R-universe search: degrees

statnet

ergm:Fit, Simulate and Diagnose Exponential-Family Models for Networks

An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.

Maintained by Pavel N. Krivitsky. Last updated 7 days ago.

67.4 match 100 stars 15.36 score 1.4k scripts 36 dependents

igraph

igraph:Network Analysis and Visualization

Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

Maintained by Kirill Müller. Last updated 5 hours ago.

complex-networks graph-algorithms graph-theory mathematics network-analysis network-graph fortran libxml2 glpk openblas cpp

41.4 match 582 stars 21.11 score 31k scripts 1.9k dependents

cran

NISTunits:Fundamental Physical Constants and Unit Conversions from NIST

Fundamental physical constants (Quantity, Value, Uncertainty, Unit) for SI (International System of Units) and non-SI units, plus unit conversions Based on the data from NIST (National Institute of Standards and Technology, USA)

Maintained by Jose Gama. Last updated 9 years ago.

151.6 match 2.85 score 10 dependents

statnet

ergm.multi:Fit, Simulate and Diagnose Exponential-Family Models for Multiple or Multilayer Networks

A set of extensions for the 'ergm' package to fit multilayer/multiplex/multirelational networks and samples of multiple networks. 'ergm.multi' is a part of the Statnet suite of packages for network analysis. See Krivitsky, Koehly, and Marcum (2020) <doi:10.1007/s11336-020-09720-7> and Krivitsky, Coletti, and Hens (2023) <doi:10.1080/01621459.2023.2242627>.

Maintained by Pavel N. Krivitsky. Last updated 4 months ago.

21.3 match 14 stars 9.67 score 11 scripts 5 dependents

benyamindsmith

ig.degree.betweenness:"Smith-Pittman Community Detection Algorithm for 'igraph' Objects (2024)"

Implements the "Smith-Pittman" community detection algorithm for network analysis using 'igraph' objects. This algorithm combines node degree and betweenness centrality measures to identify communities within networks, with a gradient evident in social partitioning. The package provides functions for community detection, visualization, and analysis of the resulting community structure. Methods are based on results from Smith, Pittman and Xu (2024) <doi:10.48550/arXiv.2411.01394>.

Maintained by Benjamin Smith. Last updated 1 days ago.

community-detection-algorithms igraph

37.2 match 38 stars 5.50 score 11 scripts

andysouth

rworldmap:Mapping Global Data

Enables mapping of country level and gridded user datasets.

Maintained by Andy South. Last updated 2 years ago.

15.2 match 30 stars 11.83 score 3.2k scripts 14 dependents

networkgroupr

fastnet:Large-Scale Social Network Analysis

We present an implementation of the algorithms required to simulate large-scale social networks and retrieve their most relevant metrics.

Maintained by Nazrul Shaikh. Last updated 8 years ago.

48.2 match 5 stars 3.37 score 47 scripts

dankelley

oce:Analysis of Oceanographic Data

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.

Maintained by Dan Kelley. Last updated 2 days ago.

oceanography fortran cpp

8.7 match 146 stars 15.42 score 4.2k scripts 18 dependents

rich-iannone

DiagrammeR:Graph/Network Visualization

Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.

Maintained by Richard Iannone. Last updated 2 months ago.

graph graph-functions network-graph property-graph visualization

8.8 match 1.7k stars 15.18 score 3.8k scripts 87 dependents

glenndavis52

colorSpec:Color Calculations with Emphasis on Spectral Data

Calculate with spectral properties of light sources, materials, cameras, eyes, and scanners. Build complex systems from simpler parts using a spectral product algebra. For light sources, compute CCT, CRI, SSI, and IES TM-30 reports. For object colors, compute optimal colors and Logvinenko coordinates. Work with the standard CIE illuminants and color matching functions, and read spectra from text files, including CGATS files. Estimate a spectrum from its response. A user guide and 9 vignettes are included.

Maintained by Glenn Davis. Last updated 1 months ago.

17.5 match 2 stars 6.34 score 73 scripts 5 dependents

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 11 months ago.

48.4 match 2.28 score 38 scripts

edzer

sp:Classes and Methods for Spatial Data

Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.

Maintained by Edzer Pebesma. Last updated 2 months ago.

5.6 match 127 stars 18.63 score 35k scripts 1.3k dependents

ropensci

CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections

Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.

Maintained by Alexander Zizka. Last updated 1 years ago.

9.0 match 82 stars 10.93 score 306 scripts 3 dependents

tidymodels

dials:Tools for Creating Tuning Parameter Values

Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for such parameters.

Maintained by Hannah Frick. Last updated 30 days ago.

6.8 match 114 stars 14.31 score 426 scripts 52 dependents

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

10.0 match 7 stars 9.11 score 1.3k scripts 6 dependents

robwschlegel

heatwaveR:Detect Heatwaves and Cold-Spells

The different methods for defining, detecting, and categorising the extreme events known as heatwaves or cold-spells, as first proposed in Hobday et al. (2016) <doi: 10.1016/j.pocean.2015.12.014> and Hobday et al. (2018) <https://www.jstor.org/stable/26542662>. The functions in this package work on both air and water temperature data. These detection algorithms may be used on non-temperature data as well.

Maintained by Robert W. Schlegel. Last updated 2 months ago.

cpp

9.7 match 46 stars 9.36 score 343 scripts

openpharma

mmrm:Mixed Models for Repeated Measures

Mixed models for repeated measures (MMRM) are a popular choice for analyzing longitudinal continuous outcomes in randomized clinical trials and beyond; see Cnaan, Laird and Slasor (1997) <doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E> for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso (2008) <doi:10.1177/009286150804200402> for a review. This package implements MMRM based on the marginal linear model without random effects using Template Model Builder ('TMB') which enables fast and robust model fitting. Users can specify a variety of covariance matrices, weight observations, fit models with restricted or standard maximum likelihood inference, perform hypothesis testing with Satterthwaite or Kenward-Roger adjustment, and extract least square means estimates by using 'emmeans'.

Maintained by Daniel Sabanes Bove. Last updated 10 days ago.

cpp

7.2 match 138 stars 12.15 score 113 scripts 4 dependents

pcruniversum

chipPCR:Toolkit of Helper Functions to Pre-Process Amplification Data

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems ('VideoScan HCU', capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

Maintained by Stefan Roediger. Last updated 4 years ago.

12.8 match 8 stars 6.84 score 97 scripts 1 dependents

bioc

glmSparseNet:Network Centrality Metrics for Elastic-Net Regularized Models

glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".

Maintained by André Veríssimo. Last updated 5 months ago.

software statisticalmethod dimensionreduction regression classification survival network graphandnetwork

11.7 match 6 stars 7.42 score 41 scripts 1 dependents

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 22 hours ago.

openblas cpp

4.9 match 64 stars 17.22 score 13k scripts 599 dependents

hojsgaard

pbkrtest:Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models

Computes p-values based on (a) Satterthwaite or Kenward-Rogers degree of freedom methods and (b) parametric bootstrap for mixed effects models as implemented in the 'lme4' package. Implements parametric bootstrap test for generalized linear mixed models as implemented in 'lme4' and generalized linear models. The package is documented in the paper by Halekoh and Højsgaard, (2012, <doi:10.18637/jss.v059.i09>). Please see 'citation("pbkrtest")' for citation details.

Maintained by Søren Højsgaard. Last updated 11 days ago.

5.6 match 5 stars 14.36 score 648 scripts 915 dependents

jokergoo

circlize:Circular Visualization

Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.

Maintained by Zuguang Gu. Last updated 1 years ago.

4.9 match 983 stars 15.62 score 10k scripts 213 dependents

comeetie

greed:Clustering and Model Selection with the Integrated Classification Likelihood

An ensemble of algorithms that enable the clustering of networks and data matrices (such as counts, categorical or continuous) with different type of generative models. Model selection and clustering is performed in combination by optimizing the Integrated Classification Likelihood (which is equivalent to minimizing the description length). Several models are available such as: Stochastic Block Model, degree corrected Stochastic Block Model, Mixtures of Multinomial, Latent Block Model. The optimization is performed thanks to a combination of greedy local search and a genetic algorithm (see <arXiv:2002:11577> for more details).

Maintained by Etienne Côme. Last updated 2 years ago.

openblas cpp openmp

12.3 match 14 stars 5.94 score 41 scripts

ropensci

parzer:Parse Messy Geographic Coordinates

Parse messy geographic coordinates from various character formats to decimal degree numeric values. Parse coordinates into their parts (degree, minutes, seconds); calculate hemisphere from coordinates; pull out individually degrees, minutes, or seconds; add and subtract degrees, minutes, and seconds. C++ code herein originally inspired from code written by Jeffrey D. Bogan, but then completely re-written.

Maintained by Alban Sagouis. Last updated 1 months ago.

geospatial data latitude longitude parser coordinates geo cpp

8.3 match 65 stars 8.45 score 162 scripts 3 dependents

cran

bnlearn:Bayesian Network Structure Learning, Parameter Learning and Inference

Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries, cross-validation, bootstrap and model averaging. Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.

Maintained by Marco Scutari. Last updated 2 months ago.

openblas

9.0 match 57 stars 7.72 score 32 dependents

aleksandarsekulic

meteo:RFSI & STRK Interpolation for Meteo and Environmental Variables

Random Forest Spatial Interpolation (RFSI, Sekulić et al. (2020) <doi:10.3390/rs12101687>) and spatio-temporal geostatistical (spatio-temporal regression Kriging (STRK)) interpolation for meteorological (Kilibarda et al. (2014) <doi:10.1002/2013JD020803>, Sekulić et al. (2020) <doi:10.1007/s00704-019-03077-3>) and other environmental variables. Contains global spatio-temporal models calculated using publicly available data.

Maintained by Aleksandar Sekulić. Last updated 6 months ago.

13.7 match 18 stars 5.06 score 64 scripts

bioc

variancePartition:Quantify and interpret drivers of variation in multilevel gene expression experiments

Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.

Maintained by Gabriel E. Hoffman. Last updated 2 months ago.

rnaseq geneexpression genesetenrichment differentialexpression batcheffect qualitycontrol regression epigenetics functionalgenomics transcriptomics normalization preprocessing microarray immunooncology software

5.7 match 7 stars 11.69 score 1.1k scripts 3 dependents

jamesramsay5

fda:Functional Data Analysis

These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer and in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions are available by ftp from <https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.

Maintained by James Ramsay. Last updated 4 months ago.

5.3 match 3 stars 12.29 score 2.0k scripts 143 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 5 months ago.

visualization graphandnetwork thirdpartyclient network

4.8 match 52 stars 13.39 score 628 scripts 15 dependents

epimodel

EpiModel:Mathematical Modeling of Infectious Disease Dynamics

Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).

Maintained by Samuel Jenness. Last updated 2 months ago.

agent-based-modeling epidemics epidemiology infectious-diseases network-graph cpp

5.3 match 250 stars 11.57 score 315 scripts

nowosad

pollen:Analysis of Aerobiological Data

Supports analysis of aerobiological data. Available features include determination of pollen season limits, replacement of outliers (Kasprzyk and Walanus (2014) <doi:10.1007/s10453-014-9332-8>), calculation of growing degree days (Baskerville and Emin (1969) <doi:10.2307/1933912>), and determination of the base temperature for growing degree days (Yang et al. (1995) <doi:10.1016/0168-1923(94)02185-M).

Maintained by Jakub Nowosad. Last updated 2 years ago.

aerobiological-data aerobiology gdd growing-degree-days pollen

12.2 match 3 stars 4.89 score 26 scripts

r-forge

Matrix:Sparse and Dense Matrix Classes and Methods

A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.

Maintained by Martin Maechler. Last updated 7 days ago.

openblas

3.4 match 1 stars 17.23 score 33k scripts 12k dependents

easystats

parameters:Processing of Model Parameters

Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).

Maintained by Daniel Lüdecke. Last updated 3 days ago.

beta bootstrap ci confidence-intervals data-reduction easystats fa feature-extraction feature-reduction hacktoberfest parameters pca pvalues regression-models robust-statistics standardize standardized-estimates statistical-models

3.8 match 453 stars 15.65 score 1.8k scripts 56 dependents

biometry

bipartite:Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.

Maintained by Carsten F. Dormann. Last updated 7 days ago.

cpp

5.2 match 37 stars 10.93 score 592 scripts 15 dependents

martirm

clustAnalytics:Cluster Evaluation on Graphs

Evaluates the stability and significance of clusters on 'igraph' graphs. Supports weighted and unweighted graphs. Implements the cluster evaluation methods defined by Arratia A, Renedo M (2021) <doi:10.7717/peerj-cs.600>. Also includes an implementation of the Reduced Mutual Information introduced by Newman et al. (2020) <doi:10.1103/PhysRevE.101.042304>.

Maintained by Martí Renedo Mirambell. Last updated 1 years ago.

cpp

11.6 match 5 stars 4.92 score 33 scripts

bioc

graph:graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Maintained by Bioconductor Package Maintainer. Last updated 11 days ago.

graphandnetwork

4.8 match 11.78 score 764 scripts 342 dependents

alexchristensen

NetworkToolbox:Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis

Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.

Maintained by Alexander Christensen. Last updated 2 years ago.

network-analysis

7.9 match 23 stars 6.99 score 101 scripts 4 dependents

tbates

umx:Structural Equation Modeling and Twin Modeling in R

Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.

Maintained by Timothy C. Bates. Last updated 2 days ago.

behavior-genetics genetics openmx psychology sem statistics structural-equation-modeling tutorials twin-models umx

5.8 match 44 stars 9.45 score 472 scripts

lrberge

fixest:Fast Fixed-Effects Estimations

Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>. Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.

Maintained by Laurent Berge. Last updated 7 months ago.

cpp openmp

3.6 match 387 stars 14.69 score 3.8k scripts 25 dependents

aphalo

photobiology:Photobiological Calculations

Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Maintained by Pedro J. Aphalo. Last updated 3 days ago.

light photobiology quantification r4photobiology-suite radiation spectra sun-position

5.6 match 4 stars 9.35 score 604 scripts 12 dependents

hwborchers

pracma:Practical Numerical Math Functions

Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.

Maintained by Hans W. Borchers. Last updated 1 years ago.

4.3 match 29 stars 12.34 score 6.6k scripts 931 dependents

ibot-geoecology

myClim:Microclimatic Data Processing

Handling the microclimatic data in R. The 'myClim' workflow begins at the reading data primary from microclimatic dataloggers, but can be also reading of meteorological station data from files. Cleaning time step, time zone settings and metadata collecting is the next step of the work flow. With 'myClim' tools one can crop, join, downscale, and convert microclimatic data formats, sort them into localities, request descriptive characteristics and compute microclimatic variables. Handy plotting functions are provided with smart defaults.

Maintained by Vojtěch Kalčík. Last updated 14 days ago.

7.4 match 7 stars 6.97 score 30 scripts

r-spatial

sf:Simple Features for R

Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.

Maintained by Edzer Pebesma. Last updated 17 days ago.

gdal geos proj spatial cpp

2.2 match 1.4k stars 22.42 score 117k scripts 1.2k dependents

quicklizard99

cheddar:Analysis and Visualisation of Ecological Communities

Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.

Maintained by Lawrence Hudson. Last updated 8 months ago.

cpp

7.3 match 15 stars 6.86 score 195 scripts

ajsmit

RmarineHeatWaves:Detect Marine Heat Waves and Marine Cold Spells

Given a time series of daily temperatures, the package provides tools to detect extreme thermal events, including marine heat waves, and to calculate the exceedances above or below specified threshold values. It outputs the properties of all detected events and exceedances.

Maintained by Albertus J. Smit. Last updated 6 years ago.

10.0 match 9 stars 4.88 score 17 scripts

zpneal

backbone:Extracts the Backbone from Graphs

An implementation of methods for extracting an unweighted unipartite graph (i.e. a backbone) from an unweighted unipartite graph, a weighted unipartite graph, the projection of an unweighted bipartite graph, or the projection of a weighted bipartite graph (Neal, 2022 <doi:10.1371/journal.pone.0269137>).

Maintained by Zachary Neal. Last updated 1 years ago.

cpp

6.8 match 41 stars 7.06 score 31 scripts 2 dependents

aaamini

nett:Network Analysis and Community Detection

Features tools for the network data analysis and community detection. Provides multiple methods for fitting, model selection and goodness-of-fit testing in degree-corrected stochastic blocks models. Most of the computations are fast and scalable for sparse networks, esp. for Poisson versions of the models. Implements the following: Amini, Chen, Bickel and Levina (2013) <doi:10.1214/13-AOS1138> Bickel and Sarkar (2015) <doi:10.1111/rssb.12117> Lei (2016) <doi:10.1214/15-AOS1370> Wang and Bickel (2017) <doi:10.1214/16-AOS1457> Zhang and Amini (2020) <arXiv:2012.15047> Le and Levina (2022) <doi:10.1214/21-EJS1971>.

Maintained by Arash A. Amini. Last updated 2 years ago.

cpp

8.7 match 8 stars 5.48 score 19 scripts

ucanr-igis

degday:Compute Degree Days

Compute degree days from daily min and max temperatures for modeling plant and insect development.

Maintained by Andy Lyons. Last updated 4 months ago.

degree-days ipm

13.2 match 3 stars 3.57 score 25 scripts

aigorahub

sensR:Thurstonian Models for Sensory Discrimination

Provides methods for sensory discrimination methods; duotrio, tetrad, triangle, 2-AFC, 3-AFC, A-not A, same-different, 2-AC and degree-of-difference. This enables the calculation of d-primes, standard errors of d-primes, sample size and power computations, and comparisons of different d-primes. Methods for profile likelihood confidence intervals and plotting are included. Most methods are described in Brockhoff, P.B. and Christensen, R.H.B. (2010) <doi:10.1016/j.foodqual.2009.04.003>.

Maintained by Dominik Rafacz. Last updated 1 years ago.

9.4 match 7 stars 4.92 score 77 scripts

mikkovihtakari

ggOceanMaps:Plot Data on Oceanographic Maps using 'ggplot2'

Allows plotting data on bathymetric maps using 'ggplot2'. Plotting oceanographic spatial data is made as simple as feasible, but also flexible for custom modifications. Data that contain geographic information from anywhere around the globe can be plotted on maps generated by the basemap() or qmap() functions using 'ggplot2' layers separated by the '+' operator. The package uses spatial shape- ('sf') and raster ('stars') files, geospatial packages for R to manipulate, and the 'ggplot2' package to plot these files. The package ships with low-resolution spatial data files and higher resolution files for detailed maps are stored in the 'ggOceanMapsLargeData' repository on GitHub and downloaded automatically when needed.

Maintained by Mikko Vihtakari. Last updated 5 months ago.

7.8 match 46 stars 5.95 score 193 scripts

briencj

dae:Functions Useful in the Design and ANOVA of Experiments

The content falls into the following groupings: (i) Data, (ii) Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions, (vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions. There is a vignette describing how to use the design functions for randomizing and assessing designs available as a vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of information when the 'Error' function has been used in the call to 'aov'. The package 'dae' can also be installed from <http://chris.brien.name/rpackages/>.

Maintained by Chris Brien. Last updated 4 months ago.

5.3 match 1 stars 8.62 score 356 scripts 7 dependents

weiliang

clusterGeneration:Random Cluster Generation (with Specified Degree of Separation)

We developed the clusterGeneration package to provide functions for generating random clusters, generating random covariance/correlation matrices, calculating a separation index (data and population version) for pairs of clusters or cluster distributions, and 1-D and 2-D projection plots to visualize clusters. The package also contains a function to generate random clusters based on factorial designs with factors such as degree of separation, number of clusters, number of variables, number of noisy variables.

Maintained by Weiliang Qiu. Last updated 2 years ago.

6.9 match 1 stars 6.45 score 225 scripts 94 dependents

crsh

papaja:Prepare American Psychological Association Journal Articles with R Markdown

Tools to create dynamic, submission-ready manuscripts, which conform to American Psychological Association manuscript guidelines. We provide R Markdown document formats for manuscripts (PDF and Word) and revision letters (PDF). Helper functions facilitate reporting statistical analyses or create publication-ready tables and plots.

Maintained by Frederik Aust. Last updated 18 days ago.

apa apa-guidelines journal manuscript psychology reproducible-paper reproducible-research rmarkdown

3.8 match 662 stars 11.74 score 1.7k scripts 1 dependents

sergiocostafh

timbeR:Calculate Wood Volumes from Taper Functions

Functions for estimation of wood volumes, number of logs, diameters along the stem and heights at which certain diameters occur, based on taper functions and other parameters. References: McTague, J. P., & Weiskittel, A. (2021). <doi:10.1139/cjfr-2020-0326>.

Maintained by Sergio Costa. Last updated 1 months ago.

8.2 match 5 stars 5.36 score 46 scripts

edwinkipruto

mfp2:Multivariable Fractional Polynomial Models with Extensions

Multivariable fractional polynomial algorithm simultaneously selects variables and functional forms in both generalized linear models and Cox proportional hazard models. Key references are Royston and Altman (1994) <doi:10.2307/2986270> and Royston and Sauerbrei (2008, ISBN:978-0-470-02842-1). In addition, it can model a sigmoid relationship between variable x and an outcome variable y using the approximate cumulative distribution transformation proposed by Royston (2014) <doi:10.1177/1536867X1401400206>. This feature distinguishes it from a standard fractional polynomial function, which lacks the ability to achieve such modeling.

Maintained by Edwin Kipruto. Last updated 10 months ago.

8.3 match 3 stars 5.26 score 4 scripts 2 dependents

bioc

CatsCradle:This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.

Maintained by Michael Shapiro. Last updated 1 months ago.

biologicalquestion statisticalmethod geneexpression singlecell transcriptomics spatial

6.5 match 3 stars 6.50 score

paulnorthrop

donut:Nearest Neighbour Search with Variables on a Torus

Finds the k nearest neighbours in a dataset of specified points, adding the option to wrap certain variables on a torus. The user chooses the algorithm to use to find the nearest neighbours. Two such algorithms, provided by the packages 'RANN' <https://cran.r-project.org/package=RANN>, and 'nabor' <https://cran.r-project.org/package=nabor>, are suggested.

Maintained by Paul J. Northrop. Last updated 2 years ago.

degrees donut edges knn-algorithm knn-search nabor nearest nearest-neighbor nearest-neighbor-search nearest-neighbors nearest-neighbour-algorithm nearest-neighbours neighbors periodicity rann torus wrap

10.0 match 1 stars 4.18 score 5 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.

3.4 match 76 stars 12.05 score 700 scripts 6 dependents

signaturescience

skater:Utilities for SNP-Based Kinship Analysis

Utilities for single nucleotide polymorphism (SNP) based kinship analysis testing and evaluation. The 'skater' package contains functions for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing identity by descent (IBD) segment data. Package functions and methods are described in Turner et al. (2021) "skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation" <doi:10.1101/2021.07.21.453083>.

Maintained by Stephen Turner. Last updated 2 years ago.

7.9 match 9 stars 5.26 score 7 scripts

cvxgrp

CVXR:Disciplined Convex Optimization

An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

3.2 match 207 stars 12.89 score 768 scripts 51 dependents

handcock

RDS:Respondent-Driven Sampling

Provides functionality for carrying out estimation with data collected using Respondent-Driven Sampling. This includes Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential Sampling estimator. The package is part of the "RDS Analyst" suite of packages for the analysis of respondent-driven sampling data. See Gile and Handcock (2010) <doi:10.1111/j.1467-9531.2010.01223.x>, Gile and Handcock (2015) <doi:10.1111/rssa.12091> and Gile, Beaudry, Handcock and Ott (2018) <doi:10.1146/annurev-statistics-031017-100704>.

Maintained by Mark S. Handcock. Last updated 6 months ago.

10.6 match 1 stars 3.87 score 82 scripts 3 dependents

paulkinyanjui01

CondMVT:Conditional Multivariate t Distribution

The packages helps sample from the conditional multivariate t distribution.

Maintained by Paul Kimani Kinyanjui. Last updated 3 years ago.

14.9 match 2.70 score

bioc

BioNAR:Biological Network Analysis in R

the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.

Maintained by Anatoly Sorokin. Last updated 19 days ago.

software graphandnetwork network

6.8 match 3 stars 5.90 score 35 scripts

gtatters

Thermimage:Thermal Image Analysis

A collection of functions and routines for inputting thermal image video files, plotting and converting binary raw data into estimates of temperature. First published 2015-03-26. Written primarily for research purposes in biological applications of thermal images. v1 included the base calculations for converting thermal image binary values to temperatures. v2 included additional equations for providing heat transfer calculations and an import function for thermal image files (v2.2.3 fixed error importing thermal image to windows OS). v3. Added numerous functions for converting thermal image, videos, rewriting and exporting. v3.1. Added new functions to convert files. v3.2. Fixed the various functions related to finding frame times. v4.0. fixed an error in atmospheric attenuation constants, affecting raw2temp and temp2raw functions. Recommend update for use with long distance calculations. v.4.1.3. changed to frameLocates to reflect change to as.character() to format().

Maintained by Glenn J. Tattersall. Last updated 3 years ago.

animal-physiology heat-exchange heat-flux image-frames temperature thermal-biology thermal-images

6.9 match 169 stars 5.85 score 83 scripts

ishidamgm

TreeRingShape:Recording Tree-Ring Shapes of Tree Disks with Manual Digitizing and Interpolating Model

Record all tree-ring Shapefile of tree disk with GIS soft ('Qgis'<https://www.qgis.org/en/site/>) and interpolating model from high resolution tree disk image.

Maintained by Megumi ISHIDA. Last updated 4 months ago.

8.9 match 4.48 score

svkucheryavski

mdatools:Multivariate Data Analysis for Chemometrics

Projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. S. Kucheryavskiy (2020) <doi:10.1016/j.chemolab.2020.103937>.

Maintained by Sergey Kucheryavskiy. Last updated 8 months ago.

5.4 match 35 stars 7.37 score 220 scripts 1 dependents

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 4 days ago.

deep-learning machine-learning nlp transformers openjdk

3.0 match 146 stars 13.16 score 436 scripts 1 dependents

trenchproject

TrenchR:Tools for Microclimate and Biophysical Ecology

Tools for translating environmental change into organismal response. Microclimate models to vertically scale weather station data to organismal heights. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. Additional functions model and temporally partition air and soil temperatures and solar radiation. Utility functions estimate the organismal and environmental parameters needed for biophysical ecology. 'TrenchR' focuses on relatively simple and modular functions so users can create transparent and flexible biophysical models. Many functions are derived from Gates (1980) <doi:10.1007/978-1-4612-6024-0> and Campbell and Norman (1988) <isbn:9780387949376>.

Maintained by Lauren Buckley. Last updated 1 years ago.

5.6 match 13 stars 6.89 score 43 scripts

asgr

celestial:Collection of Common Astronomical Conversion Routines and Functions

Contains a number of common astronomy utility functions for cosmology and angular coordinates.

Maintained by Aaron Robotham. Last updated 1 years ago.

cpp

7.3 match 9 stars 5.22 score 68 scripts 9 dependents

stewid

SimInf:A Framework for Data-Driven Stochastic Disease Spread Simulations

Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models. For more details see the paper by Widgren, Bauer, Eriksson and Engblom (2019) <doi:10.18637/jss.v091.i12>. The package also provides functionality to fit models to time series data using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm of Toni and others (2009) <doi:10.1098/rsif.2008.0172>.

Maintained by Stefan Widgren. Last updated 5 days ago.

data-driven epidemiology high-performance-computing markov-chain mathematical-modelling gsl openmp

3.8 match 35 stars 10.09 score 227 scripts

kolesarm

dfadjust:Degrees of Freedom Adjustment for Robust Standard Errors

Computes small-sample degrees of freedom adjustment for heteroskedasticity robust standard errors, and for clustered standard errors in linear regression. See Imbens and Kolesár (2016) <doi:10.1162/REST_a_00552> for a discussion of these adjustments.

Maintained by Michal Kolesár. Last updated 3 months ago.

6.6 match 31 stars 5.75 score 12 scripts

tushiqi

MAnorm2:Tools for Normalizing and Comparing ChIP-seq Samples

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the premier technology for profiling genome-wide localization of chromatin-binding proteins, including transcription factors and histones with various modifications. This package provides a robust method for normalizing ChIP-seq signals across individual samples or groups of samples. It also designs a self-contained system of statistical models for calling differential ChIP-seq signals between two or more biological conditions as well as for calling hypervariable ChIP-seq signals across samples. Refer to Tu et al. (2021) <doi:10.1101/gr.262675.120> and Chen et al. (2022) <doi:10.1186/s13059-022-02627-9> for associated statistical details.

Maintained by Shiqi Tu. Last updated 2 years ago.

chip-seq differential-analysis empirical-bayes winsorize-values

6.8 match 32 stars 5.48 score 19 scripts

bioc

RCM:Fit row-column association models with the negative binomial distribution for the microbiome

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

Maintained by Stijn Hawinkel. Last updated 5 months ago.

metagenomics dimensionreduction microbiome visualization ordination phyloseq rcm

5.3 match 16 stars 6.90 score 25 scripts

vegandevs

vegan:Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Maintained by Jari Oksanen. Last updated 17 days ago.

ecological-modelling ecology ordination fortran openblas

1.9 match 472 stars 19.41 score 15k scripts 440 dependents

beerda

lfl:Linguistic Fuzzy Logic

Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD), and forecasting time-series using fuzzy rule-based ensemble (FRBE). The package also contains basic fuzzy-related algebraic functions capable of handling missing values in different styles (Bochvar, Sobocinski, Kleene etc.), computation of Sugeno integrals and fuzzy transform.

Maintained by Michal Burda. Last updated 5 months ago.

association-rules forecast-model fuzzy-logic inference-rules cpp openmp

6.8 match 8 stars 5.35 score 28 scripts

hwarden162

rhype:Work with Hypergraphs in R

Create and manipulate hypergraph objects. This early version of rhype allows for the output of matrices associated with the hypergraphs themselves. It also uses these matrices to calculate hypergraph spectra and perform spectral comparison. Functionality coming soon includes calculation of hyperpaths and hypergraph centrality measures.

Maintained by Hugh Warden. Last updated 3 years ago.

hypergraph hypergraphs

8.6 match 3 stars 4.18 score 5 scripts

rstudio

graphframes:Interface for 'GraphFrames'

A 'sparklyr' <https://spark.rstudio.com/> extension that provides an R interface for 'GraphFrames' <https://graphframes.github.io/>. 'GraphFrames' is a package for 'Apache Spark' that provides a DataFrame-based API for working with graphs. Functionality includes motif finding and common graph algorithms, such as PageRank and Breadth-first search.

Maintained by Kevin Kuo. Last updated 6 years ago.

graphframes graphs pagerank spark sparklyr

6.8 match 38 stars 5.20 score 84 scripts

dcousin3

superb:Summary Plots with Adjusted Error Bars

Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.

Maintained by Denis Cousineau. Last updated 2 months ago.

error-bars plotting statistics summary-plots summary-statistics visualization

3.7 match 19 stars 9.55 score 155 scripts 2 dependents

satijalab

SeuratObject:Data Structures for Single Cell Data

Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

cpp

3.0 match 25 stars 11.69 score 1.2k scripts 88 dependents

robjhyndman

forecast:Forecasting Functions for Time Series and Linear Models

Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.

Maintained by Rob Hyndman. Last updated 7 months ago.

forecast forecasting openblas cpp

1.9 match 1.1k stars 18.63 score 16k scripts 239 dependents

bioxgeo

geodiv:Methods for Calculating Gradient Surface Metrics

Methods for calculating gradient surface metrics for continuous analysis of landscape features.

Maintained by Annie C. Smith. Last updated 1 years ago.

cpp

5.9 match 11 stars 5.88 score 23 scripts 1 dependents

easystats

insight:Easy Access to Model Information for Various Model Objects

A tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was used to fit the model or data from response variables. 'insight' mainly revolves around two types of functions: Functions that find (the names of) information, starting with 'find_', and functions that get the underlying data, starting with 'get_'. The package has a consistent syntax and works with many different model objects, where otherwise functions to access these information are missing.

Maintained by Daniel Lüdecke. Last updated 6 days ago.

easystats hacktoberfest insight models names predictors random

2.0 match 412 stars 17.24 score 568 scripts 210 dependents

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 Croon’s 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 17 days ago.

3.8 match 28 stars 9.11 score 56 scripts 2 dependents

bioc

ComplexHeatmap:Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing clustering complex-heatmaps heatmap

2.0 match 1.3k stars 16.93 score 16k scripts 151 dependents

eikeluedeling

chillR:Statistical Methods for Phenology Analysis in Temperate Fruit Trees

The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>). 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records (Luedeling and Gassner (2012) <doi:10.1016/j.agrformet.2011.10.020>). As of version 0.65, it also includes functions for generating weather scenarios with a weather generator, for conducting climate change analyses for temperature-based climatic metrics and for plotting results from such analyses. Since version 0.70, 'chillR' contains a function for interpolating hourly temperature records.

Maintained by Eike Luedeling. Last updated 4 months ago.

cpp

5.5 match 3 stars 6.13 score 346 scripts 1 dependents

obrl-soil

h3jsr:Access Uber's H3 Library

Provides access to Uber's H3 library for geospatial indexing via its JavaScript transpile 'h3-js' <https://github.com/uber/h3-js> and 'V8' <https://github.com/jeroen/v8>.

Maintained by Lauren OBrien. Last updated 1 years ago.

discrete-global-grids h3 spatial-indexing

4.0 match 67 stars 8.39 score 205 scripts 4 dependents

hongyuanjia

psychrolib:Psychrometric Properties of Moist and Dry Air

Implementation of 'PsychroLib' <https://github.com/psychrometrics/psychrolib> library which contains functions to enable the calculation properties of moist and dry air in both metric (SI) and imperial (IP) systems of units. References: Meyer, D. and Thevenard, D (2019) <doi:10.21105/joss.01137>.

Maintained by Hongyuan Jia. Last updated 3 years ago.

cpp

10.1 match 3.30 score 11 scripts 2 dependents

fbertran

plsdof:Degrees of Freedom and Statistical Inference for Partial Least Squares Regression

The plsdof package provides Degrees of Freedom estimates for Partial Least Squares (PLS) Regression. Model selection for PLS is based on various information criteria (aic, bic, gmdl) or on cross-validation. Estimates for the mean and covariance of the PLS regression coefficients are available. They allow the construction of approximate confidence intervals and the application of test procedures (Kramer and Sugiyama 2012 <doi:10.1198/jasa.2011.tm10107>). Further, cross-validation procedures for Ridge Regression and Principal Components Regression are available.

Maintained by Frederic Bertrand. Last updated 2 years ago.

8.9 match 3 stars 3.65 score 30 scripts

cran

sna:Tools for Social Network Analysis

A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.

Maintained by Carter T. Butts. Last updated 6 months ago.

4.8 match 8 stars 6.78 score 94 dependents

lbbe-software

MareyMap:Estimation of Meiotic Recombination Rates Using Marey Maps

Local recombination rates are graphically estimated across a genome using Marey maps.

Maintained by Aurélie Siberchicot. Last updated 14 days ago.

6.0 match 1 stars 5.30 score 20 scripts

statnet

tergm:Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models

An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) <doi:10.1111/rssb.12014> and Carnegie, Krivitsky, Hunter, and Goodreau (2015) <doi:10.1080/10618600.2014.903087>.

Maintained by Pavel N. Krivitsky. Last updated 4 months ago.

3.4 match 27 stars 9.29 score 78 scripts 3 dependents

tomasfryda

h2o:R Interface for the 'H2O' Scalable Machine Learning Platform

R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).

Maintained by Tomas Fryda. Last updated 1 years ago.

3.8 match 3 stars 8.20 score 7.8k scripts 11 dependents

rohelab

fastRG:Sample Generalized Random Dot Product Graphs in Linear Time

Samples generalized random product graphs, a generalization of a broad class of network models. Given matrices X, S, and Y with with non-negative entries, samples a matrix with expectation X S Y^T and independent Poisson or Bernoulli entries using the fastRG algorithm of Rohe et al. (2017) <https://www.jmlr.org/papers/v19/17-128.html>. The algorithm first samples the number of edges and then puts them down one-by-one. As a result it is O(m) where m is the number of edges, a dramatic improvement over element-wise algorithms that which require O(n^2) operations to sample a random graph, where n is the number of nodes.

Maintained by Alex Hayes. Last updated 7 months ago.

adjacency-matrix graph-sampling latent-factors

6.8 match 5 stars 4.52 score 22 scripts

projectmosaic

mosaicCalc:R-Language Based Calculus Operations for Teaching

Software to support the introductory *MOSAIC Calculus* textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>), one of many data- and modeling-oriented educational resources developed by Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and numerical differentiation and integration, as well as support for applied linear algebra (for data science), and differential equations/dynamics. Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc. The software is suitable for general use, but intended mainly for teaching calculus.

Maintained by Daniel Kaplan. Last updated 21 days ago.

3.5 match 13 stars 8.68 score 546 scripts

jrnold

ggthemes:Extra Themes, Scales and Geoms for 'ggplot2'

Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' themes and scales that replicate the look of plots by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and 'The Wall Street Journal', among others. Provides 'geoms' for Tufte's box plot and range frame.

Maintained by Jeffrey B. Arnold. Last updated 1 years ago.

data-visualisation ggplot2 ggplot2-themes plot plotting theme visualization

1.9 match 1.3k stars 16.17 score 40k scripts 102 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 18 hours ago.

fortran cpp

1.8 match 87 stars 16.70 score 7.7k scripts 99 dependents

runehaubo

lmerTest:Tests in Linear Mixed Effects Models

Provides p-values in type I, II or III anova and summary tables for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the pbkrtest package. Model selection methods include step, drop1 and anova-like tables for random effects (ranova). Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed effects are also available.

Maintained by Rune Haubo Bojesen Christensen. Last updated 4 years ago.

2.3 match 51 stars 13.00 score 13k scripts 90 dependents

poissonconsulting

gsdd:Calculate Growing Season Degree Days from Water Temperature Data

Calculates Growing Season Degree Days (GSDD), Growing Degree Days (GDD) and the Growing Seasons (GSS) from water temperature data. GSSD is a water temperature metric that is a useful predictor of age-0 trout size at the beginning of winter. It is the accumulated thermal units (in C) during the growing season based on the mean daily water temperature values. GDD is the GSSD to a particular date.

Maintained by Joe Thorley. Last updated 22 days ago.

8.9 match 2 stars 3.38 score 5 scripts

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-measures classification-model influence-ranking network-analysis priaritization-model

4.5 match 27 stars 6.54 score 43 scripts 1 dependents

reconhub

epicontacts:Handling, Visualisation and Analysis of Epidemiological Contacts

A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.

Maintained by Finlay Campbell. Last updated 2 months ago.

outbreak

3.3 match 15 stars 8.86 score 112 scripts 2 dependents

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 5 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

3.0 match 173 stars 9.65 score 203 scripts 2 dependents

termehs

multigraphr:Probability Models and Statistical Analysis of Random Multigraphs

Methods and models for analysing multigraphs as introduced by Shafie (2015) <doi:10.21307/joss-2019-011>, including methods to study local and global properties <doi:10.1080/0022250X.2016.1219732> and goodness of fit tests.

Maintained by Termeh Shafie. Last updated 1 years ago.

5.4 match 15 stars 5.35 score 1 scripts

statist7

sitar:Super Imposition by Translation and Rotation Growth Curve Analysis

Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales. The model was first described by Lindstrom (1995) <doi:10.1002/sim.4780141807> and developed as the SITAR method by Cole et al (2010) <doi:10.1093/ije/dyq115>.

Maintained by Tim Cole. Last updated 2 months ago.

3.3 match 13 stars 8.69 score 58 scripts 3 dependents

wilkelab

ggridges:Ridgeline Plots in 'ggplot2'

Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.

Maintained by Claus O. Wilke. Last updated 3 months ago.

1.7 match 418 stars 16.71 score 14k scripts 285 dependents

dfsp-spirit

freesurferformats:Read and Write 'FreeSurfer' Neuroimaging File Formats

Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.

Maintained by Tim Schäfer. Last updated 6 months ago.

brain brain-atlas brain-surfaces curv dti fileformats freesurfer label mesh mgh mri neuroimaging parcellation research surface voxel

3.5 match 23 stars 8.07 score 25 scripts 8 dependents

r-forge

copula:Multivariate Dependence with Copulas

Classes (S4) of commonly used elliptical, Archimedean, extreme-value and other copula families, as well as their rotations, mixtures and asymmetrizations. Nested Archimedean copulas, related tools and special functions. Methods for density, distribution, random number generation, bivariate dependence measures, Rosenblatt transform, Kendall distribution function, perspective and contour plots. Fitting of copula models with potentially partly fixed parameters, including standard errors. Serial independence tests, copula specification tests (independence, exchangeability, radial symmetry, extreme-value dependence, goodness-of-fit) and model selection based on cross-validation. Empirical copula, smoothed versions, and non-parametric estimators of the Pickands dependence function.

Maintained by Martin Maechler. Last updated 12 days ago.

2.4 match 11.83 score 1.2k scripts 86 dependents

leonawicz

tabr:Music Notation Syntax, Manipulation, Analysis and Transcription in R

Provides a music notation syntax and a collection of music programming functions for generating, manipulating, organizing, and analyzing musical information in R. Music syntax can be entered directly in character strings, for example to quickly transcribe short pieces of music. The package contains functions for directly performing various mathematical, logical and organizational operations and musical transformations on special object classes that facilitate working with music data and notation. The same music data can be organized in tidy data frames for a familiar and powerful approach to the analysis of large amounts of structured music data. Functions are available for mapping seamlessly between these formats and their representations of musical information. The package also provides an API to 'LilyPond' (<https://lilypond.org/>) for transcribing musical representations in R into tablature ("tabs") and sheet music. 'LilyPond' is open source music engraving software for generating high quality sheet music based on markup syntax. The package generates 'LilyPond' files from R code and can pass them to the 'LilyPond' command line interface to be rendered into sheet music PDF files or inserted into R markdown documents. The package offers nominal MIDI file output support in conjunction with rendering sheet music. The package can read MIDI files and attempts to structure the MIDI data to integrate as best as possible with the data structures and functionality found throughout the package.

Maintained by Matthew Leonawicz. Last updated 6 months ago.

guitar-tablature lilypond lilypond-api music-analysis music-data music-notation music-programming music-syntax music-transcription sheet-music

3.5 match 132 stars 7.87 score 94 scripts

namezys

polyMatrix:Infrastructure for Manipulation Polynomial Matrices

Implementation of class "polyMatrix" for storing a matrix of polynomials and implements basic matrix operations; including a determinant and characteristic polynomial. It is based on the package 'polynom' and uses a lot of its methods to implement matrix operations. This package includes 3 methods of triangularization of polynomial matrices: Extended Euclidean algorithm which is most classical but numerically unstable; Sylvester algorithm based on LQ decomposition; Interpolation algorithm is based on LQ decomposition and Newton interpolation. Both methods are described in D. Henrion & M. Sebek, Reliable numerical methods for polynomial matrix triangularization, IEEE Transactions on Automatic Control (Volume 44, Issue 3, Mar 1999, Pages 497-508) <doi:10.1109/9.751344> and in Salah Labhalla, Henri Lombardi & Roger Marlin, Algorithmes de calcule de la reduction de Hermite d'une matrice a coefficients polynomeaux, Theoretical Computer Science (Volume 161, Issue 1-2, July 1996, Pages 69-92) <doi:10.1016/0304-3975(95)00090-9>.

Maintained by Nikolai Ryzhkov. Last updated 4 years ago.

9.1 match 1 stars 3.00 score 2 scripts

projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

Maintained by Randall Pruim. Last updated 1 years ago.

2.0 match 93 stars 13.32 score 7.2k scripts 7 dependents

cwatson

brainGraph:Graph Theory Analysis of Brain MRI Data

A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.

Maintained by Christopher G. Watson. Last updated 1 years ago.

brain-connectivity brain-imaging complex-networks connectome connectomics fmri graph-theory mri network-analysis neuroimaging neuroscience statistics tractography

3.4 match 188 stars 7.86 score 107 scripts 3 dependents

ropensci

pathviewr:Wrangle, Analyze, and Visualize Animal Movement Data

Tools to import, clean, and visualize movement data, particularly from motion capture systems such as Optitrack's 'Motive', the Straw Lab's 'Flydra', or from other sources. We provide functions to remove artifacts, standardize tunnel position and tunnel axes, select a region of interest, isolate specific trajectories, fill gaps in trajectory data, and calculate 3D and per-axis velocity. For experiments of visual guidance, we also provide functions that use subject position to estimate perception of visual stimuli.

Maintained by Vikram B. Baliga. Last updated 2 years ago.

animal-movement flydra motion movement-data optitrack trajectories trajectory-analysis visual-guidance visual-perception

4.0 match 8 stars 6.56 score 102 scripts

moondog1969

streamDAG:Analytical Methods for Stream DAGs

Provides indices and tools for directed acyclic graphs (DAGs), particularly DAG representations of intermittent streams. A detailed introduction to the package can be found in the publication: "Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG" (Aho et al., 2023) <doi:10.1016/j.envsoft.2023.105775>, and in the introductory package vignette.

Maintained by Ken Aho. Last updated 5 months ago.

6.3 match 1 stars 4.18 score 4 scripts

bioc

Mergeomics:Integrative network analysis of omics data

The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).

Maintained by Zeyneb Kurt. Last updated 5 months ago.

software

5.9 match 4.30 score 8 scripts

billdenney

PKNCA:Perform Pharmacokinetic Non-Compartmental Analysis

Compute standard Non-Compartmental Analysis (NCA) parameters for typical pharmacokinetic analyses and summarize them.

Maintained by Bill Denney. Last updated 17 days ago.

nca noncompartmental-analysis pharmacokinetics

2.0 match 73 stars 12.61 score 214 scripts 4 dependents

bioc

EGAD:Extending guilt by association by degree

The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.

Maintained by Sara Ballouz. Last updated 5 months ago.

software functionalgenomics systemsbiology geneprediction functionalprediction networkenrichment graphandnetwork network

5.1 match 4.92 score 83 scripts

bozenne

LMMstar:Repeated Measurement Models for Discrete Times

Companion R package for the course "Statistical analysis of correlated and repeated measurements for health science researchers" taught by the section of Biostatistics of the University of Copenhagen. It implements linear mixed models where the model for the variance-covariance of the residuals is specified via patterns (compound symmetry, toeplitz, unstructured, ...). Statistical inference for mean, variance, and correlation parameters is performed based on the observed information and a Satterthwaite approximation of the degrees of freedom. Normalized residuals are provided to assess model misspecification. Statistical inference can be performed for arbitrary linear or non-linear combination(s) of model coefficients. Predictions can be computed conditional to covariates only or also to outcome values.

Maintained by Brice Ozenne. Last updated 5 months ago.

4.0 match 4 stars 6.28 score 141 scripts

jonotuke

BREADR:Estimates Degrees of Relatedness (Up to the Second Degree) for Extreme Low-Coverage Data

The goal of the package is to provide an easy-to-use method for estimating degrees of relatedness (up to the second degree) for extreme low-coverage data. The package also allows users to quantify and visualise the level of confidence in the estimated degrees of relatedness.

Maintained by Jono Tuke. Last updated 24 days ago.

5.6 match 8 stars 4.45 score 4 scripts

cran

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.

3.0 match 10 stars 8.18 score 10 dependents

wangwm2017

RLeafAngle:Estimates, Plots and Evaluates Leaf Angle Distribution Functions, Calculates Extinction Coefficients

Leaf angle distribution is described by a number of functions (e.g. ellipsoidal, Beta and rotated ellipsoidal). The parameters of leaf angle distributions functions are estimated through different empirical relationship. This package includes estimations of parameters of different leaf angle distribution function, plots and evaluates leaf angle distribution functions, calculates extinction coefficients given leaf angle distribution. Reference: Wang(2007)<doi:10.1016/j.agrformet.2006.12.003>.

Maintained by Wei-Min Wang. Last updated 8 years ago.

16.3 match 1.51 score 32 scripts

dkesada

dbnR:Dynamic Bayesian Network Learning and Inference

Learning and inference over dynamic Bayesian networks of arbitrary Markovian order. Extends some of the functionality offered by the 'bnlearn' package to learn the networks from data and perform exact inference. It offers three structure learning algorithms for dynamic Bayesian networks: Trabelsi G. (2013) <doi:10.1007/978-3-642-41398-8_34>, Santos F.P. and Maciel C.D. (2014) <doi:10.1109/BRC.2014.6880957>, Quesada D., Bielza C. and Larrañaga P. (2021) <doi:10.1007/978-3-030-86271-8_14>. It also offers the possibility to perform forecasts of arbitrary length. A tool for visualizing the structure of the net is also provided via the 'visNetwork' package.

Maintained by David Quesada. Last updated 9 months ago.

bayesian-networks dynamic-bayesian-networks forecasting inference time-series cpp

4.9 match 55 stars 5.01 score 37 scripts

bioc

mdp:Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls. It is based on the Molecular Distance to Health (Pankla et al. 2009), and expands on this algorithm by adding the options to calculate the z-score using the modified z-score (using median absolute deviation), change the z-score zeroing threshold, and look at genes that are most perturbed in the test versus control classes.

Maintained by Helder Nakaya. Last updated 5 months ago.

biomedicalinformatics qualitycontrol transcriptomics systemsbiology microarray

5.2 match 4.65 score 15 scripts

mflores72000

ILS:Interlaboratory Study

It performs interlaboratory studies (ILS) to detect those laboratories that provide non-consistent results when comparing to others. It permits to work simultaneously with various testing materials, from standard univariate, and functional data analysis (FDA) perspectives. The univariate approach based on ASTM E691-08 consist of estimating the Mandel's h and k statistics to identify those laboratories that provide more significant different results, testing also the presence of outliers by Cochran and Grubbs tests, Analysis of variance (ANOVA) techniques are provided (F and Tuckey tests) to test differences in means corresponding to different laboratories per each material. Taking into account the functional nature of data retrieved in analytical chemistry, applied physics and engineering (spectra, thermograms, etc.). ILS package provides a FDA approach for finding the Mandel's k and h statistics distribution by smoothing bootstrap resampling.

Maintained by Miguel Flores. Last updated 2 years ago.

3.8 match 6.48 score 75 scripts

agrdatasci

climatrends:Climate Variability Indices for Ecological Modelling

Supports analysis of trends in climate change, ecological and crop modelling.

Maintained by Kauê de Sousa. Last updated 11 months ago.

climate-data climatology timeseries-analysis

4.7 match 5 stars 5.18 score 8 scripts

rvlenth

emmeans:Estimated Marginal Means, aka Least-Squares Means

Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.

Maintained by Russell V. Lenth. Last updated 4 days ago.

1.3 match 377 stars 19.19 score 13k scripts 187 dependents

peekxc

simplextree:Provides Tools for Working with General Simplicial Complexes

Provides an interface to a Simplex Tree data structure, which is a data structure aimed at enabling efficient manipulation of simplicial complexes of any dimension. The Simplex Tree data structure was originally introduced by Jean-Daniel Boissonnat and Clément Maria (2014) <doi:10.1007/s00453-014-9887-3>.

Maintained by Matt Piekenbrock. Last updated 1 years ago.

rcpp simplicial-complex topological-data-analysis topology cpp

5.3 match 15 stars 4.56 score 16 scripts 1 dependents

jongheepark

NetworkChange:Bayesian Package for Network Changepoint Analysis

Network changepoint analysis for undirected network data. The package implements a hidden Markov network change point model (Park and Sohn (2020)). Functions for break number detection using the approximate marginal likelihood and WAIC are also provided.

Maintained by Jong Hee Park. Last updated 3 years ago.

bayesian changepoint latent-space network

5.2 match 5 stars 4.60 score 16 scripts

emf-creaf

indicspecies:Relationship Between Species and Groups of Sites

Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].

Maintained by Miquel De Cáceres. Last updated 25 days ago.

2.5 match 10 stars 9.49 score 386 scripts 4 dependents

roy-sr-007

bayesestdft:Estimating the Degrees of Freedom of the Student's t-Distribution under a Bayesian Framework

A Bayesian framework to estimate the Student's t-distribution's degrees of freedom is developed. Markov Chain Monte Carlo sampling routines are developed as in <doi:10.3390/axioms11090462> to sample from the posterior distribution of the degrees of freedom. A random walk Metropolis algorithm is used for sampling when Jeffrey's and Gamma priors are endowed upon the degrees of freedom. In addition, the Metropolis-adjusted Langevin algorithm for sampling is used under the Jeffrey's prior specification. The Log-normal prior over the degrees of freedom is posed as a viable choice with comparable performance in simulations and real-data application, against other prior choices, where an Elliptical Slice Sampler is used to sample from the concerned posterior.

Maintained by Somjit Roy. Last updated 2 months ago.

8.8 match 1 stars 2.70 score 1 scripts

gavinsimpson

gratia:Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'

Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.

Maintained by Gavin L. Simpson. Last updated 21 hours ago.

distributional-regression gam gamm generalized-additive-mixed-models generalized-additive-models ggplot2 glm lm mgcv penalized-spline random-effects smoothing splines

1.8 match 217 stars 12.99 score 1.6k scripts 2 dependents

cardiomoon

interpretCI:Estimate the Confidence Interval and Interpret Step by Step

Estimate confidence intervals for mean, proportion, mean difference for unpaired and paired samples and proportion difference. Plot the confidence intervals. Generate documents explaining the statistical result step by step.

Maintained by Keon-Woong Moon. Last updated 3 years ago.

3.9 match 4 stars 6.03 score 49 scripts

statnet

tsna:Tools for Temporal Social Network Analysis

Temporal SNA tools for continuous- and discrete-time longitudinal networks having vertex, edge, and attribute dynamics stored in the 'networkDynamic' format. This work was supported by grant R01HD68395 from the National Institute of Health.

Maintained by Skye Bender-deMoll. Last updated 1 years ago.

3.0 match 7 stars 7.65 score 93 scripts 2 dependents

cran

circular:Circular Statistics

Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.

Maintained by Eduardo García-Portugués. Last updated 7 months ago.

fortran

3.0 match 7 stars 7.76 score 1.1k scripts 40 dependents

jacolien

itsadug:Interpreting Time Series and Autocorrelated Data Using GAMMs

GAMM (Generalized Additive Mixed Modeling; Lin & Zhang, 1999) as implemented in the R package 'mgcv' (Wood, S.N., 2006; 2011) is a nonlinear regression analysis which is particularly useful for time course data such as EEG, pupil dilation, gaze data (eye tracking), and articulography recordings, but also for behavioral data such as reaction times and response data. As time course measures are sensitive to autocorrelation problems, GAMMs implements methods to reduce the autocorrelation problems. This package includes functions for the evaluation of GAMM models (e.g., model comparisons, determining regions of significance, inspection of autocorrelational structure in residuals) and interpreting of GAMMs (e.g., visualization of complex interactions, and contrasts).

Maintained by Jacolien van Rij. Last updated 3 years ago.

3.6 match 1 stars 6.45 score 576 scripts 2 dependents

cran

mable:Maximum Approximate Bernstein/Beta Likelihood Estimation

Fit data from a continuous population with a smooth density on finite interval by an approximate Bernstein polynomial model which is a mixture of certain beta distributions and find maximum approximate Bernstein likelihood estimator of the unknown coefficients. Consequently, maximum likelihood estimates of the unknown density, distribution functions, and more can be obtained. If the support of the density is not the unit interval then transformation can be applied. This is an implementation of the methods proposed by the author of this package published in the Journal of Nonparametric Statistics: Guan (2016) <doi:10.1080/10485252.2016.1163349> and Guan (2017) <doi:10.1080/10485252.2017.1374384>. For data with covariates, under some semiparametric regression models such as Cox proportional hazards model and the accelerated failure time model, the baseline survival function can be estimated smoothly based on general interval censored data.

Maintained by Zhong Guan. Last updated 6 months ago.

10.0 match 2.30 score

bioc

MAST:Model-based Analysis of Single Cell Transcriptomics

Methods and models for handling zero-inflated single cell assay data.

Maintained by Andrew McDavid. Last updated 5 months ago.

geneexpression differentialexpression genesetenrichment rnaseq transcriptomics singlecell

1.8 match 230 stars 12.75 score 1.8k scripts 5 dependents

lmarusich

rmcorr:Repeated Measures Correlation

Compute the repeated measures correlation, a statistical technique for determining the overall within-individual relationship among paired measures assessed on two or more occasions, first introduced by Bland and Altman (1995). Includes functions for diagnostics, p-value, effect size with confidence interval including optional bootstrapping, as well as graphing. Also includes several example datasets. For more details, see the web documentation <https://lmarusich.github.io/rmcorr/index.html> and the original paper: Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.

Maintained by Laura R. Marusich. Last updated 7 months ago.

2.5 match 7 stars 9.18 score 304 scripts

flh3

CR2:Compute Cluster Robust Standard Errors with Degrees of Freedom Adjustments

Estimate different types of cluster robust standard errors (CR0, CR1, CR2) with degrees of freedom adjustments. Standard errors are computed based on 'Liang and Zeger' (1986) <doi:10.1093/biomet/73.1.13> and Bell and 'McCaffrey' <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2002002/article/9058-eng.pdf?st=NxMjN1YZ>. Functions used in Huang and Li <doi:10.3758/s13428-021-01627-0>, Huang, 'Wiedermann', and 'Zhang' <doi:10.1080/00273171.2022.2077290>, and Huang, 'Zhang', and Li (forthcoming: Journal of Research on Educational Effectiveness).

Maintained by Francis Huang. Last updated 1 years ago.

8.5 match 1 stars 2.70 score 7 scripts

cran

VCA:Variance Component Analysis

ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.

Maintained by Andre Schuetzenmeister. Last updated 1 years ago.

fortran openblas

5.0 match 2 stars 4.51 score 5 dependents

midfieldr

midfieldr:Tools and Methods for Working with MIDFIELD Data in 'R'

Provides tools and demonstrates methods for working with individual undergraduate student-level records (registrar's data) in 'R'. Tools include filters for program codes, data sufficiency, and timely completion. Methods include gathering blocs of records, computing quantitative metrics such as graduation rate, and creating charts to visualize comparisons. 'midfieldr' interacts with practice data provided in 'midfielddata', an R data package available at <https://midfieldr.github.io/midfielddata/>. 'midfieldr' also interacts with the full MIDFIELD database for users who have access. This work is supported by the US National Science Foundation through grant numbers 1545667 and 2142087.

Maintained by Richard Layton. Last updated 2 months ago.

4.0 match 2 stars 5.56 score 26 scripts

r-forge

sirad:Functions for Calculating Daily Solar Radiation and Evapotranspiration

Calculating daily global solar radiation at horizontal surface using several well-known models (i.e. Angstrom-Prescott, Supit-Van Kappel, Hargreaves, Bristow and Campbell, and Mahmood-Hubbard), and model calibration based on ground-truth data, and (3) model auto-calibration. The FAO Penmann-Monteith equation to calculate evapotranspiration is also included.

Maintained by Jedrzej S. Bojanowski. Last updated 8 years ago.

7.0 match 3.18 score 64 scripts

ocean-tracking-network

glatos:A package for the Great Lakes Acoustic Telemetry Observation System

Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.

Maintained by Christopher Holbrook. Last updated 6 months ago.

3.5 match 10 stars 6.38 score 112 scripts

glenndavis52

colorscience:Color Science Methods and Data

Methods and data for color science - color conversions by observer, illuminant, and gamma. Color matching functions and chromaticity diagrams. Color indices, color differences, and spectral data conversion/analysis. This package is deprecated and will someday be removed; for reasons and details please see the README file.

Maintained by Glenn Davis. Last updated 11 months ago.

5.6 match 4 stars 3.93 score 214 scripts

gaborcsardi

simplegraph:Simple Graph Data Types and Basic Algorithms

Simple classic graph algorithms for simple graph classes. Graphs may possess vertex and edge attributes. 'simplegraph' has no dependencies and it is written entirely in R, so it is easy to install.

Maintained by Gabor Csardi. Last updated 2 years ago.

5.3 match 2 stars 4.19 score 26 scripts 1 dependents

agandy

systemicrisk:Systemic Risk and Network Reconstruction

Analysis of risk through liability matrices. Contains a Gibbs sampler for network reconstruction, where only row and column sums of the liabilities matrix as well as some other fixed entries are observed, following the methodology of Gandy&Veraart (2016) <doi:10.1287/mnsc.2016.2546>. It also incorporates models that use a power law distribution on the degree distribution.

Maintained by Axel Gandy. Last updated 11 months ago.

cpp

5.7 match 5 stars 3.88 score 51 scripts

cjerzak

DescriptiveRepresentationCalculator:Characterizing Observed and Expected Representation

A system for analyzing descriptive representation, especially for comparing the composition of a political body to the population it represents. Users can compute the expected degree of representation for a body under a random sampling model, the expected degree of representation variability, as well as representation scores from observed political bodies. The package is based on Gerring, Jerzak, and Oncel (2024) <doi:10.1017/S0003055423000680>.

Maintained by Connor Jerzak. Last updated 1 months ago.

descriptive-representation leadership society

4.2 match 6 stars 5.18 score 2 scripts

jmw86069

jamba:Just Analysis Methods Base

Just analysis methods ('jam') base functions focused on bioinformatics. Version- and gene-centric alphanumeric sort, unique name and version assignment, colorized console and 'HTML' output, color ramp and palette manipulation, 'Rmarkdown' cache import, styled 'Excel' worksheet import and export, interpolated raster output from smooth scatter and image plots, list to delimited vector, efficient list tools.

Maintained by James M. Ward. Last updated 10 days ago.

bioinformatics

4.0 match 6 stars 5.43 score

cran

mgcv:Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.

Maintained by Simon Wood. Last updated 1 years ago.

openblas openmp

1.7 match 32 stars 12.71 score 17k scripts 7.8k dependents

tyee001

VGAM:Vector Generalized Linear and Additive Models

An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted least squares. At the heart of this package are the vector generalized linear and additive model (VGLM/VGAM) classes. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs that use smoothing. The book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of the statistical framework and the package. Currently only fixed-effects models are implemented. Many (100+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE. The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, doubly constrained RR-VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Hauck-Donner effect detection is implemented. Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.

Maintained by Thomas Yee. Last updated 1 months ago.

fortran

2.0 match 10 stars 10.67 score 3.6k scripts 169 dependents

nicebread

RSA:Response Surface Analysis

Advanced response surface analysis. The main function RSA computes and compares several nested polynomial regression models (full second- or third-order polynomial, shifted and rotated squared difference model, rising ridge surfaces, basic squared difference model, asymmetric or level-dependent congruence effect models). The package provides plotting functions for 3d wireframe surfaces, interactive 3d plots, and contour plots. Calculates many surface parameters (a1 to a5, principal axes, stationary point, eigenvalues) and provides standard, robust, or bootstrapped standard errors and confidence intervals for them.

Maintained by Felix Schönbrodt. Last updated 11 months ago.

3.4 match 17 stars 6.30 score 26 scripts 1 dependents

mkoohafkan

cimir:Interface to the CIMIS Web API

Connect to the California Irrigation Management Information System (CIMIS) Web API. See the CIMIS main page <https://cimis.water.ca.gov> and web API documentation <https://et.water.ca.gov> for more information.

Maintained by Michael Koohafkan. Last updated 6 months ago.

weather-api

4.0 match 6 stars 5.31 score 34 scripts

inlabru-org

fmesher:Triangle Meshes and Related Geometry Tools

Generate planar and spherical triangle meshes, compute finite element calculations for 1- and 2-dimensional flat and curved manifolds with associated basis function spaces, methods for lines and polygons, and transparent handling of coordinate reference systems and coordinate transformation, including 'sf' and 'sp' geometries. The core 'fmesher' library code was originally part of the 'INLA' package, and implements parts of "Triangulations and Applications" by Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.

Maintained by Finn Lindgren. Last updated 3 days ago.

cpp

1.9 match 16 stars 11.18 score 261 scripts 26 dependents

petebaker

cropgrowdays:Crop Growing Degree Days and Agrometeorological Calculations

Calculate agrometeorological variables for crops including growing degree days (McMaster, GS & Wilhelm, WW (1997) <doi:10.1016/S0168-1923(97)00027-0>), cumulative rainfall, number of stress days and cumulative or mean radiation and evaporation. Convert dates to day of year and vice versa. Also, download curated and interpolated Australian weather data from the Queensland Government DES longpaddock website <https://www.longpaddock.qld.gov.au/>. This data is freely available under the Creative Commons 4.0 licence.

Maintained by Peter Baker. Last updated 1 years ago.

5.1 match 4.11 score 13 scripts

grosssbm

missSBM:Handling Missing Data in Stochastic Block Models

When a network is partially observed (here, NAs in the adjacency matrix rather than 1 or 0 due to missing information between node pairs), it is possible to account for the underlying process that generates those NAs. 'missSBM', presented in 'Barbillon, Chiquet and Tabouy' (2022) <doi:10.18637/jss.v101.i12>, adjusts the popular stochastic block model from network data sampled under various missing data conditions, as described in 'Tabouy, Barbillon and Chiquet' (2019) <doi:10.1080/01621459.2018.1562934>.

Maintained by Julien Chiquet. Last updated 4 days ago.

missing-data nas network-analysis network-dataset stochastic-block-model cpp

3.8 match 12 stars 5.53 score 19 scripts

gi0na

ghypernet:Fit and Simulate Generalised Hypergeometric Ensembles of Graphs

Provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG). To learn how to use it, check the vignettes for a quick tutorial. Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300> together with those relevant references from the one listed below. The package is based on the research developed at the Chair of Systems Design, ETH Zurich. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arXiv:1607.02441>. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>. Casiraghi, G., (2017) <arXiv:1702.02048> Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926> Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>. Casiraghi, G., Nanumyan, V. (2021) <doi:10.1038/s41598-021-92519-y>. Casiraghi, G. (2021) <doi:10.1088/2632-072X/ac0493>.

Maintained by Giona Casiraghi. Last updated 11 months ago.

data-mining data-science graphs network network-analysis random-graph-generation random-graphs

3.7 match 8 stars 5.68 score 20 scripts

trevorld

affiner:A Finer Way to Render 3D Illustrated Objects in 'grid' Using Affine Transformations

Dilate, permute, project, reflect, rotate, shear, and translate 2D and 3D points. Supports parallel projections including oblique projections such as the cabinet projection as well as axonometric projections such as the isometric projection. Use 'grid's "affine transformation" feature to render illustrated flat surfaces.

Maintained by Trevor L. Davis. Last updated 3 months ago.

3.0 match 9 stars 6.91 score 1 scripts 5 dependents

jlmelville

rnndescent:Nearest Neighbor Descent Method for Approximate Nearest Neighbors

The Nearest Neighbor Descent method for finding approximate nearest neighbors by Dong and co-workers (2010) <doi:10.1145/1963405.1963487>. Based on the 'Python' package 'PyNNDescent' <https://github.com/lmcinnes/pynndescent>.

Maintained by James Melville. Last updated 8 months ago.

approximate-nearest-neighbor-search cpp

2.8 match 11 stars 7.31 score 75 scripts

friendly

heplots:Visualizing Hypothesis Tests in Multivariate Linear Models

Provides HE plot and other functions for visualizing hypothesis tests in multivariate linear models. HE plots represent sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions). The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when there are more than a few response variables.

Maintained by Michael Friendly. Last updated 9 days ago.

linear-hypotheses matrices multivariate-linear-models plot repeated-measure-designs visualizing-hypothesis-tests

1.8 match 9 stars 11.49 score 1.1k scripts 7 dependents

convexfi

fitHeavyTail:Mean and Covariance Matrix Estimation under Heavy Tails

Robust estimation methods for the mean vector, scatter matrix, and covariance matrix (if it exists) from data (possibly containing NAs) under multivariate heavy-tailed distributions such as angular Gaussian (via Tyler's method), Cauchy, and Student's t distributions. Additionally, a factor model structure can be specified for the covariance matrix. The latest revision also includes the multivariate skewed t distribution. The package is based on the papers: Sun, Babu, and Palomar (2014); Sun, Babu, and Palomar (2015); Liu and Rubin (1995); Zhou, Liu, Kumar, and Palomar (2019); Pascal, Ollila, and Palomar (2021).

Maintained by Daniel P. Palomar. Last updated 2 years ago.

cauchy covariance-estimation covariance-matrix heavy-tailed-distributions outliers robust-estimation student-t tyler

3.3 match 22 stars 6.27 score 28 scripts 1 dependents

symbolixau

h3r:Hexagonal Hierarchical Geospatial Indexing System

Provides access to Uber's 'H3' geospatial indexing system via 'h3lib' <https://CRAN.R-project.org/package=h3lib>. 'h3r' is designed to mimic the 'H3' Application Programming Interface (API) <https://h3geo.org/docs/api/indexing/>, so that any function in the API is also available in 'h3r'.

Maintained by David Cooley. Last updated 3 months ago.

4.5 match 5 stars 4.52 score 33 scripts

gamlss-dev

gamlss:Generalized Additive Models for Location Scale and Shape

Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.

Maintained by Mikis Stasinopoulos. Last updated 4 months ago.

1.8 match 16 stars 11.23 score 2.0k scripts 49 dependents

nwaller

fungible:Psychometric Functions from the Waller Lab

Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications: Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>. Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights. Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>. Waller, N. G. (2016). Fungible Correlation Matrices: A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568. Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF) covariance matrix of standardized regression coefficients: theoretical extensions and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>. Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.

Maintained by Niels Waller. Last updated 1 years ago.

4.0 match 5.01 score 136 scripts 8 dependents

rapler

dst:Using the Theory of Belief Functions

Using the Theory of Belief Functions for evidence calculus. Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values and combined. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.

Maintained by Peiyuan Zhu. Last updated 3 months ago.

3.4 match 6 stars 5.96 score 126 scripts

arni-magnusson

gmt:Interface Between GMT Map-Making Software and R

Interface between the 'GMT' map-making software and R, enabling the user to manipulate geographic data within R and call GMT commands to draw and annotate maps in postscript format. The gmt package is about interactive data analysis, rapidly visualizing subsets and summaries of geographic data, while performing statistical analysis in the R console.

Maintained by Arni Magnusson. Last updated 2 years ago.

4.0 match 1 stars 4.97 score 52 scripts 1 dependents

claudioagostinelli

CircStats:Circular Statistics, from "Topics in Circular Statistics" (2001)

Circular Statistics, from "Topics in Circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.

Maintained by Claudio Agostinelli. Last updated 7 years ago.

3.0 match 2 stars 6.60 score 261 scripts 36 dependents

nasserdr

digiRhythm:Analyzing Animal's Rhythmicity

Analyze and visualize the rhythmic behavior of animals using the degree of functional coupling (See Scheibe (1999) <doi:10.1076/brhm.30.2.216.1420>), compute and visualize harmonic power, actograms, average activity and diurnality index.

Maintained by Hassan-Roland Nasser. Last updated 6 days ago.

3.2 match 6.06 score 22 scripts

chrisaberson

pwr2ppl:Power Analyses for Common Designs (Power to the People)

Statistical power analysis for designs including t-tests, correlations, multiple regression, ANOVA, mediation, and logistic regression. Functions accompany Aberson (2019) <doi:10.4324/9781315171500>.

Maintained by Chris Aberson. Last updated 3 years ago.

4.7 match 17 stars 4.16 score 17 scripts

euctrl-pru

nvctr:The n-vector Approach to Geographical Position Calculations using an Ellipsoidal Model of Earth

The n-vector framework uses the normal vector to the Earth ellipsoid (called n-vector) as a non-singular position representation that turns out to be very convenient for practical position calculations. The n-vector is simple to use and gives exact answers for all global positions, and all distances, for both ellipsoidal and spherical Earth models. This package is a translation of the 'Matlab' library from FFI, the Norwegian Defence Research Establishment, as described in Gade (2010) <doi:10.1017/S0373463309990415>.

Maintained by Enrico Spinielli. Last updated 11 months ago.

geographical-positions n-vector

3.8 match 10 stars 5.19 score 31 scripts

eitsupi

neopolars:R Bindings for the 'polars' Rust Library

Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.

Maintained by Tatsuya Shima. Last updated 2 days ago.

rust cargo

4.0 match 40 stars 4.86 score 1 scripts

dmurdoch

plotrix:Various Plotting Functions

Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.

Maintained by Duncan Murdoch. Last updated 1 years ago.

1.7 match 5 stars 11.31 score 9.2k scripts 361 dependents

adwolfer

santaR:Short Asynchronous Time-Series Analysis

A graphical and automated pipeline for the analysis of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous time sampling (i.e. different time points for different individuals), inter-individual variability, noisy measurements and large numbers of variables. Based on a smoothing splines functional model, 'santaR' is able to detect variables highlighting significantly different temporal trajectories between study groups. Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting options for non-specialist users.

Maintained by Arnaud Wolfer. Last updated 1 years ago.

pcamethods (>= 1.92.0)

3.0 match 11 stars 6.44 score 63 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.

3.8 match 4 stars 5.10 score 21 scripts

adamlilith

enmSdmX:Species Distribution Modeling and Ecological Niche Modeling

Implements species distribution modeling and ecological niche modeling, including: bias correction, spatial cross-validation, model evaluation, raster interpolation, biotic "velocity" (speed and direction of movement of a "mass" represented by a raster), interpolating across a time series of rasters, and use of spatially imprecise records. The heart of the package is a set of "training" functions which automatically optimize model complexity based number of available occurrences. These algorithms include MaxEnt, MaxNet, boosted regression trees/gradient boosting machines, generalized additive models, generalized linear models, natural splines, and random forests. To enhance interoperability with other modeling packages, no new classes are created. The package works with 'PROJ6' geodetic objects and coordinate reference systems.

Maintained by Adam B. Smith. Last updated 25 days ago.

bias-correction biogeography ecological-niche-modeling ecological-niche-modelling niche-modeling niche-modelling species-distribution-modeling openjdk

3.4 match 25 stars 5.62 score 37 scripts

bioc

pandaR:PANDA Algorithm

Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.

Maintained by Joseph N. Paulson. Last updated 5 months ago.

statisticalmethod graphandnetwork microarray generegulation networkinference geneexpression transcription network

5.7 match 3.30 score 8 scripts

venpopov

bmm:Easy and Accessible Bayesian Measurement Models Using 'brms'

Fit computational and measurement models using full Bayesian inference. The package provides a simple and accessible interface by translating complex domain-specific models into 'brms' syntax, a powerful and flexible framework for fitting Bayesian regression models using 'Stan'. The package is designed so that users can easily apply state-of-the-art models in various research fields, and so that researchers can use it as a new model development framework. References: Frischkorn and Popov (2023) <doi:10.31234/osf.io/umt57>.

Maintained by Vencislav Popov. Last updated 14 days ago.

3.1 match 15 stars 5.92 score 35 scripts

vlyubchich

snowboot:Bootstrap Methods for Network Inference

Functions for analysis of network objects, which are imported or simulated by the package. The non-parametric methods of analysis center on snowball and bootstrap sampling for estimating functions of network degree distribution. For other parameters of interest, see, e.g., 'bootnet' package.

Maintained by Vyacheslav Lyubchich. Last updated 5 years ago.

cpp

10.9 match 2 stars 1.68 score 24 scripts

bioc

miloR:Differential neighbourhood abundance testing on a graph

Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using either a negative bionomial generalized linear model or negative binomial generalized linear mixed model.

Maintained by Mike Morgan. Last updated 5 months ago.

singlecell multiplecomparison functionalgenomics software openblas cpp openmp

1.8 match 357 stars 10.49 score 340 scripts 1 dependents

dankelley

ocedata:Oceanographic Data Sets for 'oce' Package

Several Oceanographic data sets are provided for use by the 'oce' package, and for other purposes.

Maintained by Dan Kelley. Last updated 2 years ago.

3.6 match 8 stars 5.07 score 146 scripts

anespinosa

netmem:Social Network Measures using Matrices

Measures to describe and manipulate networks using matrices.

Maintained by Alejandro Espinosa-Rada. Last updated 6 days ago.

matrices multilayer-networks network-analysis network-science sna social-network social-network-analysis sociology

4.1 match 11 stars 4.33 score 13 scripts

rafael-ayala

asteRisk:Computation of Satellite Position

Provides basic functionalities to calculate the position of satellites given a known state vector. The package includes implementations of the SGP4 and SDP4 simplified perturbation models to propagate orbital state vectors, as well as utilities to read TLE files and convert coordinates between different frames of reference. Several of the functionalities of the package (including the high-precision numerical orbit propagator) require the coefficients and data included in the 'asteRiskData' package, available in a 'drat' repository. To install this data package, run 'install.packages("asteRiskData", repos="https://rafael-ayala.github.io/drat/")'. Felix R. Hoots, Ronald L. Roehrich and T.S. Kelso (1988) <https://celestrak.org/NORAD/documentation/spacetrk.pdf>. David Vallado, Paul Crawford, Richard Hujsak and T.S. Kelso (2012) <doi:10.2514/6.2006-6753>. Felix R. Hoots, Paul W. Schumacher Jr. and Robert A. Glover (2014) <doi:10.2514/1.9161>.

Maintained by Rafael Ayala. Last updated 10 months ago.

cpp

3.8 match 6 stars 4.74 score 23 scripts

nunzioknerr

pannotator:Visualisation and Annotation of 360 Degree Imagery

Provides a customisable R 'shiny' app for immersively visualising, mapping and annotating panospheric (360 degree) imagery. The flexible interface allows annotation of any geocoded images using up to 4 user specified dropdown menus. The app uses 'leaflet' to render maps that display the geo-locations of images and panellum <https://pannellum.org/>, a lightweight panorama viewer for the web, to render images in virtual 360 degree viewing mode. Key functions include the ability to draw on & export parts of 360 images for downstream applications. Users can also draw polygons and points on map imagery related to the panoramic images and export them for further analysis. Downstream applications include using annotations to train Artificial Intelligence/Machine Learning (AI/ML) models and geospatial modelling and analysis of camera based survey data.

Maintained by Nunzio Knerr. Last updated 4 months ago.

3.8 match 2 stars 4.70 score 8 scripts

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 16 days ago.

2.3 match 10 stars 7.86 score 139 scripts 1 dependents

neon-biodiversity

Ostats:O-Stats, or Pairwise Community-Level Niche Overlap Statistics

O-statistics, or overlap statistics, measure the degree of community-level trait overlap. They are estimated by fitting nonparametric kernel density functions to each species’ trait distribution and calculating their areas of overlap. For instance, the median pairwise overlap for a community is calculated by first determining the overlap of each species pair in trait space, and then taking the median overlap of each species pair in a community. This median overlap value is called the O-statistic (O for overlap). The Ostats() function calculates separate univariate overlap statistics for each trait, while the Ostats_multivariate() function calculates a single multivariate overlap statistic for all traits. O-statistics can be evaluated against null models to obtain standardized effect sizes. 'Ostats' is part of the collaborative Macrosystems Biodiversity Project "Local- to continental-scale drivers of biodiversity across the National Ecological Observatory Network (NEON)." For more information on this project, see the Macrosystems Biodiversity Website (<https://neon-biodiversity.github.io/>). Calculation of O-statistics is described in Read et al. (2018) <doi:10.1111/ecog.03641>, and a teaching module for introducing the underlying biological concepts at an undergraduate level is described in Grady et al. (2018) <http://tiee.esa.org/vol/v14/issues/figure_sets/grady/abstract.html>.

Maintained by Quentin D. Read. Last updated 4 months ago.

ecology

2.6 match 7 stars 6.69 score 28 scripts

ilaga

networkscaleup:Network Scale-Up Models for Aggregated Relational Data

Provides a variety of Network Scale-up Models for researchers to analyze Aggregated Relational Data, mostly through the use of Stan. In this version, the package implements models from Laga, I., Bao, L., and Niu, X (2021) <arXiv:2109.10204>, Zheng, T., Salganik, M. J., and Gelman, A. (2006) <doi:10.1198/016214505000001168>, Killworth, P. D., Johnsen, E. C., McCarty, C., Shelley, G. A., and Bernard, H. R. (1998) <doi:10.1016/S0378-8733(96)00305-X>, and Killworth, P. D., McCarty, C., Bernard, H. R., Shelley, G. A., and Johnsen, E. C. (1998) <doi:10.1177/0193841X9802200205>.

Maintained by Ian Laga. Last updated 1 years ago.

cpp

4.9 match 4 stars 3.60 score 4 scripts

murrayefford

secr:Spatially Explicit Capture-Recapture

Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

Maintained by Murray Efford. Last updated 5 hours ago.

cpp

1.7 match 3 stars 10.16 score 410 scripts 5 dependents

mlampros

OpenImageR:An Image Processing Toolkit

Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform, the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library. The Gabor Feature Extraction functions are based on 'Matlab' code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>. The 'SLIC' and 'SLICO' superpixel algorithms were explained in detail in (i) "SLIC Superpixels Compared to State-of-the-art Superpixel Methods", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274-2282, May 2012, <doi:10.1109/TPAMI.2012.120> and (ii) "SLIC Superpixels", Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Suesstrunk, EPFL Technical Report no. 149300, June 2010.

Maintained by Lampros Mouselimis. Last updated 2 years ago.

filtering gabor-feature-extraction gabor-filters hog-features image image-hashing processing rcpparmadillo recognition slic slico superpixels openblas cpp openmp

1.8 match 60 stars 9.86 score 358 scripts 8 dependents

derek-corcoran-barrios

NetworkExtinction:Extinction Simulation in Ecological Networks

Simulates the extinction of species in ecological networks and it analyzes its cascading effects, described in Dunne et al. (2002) <doi:10.1073/pnas.192407699>.

Maintained by Derek Corcoran. Last updated 4 months ago.

3.3 match 5 stars 5.15 score 19 scripts

tlverse

hal9001:The Scalable Highly Adaptive Lasso

A scalable implementation of the highly adaptive lasso algorithm, including routines for constructing sparse matrices of basis functions of the observed data, as well as a custom implementation of Lasso regression tailored to enhance efficiency when the matrix of predictors is composed exclusively of indicator functions. For ease of use and increased flexibility, the Lasso fitting routines invoke code from the 'glmnet' package by default. The highly adaptive lasso was first formulated and described by MJ van der Laan (2017) <doi:10.1515/ijb-2015-0097>, with practical demonstrations of its performance given by Benkeser and van der Laan (2016) <doi:10.1109/DSAA.2016.93>. This implementation of the highly adaptive lasso algorithm was described by Hejazi, Coyle, and van der Laan (2020) <doi:10.21105/joss.02526>.

Maintained by Jeremy Coyle. Last updated 4 months ago.

cross-validation lasso-regression machine-learning-algorithms nonparametric-regression cpp

1.9 match 49 stars 9.16 score 368 scripts 6 dependents

pboutros

VennDiagram:Generate High-Resolution Venn and Euler Plots

A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

Maintained by Paul Boutros. Last updated 3 years ago.

2.0 match 3 stars 8.53 score 5.7k scripts 41 dependents

gergness

srvyr:'dplyr'-Like Syntax for Summary Statistics of Survey Data

Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.

Maintained by Greg Freedman Ellis. Last updated 1 months ago.

survey

1.2 match 215 stars 13.88 score 1.8k scripts 15 dependents

usccana

netdiffuseR:Analysis of Diffusion and Contagion Processes on Networks

Empirical statistical analysis, visualization and simulation of diffusion and contagion processes on networks. The package implements algorithms for calculating network diffusion statistics such as transmission rate, hazard rates, exposure models, network threshold levels, infectiousness (contagion), and susceptibility. The package is inspired by work published in Valente, et al., (2015) <DOI:10.1016/j.socscimed.2015.10.001>; Valente (1995) <ISBN: 9781881303213>, Myers (2000) <DOI:10.1086/303110>, Iyengar and others (2011) <DOI:10.1287/mksc.1100.0566>, Burt (1987) <DOI:10.1086/228667>; among others.

Maintained by George Vega Yon. Last updated 3 months ago.

contagion diffusion-network network-analysis network-visualization openblas cpp openmp

1.9 match 88 stars 8.88 score 217 scripts

lucasvenez

precintcon:Precipitation Intensity, Concentration and Anomaly Analysis

It contains functions to analyze the precipitation intensity, concentration and anomaly.

Maintained by Lucas Venezian Povoa. Last updated 9 years ago.

3.9 match 10 stars 4.28 score 38 scripts

toreopsahl

tnet:Weighted, Two-Mode, and Longitudinal Networks Analysis

Binary ties limit the richness of network analyses as relations are unique. The two-mode structure contains a number of features lost when projection it to a one-mode network. Longitudinal datasets allow for an understanding of the causal relationship among ties, which is not the case in cross-sectional datasets as ties are dependent upon each other.

Maintained by Tore Opsahl. Last updated 5 years ago.

3.7 match 1 stars 4.48 score 145 scripts 6 dependents

carlos-alberto-silva

ICESat2VegR:NASA's Ice, Cloud, and Elevation Satellite (ICESat-2) Data Analysis for Land and Vegetation Applications

Set of tools for downloading, reading, visualizing, processing and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon Data) and ATL08 (Land and Vegetation Height) products for Land and Vegetation Applications.

Maintained by Caio Hamamura. Last updated 6 months ago.

gdal proj cpp

3.6 match 11 stars 4.57 score 21 scripts

tobiste

tectonicr:Analyzing the Orientation of Maximum Horizontal Stress

Models the direction of the maximum horizontal stress using relative plate motion parameters. Statistical algorithms to evaluate the modeling results compared with the observed data. Provides plots to visualize the results. Methods described in Stephan et al. (2023) <doi:10.1038/s41598-023-42433-2> and Wdowinski (1998) <doi:10.1016/S0079-1946(98)00091-3>.

Maintained by Tobias Stephan. Last updated 14 days ago.

geology structural-geology tectonics

2.3 match 7 stars 7.26 score 33 scripts

wjschne

ggdiagram:Object-Oriented Diagram Plots with ggplot2

The ggdiagram package creates path diagrams with an object-oriented approach and plots diagrams with ggplot2.

Maintained by W. Joel Schneider. Last updated 12 days ago.

diagrams factor-analysis ggplot2 path-analysis s7 structural-equation-modeling

3.0 match 32 stars 5.41 score

carm1r

fruclimadapt:Evaluation Tools for Assessing Climate Adaptation of Fruit Tree Species

Climate is a critical component limiting growing range of plant species, which also determines cultivar adaptation to a region. The evaluation of climate influence on fruit production is critical for decision-making in the design stage of orchards and vineyards and in the evaluation of the potential consequences of future climate. Bio- climatic indices and plant phenology are commonly used to describe the suitability of climate for growing quality fruit and to provide temporal and spatial information about regarding ongoing and future changes. 'fruclimadapt' streamlines the assessment of climate adaptation and the identification of potential risks for grapevines and fruit trees. Procedures in the package allow to i) downscale daily meteorological variables to hourly values (Forster et al (2016) <doi:10.5194/gmd-9-2315-2016>), ii) estimate chilling and forcing heat accumulation (Miranda et al (2019) <https://ec.europa.eu/eip/agriculture/sites/default/files/fg30_mp5_phenology_critical_temperatures.pdf>), iii) estimate plant phenology (Schwartz (2012) <doi:10.1007/978-94-007-6925-0>), iv) calculate bioclimatic indices to evaluate fruit tree and grapevine adaptation (e.g. Badr et al (2017) <doi:10.3354/cr01532>), v) estimate the incidence of weather-related disorders in fruits (e.g. Snyder and de Melo-Abreu (2005, ISBN:92-5-105328-6) and vi) estimate plant water requirements (Allen et al (1998, ISBN:92-5-104219-5)).

Maintained by Carlos Miranda. Last updated 2 years ago.

chill-models chill-requirement climate-adaptation climate-analysis estimate fruit fruit-trees grapevine horticulture phenology

5.1 match 3 stars 3.18 score 4 scripts

r-forge

fuzzySim:Fuzzy Similarity in Species Distributions

Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially described in Barbosa (2015) <doi:10.1111/2041-210X.12372>.

Maintained by A. Marcia Barbosa. Last updated 21 days ago.

3.0 match 2 stars 5.35 score 156 scripts

ha-pu

globaltrends:Download and Measure Global Trends Through Google Search Volumes

Google offers public access to global search volumes from its search engine through the Google Trends portal. The package downloads these search volumes provided by Google Trends and uses them to measure and analyze the distribution of search scores across countries or within countries. The package allows researchers and analysts to use these search scores to investigate global trends based on patterns within these scores. This offers insights such as degree of internationalization of firms and organizations or dissemination of political, social, or technological trends across the globe or within single countries. An outline of the package's methodological foundations and potential applications is available as a working paper: <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3969013>.

Maintained by Harald Puhr. Last updated 2 years ago.

google-trends internationalization

3.2 match 18 stars 5.00 score 11 scripts

insightsengineering

rbmi:Reference Based Multiple Imputation

Implements standard and reference based multiple imputation methods for continuous longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular, this package supports deterministic conditional mean imputation and jackknifing as described in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.

Maintained by Isaac Gravestock. Last updated 24 days ago.

1.8 match 18 stars 8.78 score 33 scripts 1 dependents

cran

JGL:Performs the Joint Graphical Lasso for Sparse Inverse Covariance Estimation on Multiple Classes

The Joint Graphical Lasso is a generalized method for estimating Gaussian graphical models/ sparse inverse covariance matrices/ biological networks on multiple classes of data. We solve JGL under two penalty functions: The Fused Graphical Lasso (FGL), which employs a fused penalty to encourage inverse covariance matrices to be similar across classes, and the Group Graphical Lasso (GGL), which encourages similar network structure between classes. FGL is recommended over GGL for most applications. Reference: Danaher P, Wang P, Witten DM. (2013) <doi:10.1111/rssb.12033>.

Maintained by Patrick Danaher. Last updated 1 years ago.

5.9 match 1 stars 2.65 score 1 dependents