schwartz.
Maintained by Giuseppe Corbelli. Last updated 7 months ago.
assessmentpersonalitypsychologypsychometricsquestionnaire-surveyvalues
10.0 match 2 stars 3.30 scoreices-tools-prod
TAF:Transparent Assessment Framework for Reproducible Research
General framework to organize data, methods, and results used in reproducible scientific analyses. A TAF analysis consists of four scripts (data.R, model.R, output.R, report.R) that are run sequentially. Each script starts by reading files from a previous step and ends with writing out files for the next step. Convenience functions are provided to version control the required data and software, run analyses, clean residues from previous runs, manage files, manipulate tables, and produce figures. With a focus on stability and reproducible analyses, the TAF package comes with no dependencies. TAF forms a base layer for the 'icesTAF' package and other scientific applications.
Maintained by Arni Magnusson. Last updated 4 months ago.
4.8 match 3 stars 6.85 score 282 scripts 2 dependents
weirichs
eatRep:Educational Assessment Tools for Replication Methods
Replication methods to compute some basic statistic operations (means, standard deviations, frequency tables, percentiles, mean comparisons using weighted effect coding, generalized linear models, and linear multilevel models) in complex survey designs comprising multiple imputed or nested imputed variables and/or a clustered sampling structure which both deserve special procedures at least in estimating standard errors. See the package documentation for a more detailed description along with references.
Maintained by Sebastian Weirich. Last updated 17 days ago.
6.4 match 1 stars 5.16 score 13 scripts
edzer
intervals:Tools for Working with Points and Intervals
Tools for working with and comparing sets of points and intervals.
Maintained by Edzer Pebesma. Last updated 7 months ago.
3.5 match 11 stars 9.40 score 122 scripts 90 dependentsr-forge
Rmpfr:Interface R to MPFR - Multiple Precision Floating-Point Reliable
Arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental ("special") functions. To this end, the package interfaces to the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Maintained by Martin Maechler. Last updated 4 months ago.
2.9 match 11.30 score 316 scripts 141 dependents
veronica0206
nlpsem:Linear and Nonlinear Longitudinal Process in Structural Equation Modeling Framework
Provides computational tools for nonlinear longitudinal models, in particular the intrinsically nonlinear models, in four scenarios: (1) univariate longitudinal processes with growth factors, with or without covariates including time-invariant covariates (TICs) and time-varying covariates (TVCs); (2) multivariate longitudinal processes that facilitate the assessment of correlation or causation between multiple longitudinal variables; (3) multiple-group models for scenarios (1) and (2) to evaluate differences among manifested groups, and (4) longitudinal mixture models for scenarios (1) and (2), with an assumption that trajectories are from multiple latent classes. The methods implemented are introduced in Jin Liu (2023) <arXiv:2302.03237v2>.
Maintained by Jin Liu. Last updated 4 months ago.
4.6 match 145 stars 6.91 score 16 scripts
manuhuth
coconots:Convolution-Closed Models for Count Time Series
Useful tools for fitting, validating, and forecasting of practical convolution-closed time series models for low counts are provided. Marginal distributions of the data can be modelled via Poisson and Generalized Poisson innovations. Regression effects can be incorprated through time varying innovation rates. The models are described in Jung and Tremayne (2011) <doi:10.1111/j.1467-9892.2010.00697.x> and the model assessment tools are presented in Czado et al. (2009) <doi:10.1111/j.1541-0420.2009.01191.x> and, Tsay (1992) <doi:10.2307/2347612>.
Maintained by Manuel Huth. Last updated 1 months ago.
7.6 match 3 stars 4.18 score 4 scripts
msainsburydale
NeuralEstimators:Likelihood-Free Parameter Estimation using Neural Networks
An 'R' interface to the 'Julia' package 'NeuralEstimators.jl'. The package facilitates the user-friendly development of neural Bayes estimators, which are neural networks that map data to a point summary of the posterior distribution (Sainsbury-Dale et al., 2024, <doi:10.1080/00031305.2023.2249522>). These estimators are likelihood-free and amortised, in the sense that, once the neural networks are trained on simulated data, inference from observed data can be made in a fraction of the time required by conventional approaches. The package also supports amortised Bayesian or frequentist inference using neural networks that approximate the posterior or likelihood-to-evidence ratio (Zammit-Mangion et al., 2025, Sec. 3.2, 5.2, <doi:10.48550/arXiv.2404.12484>). The package accommodates any model for which simulation is feasible by allowing users to define models implicitly through simulated data.
Maintained by Matthew Sainsbury-Dale. Last updated 14 days ago.
5.3 match 9 stars 5.95 score 3 scripts
bozenne
BuyseTest:Generalized Pairwise Comparisons
Implementation of the Generalized Pairwise Comparisons (GPC) as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations, and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring. GPC compare two groups of observations (intervention vs. control group) regarding several prioritized endpoints to estimate the probability that a random observation drawn from one group performs better/worse/equivalently than a random observation drawn from the other group. Summary statistics such as the net treatment benefit, win ratio, or win odds are then deduced from these probabilities. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>), non-parametric bootstrap, or permutations. The software enables the use of thresholds of minimal importance difference, stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Maintained by Brice Ozenne. Last updated 4 days ago.
generalized-pairwise-comparisonsnon-parametricstatisticscpp
5.3 match 5 stars 5.91 score 90 scripts
chgrl
bReeze:Functions for Wind Resource Assessment
A collection of functions to analyse, visualize and interpret wind data and to calculate the potential energy production of wind turbines.
Maintained by Christian Graul. Last updated 1 years ago.
7.3 match 20 stars 4.34 score 22 scripts
r-lum
Luminescence:Comprehensive Luminescence Dating Data Analysis
A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Maintained by Sebastian Kreutzer. Last updated 16 hours ago.
bayesian-statisticsdata-sciencegeochronologyluminescenceluminescence-datingopen-scienceoslplottingradiofluorescencetlxsygcpp
2.9 match 15 stars 10.77 score 178 scripts 8 dependents
mhahsler
seriation:Infrastructure for Ordering Objects Using Seriation
Infrastructure for ordering objects with an implementation of several seriation/sequencing/ordination techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Maintained by Michael Hahsler. Last updated 3 months ago.
combinatorial-optimizationordinationseriationfortran
2.2 match 77 stars 14.07 score 640 scripts 79 dependents
rudeboybert
forestecology:Fitting and Assessing Neighborhood Models of the Effect of Interspecific Competition on the Growth of Trees
Code for fitting and assessing models for the growth of trees. In particular for the Bayesian neighborhood competition linear regression model of Allen (2020): methods for model fitting and generating fitted/predicted values, evaluating the effect of competitor species identity using permutation tests, and evaluating model performance using spatial cross-validation.
Maintained by Albert Y. Kim. Last updated 3 years ago.
6.0 match 12 stars 5.12 score 11 scripts
apguthrie
BRcal:Boldness-Recalibration of Binary Events
Boldness-recalibration maximally spreads out probability predictions while maintaining a user specified level of calibration, facilitated the brcal() function. Supporting functions to assess calibration via Bayesian and Frequentist approaches, Maximum Likelihood Estimator (MLE) recalibration, Linear in Log Odds (LLO)-adjust via any specified parameters, and visualize results are also provided. Methodological details can be found in Guthrie & Franck (2024) <doi:10.1080/00031305.2024.2339266>.
Maintained by Adeline P. Guthrie. Last updated 4 months ago.
6.4 match 4.81 score 5 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.
3.6 match 8 stars 8.39 score 1.4k scripts 28 dependents
jwb133
smcfcs:Multiple Imputation of Covariates by Substantive Model Compatible Fully Conditional Specification
Implements multiple imputation of missing covariates by Substantive Model Compatible Fully Conditional Specification. This is a modification of the popular FCS/chained equations multiple imputation approach, and allows imputation of missing covariate values from models which are compatible with the user specified substantive model.
Maintained by Jonathan Bartlett. Last updated 2 days ago.
3.4 match 11 stars 9.00 score 59 scripts 1 dependentsmaelstrom-research
Rmonize:Support Retrospective Harmonization of Data
Functions to support rigorous retrospective data harmonization processing, evaluation, and documentation across datasets from different studies based on Maelstrom Research guidelines. The package includes the core functions to evaluate and format the main inputs that define the harmonization process, apply specified processing rules to generate harmonized data, diagnose processing errors, and summarize and evaluate harmonized outputs. The main inputs that define the processing are a DataSchema (list and definitions of harmonized variables to be generated) and Data Processing Elements (processing rules to be applied to generate harmonized variables from study-specific variables). The main outputs of processing are harmonized datasets, associated metadata, and tabular and visual summary reports. As described in Maelstrom Research guidelines for rigorous retrospective data harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).
Maintained by Guillaume Fabre. Last updated 12 months ago.
5.4 match 5 stars 5.58 score 51 scriptsr-forge
tscount:Analysis of Count Time Series
Likelihood-based methods for model fitting and assessment, prediction and intervention analysis of count time series following generalized linear models are provided, see Liboschik et al. (2017) <doi:10.18637/jss.v082.i05>. Models with the identity and with the logarithmic link function are allowed. The conditional distribution can be Poisson or Negative Binomial.
Maintained by Tobias Liboschik. Last updated 2 years ago.
5.7 match 5.28 score 91 scripts 1 dependents
ss3sim
ss3sim:Fisheries Stock Assessment Simulation Testing with Stock Synthesis
A framework for fisheries stock assessment simulation testing with Stock Synthesis (SS3) as described in Anderson et al. (2014) <doi:10.1371/journal.pone.0092725>.
Maintained by Kelli F. Johnson. Last updated 5 months ago.
fisheriessimulationstock-synthesis
3.4 match 39 stars 8.89 score 149 scripts
r-spatial
classInt:Choose Univariate Class Intervals
Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Maintained by Roger Bivand. Last updated 3 months ago.
1.9 match 34 stars 16.02 score 3.2k scripts 1.2k dependents
mrc-ide
epireview:Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)
Contains the latest open access pathogen data from the Pathogen Epidemiology Review Group (PERG). Tools are available to update pathogen databases with new peer-reviewed data as it becomes available, and to summarise the latest data using tables and figures.
Maintained by Sangeeta Bhatia. Last updated 2 days ago.
4.4 match 30 stars 6.76 score 6 scripts
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.
3.3 match 7 stars 9.11 score 1.3k scripts 6 dependents
giscience-fsu
sperrorest:Perform Spatial Error Estimation and Variable Importance Assessment
Implements spatial error estimation and permutation-based variable importance measures for predictive models using spatial cross-validation and spatial block bootstrap.
Maintained by Alexander Brenning. Last updated 2 years ago.
cross-validationmachine-learningspatial-statisticsspatio-temporal-modelingstatistical-learning
4.6 match 19 stars 6.46 score 46 scripts
eldafani
intsvy:International Assessment Data Manager
Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA, ICILS, and PIAAC).
Maintained by Daniel Caro. Last updated 12 months ago.
5.5 match 22 stars 5.29 score 88 scripts
pik-piam
remind2:The REMIND R package (2nd generation)
Contains the REMIND-specific routines for data and model output manipulation.
Maintained by Renato Rodrigues. Last updated 6 days ago.
3.3 match 8.88 score 161 scripts 5 dependents
rvlenth
estimability:Tools for Assessing Estimability of Linear Predictions
Provides tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly. Estimability theory is discussed in many linear-models textbooks including Chapter 3 of Monahan, JF (2008), "A Primer on Linear Models", Chapman and Hall (ISBN 978-1-4200-6201-4).
Maintained by Russell Lenth. Last updated 9 months ago.
3.0 match 2 stars 9.64 score 18 scripts 242 dependents
martin3141
spant:MR Spectroscopy Analysis Tools
Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Maintained by Martin Wilson. Last updated 30 days ago.
brainmrimrsmrshubspectroscopyfortran
3.4 match 25 stars 8.52 score 81 scripts
usepa
spmodel:Spatial Statistical Modeling and Prediction
Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Maintained by Michael Dumelle. Last updated 3 days ago.
3.8 match 15 stars 7.66 score 112 scripts 3 dependentskwb-r
kwb.lca:Functions to Be Used in Life Cycle Assessment (LCA) Projects
This package contains a function to read LCA. parameters from an Excel file that was sent to and received from a project partner. The parameters are read into a data frame. Another function can be used to write the dataframe into an Excel file with different sheets and data.
Maintained by Hauke Sonnenberg. Last updated 5 years ago.
data-aggregationdata-exportdata-importdata-visualisationexcellife-cycle-assessmentmodellingproject-fakinproject-smartplantquestionairesspreadsheetstemplate
9.5 match 2 stars 3.00 score 1 scripts
boehringer-ingelheim
tipmap:Tipping Point Analysis for Bayesian Dynamic Borrowing
Tipping point analysis for clinical trials that employ Bayesian dynamic borrowing via robust meta-analytic predictive (MAP) priors. Further functions facilitate expert elicitation of a primary weight of the informative component of the robust MAP prior and computation of operating characteristics. Intended use is the planning, analysis and interpretation of extrapolation studies in pediatric drug development, but applicability is generally wider.
Maintained by Christian Stock. Last updated 12 months ago.
bayesian-borrowingbayesian-methodsclinical-trialevidence-synthesisextrapolationpediatricspharmaceutical-developmentprior-elicitationtipping-pointweighting
6.5 match 2 stars 4.38 score 12 scriptsweirichs
eatTools:Miscellaneous Functions for the Analysis of Educational Assessments
Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep', 'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN'). The function for defining (weighted) contrasts in weighted effect coding refers to te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>. Functions for weighted statistics refer to Wolter (2007) <doi:10.1007/978-0-387-35099-8>.
Maintained by Sebastian Weirich. Last updated 3 months ago.
5.3 match 2 stars 5.38 score 11 scripts 2 dependents
kassambara
factoextra:Extract and Visualize the Results of Multivariate Data Analyses
Provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides 'ggplot2' - based elegant data visualization.
Maintained by Alboukadel Kassambara. Last updated 5 years ago.
2.0 match 363 stars 14.13 score 15k scripts 52 dependents
overton-group
eHDPrep:Quality Control and Semantic Enrichment of Datasets
A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023) <doi:10.1093/gigascience/giad030>). Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
Maintained by Ian Overton. Last updated 2 years ago.
data-qualityhealth-informaticssemantic-enrichment
5.8 match 8 stars 4.90 score 10 scripts
slzhang-fd
mirtjml:Joint Maximum Likelihood Estimation for High-Dimensional Item Factor Analysis
Provides constrained joint maximum likelihood estimation algorithms for item factor analysis (IFA) based on multidimensional item response theory models. So far, we provide functions for exploratory and confirmatory IFA based on the multidimensional two parameter logistic (M2PL) model for binary response data. Comparing with traditional estimation methods for IFA, the methods implemented in this package scale better to data with large numbers of respondents, items, and latent factors. The computation is facilitated by multiprocessing 'OpenMP' API. For more information, please refer to: 1. Chen, Y., Li, X., & Zhang, S. (2018). Joint Maximum Likelihood Estimation for High-Dimensional Exploratory Item Factor Analysis. Psychometrika, 1-23. <doi:10.1007/s11336-018-9646-5>; 2. Chen, Y., Li, X., & Zhang, S. (2019). Structured Latent Factor Analysis for Large-scale Data: Identifiability, Estimability, and Their Implications. Journal of the American Statistical Association, <doi: 10.1080/01621459.2019.1635485>.
Maintained by Siliang Zhang. Last updated 4 years ago.
ifaitem-factor-analysislarge-scale-assessmentparallel-computingpsychometricsopenblascppopenmp
6.7 match 9 stars 4.21 score 12 scripts 1 dependents
fitzlab-al
gdm:Generalized Dissimilarity Modeling
A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models. Mokany K, Ware C, Woolley SNC, Ferrier S, Fitzpatrick MC (2022) <doi:10.1111/geb.13459> Ferrier S, Manion G, Elith J, Richardson K (2007) <doi:10.1111/j.1472-4642.2007.00341.x>.
Maintained by Matt Fitzpatrick. Last updated 2 months ago.
3.5 match 35 stars 8.12 score 145 scripts
angabrio
missingHE:Missing Outcome Data in Health Economic Evaluation
Contains a suite of functions for health economic evaluations with missing outcome data. The package can fit different types of statistical models under a fully Bayesian approach using the software 'JAGS' (which should be installed locally and which is loaded in 'missingHE' via the 'R' package 'R2jags'). Three classes of models can be fitted under a variety of missing data assumptions: selection models, pattern mixture models and hurdle models. In addition to model fitting, 'missingHE' provides a set of specialised functions to assess model convergence and fit, and to summarise the statistical and economic results using different types of measures and graphs. The methods implemented are described in Mason (2018) <doi:10.1002/hec.3793>, Molenberghs (2000) <doi:10.1007/978-1-4419-0300-6_18> and Gabrio (2019) <doi:10.1002/sim.8045>.
Maintained by Andrea Gabrio. Last updated 2 years ago.
cost-effectiveness-analysishealth-economic-evaluationindividual-level-datajagsmissing-dataparametric-modellingsensitivity-analysiscpp
5.2 match 5 stars 5.38 score 24 scriptsjbryer
PSAboot:Bootstrapping for Propensity Score Analysis
It is often advantageous to test a hypothesis more than once in the context of propensity score analysis (Rosenbaum, 2012) <doi:10.1093/biomet/ass032>. The functions in this package facilitate bootstrapping for propensity score analysis (PSA). By default, bootstrapping using two classification tree methods (using 'rpart' and 'ctree' functions), two matching methods (using 'Matching' and 'MatchIt' packages), and stratification with logistic regression. A framework is described for users to implement additional propensity score methods. Visualizations are emphasized for diagnosing balance; exploring the correlation relationships between bootstrap samples and methods; and to summarize results.
Maintained by Jason Bryer. Last updated 1 years ago.
6.7 match 12 stars 4.14 score 23 scriptsbioc
MetaboCoreUtils:Core Utils for Metabolomics Data
MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.
Maintained by Johannes Rainer. Last updated 5 months ago.
infrastructuremetabolomicsmassspectrometrymass-spectrometry
2.9 match 9 stars 9.40 score 58 scripts 36 dependents
ngreifer
cobalt:Covariate Balance Tables and Plots
Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'WeightIt', 'MatchThem', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'cem', 'sbw', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with multi-category, continuous, or longitudinal treatments.
Maintained by Noah Greifer. Last updated 11 months ago.
causal-inferencepropensity-scores
2.1 match 75 stars 12.98 score 1.0k scripts 8 dependents
kenhanscombe
ukbtools:Manipulate and Explore UK Biobank Data
A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html), visualize primary demographic data for a sample subset, query ICD diagnoses, retrieve genetic metadata, read and write standard file formats for genetic analyses.
Maintained by Ken Hanscombe. Last updated 2 years ago.
4.0 match 101 stars 6.78 score 118 scripts
khliland
multiblock:Multiblock Data Fusion in Statistics and Machine Learning
Functions and datasets to support Smilde, Nรฆs and Liland (2021, ISBN: 978-1-119-60096-1) "Multiblock Data Fusion in Statistics and Machine Learning - Applications in the Natural and Life Sciences". This implements and imports a large collection of methods for multiblock data analysis with common interfaces, result- and plotting functions, several real data sets and six vignettes covering a range different applications.
Maintained by Kristian Hovde Liland. Last updated 2 months ago.
4.0 match 14 stars 6.68 score 19 scripts
cfwp
FMradio:Factor Modeling for Radiomics Data
Functions that support stable prediction and classification with radiomics data through factor-analytic modeling. For details, see Peeters et al. (2019) <arXiv:1903.11696>.
Maintained by Carel F.W. Peeters. Last updated 5 years ago.
factor-analysismachine-learningradiomics
7.1 match 11 stars 3.74 score 2 scriptsalexanderrobitzsch
BIFIEsurvey:Tools for Survey Statistics in Educational Assessment
Contains tools for survey statistics (especially in educational assessment) for datasets with replication designs (jackknife, bootstrap, replicate weights; see Kolenikov, 2010; Pfefferman & Rao, 2009a, 2009b, <doi:10.1016/S0169-7161(09)70003-3>, <doi:10.1016/S0169-7161(09)70037-9>); Shao, 1996, <doi:10.1080/02331889708802523>). Descriptive statistics, linear and logistic regression, path models for manifest variables with measurement error correction and two-level hierarchical regressions for weighted samples are included. Statistical inference can be conducted for multiply imputed datasets and nested multiply imputed datasets and is in particularly suited for the analysis of plausible values (for details see George, Oberwimmer & Itzlinger-Bruneforth, 2016; Bruneforth, Oberwimmer & Robitzsch, 2016; Robitzsch, Pham & Yanagida, 2016). The package development was supported by BIFIE (Federal Institute for Educational Research, Innovation and Development of the Austrian School System; Salzburg, Austria).
Maintained by Alexander Robitzsch. Last updated 11 months ago.
5.3 match 4 stars 4.99 score 85 scripts 1 dependentsbioc
beadarray:Quality assessment and low-level analysis for Illumina BeadArray data
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Maintained by Mark Dunning. Last updated 5 months ago.
microarrayonechannelqualitycontrolpreprocessing
3.3 match 7.88 score 70 scripts 4 dependents
gasparrini
mvmeta:Multivariate and Univariate Meta-Analysis and Meta-Regression
Collection of functions to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression.
Maintained by Antonio Gasparrini. Last updated 5 years ago.
3.6 match 6 stars 7.29 score 151 scripts 10 dependentsbioc
RTN:RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.
Maintained by Mauro Castro. Last updated 5 months ago.
transcriptionnetworknetworkinferencenetworkenrichmentgeneregulationgeneexpressiongraphandnetworkgenesetenrichmentgeneticvariability
4.5 match 5.80 score 53 scripts 2 dependents
talgalili
gplots:Various R Programming Tools for Plotting Data
Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to 'stats::lowess' function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting dots whose size reflects the relative magnitude of the elements ('balloonplot', 'bubbleplot'), - plotting "Venn" diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space').
Maintained by Tal Galili. Last updated 5 months ago.
1.7 match 13 stars 15.11 score 13k scripts 482 dependentsbioc
limma:Linear Models for Microarray and Omics Data
Data analysis, linear models and differential expression for omics data.
Maintained by Gordon Smyth. Last updated 5 days ago.
exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomics
1.9 match 13.81 score 16k scripts 585 dependents
mvesuviusc
primerTree:Visually Assessing the Specificity and Informativeness of Primer Pairs
Identifies potential target sequences for a given set of primers and generates phylogenetic trees annotated with the taxonomies of the predicted amplification products.
Maintained by Matt Cannon. Last updated 1 years ago.
4.6 match 51 stars 5.56 score 16 scripts
hanel
musica:Multiscale Climate Model Assessment
Provides functions allowing for (1) easy aggregation of multivariate time series into custom time scales, (2) comparison of statistical summaries between different data sets at multiple time scales (e.g. observed and bias-corrected data), (3) comparison of relations between variables and/or different data sets at multiple time scales (e.g. correlation of precipitation and temperature in control and scenario simulation) and (4) transformation of time series at custom time scales.
Maintained by Martin Hanel. Last updated 8 years ago.
6.7 match 3.85 score 14 scriptsflr
a4adiags:Additional Diagnostics for FLa4a stock Assessment Models
A series of extra diagnostics for the FLa4a model, including prediction skill through restrospective prediction of model inputs and runs tests. Contains ggplot-based plot funtions of diagnostics outputs.
Maintained by Iago Mosqueira. Last updated 12 days ago.
9.5 match 2.70 score 7 scriptspharmaverse
admiralvaccine:Vaccine Extension Package for ADaM in 'R' Asset Library
Programming vaccine specific Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. Flat model is followed as per Center for Biologics Evaluation and Research (CBER) guidelines for creating vaccine specific domains. 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/adamig-v1-3-release-package>). The package is an extension package of the 'admiral' package.
Maintained by Sukalpo Saha. Last updated 2 months ago.
3.4 match 6 stars 7.44 score 23 scripts
dbosak01
pkgdiff:Identifies Package Differences
Identifies differences between versions of a package. Specifically, the functions help determine if there are breaking changes from one package version to the next. The package also includes a stability assessment, to help you determine the overall stability of a package, or even an entire repository.
Maintained by David Bosak. Last updated 3 days ago.
4.9 match 5.26 score
bioc
gDNAx:Diagnostics for assessing genomic DNA contamination in RNA-seq data
Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.
Maintained by Robert Castelo. Last updated 1 months ago.
transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomicssplicedalignmentalignment
5.0 match 1 stars 5.08 score 3 scripts
klauslehmann
calidad:Assesses the Quality of Estimates Made by Complex Sample Designs
Assesses the quality of estimates made by complex sample designs, following the methodology developed by the National Institute of Statistics Chile (2020, <https://www.ine.cl/docs/default-source/institucionalidad/buenas-pr%C3%A1cticas/clasificaciones-y-estandares/est%C3%A1ndar-evaluaci%C3%B3n-de-calidad-de-estimaciones-publicaci%C3%B3n-27022020.pdf>) and by Economic Commission for Latin America and Caribbean (2020, <https://repositorio.cepal.org/bitstream/handle/11362/45681/1/S2000293_es.pdf>), (2024, <https://repositorio.cepal.org/server/api/core/bitstreams/f04569e6-4f38-42e7-a32b-e0b298e0ab9c/content>).
Maintained by Klaus Lehmann. Last updated 26 days ago.
10.5 match 2.38 score 12 scriptsgasparrini
mixmeta:An Extended Mixed-Effects Framework for Meta-Analysis
A collection of functions to perform various meta-analytical models through a unified mixed-effects framework, including standard univariate fixed and random-effects meta-analysis and meta-regression, and non-standard extensions such as multivariate, multilevel, longitudinal, and dose-response models.
Maintained by Antonio Gasparrini. Last updated 3 years ago.
3.6 match 13 stars 6.96 score 63 scripts 13 dependents
alexander-pastukhov
BiDimRegression:Calculates the Bidimensional Regression Between Two 2D Configurations
Calculates the bidimensional regression between two 2D configurations following the approach by Tobler (1965).
Maintained by Alexander Pastukhov. Last updated 3 years ago.
6.3 match 4.00 score 20 scriptsbioc
xcms:LC-MS and GC-MS Data Analysis
Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.
Maintained by Steffen Neumann. Last updated 2 days ago.
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp
1.8 match 196 stars 14.31 score 984 scripts 11 dependents
cvasi-tktd
cvasi:Calibration, Validation, and Simulation of TKTD Models
Eases the use of ecotoxicological effect models. Can simulate common toxicokinetic-toxicodynamic (TK/TD) models such as General Unified Threshold models of Survival (GUTS) and Lemna. It can derive effects and effect profiles (EPx) from scenarios. It supports the use of 'tidyr' workflows employing the pipe symbol. Time-consuming tasks can be parallelized.
Maintained by Nils Kehrein. Last updated 4 days ago.
ecotoxicologymodelingsimulation
4.0 match 2 stars 6.26 score 12 scripts
ohdsi
PhenotypeR:Assess Study Cohorts Using a Common Data Model
Phenotype study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model. Diagnostics are run at the database, code list, cohort, and population level to assess whether study cohorts are ready for research.
Maintained by Edward Burn. Last updated 4 days ago.
3.4 match 2 stars 7.40 score 57 scripts
wjbraun
DAAG:Data Analysis and Graphics Data and Functions
Functions and data sets used in examples and exercises in the text Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data Analysis and Graphics Using R", and in an upcoming Maindonald, Braun, and Andrews text that builds on this earlier text.
Maintained by W. John Braun. Last updated 11 months ago.
3.0 match 8.25 score 1.2k scripts 1 dependents
brechtdv
prevalence:Tools for Prevalence Assessment Studies
The prevalence package provides Frequentist and Bayesian methods for prevalence assessment studies. IMPORTANT: the truePrev functions in the prevalence package call on JAGS (Just Another Gibbs Sampler), which therefore has to be available on the user's system. JAGS can be downloaded from <https://mcmc-jags.sourceforge.io/>.
Maintained by Brecht Devleesschauwer. Last updated 3 years ago.
5.5 match 2 stars 4.48 score 38 scripts
nutriverse
zscorer:Child Anthropometry z-Score Calculator
A tool for calculating z-scores and centiles for weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age, head circumference-for-age, age circumference-for-age, subscapular skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth Standards.
Maintained by Ernest Guevarra. Last updated 4 years ago.
anthropometric-indicesanthropometrygrowth-chartsgrowth-standardsheight-for-agenutritionweight-for-ageweight-for-heightz-score
3.4 match 14 stars 7.30 score 47 scripts 1 dependentstidymodels
spatialsample:Spatial Resampling Infrastructure
Functions and classes for spatial resampling to use with the 'rsample' package, such as spatial cross-validation (Brenning, 2012) <doi:10.1109/IGARSS.2012.6352393>. The scope of 'rsample' and 'spatialsample' is to provide the basic building blocks for creating and analyzing resamples of a spatial data set, but neither package includes functions for modeling or computing statistics. The resampled spatial data sets created by 'spatialsample' do not contain much overhead in memory.
Maintained by Michael Mahoney. Last updated 5 months ago.
3.0 match 73 stars 8.19 score 118 scripts 2 dependents