Showing 125 of total 125 results (show query)
stan-dev
rstanarm:Bayesian Applied Regression Modeling via Stan
Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
Maintained by Ben Goodrich. Last updated 11 days ago.
bayesianbayesian-data-analysisbayesian-inferencebayesian-methodsbayesian-statisticsmultilevel-modelsrstanrstanarmstanstatistical-modelingcpp
393 stars 15.70 score 5.0k scripts 13 dependentsstan-dev
shinystan:Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
A graphical user interface for interactive Markov chain Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a posterior sample. The interface is powered by the 'Shiny' web application framework from 'RStudio' and works with the output of MCMC programs written in any programming language (and has extended functionality for 'Stan' models fit using the 'rstan' and 'rstanarm' packages).
Maintained by Jonah Gabry. Last updated 3 years ago.
bayesianbayesian-data-analysisbayesian-inferencebayesian-methodsbayesian-statisticsmcmcshiny-appsstanstatistical-graphics
200 stars 13.13 score 1.6k scripts 15 dependents
immunomind
immunarch:Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Maintained by Vadim I. Nazarov. Last updated 1 years ago.
airr-analysisb-cell-receptorbcrbcr-repertoirebioinformaticsigig-repertoireimmune-repertoireimmune-repertoire-analysisimmune-repertoire-dataimmunoglobulinimmunoinformaticsimmunologyrep-seqrepertoire-analysissingle-cellsingle-cell-analysist-cell-receptortcrtcr-repertoirecpp
316 stars 9.49 score 203 scripts
didiermurillof
FielDHub:A Shiny App for Design of Experiments in Life Sciences
A shiny design of experiments (DOE) app that aids in the creation of traditional, un-replicated, augmented and partially-replicated designs applied to agriculture, plant breeding, forestry, animal and biological sciences.
Maintained by Didier Murillo. Last updated 8 months ago.
agriculturalbreedingdesigndoeexperimentalplantbreedingshiny
47 stars 9.09 score 70 scripts 1 dependents
bioc
BatchQC:Batch Effects Quality Control Software
Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.
Maintained by Jessica Anderson. Last updated 12 days ago.
batcheffectgraphandnetworkmicroarraynormalizationprincipalcomponentsequencingsoftwarevisualizationqualitycontrolrnaseqpreprocessingdifferentialexpressionimmunooncology
7 stars 9.06 score 54 scripts
tidymodels
tidyposterior:Bayesian Analysis to Compare Models using Resampling Statistics
Bayesian analysis used here to answer the question: "when looking at resampling results, are the differences between models 'real'?" To answer this, a model can be created were the performance statistic is the resampling statistics (e.g. accuracy or RMSE). These values are explained by the model types. In doing this, we can get parameter estimates for each model's affect on performance and make statistical (and practical) comparisons between models. The methods included here are similar to Benavoli et al (2017) <https://jmlr.org/papers/v18/16-305.html>.
Maintained by Max Kuhn. Last updated 5 months ago.
102 stars 8.44 score 273 scripts
florale
multilevelcoda:Estimate Bayesian Multilevel Models for Compositional Data
Implement Bayesian Multilevel Modelling for compositional data in a multilevel framework. Compute multilevel compositional data and Isometric log ratio (ILR) at between and within-person levels, fit Bayesian multilevel models for compositional predictors and outcomes, and run post-hoc analyses such as isotemporal substitution models. References: Le, Stanford, Dumuid, and Wiley (2024) <doi:10.48550/arXiv.2405.03985>, Le, Dumuid, Stanford, and Wiley (2024) <doi:10.48550/arXiv.2411.12407>.
Maintained by Flora Le. Last updated 3 days ago.
bayesian-inferencecompositional-data-analysismultilevel-modelsmultilevelcoda
15 stars 8.34 score 118 scripts
bayes-rules
bayesrules:Datasets and Supplemental Functions from Bayes Rules! Book
Provides datasets and functions used for analysis and visualizations in the Bayes Rules! book (<https://www.bayesrulesbook.com>). The package contains a set of functions that summarize and plot Bayesian models from some conjugate families and another set of functions for evaluation of some Bayesian models.
Maintained by Mine Dogucu. Last updated 3 years ago.
72 stars 8.06 score 466 scriptsbioc
LACE:Longitudinal Analysis of Cancer Evolution (LACE)
LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.
Maintained by Davide Maspero. Last updated 15 days ago.
biomedicalinformaticssinglecellsomaticmutation
15 stars 7.75 score 3 scripts
sebastien-plutniak
archeoViz:Visualisation, Exploration, and Web Communication of Archaeological Spatial Data
An R 'Shiny' application for visual and statistical exploration and web communication of archaeological spatial data, either remains or sites. It offers interactive 3D and 2D visualisations (cross sections and maps of remains, timeline of the work made in a site) which can be exported in SVG and HTML formats. It performs simple spatial statistics (convex hull, regression surfaces, 2D kernel density estimation) and allows exporting data to other online applications for more complex methods. 'archeoViz' can be used offline locally or deployed on a server, either with interactive input of data or with a static data set. Example is provided at <https://analytics.huma-num.fr/archeoviz/en>.
Maintained by Sebastien Plutniak. Last updated 2 months ago.
archaeologyarcheologydata-visualization
19 stars 7.23 score 6 scriptsbioc
ChAMP:Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.
Maintained by Yuan Tian. Last updated 5 months ago.
microarraymethylationarraynormalizationtwochannelcopynumberdnamethylation
6.50 score 278 scriptsbioc
Prostar:Provides a GUI for DAPAR
This package provides a GUI interface for the DAPAR package. The package Prostar (Proteomics statistical analysis with R) is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required.
Maintained by Samuel Wieczorek. Last updated 5 months ago.
proteomicsmassspectrometrynormalizationpreprocessingsoftwareguiprostar1
1 stars 6.48 score 15 scripts
jensharbers
agricolaeplotr:Visualization of Design of Experiments from the 'agricolae' Package
Visualization of Design of Experiments from the 'agricolae' package with 'ggplot2' framework The user provides an experiment design from the 'agricolae' package, calls the corresponding function and will receive a visualization with 'ggplot2' based functions that are specific for each design. As there are many different designs, each design is tested on its type. The output can be modified with standard 'ggplot2' commands or with other packages with 'ggplot2' function extensions.
Maintained by Jens Harbers. Last updated 2 months ago.
8 stars 6.27 score 78 scriptsbioc
VariantFiltering:Filtering of coding and non-coding genetic variants
Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.
Maintained by Robert Castelo. Last updated 2 months ago.
geneticshomo_sapiensannotationsnpsequencinghighthroughputsequencing
4 stars 6.23 score 21 scriptsbioc
omicsViewer:Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer
omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existing ExpressionSet object. The pure dependency on R/Bioconductor guarantees maximum flexibility in the statistical analysis in the back-end. Once the ExpressionSet is prepared, it can be visualized using the front-end, implemented by shiny and plotly. Both features and samples could be selected from (data) tables or graphs (scatter plot/heatmap). Different types of analyses, such as enrichment analysis (using Bioconductor package fgsea or fisher's exact test) and STRING network analysis, will be performed on the fly and the results are visualized simultaneously. When a subset of samples and a phenotype variable is selected, a significance test on means (t-test or ranked based test; when phenotype variable is quantitative) or test of independence (chi-square or fisher’s exact test; when phenotype data is categorical) will be performed to test the association between the phenotype of interest with the selected samples. Additionally, other analyses can be easily added as extra shiny modules. Therefore, omicsViewer will greatly facilitate data exploration, many different hypotheses can be explored in a short time without the need for knowledge of R. In addition, the resulting data could be easily shared using a shiny server. Otherwise, a standalone version of omicsViewer together with designated omics data could be easily created by integrating it with portable R, which can be shared with collaborators or submitted as supplementary data together with a manuscript.
Maintained by Chen Meng. Last updated 2 months ago.
softwarevisualizationgenesetenrichmentdifferentialexpressionmotifdiscoverynetworknetworkenrichment
4 stars 6.02 score 22 scripts
malcolmbarrett
precisely:Estimate Sample Size Based on Precision Rather than Power
Estimate sample size based on precision rather than power. 'precisely' is a study planning tool to calculate sample size based on precision. Power calculations are focused on whether or not an estimate will be statistically significant; calculations of precision are based on the same principles as power calculation but turn the focus to the width of the confidence interval. 'precisely' is based on the work of 'Rothman and Greenland' (2018).
Maintained by Malcolm Barrett. Last updated 3 years ago.
94 stars 5.93 score 18 scripts
insee-psar-at
oceanis:Cartography for Statistical Analysis
Creating maps for statistical analysis such as proportional circles, choropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity. The great features are : - Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technologies). - Create interactive maps through zoom and pop-up ('leaflet' technology). - Create frozen maps with the possibility to add labels.
Maintained by Sébastien Novella. Last updated 2 months ago.
12 stars 5.79 score 17 scriptsbioc
bioCancer:Interactive Multi-Omics Cancers Data Visualization and Analysis
This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.
Maintained by Karim Mezhoud. Last updated 5 months ago.
guidatarepresentationnetworkmultiplecomparisonpathwaysreactomevisualizationgeneexpressiongenetargetanalysisbiocancer-interfacecancercancer-studiesrmarkdown
20 stars 5.78 score 7 scripts
giopogg
webSDM:Including Known Interactions in Species Distribution Models
A collection of tools to fit and work with trophic Species Distribution Models. Trophic Species Distribution Models combine knowledge of trophic interactions with Bayesian structural equation models that model each species as a function of its prey (or predators) and environmental conditions. It exploits the topological ordering of the known trophic interaction network to predict species distribution in space and/or time, where the prey (or predator) distribution is unavailable. The method implemented by the package is described in Poggiato, Andréoletti, Pollock and Thuiller (2022) <doi:10.22541/au.166853394.45823739/v1>.
Maintained by Giovanni Poggiato. Last updated 9 months ago.
17 stars 5.71 score 9 scripts
bernhard-da
sdcHierarchies:Create and (Interactively) Modify Nested Hierarchies
Provides functionality to generate, (interactively) modify (by adding, removing and renaming nodes) and convert nested hierarchies between different formats. These tree like structures can be used to define for example complex hierarchical tables used for statistical disclosure control.
Maintained by Bernhard Meindl. Last updated 1 years ago.
2 stars 5.70 score 28 scripts 3 dependents
danielmork
dlmtree:Bayesian Treed Distributed Lag Models
Estimation of distributed lag models (DLMs) based on a Bayesian additive regression trees framework. Includes several extensions of DLMs: treed DLMs and distributed lag mixture models (Mork and Wilson, 2023) <doi:10.1111/biom.13568>; treed distributed lag nonlinear models (Mork and Wilson, 2022) <doi:10.1093/biostatistics/kxaa051>; heterogeneous DLMs (Mork, et. al., 2024) <doi:10.1080/01621459.2023.2258595>; monotone DLMs (Mork and Wilson, 2024) <doi:10.1214/23-BA1412>. The package also includes visualization tools and a 'shiny' interface to help interpret results.
Maintained by Daniel Mork. Last updated 2 months ago.
21 stars 5.40 score 17 scripts
maialba3
LipidMS:Lipid Annotation for LC-MS/MS DDA or DIA Data
Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Maintained by M Isabel Alcoriza-Balaguer. Last updated 7 months ago.
2 stars 5.33 score 12 scripts 1 dependents
forsterepi
epicmodel:Causal Modeling in Epidemiology
Create causal models for use in epidemiological studies, including sufficient-component cause models as introduced by Rothman (1976) <doi:10.1093/oxfordjournals.aje.a112335>.
Maintained by Felix Forster. Last updated 4 months ago.
5.24 score 6 scripts
manueleleonelli
bnRep:A Repository of Bayesian Networks from the Academic Literature
A collection of Bayesian networks (discrete, Gaussian, and conditional linear Gaussian) collated from recent academic literature. The 'bnRep_summary' object provides an overview of the Bayesian networks in the repository and the package documentation includes details about the variables in each network. A Shiny app to explore the repository can be launched with 'bnRep_app()' and is available online at <https://manueleleonelli.shinyapps.io/bnRep>. For details see <https://github.com/manueleleonelli/bnRep>.
Maintained by Manuele Leonelli. Last updated 6 months ago.
6 stars 5.18 score 7 scripts
markheckmann
gridsampler:A Simulation Tool to Determine the Required Sample Size for Repertory Grid Studies
Simulation tool to facilitate determination of required sample size to achieve category saturation for studies using multiple repertory grids in conjunction with content analysis.
Maintained by Mark Heckmann. Last updated 5 years ago.
4 stars 5.10 score 21 scripts
ropensci
qcoder:Lightweight Qualitative Coding
A free, lightweight, open source option for analyzing text-based qualitative data. Enables analysis of interview transcripts, observation notes, memos, and other sources. Supports the work of social scientists, historians, humanists, and other researchers who use qualitative methods. Addresses the unique challenges faced in analyzing qualitative data analysis. Provides opportunities for researchers who otherwise might not develop software to build software development skills.
Maintained by Elin Waring. Last updated 3 years ago.
135 stars 5.06 score 13 scripts
vinhdizzo
IRexamples:Collection of Practical Institutional Research Examples and Tutorials
Provides examples of code for analyzing data or accomplishing tasks that may be useful to institutional or educational researchers.
Maintained by Vinh Nguyen. Last updated 2 years ago.
4 stars 5.00 score 4 scriptsbioc
shinyepico:ShinyÉPICo
ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis.
Maintained by Octavio Morante-Palacios. Last updated 5 months ago.
differentialmethylationdnamethylationmicroarraypreprocessingqualitycontrol
5 stars 5.00 score 1 scripts
traitecoevo
infinitylists:A Shiny-Based Application for Generating Place-Based Species Lists
This shiny-based application allows users to extract species occurrence records from the Atlas of Living Australia or GBIF and generate a species list for a defined area. All records associated with either a physical voucher (stored in herbaria or museums) or a photographic or audio voucher (stored in iNaturalist) are extracted. For each species within the defined area, the application will return voucher type, number of vouchers, date of the most recent voucher, spatial coordinates, voucher location, and the voucher collector. Records are displayed both in a table and on a map, and are downloadable as a CSV.
Maintained by Thomas Mesaglio. Last updated 6 days ago.
4 stars 4.98 score 7 scripts
fpaskali
LFApp:Shiny Apps for Lateral Flow Assays
Shiny apps for the quantitative analysis of images from lateral flow assays (LFAs). The images are segmented and background corrected and color intensities are extracted. The apps can be used to import and export intensity data and to calibrate LFAs by means of linear, loess, or gam models. The calibration models can further be saved and applied to intensity data from new images for determining concentrations.
Maintained by Filip Paskali. Last updated 10 months ago.
calibrationimage-processingmedical-image-processingshiny
3 stars 4.78 score 2 scripts
genentech
BayesERtools:Bayesian Exposure-Response Analysis Tools
Suite of tools that facilitate exposure-response analysis using Bayesian methods. The package provides a streamlined workflow for fitting types of models that are commonly used in exposure-response analysis - linear and Emax for continuous endpoints, logistic linear and logistic Emax for binary endpoints, as well as performing simulation and visualization. Learn more about the workflow at <https://genentech.github.io/BayesERbook/>.
Maintained by Kenta Yoshida. Last updated 1 months ago.
2 stars 4.78 score 20 scriptsbioc
plotGrouper:Shiny app GUI wrapper for ggplot with built-in statistical analysis
A shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed).
Maintained by John D. Gagnon. Last updated 5 months ago.
immunooncologyflowcytometrygraphandnetworkstatisticalmethoddataimportguimultiplecomparisonbioconductorggplot2plottingshiny
6 stars 4.78 score 10 scripts
nspyrison
cheem:Interactively Explore Local Explanations with the Radial Tour
Given a non-linear model, calculate the local explanation. We purpose view the data space, explanation space, and model residuals as ensemble graphic interactive on a shiny application. After an observation of interest is identified, the normalized variable importance of the local explanation is used as a 1D projection basis. The support of the local explanation is then explored by changing the basis with the use of the radial tour <doi:10.32614/RJ-2020-027>; <doi:10.1080/10618600.1997.10474754>.
Maintained by Nicholas Spyrison. Last updated 1 years ago.
2 stars 4.73 score 54 scripts
mreginato
monographaR:Taxonomic Monographs Tools
Contains functions intended to facilitate the production of plant taxonomic monographs. The package includes functions to convert tables into taxonomic descriptions, lists of collectors, examined specimens, identification keys (dichotomous and interactive), and can generate a monograph skeleton. Additionally, wrapper functions to batch the production of phenology histograms and distributional and diversity maps are also available.
Maintained by Marcelo Reginato. Last updated 1 years ago.
3 stars 4.73 score 18 scripts
zjg540066169
AuxSurvey:Survey Analysis with Auxiliary Discretized Variables
Probability surveys often use auxiliary continuous data from administrative records, but the utility of this data is diminished when it is discretized for confidentiality. We provide a set of survey estimators to make full use of information from the discretized variables. See Williams, S.Z., Zou, J., Liu, Y., Si, Y., Galea, S. and Chen, Q. (2024), Improving Survey Inference Using Administrative Records Without Releasing Individual-Level Continuous Data. Statistics in Medicine, 43: 5803-5813. <doi:10.1002/sim.10270> for details.
Maintained by Jungang Zou. Last updated 3 months ago.
auxilary-variablescategorical-variablessurvey-analysis
1 stars 4.70 score 5 scripts
aurelienroyer
SEAHORS:Spatial Exploration of ArcHaeological Objects in R Shiny
An R 'Shiny' application dedicated to the intra-site spatial analysis of piece-plotted archaeological remains, making the two and three-dimensional spatial exploration of archaeological data as user-friendly as possible. Documentation about 'SEAHORS' is provided by the vignette included in this package and by the companion scientific paper: Royer, Discamps, Plutniak, Thomas (2023, PCI Archaeology, <doi:10.5281/zenodo.7674698>).
Maintained by Sebastien Plutniak. Last updated 1 years ago.
archaeologyspatial-visualizations
5 stars 4.70 score 4 scripts
kfinucane
MetSizeR:A Shiny App for Sample Size Estimation in Metabolomic Experiments
Provides a Shiny application to estimate the sample size required for a metabolomic experiment to achieve a desired statistical power. Estimation is possible with or without available data from a pilot study.
Maintained by Kate Finucane. Last updated 4 years ago.
4.65 score 7 scriptssebastien-plutniak
archeofrag.gui:Spatial Analysis in Archaeology from Refitting Fragments (GUI)
A 'Shiny' application to access the functionalities and datasets of the 'archeofrag' package for spatial analysis in archaeology from refitting data. Quick and seamless exploration of archaeological refitting datasets, focusing on physical refits only. Features include: built-in documentation and convenient workflow, plot generation and exports, exploration of spatial units merging solutions, simulation of archaeological site formation processes, support for parallel computing, R code generation to re-execute simulations and ensure reproducibility, code generation for the 'openMOLE' model exploration software. A demonstration of the app is available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.
Maintained by Sebastien Plutniak. Last updated 7 days ago.
archaeologyfragmentationshiny-appstaphonomy
5 stars 4.65 scorebioc
GA4GHshiny:Shiny application for interacting with GA4GH-based data servers
GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.
Maintained by Welliton Souza. Last updated 5 months ago.
2 stars 4.60 score 3 scripts
jessieyeung
rcbayes:Estimate Rogers-Castro Migration Age Schedules with Bayesian Models
A collection of functions to estimate Rogers-Castro migration age schedules using 'Stan'. This model which describes the fundamental relationship between migration and age in the form of a flexible multi-exponential migration model was most notably proposed in Rogers and Castro (1978) <doi:10.1068/a100475>.
Maintained by Jessie Yeung. Last updated 1 years ago.
2 stars 4.60 score 8 scripts
shabbychef
cocktailApp:'shiny' App to Discover Cocktails
A 'shiny' app to discover cocktails. The app allows one to search for cocktails by ingredient, filter on rating, and number of ingredients. The package also contains data with the ingredients of nearly 26 thousand cocktails scraped from the web.
Maintained by Steven E. Pav. Last updated 3 years ago.
43 stars 4.33 score 5 scripts
mightymetrika
npboottprm:Nonparametric Bootstrap Test with Pooled Resampling
Addressing crucial research questions often necessitates a small sample size due to factors such as distinctive target populations, rarity of the event under study, time and cost constraints, ethical concerns, or group-level unit of analysis. Many readily available analytic methods, however, do not accommodate small sample sizes, and the choice of the best method can be unclear. The 'npboottprm' package enables the execution of nonparametric bootstrap tests with pooled resampling to help fill this gap. Grounded in the statistical methods for small sample size studies detailed in Dwivedi, Mallawaarachchi, and Alvarado (2017) <doi:10.1002/sim.7263>, the package facilitates a range of statistical tests, encompassing independent t-tests, paired t-tests, and one-way Analysis of Variance (ANOVA) F-tests. The nonparboot() function undertakes essential computations, yielding detailed outputs which include test statistics, effect sizes, confidence intervals, and bootstrap distributions. Further, 'npboottprm' incorporates an interactive 'shiny' web application, nonparboot_app(), offering intuitive, user-friendly data exploration.
Maintained by Mackson Ncube. Last updated 6 months ago.
datasciencenonparametricstatistics
1 stars 4.26 score 5 scripts 2 dependents
statisticsnorway
easySdcTable:Easy Interface to the Statistical Disclosure Control Package 'sdcTable' Extended with Own Implementation of 'GaussSuppression'
The main function, ProtectTable(), performs table suppression according to a frequency rule with a data set as the only required input. Within this function, protectTable(), protect_linked_tables() or runArgusBatchFile() in package 'sdcTable' is called. Lists of level-hierarchy (parameter 'dimList') and other required input to these functions are created automatically. The suppression method Gauss (default) is implemented independently of 'sdcTable'. The function, PTgui(), starts a graphical user interface based on the 'shiny' package.
Maintained by Øyvind Langsrud. Last updated 13 days ago.
1 stars 4.20 score 16 scripts
green-striped-gecko
dartR.sim:Computer Simulations of 'SNP' Data
Allows to simulate SNP data using genlight objects. For example, it is straight forward to simulate a simple drift scenario with exchange of individuals between two populations or create a new genlight object based on allele frequencies of an existing genlight object.
Maintained by Jose L. Mijangos. Last updated 1 years ago.
4.18 score 1 scripts 1 dependents
nassimayad87
EpiSimR:A 'Shiny' App to Simulate the Dynamics of Epidemic and Endemic Diseases Spread
The 'EpiSimR' package provides an interactive 'shiny' app based on deterministic compartmental mathematical modeling for simulating and visualizing the dynamics of epidemic and endemic disease spread. It allows users to explore various intervention strategies, including vaccination and isolation, by adjusting key epidemiological parameters. The methodology follows the approach described by Brauer (2008) <doi:10.1007/978-3-540-78911-6_2>. Thanks to 'shiny' package.
Maintained by Nassim AYAD. Last updated 29 days ago.
infectious-disease-modelsseir-modelshiny-appssimulationsir-model
4.18 score 1 scripts
arliph
SPARTAAS:Statistical Pattern Recognition and daTing using Archaeological Artefacts assemblageS
Statistical pattern recognition and dating using archaeological artefacts assemblages. Package of statistical tools for archaeology. hclustcompro(perioclust): Bellanger Lise, Coulon Arthur, Husi Philibrary(SPARTlippe (2021, ISBN:978-3-030-60103-4). mapclust: Bellanger Lise, Coulon Arthur, Husi Philippe (2021) <doi:10.1016/j.jas.2021.105431>. seriograph: Desachy Bruno (2004) <doi:10.3406/pica.2004.2396>. cerardat: Bellanger Lise, Husi Philippe (2012) <doi:10.1016/j.jas.2011.06.031>.
Maintained by Arthur Coulon. Last updated 10 months ago.
6 stars 4.14 score 46 scripts
kwb-r
aquanes.report:Automated Reporting Tool for Water Suppliers
Collects, aggregates and visualises operational and analytical data from water suppliers (including a standardised reporting document).
Maintained by Michael Rustler. Last updated 6 years ago.
automated-reportingdata-aggregationdata-exportdata-importdata-visualisationpilot-plantproject-aquanesshiny-app
4.01 score 23 scriptskwb-r
kwb.pilot:Importing, Aggregating and Visualising Data From KWB Pilot Plants
Collects, aggregates and visualises operational and analytical data from water suppliers (including a standardised reporting document).
Maintained by Michael Rustler. Last updated 2 years ago.
data-aggregationdata-importdata-visualisationproject-aquanesproject-mbr40project-sulemanproject-ultimate
1 stars 4.01 score 17 scriptsmightymetrika
bootwar:Nonparametric Bootstrap Test with Pooled Resampling Card Game
The card game War is simple in its rules but can be lengthy. In another domain, the nonparametric bootstrap test with pooled resampling (nbpr) methods, as outlined in Dwivedi, Mallawaarachchi, and Alvarado (2017) <doi:10.1002/sim.7263>, is optimal for comparing paired or unpaired means in non-normal data, especially for small sample size studies. However, many researchers are unfamiliar with these methods. The 'bootwar' package bridges this gap by enabling users to grasp the concepts of nbpr via Boot War, a variation of the card game War designed for small samples. The package provides functions like score_keeper() and play_round() to streamline gameplay and scoring. Once a predetermined number of rounds concludes, users can employ the analyze_game() function to derive game results. This function leverages the 'npboottprm' package's nonparboot() to report nbpr results and, for comparative analysis, also reports results from the 'stats' package's t.test() function. Additionally, 'bootwar' features an interactive 'shiny' web application, bootwar(). This offers a user-centric interface to experience Boot War, enhancing understanding of nbpr methods across various distributions, sample sizes, number of bootstrap resamples, and confidence intervals.
Maintained by Mackson Ncube. Last updated 1 years ago.
bootstrapdata-scienceresamplingstatistics
4.00 score 6 scripts
mmollina
viewpoly:A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
Provides a graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.
Maintained by Cristiane Taniguti. Last updated 30 days ago.
4 stars 3.90 score 2 scriptsbioc
BiocHubsShiny:View AnnotationHub and ExperimentHub Resources Interactively
A package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.
Maintained by Marcel Ramos. Last updated 26 days ago.
3.90 score 1 scripts
abhrastat
heiscore:Score and Plot the Healthy Eating Index from NHANES Data
Calculate and visualize Healthy Eating Index (HEI) scores from National Health and Nutrition Examination Survey 24-hour dietary recall data utilizing three methods recommended by the National Cancer Institute (2024) <https://epi.grants.cancer.gov/hei/hei-methods-and-calculations.html#:~:text=To%20use%20the%20simple%20HEI,the%20total%20scores%20across%20individuals.>. Effortlessly analyze HEI scores across different demographic groups and years.
Maintained by Vijetha Ramdas. Last updated 2 months ago.
3.85 score 2 scripts
sciurus365
quadVAR:Quadratic Vector Autoregression
Estimate quadratic vector autoregression models with the strong hierarchy using the Regularization Algorithm under Marginality Principle (RAMP) by Hao et al. (2018) <doi:10.1080/01621459.2016.1264956>, compare the performance with linear models, and construct networks with partial derivatives.
Maintained by Jingmeng Cui. Last updated 2 months ago.
3.78 score 3 scripts
openvolley
ovscout2:An R Shiny App for Scouting Volleyball Match Files
Functions for scouting volleyball match files.
Maintained by Ben Raymond. Last updated 11 months ago.
6 stars 3.78 score 8 scriptsmaialba3
FAMetA:Fatty Acid Metabolic Analysis
Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.
Maintained by Maribel Alcoriza-Balaguer. Last updated 1 years ago.
1 stars 3.70 score 2 scripts
moshejasper
kindisperse:Simulate and Estimate Close-Kin Dispersal Kernels
Functions for simulating and estimating kinship-related dispersal. Based on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A. Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito". Assumes an additive variance model of dispersal in two dimensions, compatible with Wright's neighbourhood area. Simple and composite dispersal simulations are supplied, as well as the functions needed to estimate parent-offspring dispersal for simulated or empirical data, and to undertake sampling design for future field studies of dispersal. For ease of use an integrated Shiny app is also included.
Maintained by Moshe-Elijah Jasper. Last updated 5 months ago.
1 stars 3.70 score 5 scripts
stla
html2R:Convert 'HTML' to 'R' with a 'Shiny' App
Provides a 'Shiny' app allowing to convert 'HTML' code to 'R' code (e.g. '<span>Hello</span>' to 'tags$span("Hello")'), for usage in a 'Shiny' UI.
Maintained by Stéphane Laurent. Last updated 5 years ago.
9 stars 3.65 score
henry-heppe
adproclus:Additive Profile Clustering Algorithms
Obtain overlapping clustering models for object-by-variable data matrices using the Additive Profile Clustering (ADPROCLUS) method. Also contains the low dimensional ADPROCLUS method for simultaneous dimension reduction and overlapping clustering. For reference see Depril, Van Mechelen, Mirkin (2008) <doi:10.1016/j.csda.2008.04.014> and Depril, Van Mechelen, Wilderjans (2012) <doi:10.1007/s00357-012-9112-5>.
Maintained by Henry Heppe. Last updated 7 months ago.
2 stars 3.60 score 2 scriptsmightymetrika
holi:Higher Order Likelihood Inference Web Applications
Higher order likelihood inference is a promising approach for analyzing small sample size data. The 'holi' package provides web applications for higher order likelihood inference. It currently supports linear, logistic, and Poisson generalized linear models through the rstar_glm() function, based on Pierce and Bellio (2017) <doi:10.1111/insr.12232> and 'likelihoodAsy'. The package offers two main features: LA_rstar(), which launches an interactive 'shiny' application allowing users to fit models with rstar_glm() through their web browser, and sim_rstar_glm_pgsql(), which streamlines the process of launching a web-based 'shiny' simulation application that saves results to a user-created 'PostgreSQL' database.
Maintained by Mackson Ncube. Last updated 7 months ago.
3.48 score 5 scripts
dzangri
stmgui:Shiny Application for Creating STM Models
Provides an application that acts as a GUI for the 'stm' text analysis package.
Maintained by Dan Zangri. Last updated 8 years ago.
5 stars 3.40 score 4 scripts
r-forge
Eagle:Multiple Locus Association Mapping on a Genome-Wide Scale
An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred or outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. To perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Maintained by Andrew George. Last updated 5 years ago.
3.34 score 22 scriptsbernhard-da
sdcTable:Methods for Statistical Disclosure Control in Tabular Data
Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression as described for example in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.
Maintained by Bernhard Meindl. Last updated 19 days ago.
1 stars 3.32 score 25 scripts 2 dependentsmightymetrika
mmibain:Bayesian Informative Hypotheses Evaluation Web Applications
Researchers often have expectations about the relations between means of different groups or standardized regression coefficients; using informative hypothesis testing to incorporate these expectations into the analysis through order constraints increases statistical power Vanbrabant and Rosseel (2020) <doi:10.4324/9780429273872-14>. Another valuable tool, the Bayes factor, can evaluate evidence for multiple hypotheses without concerns about multiple testing, and can be used in Bayesian updating Hoijtink, Mulder, van Lissa & Gu (2019) <doi:10.1037/met0000201>. The 'bain' R package enables informative hypothesis testing using the Bayes factor. The 'mmibain' package provides 'shiny' web applications based on 'bain'. The RepliCrisis() function launches a 'shiny' card game to simulate the evaluation of replication studies while the mmibain() function launches a 'shiny' application to fit Bayesian informative hypotheses evaluation models from 'bain'.
Maintained by Mackson Ncube. Last updated 10 months ago.
bayes-factorbayesianhypothesisinformativestatistics
3.30 score 2 scriptsmightymetrika
mmirestriktor:Informative Hypothesis Testing Web Applications
Offering enhanced statistical power compared to traditional hypothesis testing methods, informative hypothesis testing allows researchers to explicitly model their expectations regarding the relationships among parameters. An important software tool for this framework is 'restriktor'. The 'mmirestriktor' package provides 'shiny' web applications to implement some of the basic functionality of 'restriktor'. The mmirestriktor() function launches a 'shiny' application for fitting and analyzing models with constraints. The FbarCards() function launches a card game application which can help build intuition about informative hypothesis testing. The iht_interpreter() helps interpret informative hypothesis testing results based on guidelines in Vanbrabant and Rosseel (2020) <doi:10.4324/9780429273872-14>.
Maintained by Mackson Ncube. Last updated 8 months ago.
datahypothesisinfomativepowerrestriktorstatisticstesting
3.30 score 5 scriptssciurus365
Isinglandr:Landscape Construction and Simulation for Ising Networks
A toolbox for constructing potential landscapes for Ising networks. The parameters of the networks can be directly supplied by users or estimated by the 'IsingFit' package by van Borkulo and Epskamp (2016) <https://CRAN.R-project.org/package=IsingFit> from empirical data. The Ising model's Boltzmann distribution is preserved for the potential landscape function. The landscape functions can be used for quantifying and visualizing the stability of network states, as well as visualizing the simulation process.
Maintained by Jingmeng Cui. Last updated 6 months ago.
1 stars 3.30 score 3 scripts
therfrog
shinyNORRRM:The Ultimate Igneous Norm
The computer program is an efficient igneous norm algorithm and rock classification system written in R but run as shiny app.
Maintained by Reneé González-Guzmán. Last updated 2 years ago.
3 stars 3.18 score 3 scripts
cran
MuPETFlow:Multiple Ploidy Estimation Tool for all Species Compatible with Flow Cytometry
A graphical user interface tool to estimate ploidy from DNA cells stained with fluorescent dyes and analyzed by flow cytometry, following the methodology of Gómez-Muñoz and Fischer (2024) <doi:10.1101/2024.01.24.577056>. Features include multiple file uploading and configuration, peak fluorescence intensity detection, histogram visualizations, peak error curation, ploidy and genome size calculations, and easy results export.
Maintained by Cintia Gómez-Muñoz. Last updated 2 months ago.
3.00 score
ptuc-stats
shinyCLT:Central Limit Theorem 'shiny' Application
A 'shiny' application estimating the operating characteristics of the Student's t-test by Student (1908) <doi:10.1093/biomet/6.1.1>, Welch's t-test by Welch (1947) <doi:10.1093/biomet/34.1-2.28>, and Wilcoxon test by Wilcoxon (1945) <doi:10.2307/3001968> in one-sample or two-sample cases, in settings defined by the user (conditional distribution, sample size per group, location parameter per group, nuisance parameter per group), using Monte Carlo simulations Malvin H. Kalos, Paula A. Whitlock (2008) <doi:10.1002/9783527626212>.
Maintained by Dominique-Laurent Couturier. Last updated 1 months ago.
3.00 scoremarkheckmann
OpenRepGrid.ic:Interpretive Clustering for Repertory Grids
Shiny UI to identify cliques of related constructs in repertory grid data. See Burr, King, & Heckmann (2020) <doi:10.1080/14780887.2020.1794088> for a description of the interpretive clustering (IC) method.
Maintained by Mark Heckmann. Last updated 1 years ago.
clusteringconstructsgridrepertoryrepgridshiny
2 stars 3.00 score 8 scripts
amalan-constat
OlympicRshiny:'Shiny' Application for Olympic Data
'Shiny' Application to visualize Olympic Data. From 1896 to 2016. Even Winter Olympics events are included. Data is from Kaggle at <https://www.kaggle.com/heesoo37/120-years-of-olympic-history-athletes-and-results>.
Maintained by Amalan Mahendran. Last updated 4 months ago.
1 stars 3.00 score
rikoke
fbst:The Full Bayesian Evidence Test, Full Bayesian Significance Test and the e-Value
Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available.
Maintained by Riko Kelter. Last updated 1 years ago.
1 stars 2.95 score 6 scripts 1 dependents
ugranziol
appRiori:Code and Obtain Customized Planned Comparisons with 'appRiori'
With 'appRiori' <doi:10.1177/25152459241293110>, users upload the research variables and the app guides them to the best set of comparisons fitting the hypotheses, for both main and interaction effects. Through a graphical explanation and empirical examples on reproducible data, it is shown that it is possible to understand both the logic behind the planned comparisons and the way to interpret them when a model is tested.
Maintained by Umberto Granziol. Last updated 1 months ago.
2 stars 2.90 score 7 scripts
kwb-r
kwb.flusshygiene:Functions used within FLUSSHYGIENE project (BMBF)
Easy and transferable functions for creating and managing models for hygiene data in rivers. This package is developed within the FLUSSHYGIENE project. See https://bmbf.nawam-rewam.de/en/projekt/flusshygiene/ for details.
Maintained by Hauke Sonnenberg. Last updated 5 years ago.
1 stars 2.70 score 1 scriptsmightymetrika
exactamente:Explore the Exact Bootstrap Method
Researchers often use the bootstrap to understand a sample drawn from a population with unknown distribution. The exact bootstrap method is a practical tool for exploring the distribution of small sample size data. For a sample of size n, the exact bootstrap method generates the entire space of n to the power of n resamples and calculates all realizations of the selected statistic. The 'exactamente' package includes functions for implementing two bootstrap methods, the exact bootstrap and the regular bootstrap. The exact_bootstrap() function applies the exact bootstrap method following methodologies outlined in Kisielinska (2013) <doi:10.1007/s00180-012-0350-0>. The regular_bootstrap() function offers a more traditional bootstrap approach, where users can determine the number of resamples. The e_vs_r() function allows users to directly compare results from these bootstrap methods. To augment user experience, 'exactamente' includes the function exactamente_app() which launches an interactive 'shiny' web application. This application facilitates exploration and comparison of the bootstrap methods, providing options for modifying various parameters and visualizing results.
Maintained by Mackson Ncube. Last updated 2 years ago.
bootstrapprobabilityresamplestatistics
2.70 score 2 scripts
phamdn
centrifugeR:Non-Trivial Balance of Centrifuge Rotors
Find the numbers of test tubes that can be balanced in centrifuge rotors and show various ways to load them. Refer to Pham (2020) <doi:10.31224/osf.io/4xs38> for more information on package functionality.
Maintained by Duy Nghia Pham. Last updated 8 months ago.
2.70 score 2 scripts
ifpri
ARIA:App for IMPACT (App foR ImpAct)
App for IMPACT (App foR ImpAct).
Maintained by Abhijeet Mishra. Last updated 10 months ago.
2.70 score 6 scripts
andeek
protoshiny:Interactive Dendrograms for Visualizing Hierarchical Clusters with Prototypes
Shiny app to interactively visualize hierarchical clustering with prototypes. For details on hierarchical clustering with prototypes, see Bien and Tibshirani (2011) <doi:10.1198/jasa.2011.tm10183>. This package currently launches the application.
Maintained by Andee Kaplan. Last updated 3 years ago.
1 stars 2.70 score 4 scripts
kidoishi
MadanTextNetwork:Persian Textmining Tool for Co-Occurrence_Network
MadanText_co-occurrence_network is an open-source software designed specifically for text mining in the Persian language. It adds co-occurrence network functionality to MadanText. The input file replaces the text format with an Excel format.
Maintained by Kido Ishikawa. Last updated 1 years ago.
2.70 scorekidoishi
MadanText:Persian Textmining Tool for Frequency Analysis, Statistical Analysis, and Word Clouds
MadanText is an open-source software designed specifically for text mining in the Persian language. It allows users to examine word frequencies, download data for analysis, and generate word clouds. This tool is particularly useful for researchers and analysts working with Persian language data.
Maintained by Kido Ishikawa. Last updated 1 years ago.
2.70 score
jamescbell
gestate:Generalised Survival Trial Assessment Tool Environment
Provides tools to assist planning and monitoring of time-to-event trials under complicated censoring assumptions and/or non-proportional hazards. There are three main components: The first is analytic calculation of predicted time-to-event trial properties, providing estimates of expected hazard ratio, event numbers and power under different analysis methods. The second is simulation, allowing stochastic estimation of these same properties. Thirdly, it provides parametric event prediction using blinded trial data, including creation of prediction intervals. Methods are based upon numerical integration and a flexible object-orientated structure for defining event, censoring and recruitment distributions (Curves).
Maintained by James Bell. Last updated 2 years ago.
2 stars 2.60 score 8 scripts
julienrocheigepp
APIS:Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents
Parentage assignment package. Parentage assignment is performed based on observed average Mendelian transmission probability distributions or Exclusion. The main functions of this package are the function APIS_2n(), APIS_3n() and launch_APIShiny(), which perform parentage assignment.
Maintained by Julien Roche. Last updated 5 months ago.
2.60 score
riko-k
brada:Bayesian Response-Adaptive Design Analysis
Provides access to a range of functions for analyzing, applying and visualizing Bayesian response-adaptive trial designs for a binary endpoint. Includes the predictive probability approach and the predictive evidence value designs for binary endpoints.
Maintained by Riko Kelter. Last updated 2 years ago.
2.30 score 4 scripts
vharntzen
doublIn:Estimate Incubation or Latency Time using Doubly Interval Censored Observations
Visualize contact tracing data using a 'shiny' app and estimate the incubation or latency time of an infectious disease respecting the following characteristics in the analysis; (i) doubly interval censoring with (partly) overlapping or distinct windows; (ii) an infection risk corresponding to exponential growth; (iii) right truncation allowing for individual truncation times; (iv) different choices concerning the family of the distribution. For our earlier work, we refer to Arntzen et al. (2023) <doi:10.1002/sim.9726>. A paper describing our approach in detail will follow.
Maintained by Vera Arntzen. Last updated 10 months ago.
2.30 score 3 scripts
aybekec
RSP:'shiny' Applications for Statistical and Psychometric Analysis
Toolbox with 'shiny' applications for widely used psychometric methods. Those methods include following analysis: Item analysis, item response theory calibration, principal component analysis, confirmatory factor analysis - structural equation modeling, generating simulated data. References: Chalmers (2012, <doi:10.18637/jss.v048.i06>); Revelle (2022, <https://CRAN.R-project.org/package=psych Version = 2.2.9.>); Rosseel (2012, <doi:10.18637/jss.v048.i02>); Magis & Raiche (2012, <doi:10.18637/jss.v048.i08>); Magis & Barrada (2017, <doi:10.18637/jss.v076.c01>).
Maintained by Eren Can Aybek. Last updated 2 years ago.
2.28 score 19 scriptscran
multichull:A Generic Convex-Hull-Based Model Selection Method
Given a set of models for which a measure of model (mis)fit and model complexity is provided, CHull(), developed by Ceulemans and Kiers (2006) <doi:10.1348/000711005X64817>, determines the models that are located on the boundary of the convex hull and selects an optimal model by means of the scree test values.
Maintained by Kristof Meers. Last updated 5 months ago.
2.08 score 2 dependents
mattkumar
abstractr:An R-Shiny Application for Creating Visual Abstracts
An R-Shiny application to create visual abstracts for original research. A variety of user defined options and formatting are included.
Maintained by Matthew Kumar. Last updated 6 years ago.
2.00 score 1 scriptsgreen-striped-gecko
dartR.captive:Analysing 'SNP' Data to Support Captive Breeding
Functions are provided that facilitate the analysis of SNP (single nucleotide polymorphism) data to answer questions regarding captive breeding and relatedness between individuals. 'dartR.captive' is part of the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.
Maintained by Bernd Gruber. Last updated 1 months ago.
1 stars 2.00 score 3 scriptscran
GFD:Tests for General Factorial Designs
Implemented are the Wald-type statistic, a permuted version thereof as well as the ANOVA-type statistic for general factorial designs, even with non-normal error terms and/or heteroscedastic variances, for crossed designs with an arbitrary number of factors and nested designs with up to three factors. Friedrich et al. (2017) <doi:10.18637/jss.v079.c01>.
Maintained by Sarah Friedrich. Last updated 3 years ago.
2.00 scorecran
NiLeDAM:Monazite Dating for the NiLeDAM Team
Th-U-Pb electron microprobe age dating of monazite, as originally described in <doi:10.1016/0009-2541(96)00024-1>.
Maintained by Nathalie Vialaneix. Last updated 2 years ago.
2.00 score
lrcastro
spANOVA:Analysis of Field Trials with Geostatistics & Spatial AR Models
Perform analysis of variance when the experimental units are spatially correlated. There are two methods to deal with spatial dependence: Spatial autoregressive models (see Rossoni, D. F., & Lima, R. R. (2019) <doi:10.28951/rbb.v37i2.388>) and geostatistics (see Pontes, J. M., & Oliveira, M. S. D. (2004) <doi:10.1590/S1413-70542004000100018>). For both methods, there are three multicomparison procedure available: Tukey, multivariate T, and Scott-Knott.
Maintained by Castro L. R.. Last updated 1 years ago.
1.70 score 2 scriptsshabbychef
faroutman:Shiny Fractal Viewer
a shiny page to page around in fractals.
Maintained by Steven E. Pav. Last updated 2 years ago.
1.70 score 2 scripts
rvhulst
evidence:Analysis of Scientific Evidence Using Bayesian and Likelihood Methods
Bayesian (and some likelihoodist) functions as alternatives to hypothesis-testing functions in R base using a user interface patterned after those of R's hypothesis testing functions. See McElreath (2016, ISBN: 978-1-4822-5344-3), Gelman and Hill (2007, ISBN: 0-521-68689-X) (new edition in preparation) and Albert (2009, ISBN: 978-0-387-71384-7) for good introductions to Bayesian analysis and Pawitan (2002, ISBN: 0-19-850765-8) for the Likelihood approach. The functions in the package also make extensive use of graphical displays for data exploration and model comparison.
Maintained by Robert van Hulst. Last updated 7 years ago.
1.63 score 43 scripts
hanase
wppExplorer:Explorer of World Population Prospects
Explore data in the 'wpp2019' (or 2017, 2015, ...) package using a 'shiny' interface.
Maintained by Hana Sevcikova. Last updated 5 years ago.
1.53 score 34 scriptsjulienrocheigepp
GenoTriplo:Genotyping Triploids (or Diploids) from Luminescence Data
Genotyping of triploid individuals from luminescence data (marker probeset A and B). Works also for diploids. Two main functions: Run_Clustering() that regroups individuals with a same genotype based on proximity and Run_Genotyping() that assigns a genotype to each cluster. For Shiny interface use: launch_GenoShiny().
Maintained by Julien Roche. Last updated 5 days ago.
1.48 score
merlemunko
GFDrmst:Multiple RMST-Based Tests in General Factorial Designs
We implemented multiple tests based on the restricted mean survival time (RMST) for general factorial designs as described in Munko et al. (2024) <doi:10.1002/sim.10017>. Therefore, an asymptotic test, a groupwise bootstrap test, and a permutation test are incorporated with a Wald-type test statistic. The asymptotic and groupwise bootstrap test take the asymptotic exact dependence structure of the test statistics into account to gain more power. Furthermore, confidence intervals for RMST contrasts can be calculated and plotted and a stepwise extension that can improve the power of the multiple tests is available.
Maintained by Merle Munko. Last updated 7 months ago.
1.48 score 1 scripts 1 dependents
rosarialo
CA3variants:Three-Way Correspondence Analysis Variants
Provides four variants of three-way correspondence analysis (ca): three-way symmetrical ca, three-way non-symmetrical ca, three-way ordered symmetrical ca and three-way ordered non-symmetrical ca.
Maintained by Rosaria Lombardo. Last updated 2 years ago.
1.04 score 11 scripts
mansukoh
bayesMRM:Bayesian Multivariate Receptor Modeling
Bayesian analysis of multivariate receptor modeling. The package consists of implementations of the methods of Park and Oh (2015) <doi:10.1016/j.chemolab.2015.08.021>.The package uses 'JAGS'(Just Another Gibbs Sampler) to generate Markov chain Monte Carlo samples of parameters.
Maintained by Man-Suk Oh. Last updated 2 years ago.
1.00 scorecran
icertool:Calculate and Plot ICER
The app will calculate the ICER (incremental cost-effectiveness ratio) Rawlins (2012) <doi:10.1016/B978-0-7020-4084-9.00044-6> from the mean costs and quality-adjusted life years (QALY) Torrance and Feeny (2009) <doi:10.1017/S0266462300008461> for a set of treatment options, and draw the efficiency frontier in the costs-effectiveness plane. The app automatically identifies and excludes dominated and extended-dominated options from the ICER calculation.
Maintained by Daniel Perez-Troncoso. Last updated 3 years ago.
1.00 score
robstine
qqvases:Animated Normal Quantile-Quantile Plots
Presents an explanatory animation of normal quantile-quantile plots based on a water-filling analogy. The animation presents a normal QQ plot as the parametric plot of the water levels in vases defined by two distributions. The distributions decorate the axes in the normal QQ plot and are optionally shown as vases adjacent to the plot. The package draws QQ plots for several distributions, either as samples or continuous functions.
Maintained by Robert Stine. Last updated 9 years ago.
1.00 score 4 scriptsshabbychef
HappyCampR:Shiny App to Find Campgrounds
A Shiny app to find campgrounds.
Maintained by Steven E. Pav. Last updated 1 years ago.
1.00 scoremerlemunko
GFDrmtl:Multiple RMTL-Based Tests for Competing Risks Data in General Factorial Designs
We implemented multiple tests based on the restricted mean time lost (RMTL) for general factorial designs as described in Munko et al. (2024) <doi:10.48550/arXiv.2409.07917>. Therefore, an asymptotic test and a permutation test are incorporated with a Wald-type test statistic. The asymptotic test takes the asymptotic exact dependence structure of the test statistics into account to gain more power. Furthermore, confidence intervals for RMTL contrasts can be calculated and plotted and a stepwise extension that can improve the power of the multiple tests is available.
Maintained by Merle Munko. Last updated 6 months ago.
1.00 score
mansukoh
bayMDS:Bayesian Multidimensional Scaling and Choice of Dimension
Bayesian approach to multidimensional scaling. The package consists of implementations of the methods of Oh and Raftery (2001) <doi:10.1198/016214501753208690>.
Maintained by Man-Suk Oh. Last updated 2 years ago.
1.00 score 1 scripts
atanubhattacharjee
JMbdirect:Joint Model for Longitudinal and Multiple Time to Events Data
Provides model fitting, prediction, and plotting for joint models of longitudinal and multiple time-to-event data, including methods from Rizopoulos (2012) <doi:10.1201/b12208>. Useful for handling complex survival and longitudinal data in clinical research.
Maintained by Atanu Bhattacharjee. Last updated 19 days ago.
1.00 score