Showing 53 of total 53 results (show query)
brianstock
MixSIAR:Bayesian Mixing Models in R
Creates and runs Bayesian mixing models to analyze biological tracer data (i.e. stable isotopes, fatty acids), which estimate the proportions of source (prey) contributions to a mixture (consumer). 'MixSIAR' is not one model, but a framework that allows a user to create a mixing model based on their data structure and research questions, via options for fixed/ random effects, source data types, priors, and error terms. 'MixSIAR' incorporates several years of advances since 'MixSIR' and 'SIAR'.
Maintained by Brian Stock. Last updated 4 years ago.
98 stars 9.27 score 122 scripts
beatrizpateiro
alphahull:Generalization of the Convex Hull of a Sample of Points in the Plane
Computation of the alpha-shape and alpha-convex hull of a given sample of points in the plane. The concepts of alpha-shape and alpha-convex hull generalize the definition of the convex hull of a finite set of points. The programming is based on the duality between the Voronoi diagram and Delaunay triangulation. The package also includes a function that returns the Delaunay mesh of a given sample of points and its dual Voronoi diagram in one single object.
Maintained by Beatriz Pateiro-Lopez. Last updated 2 years ago.
1 stars 7.91 score 251 scripts 12 dependents
paulojus
geoR:Analysis of Geostatistical Data
Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Maintained by Paulo Justiniano Ribeiro Jr. Last updated 1 years ago.
10 stars 7.57 score 1.8k scripts 12 dependents
mu-sigma
HVT:Constructing Hierarchical Voronoi Tessellations and Overlay Heatmaps for Data Analysis
Facilitates building topology preserving maps for data analysis.
Maintained by "Mu Sigma, Inc.". Last updated 7 days ago.
4 stars 6.20 score 1 scripts
fridleylab
spatialTIME:Spatial Analysis of Vectra Immunoflourescent Data
Visualization and analysis of Vectra Immunoflourescent data. Options for calculating both the univariate and bivariate Ripley's K are included. Calculations are performed using a permutation-based approach presented by Wilson et al. <doi:10.1101/2021.04.27.21256104>.
Maintained by Fridley Lab. Last updated 8 months ago.
4 stars 6.08 score 30 scripts
numbats
cassowaryr:Compute Scagnostics on Pairs of Numeric Variables in a Data Set
Computes a range of scatterplot diagnostics (scagnostics) on pairs of numerical variables in a data set. A range of scagnostics, including graph and association-based scagnostics described by Leland Wilkinson and Graham Wills (2008) <doi:10.1198/106186008X320465> and association-based scagnostics described by Katrin Grimm (2016,ISBN:978-3-8439-3092-5) can be computed. Summary and plotting functions are provided.
Maintained by Harriet Mason. Last updated 30 days ago.
data-sciencedata-visualizationedahigh-dimensional-datamultivariate
3 stars 6.02 score 26 scripts 1 dependents
blakedickson
Morphoscape:Computation and Visualization of Adaptive Landscapes
Implements adaptive landscape methods first described by Polly et al. (2016) <doi:10.1080/02724634.2016.1111225> for the integration, analysis and visualization of biological trait data on a phenotypic morphospace - typically defined by shape metrics.
Maintained by Blake Dickson. Last updated 10 months ago.
4 stars 5.56 score 8 scripts
swarm-lab
swaRm:Processing Collective Movement Data
Function library for processing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.
Maintained by Simon Garnier. Last updated 1 years ago.
animal-behavioranimal-behaviourcollective-behaviorcollective-behaviour
21 stars 5.50 score 8 scripts 1 dependents
marinapapa
swaRmverse:Swarm Space Creation
Provides a pipeline for the comparative analysis of collective movement data (e.g. fish schools, bird flocks, baboon troops) by processing 2-dimensional positional data (x,y,t) from GPS trackers or computer vision tracking systems, discretizing events of collective motion, calculating a set of established metrics that characterize each event, and placing the events in a multi-dimensional swarm space constructed from these metrics. The swarm space concept, the metrics and data sets included are described in: Papadopoulou Marina, Furtbauer Ines, O'Bryan Lisa R., Garnier Simon, Georgopoulou Dimitra G., Bracken Anna M., Christensen Charlotte and King Andrew J. (2023) <doi:10.1098/rstb.2022.0068>.
Maintained by Marina Papadopoulou. Last updated 6 months ago.
2 stars 5.13 score 15 scripts
waynegitshell
GWSDAT:GroundWater Spatiotemporal Data Analysis Tool (GWSDAT)
Shiny application for the analysis of groundwater monitoring data, designed to work with simple time-series data for solute concentration and ground water elevation, but can also plot non-aqueous phase liquid (NAPL) thickness if required. Also provides the import of a site basemap in GIS shapefile format.
Maintained by Wayne Jones. Last updated 1 years ago.
contamination-detectiongroundwater-flowplumeshinyspatio-temporal-analysis
32 stars 5.02 score 11 scripts
ptitle
rangeBuilder:Occurrence Filtering, Geographic Standardization and Generation of Species Range Polygons
Provides tools for filtering occurrence records, generating alpha-hull-derived range polygons and mapping species distributions.
Maintained by Pascal Title. Last updated 5 months ago.
9 stars 4.99 score 72 scripts 1 dependents
mpadge
spatialcluster:R port of redcap
R port of redcap (Regionalization with dynamically constrained agglomerative clustering and partitioning).
Maintained by Mark Padgham. Last updated 2 months ago.
clusterclustering-algorithmspatialcpp
31 stars 4.97 score 1 scripts
statnmap
GeoDist:Constrained distance calculation and associated geotools
This package allows the calculation of distances that are constrained by frontiers, islands, mountains, ... These distances are then implemented in classical geotools like kriging with a modified version of geoR functions.
Maintained by Sébastien Rochette. Last updated 5 years ago.
7 stars 4.94 score 251 scripts
drammock
phonR:Tools for Phoneticians and Phonologists
Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels.
Maintained by Daniel R. McCloy. Last updated 6 years ago.
31 stars 4.85 score 23 scripts
levisc8
spind:Spatial Methods and Indices
Functions for spatial methods based on generalized estimating equations (GEE) and wavelet-revised methods (WRM), functions for scaling by wavelet multiresolution regression (WMRR), conducting multi-model inference, and stepwise model selection. Further, contains functions for spatially corrected model accuracy measures.
Maintained by Sam Levin. Last updated 1 years ago.
3 stars 4.84 score 46 scripts
ericmarcon
divent:Entropy Partitioning to Measure Diversity
Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'divent' provides functions to estimate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
Maintained by Eric Marcon. Last updated 6 days ago.
1 stars 4.81 score 1 scripts
leondap
recluster:Ordination Methods for the Analysis of Beta-Diversity Indices
The analysis of different aspects of biodiversity requires specific algorithms. For example, in regionalisation analyses, the high frequency of ties and zero values in dissimilarity matrices produced by Beta-diversity turnover produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. Moreover, visualisation of biogeographical regionalisation can be facilitated by a combination of hierarchical clustering and multi-dimensional scaling. The recluster package provides robust techniques to visualise and analyse pattern of biodiversity and to improve occurrence data for cryptic taxa.
Maintained by Leonardo Dapporto. Last updated 5 months ago.
4 stars 4.69 score 41 scripts
timcdlucas
disaggregation:Disaggregation Modelling
Fits disaggregation regression models using 'TMB' ('Template Model Builder'). When the response data are aggregated to polygon level but the predictor variables are at a higher resolution, these models can be useful. Regression models with spatial random fields. The package is described in detail in Nandi et al. (2023) <doi:10.18637/jss.v106.i11>.
Maintained by Tim Lucas. Last updated 5 months ago.
2 stars 4.60 score 9 scripts
giorgilancs
PrevMap:Geostatistical Modelling of Spatially Referenced Prevalence Data
Provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data. For a tutorial on the use of the R package, see Giorgi and Diggle (2017) <doi:10.18637/jss.v078.i08>.
Maintained by Emanuele Giorgi. Last updated 2 years ago.
4.36 score 46 scripts
tengmcing
autovi:Auto Visual Inference with Computer Vision Models
Provides automated visual inference of residual plots using computer vision models, facilitating diagnostic checks for classical normal linear regression models.
Maintained by Weihao Li. Last updated 4 months ago.
1 stars 4.08 score 16 scripts
berndbischl
tspmeta:Instance Feature Calculation and Evolutionary Instance Generation for the Traveling Salesman Problem
Instance feature calculation and evolutionary instance generation for the traveling salesman problem. Also contains code to "morph" two TSP instances into each other. And the possibility to conveniently run a couple of solvers on TSP instances.
Maintained by Bernd Bischl. Last updated 9 years ago.
5 stars 4.08 score 24 scripts
cysouw
qlcVisualize:Visualization for Quantitative Language Comparison
Collection of visualizations as used in quantitative language comparison. Currently implemented are visualisations dealing nominal data with multiple levels ("level map" and "factor map"), and assistance for making weighted geographical Voronoi-maps ("weighted map").
Maintained by Michael Cysouw. Last updated 6 months ago.
4.03 score 24 scripts
mechantrouquin
landsepi:Landscape Epidemiology and Evolution
A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. It is based on a spatial geometry for describing the landscape and allocation of different cultivars, a dispersal kernel for the dissemination of the pathogen, and a SEIR ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step. It provides a useful tool to assess the performance of a wide range of deployment options with respect to their epidemiological, evolutionary and economic outcomes. Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Maintained by Jean-François Rey. Last updated 6 months ago.
3.40 score 18 scripts
garciapintado
SpatialGraph:The SpatialGraph Class and Utilities
Provision of the S4 SpatialGraph class built on top of objects provided by 'igraph' and 'sp' packages, and associated utilities. See the documentation of the SpatialGraph-class within this package for further description. An example of how from a few points one can arrive to a SpatialGraph is provided in the function sl2sg().
Maintained by Javier Garcia-Pintado. Last updated 2 years ago.
5 stars 3.40 score 3 scripts
bioc
GateFinder:Projection-based Gating Strategy Optimization for Flow and Mass Cytometry
Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.
Maintained by Nima Aghaeepour. Last updated 5 months ago.
immunooncologyflowcytometrycellbiologyclustering
3.30 score 7 scripts
bryanhanson
SpecHelpers:Spectroscopy Related Utilities
Utility functions for spectroscopy. 1. Functions to simulate spectra for use in teaching or testing. 2. Functions to process files created by 'LoggerPro' and 'SpectraSuite' software.
Maintained by Bryan A. Hanson. Last updated 28 days ago.
2 stars 3.04 score 11 scripts
joalor93
CensSpatial:Censored Spatial Models
It fits linear regression models for censored spatial data. It provides different estimation methods as the SAEM (Stochastic Approximation of Expectation Maximization) algorithm and seminaive that uses Kriging prediction to estimate the response at censored locations and predict new values at unknown locations. It also offers graphical tools for assessing the fitted model. More details can be found in Ordonez et al. (2018) <doi:10.1016/j.spasta.2017.12.001>.
Maintained by Alejandro Ordonez. Last updated 2 years ago.
2.93 score 17 scripts
cran
stpp:Space-Time Point Pattern Simulation, Visualisation and Analysis
Many of the models encountered in applications of point process methods to the study of spatio-temporal phenomena are covered in 'stpp'. This package provides statistical tools for analyzing the global and local second-order properties of spatio-temporal point processes, including estimators of the space-time inhomogeneous K-function and pair correlation function. It also includes tools to get static and dynamic display of spatio-temporal point patterns. See Gabriel et al (2013) <doi:10.18637/jss.v053.i02>.
Maintained by Edith Gabriel. Last updated 9 months ago.
2 stars 2.78 score 1 dependents
guidoamoreira
pompp:Presence-Only for Marked Point Process
Inspired by Moreira and Gamerman (2022) <doi:10.1214/21-AOAS1569>, this methodology expands the idea by including Marks in the point process. Using efficient 'C++' code, the estimation is possible and made faster with 'OpenMP' <https://www.openmp.org/> enabled computers. This package was developed under the project PTDC/MAT-STA/28243/2017, supported by Portuguese funds through the Portuguese Foundation for Science and Technology (FCT).
Maintained by Guido Alberti Moreira. Last updated 2 years ago.
2.70 score
markdrisser
convoSPAT:Convolution-Based Nonstationary Spatial Modeling
Fits convolution-based nonstationary Gaussian process models to point-referenced spatial data. The nonstationary covariance function allows the user to specify the underlying correlation structure and which spatial dependence parameters should be allowed to vary over space: the anisotropy, nugget variance, and process variance. The parameters are estimated via maximum likelihood, using a local likelihood approach. Also provided are functions to fit stationary spatial models for comparison, calculate the Kriging predictor and standard errors, and create various plots to visualize nonstationarity.
Maintained by Mark D. Risser. Last updated 7 years ago.
2 stars 2.70 score 25 scripts
tpourmohamad
BayesDissolution:Bayesian Models for Dissolution Testing
Fits Bayesian models (amongst others) to dissolution data sets that can be used for dissolution testing. The package was originally constructed to include only the Bayesian models outlined in Pourmohamad et al. (2022) <doi:10.1111/rssc.12535>. However, additional Bayesian and non-Bayesian models (based on bootstrapping and generalized pivotal quanties) have also been added. More models may be added over time.
Maintained by Tony Pourmohamad. Last updated 1 years ago.
2.70 score
jiri-dvorak
NTSS:Nonparametric Tests in Spatial Statistics
Nonparametric test of independence between a pair of spatial objects (random fields, point processes) based on random shifts with torus or variance correction. See Mrkvička et al. (2021) <doi:10.1016/j.spasta.2020.100430>, Dvořák et al. (2022) <doi:10.1111/insr.12503>, Dvořák and Mrkvička (2022) <arxiv:2210.05424>.
Maintained by Jiří Dvořák. Last updated 2 years ago.
2.70 score
santostbio
PVR:Phylogenetic Eigenvectors Regression and Phylogentic Signal-Representation Curve
Estimates (and controls for) phylogenetic signal through phylogenetic eigenvectors regression (PVR) and phylogenetic signal-representation (PSR) curve, along with some plot utilities.
Maintained by Thiago Santos. Last updated 7 years ago.
2.64 score 73 scriptscran
molaR:Dental Surface Complexity Measurement Tools
Surface topography calculations of Dirichlet's normal energy, relief index, surface slope, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.
Maintained by James D. Pampush. Last updated 2 years ago.
1 stars 2.48 score 1 dependents
jisunjang19
JSDNE:Estimating the Age using Auricular Surface by DNE
The age is estimated by calculating the Dirichlet Normal Energy (DNE) on the whole auricular surface and the apex of the auricular surface. It involves three estimation methods: principal component discriminant analysis (PCQDA), principal component regression analysis (PCR), and principal component logistic regression analysis (PCLR) methods. The package is created with the data from the Louis Lopes Collection in Lisbon, the 21st Century Identified Human Remains Collection in Coimbra, and the CAL Milano Cemetery Skeletal Collection in Milan.
Maintained by Jisun Jang. Last updated 7 months ago.
2.48 score 3 scripts
filzmoserp
StatDA:Statistical Analysis for Environmental Data
Statistical analysis methods for environmental data are implemented. There is a particular focus on robust methods, and on methods for compositional data. In addition, larger data sets from geochemistry are provided. The statistical methods are described in Reimann, Filzmoser, Garrett, Dutter (2008, ISBN:978-0-470-98581-6).
Maintained by Peter Filzmoser. Last updated 2 years ago.
2.45 score 141 scripts
famuvie
geoRcb:An Extension of Package geoR that Works with Cost-Based Distances
Mainly, three functions are adapted in order to admit custom distance matrices as additional arguments. Namely variog, to produce empirical variograms; likfit, to fit theoretical variograms and krige.conv, to preform kriging.
Maintained by Facundo Muñoz. Last updated 9 years ago.
4 stars 2.30 score 3 scripts
jfrench
ExceedanceTools:Confidence/Credible Regions for Exceedance Sets and Contour Lines
Provides methods for constructing confidence or credible regions for exceedance sets and contour lines.
Maintained by Joshua French. Last updated 2 years ago.
1 stars 2.00 score 7 scripts
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 scripts
cran
dixon:Nearest Neighbour Contingency Table Analysis
Function to test spatial segregation and association based in contingency table analysis of nearest neighbour counts following Dixon (2002) <doi:10.1080/11956860.2002.11682700>. Some 'Fortran' code has been included to the original dixon2002() function of the 'ecespa' package to improve speed.
Maintained by Marcelino de la Cruz Rot. Last updated 1 years ago.
1.48 score 1 dependents
jlswall
aqfig:Display Air Quality Model Output and Monitoring Data
Display air quality model output and monitoring data using scatterplots, grids, and legends.
Maintained by Jenise Swall. Last updated 9 months ago.
1 stars 1.41 score 26 scriptscran
EcoIndR:Ecological Indicators
Calculates several indices, such as of diversity, fluctuation, etc., and they are used to estimate ecological indicators.
Maintained by Castor Guisande Gonzalez. Last updated 1 years ago.
1 stars 1.30 scoremechantrouquin
RCALI:Calculation of the Integrated Flow of Particles Between Polygons
Calculate the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points. Annie Bouvier, Kien Kieu, Kasia Adamczyk and Herve Monod (2009) <doi:10.1016/j.envsoft.2008.11.006>.
Maintained by Jean-Francois Rey. Last updated 5 months ago.
1.08 score 12 scriptscran
highriskzone:Determining and Evaluating High-Risk Zones
Functions for determining and evaluating high-risk zones and simulating and thinning point process data, as described in 'Determining high risk zones using point process methodology - Realization by building an R package' Seibold (2012) <http://highriskzone.r-forge.r-project.org/Bachelorarbeit.pdf> and 'Determining high-risk zones for unexploded World War II bombs by using point process methodology', Mahling et al. (2013) <doi:10.1111/j.1467-9876.2012.01055.x>.
Maintained by Rickmer Schulte. Last updated 2 years ago.
1.00 scorecran
geotoolsR:Tools to Improve the Use of Geostatistic
The basic idea of this package is provides some tools to help the researcher to work with geostatistics. Initially, we present a collection of functions that allow the researchers to deal with spatial data using bootstrap procedure. There are five methods available and two ways to display them: bootstrap confidence interval - provides a two-sided bootstrap confidence interval; bootstrap plot - a graphic with the original variogram and each of the B bootstrap variograms.
Maintained by Diogo Francisco Rossoni. Last updated 9 months ago.
1.00 score