Showing 113 of total 113 results (show query)
bioc
velociraptor:Toolkit for Single-Cell Velocity
This package provides Bioconductor-friendly wrappers for RNA velocity calculations in single-cell RNA-seq data. We use the basilisk package to manage Conda environments, and the zellkonverter package to convert data structures between SingleCellExperiment (R) and AnnData (Python). The information produced by the velocity methods is stored in the various components of the SingleCellExperiment class.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
singlecellgeneexpressionsequencingcoveragerna-velocity
21.8 match 55 stars 8.06 score 52 scripts
carriedaymont
growthcleanr:Data Cleaner for Anthropometric Measurements
Identifies implausible anthropometric (e.g., height, weight) measurements in irregularly spaced longitudinal datasets, such as those from electronic health records.
Maintained by Carrie Daymont. Last updated 1 months ago.
18.5 match 14 stars 6.68 score 41 scripts 1 dependents
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 5 days ago.
7.1 match 146 stars 15.34 score 4.2k scripts 18 dependents
robinhankin
lorentz:The Lorentz Transform in Relativistic Physics
The Lorentz transform in special relativity; also the gyrogroup structure of three-velocities. Performs active and passive transforms and has the ability to use units in which the speed of light is not unity. Includes some experimental functionality for celerity and rapidity. For general relativity, see the 'schwarzschild' package.
Maintained by Robin K. S. Hankin. Last updated 2 months ago.
16.5 match 4 stars 5.26 score 15 scripts
thomasp85
particles:A Graph Based Particle Simulator Based on D3-Force
Simulating particle movement in 2D space has many application. The 'particles' package implements a particle simulator based on the ideas behind the 'd3-force' 'JavaScript' library. 'particles' implements all forces defined in 'd3-force' as well as others such as vector fields, traps, and attractors.
Maintained by Thomas Lin Pedersen. Last updated 4 months ago.
d3jsgraph-layoutnetworknetwork-visualizationparticlessimulationcpp
11.9 match 119 stars 7.19 score 43 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 20 days ago.
9.1 match 13 stars 8.90 score 58 scripts 3 dependents
gfellerlab
SuperCell:Simplification of scRNA-seq data by merging together similar cells
Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells.
Maintained by The package maintainer. Last updated 9 months ago.
softwarecoarse-grainingscrna-seq-analysisscrna-seq-data
8.6 match 72 stars 8.08 score 93 scripts
alanarnholt
BSDA:Basic Statistics and Data Analysis
Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.
Maintained by Alan T. Arnholt. Last updated 2 years ago.
7.0 match 7 stars 9.11 score 1.3k scripts 6 dependents
jonathanlees
RSEIS:Seismic Time Series Analysis Tools
Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Maintained by Jonathan M. Lees. Last updated 7 months ago.
14.1 match 3 stars 4.27 score 262 scripts 4 dependents
flujoo
gm:Create Music with Ease
Provides a simple and intuitive high-level language for music representation. Generates and embeds music scores and audio files in 'RStudio', 'R Markdown' documents, and R 'Jupyter Notebooks'. Internally, uses 'MusicXML' <https://github.com/w3c/musicxml> to represent music, and 'MuseScore' <https://musescore.org/> to convert 'MusicXML'.
Maintained by Renfei Mao. Last updated 9 months ago.
algorithmic-compositionmusic-programmingmusicxml
7.0 match 207 stars 8.06 score 35 scripts
mitchelloharawild
ggquiver:Quiver Plots for 'ggplot2'
An extension of 'ggplot2' to provide quiver plots to visualise vector fields. This functionality is implemented using a geom to produce a new graphical layer, which allows aesthetic options. This layer can be overlaid on a map to improve visualisation of mapped data.
Maintained by Mitchell OHara-Wild. Last updated 1 years ago.
10.0 match 52 stars 5.57 score 48 scripts 1 dependents
welch-lab
cytosignal:What the Package Does (One Line, Title Case)
What the package does (one paragraph).
Maintained by Jialin Liu. Last updated 11 hours ago.
8.7 match 17 stars 6.11 score 6 scripts
friendly
HistData:Data Sets from the History of Statistics and Data Visualization
The 'HistData' package provides a collection of small data sets that are interesting and important in the history of statistics and data visualization. The goal of the package is to make these available, both for instructional use and for historical research. Some of these present interesting challenges for graphics or analysis in R.
Maintained by Michael Friendly. Last updated 11 months ago.
5.6 match 63 stars 9.19 score 732 scripts 2 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-movementflydramotionmovement-dataoptitracktrajectoriestrajectory-analysisvisual-guidancevisual-perception
7.7 match 8 stars 6.56 score 102 scripts
jimmcl
trajr:Animal Trajectory Analysis
A toolbox to assist with statistical analysis of animal trajectories. It provides simple access to algorithms for calculating and assessing a variety of characteristics such as speed and acceleration, as well as multiple measures of straightness or tortuosity. Some support is provided for 3-dimensional trajectories. McLean & Skowron Volponi (2018) <doi:10.1111/eth.12739>.
Maintained by Jim McLean. Last updated 8 months ago.
6.5 match 27 stars 7.69 score 151 scripts
smac-group
gmwmx2:Estimate Functional and Stochastic Parameters of Linear Models with Correlated Residuals and Missing Data
Implements the Generalized Method of Wavelet Moments with Exogenous Inputs estimator (GMWMX) presented in Voirol, L., Xu, H., Zhang, Y., Insolia, L., Molinari, R. and Guerrier, S. (2024) <doi:10.48550/arXiv.2409.05160>. The GMWMX estimator allows to estimate functional and stochastic parameters of linear models with correlated residuals in presence of missing data. The 'gmwmx2' package provides functions to load and plot Global Navigation Satellite System (GNSS) data from the Nevada Geodetic Laboratory and functions to estimate linear model model with correlated residuals in presence of missing data.
Maintained by Lionel Voirol. Last updated 11 days ago.
8.5 match 2 stars 5.38 score
adokter
bioRad:Biological Analysis and Visualization of Weather Radar Data
Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.
Maintained by Adriaan M. Dokter. Last updated 4 hours ago.
aeroecologyenrameumetnet-operalifewatchmovement-ecologynexradoscibioradarweather-radarwsr-88d
5.2 match 29 stars 8.73 score 56 scripts
cran
MASS:Support Functions and Datasets for Venables and Ripley's MASS
Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).
Maintained by Brian Ripley. Last updated 1 months ago.
4.0 match 19 stars 10.64 score 11k dependents
spsanderson
healthyR.ts:The Time Series Modeling Companion to 'healthyR'
Hospital time series data analysis workflow tools, modeling, and automations. This library provides many useful tools to review common administrative time series hospital data. Some of these include average length of stay, and readmission rates. The aim is to provide a simple and consistent verb framework that takes the guesswork out of everything.
Maintained by Steven Sanderson. Last updated 6 months ago.
aiarima-forecastingarima-modeletsforecastingggplot2machine-learningmodelingprophettime-seriestime-series-analysisworkflows
5.5 match 19 stars 7.58 score 56 scripts 1 dependents
openintrostat
openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs
Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.
Maintained by Mine Çetinkaya-Rundel. Last updated 3 months ago.
3.5 match 240 stars 11.29 score 6.0k scriptsbioc
scMultiSim:Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions
scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments.
Maintained by Hechen Li. Last updated 5 months ago.
singlecelltranscriptomicsgeneexpressionsequencingexperimentaldesign
5.5 match 23 stars 7.08 score 11 scriptsbioc
veloviz:VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories.
Maintained by Lyla Atta. Last updated 5 months ago.
transcriptomicsvisualizationgeneexpressionsequencingrnaseqdimensionreductioncpp
9.0 match 4.00 score 6 scriptsbioc
BUSpaRse:kallisto | bustools R utilities
The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.
Maintained by Lambda Moses. Last updated 5 months ago.
singlecellrnaseqworkflowstepcpp
5.9 match 9 stars 5.87 score 165 scripts
shirintaheri
climetrics:Climate Change Metrics
A framework that facilitates spatio-temporal analysis of climate dynamics through exploring and measuring different dimensions of climate change in space and time.
Maintained by Shirin Taheri. Last updated 12 months ago.
8.6 match 15 stars 3.88 score 9 scripts
jdtuck
fdasrvf:Elastic Functional Data Analysis
Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <doi:10.48550/arXiv.1103.3817> and Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.
Maintained by J. Derek Tucker. Last updated 1 months ago.
4.3 match 13 stars 7.79 score 83 scripts 3 dependentsjonathanlees
Rquake:Seismic Hypocenter Determination
Non-linear inversion for hypocenter estimation and analysis of seismic data collected continuously, or in trigger mode. The functions organize other functions from 'RSEIS' and 'GEOmap' to help researchers pick, locate, and store hypocenters for detailed seismic investigation. Error ellipsoids and station influence are estimated via jackknife analysis. References include Iversen, E. S., and J. M. Lees (1996)<doi:10.1785/BSSA0860061853>.
Maintained by Jonathan M. Lees. Last updated 1 years ago.
18.0 match 1.76 score 57 scripts
gleon
LakeMetabolizer:Tools for the Analysis of Ecosystem Metabolism
A collection of tools for the calculation of freewater metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models).
Maintained by Jake Zwart. Last updated 2 years ago.
5.3 match 18 stars 5.94 score 122 scripts
alexander-pastukhov
saccadr:Extract Saccades via an Ensemble of Methods Approach
A modular and extendable approach to extract (micro)saccades from gaze samples via an ensemble of methods. Although there is an agreement about a general definition of a saccade, the more specific details are harder to agree upon. Therefore, there are numerous algorithms that extract saccades based on various heuristics, which differ in the assumptions about velocity, acceleration, etc. The package uses three methods (Engbert and Kliegl (2003) <doi:10.1016/S0042-6989(03)00084-1>, Otero-Millan et al. (2014)<doi:10.1167/14.2.18>, and Nyström and Holmqvist (2010) <doi:10.3758/BRM.42.1.188>) to label individual samples and then applies a majority vote approach to identify saccades. The package includes three methods but can be extended via custom functions. It also uses a modular approach to compute velocity and acceleration from noisy samples. Finally, you can obtain methods votes per gaze sample instead of saccades.
Maintained by Alexander Pastukhov. Last updated 2 years ago.
6.2 match 4 stars 4.90 score 8 scripts
dynverse
dynwrap:Representing and Inferring Single-Cell Trajectories
Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Maintained by Robrecht Cannoodt. Last updated 2 years ago.
4.0 match 16 stars 7.48 score 159 scripts 1 dependents
haoranpopevo
ecode:Ordinary Differential Equation Systems in Ecology
A framework to simulate ecosystem dynamics through ordinary differential equations (ODEs). You create an ODE model, tells 'ecode' to explore its behaviour, and perform numerical simulations on the model. 'ecode' also allows you to fit model parameters by machine learning algorithms. Potential users include researchers who are interested in the dynamics of ecological community and biogeochemical cycles.
Maintained by Haoran Wu. Last updated 8 months ago.
7.6 match 7 stars 3.85 score 3 scripts
marinapapa
swaRmverse:Swarm Space Creation
Provides a pipeline for the comparative analysis of collective movement data (e.g. fish schools, bird flocks, baboon troops) by processing 2-dimensional positional data (x,y,t) from GPS trackers or computer vision tracking systems, discretizing events of collective motion, calculating a set of established metrics that characterize each event, and placing the events in a multi-dimensional swarm space constructed from these metrics. The swarm space concept, the metrics and data sets included are described in: Papadopoulou Marina, Furtbauer Ines, O'Bryan Lisa R., Garnier Simon, Georgopoulou Dimitra G., Bracken Anna M., Christensen Charlotte and King Andrew J. (2023) <doi:10.1098/rstb.2022.0068>.
Maintained by Marina Papadopoulou. Last updated 6 months ago.
5.0 match 2 stars 5.13 score 15 scripts
drizopoulos
JMbayes2:Extended Joint Models for Longitudinal and Time-to-Event Data
Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Maintained by Dimitris Rizopoulos. Last updated 27 days ago.
competing-riskslongitudinal-analysismixed-modelsmulti-statepersonalized-medicineprecision-medicineprediction-modelsurvival-modelsopenblascppopenmp
3.0 match 84 stars 8.27 score 264 scripts 2 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.
2.0 match 29 stars 12.34 score 6.6k scripts 931 dependents
welch-lab
CytoSimplex:Simplex Visualization of Cell Fate Similarity in Single-Cell Data
Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) <doi:10.1101/2023.12.07.570655> for more details.
Maintained by Yichen Wang. Last updated 11 hours ago.
5.1 match 4 stars 4.78 score 3 scripts
mladenjovanovic
shorts:Short Sprints
Create short sprint acceleration-velocity (AVP) and force-velocity (FVP) profiles and predict kinematic and kinetic variables using the timing-gate split times, laser or radar gun data, tether devices data, as well as the data provided by the GPS and LPS monitoring systems. The modeling method utilized in this package is based on the works of Furusawa K, Hill AV, Parkinson JL (1927) <doi: 10.1098/rspb.1927.0035>, Greene PR. (1986) <doi: 10.1016/0025-5564(86)90063-5>, Chelly SM, Denis C. (2001) <doi: 10.1097/00005768-200102000-00024>, Clark KP, Rieger RH, Bruno RF, Stearne DJ. (2017) <doi: 10.1519/JSC.0000000000002081>, Samozino P. (2018) <doi: 10.1007/978-3-319-05633-3_11>, Samozino P. and Peyrot N., et al (2022) <doi: 10.1111/sms.14097>, Clavel, P., et al (2023) <doi: 10.1016/j.jbiomech.2023.111602>, Jovanovic M. (2023) <doi: 10.1080/10255842.2023.2170713>, Jovanovic M., et al (2024) <doi: 10.3390/s24092894>, and Jovanovic M., et al (2024) <doi: 10.3390/s24196192>.
Maintained by Mladen Jovanović. Last updated 5 months ago.
5.4 match 14 stars 4.45 score 4 scripts
paocorrales
rvad:Velocity Azimuth Display of Meteorological Radars
This package implement an algorithm to process radial wind from Doppler radars obtainning the proper horizontal wind. The implementation is based on Browning and Wexler (1968) <doi: 10.1175/1520-0450(1968)007%3C0105:TDOKPO%3E2.0.CO;2> with the addition of several quality controls.
Maintained by Paola Corrales. Last updated 5 years ago.
8.8 match 4 stars 2.53 score 17 scripts
albandelavenne
transfR:Transfer of Hydrograph from Gauged to Ungauged Catchments
A geomorphology-based hydrological modelling for transferring streamflow measurements from gauged to ungauged catchments. Inverse modelling enables to estimate net rainfall from streamflow measurements following Boudhraâ et al. (2018) <doi:10.1080/02626667.2018.1425801>. Resulting net rainfall is then estimated on the ungauged catchments by spatial interpolation in order to finally simulate streamflow following de Lavenne et al. (2016) <doi:10.1002/2016WR018716>.
Maintained by Alban de Lavenne. Last updated 12 days ago.
6.3 match 3.48 score 6 scripts
lightbluetitan
MedDataSets:Comprehensive Medical, Disease, Treatment, and Drug Datasets
Provides an extensive collection of datasets related to medicine, diseases, treatments, drugs, and public health. This package covers topics such as drug effectiveness, vaccine trials, survival rates, infectious disease outbreaks, and medical treatments. The included datasets span various health conditions, including AIDS, cancer, bacterial infections, and COVID-19, along with information on pharmaceuticals and vaccines. These datasets are sourced from the R ecosystem and other R packages, remaining unaltered to ensure data integrity. This package serves as a valuable resource for researchers, analysts, and healthcare professionals interested in conducting medical and public health data analysis in R.
Maintained by Renzo Caceres Rossi. Last updated 5 months ago.
3.8 match 8 stars 5.68 score 60 scripts
jose-ameijeiras
multimode:Mode Testing and Exploring
Different examples and methods for testing (including different proposals described in Ameijeiras-Alonso et al., 2019 <DOI:10.1007/s11749-018-0611-5>) and exploring (including the mode tree, mode forest and SiZer) the number of modes using nonparametric techniques <DOI:10.18637/jss.v097.i09>.
Maintained by Jose Ameijeiras-Alonso. Last updated 4 years ago.
7.2 match 1 stars 2.85 score 76 scripts 2 dependents
josie-athens
pubh:A Toolbox for Public Health and Epidemiology
A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand 'ggplot2' plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.
Maintained by Josie Athens. Last updated 6 months ago.
3.5 match 5 stars 5.73 score 72 scripts
stefanocoretta
rticulate:Articulatory Data Processing in R
A tool for processing Articulate Assistant Advanced™ (AAA) ultrasound tongue imaging data and Carstens AG500/1 electro-magnetic articulographic data.
Maintained by Stefano Coretta. Last updated 1 months ago.
phoneticssoftwaretongue-imageultrasoundultrasound-tongue-imaging
3.3 match 5 stars 5.88 score 17 scriptsbioc
cellmigRation:Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.
Maintained by Waldir Leoncio. Last updated 5 months ago.
cellbiologydatarepresentationdataimportbioconductor-packagecell-trackingshinytrajectory-analysis
4.3 match 4.60 score 4 scripts
tombeesley
eyetools:Analyse Eye Data
Enables the automation of actions across the pipeline, including initial steps of transforming binocular data and gap repair to event-based processing such as fixations, saccades, and entry/duration in Areas of Interest (AOIs). It also offers visualisation of eye movement and AOI entries. These tools take relatively raw (trial, time, x, and y form) data and can be used to return fixations, saccades, and AOI entries and time spent in AOIs. As the tools rely on this basic data format, the functions can work with data from any eye tracking device. Implements fixation and saccade detection using methods proposed by Salvucci and Goldberg (2000) <doi:10.1145/355017.355028>.
Maintained by Tom Beesley. Last updated 3 months ago.
areas-of-interestattention-visualizationcognitive-sciencedwell-time-algorithmeye-trackereye-trackingeyetrackingggplot2psychologypsychology-experimentssaccadestobiitobii-eye-trackervisualization
3.6 match 4 stars 5.45 score 8 scripts
trafficonese
leaflet.extras2:Extra Functionality for 'leaflet' Package
Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Maintained by Gatscha Sebastian. Last updated 27 days ago.
data-visualizationgeospatialgeospatial-visualizationleafletleaflet-plugins
2.0 match 87 stars 9.70 score 432 scripts 1 dependents
garciadejalon
TreeDep:Air Pollution Removal by Dry Deposition on Trees
The model estimates air pollution removal by dry deposition on trees. It also estimates or uses hourly values for aerodynamic resistance, boundary layer resistance, canopy resistance, stomatal resistance, cuticular resistance, mesophyll resistance, soil resistance, friction velocity and deposition velocity. It also allows plotting graphical results for a specific time period. The pollutants are nitrogen dioxide, ozone, sulphur dioxide, carbon monoxide and particulate matter. Baldocchi D (1994) <doi:10.1093/treephys/14.7-8-9.1069>. Farquhar GD, von Caemmerer S, Berry JA (1980) Planta 149: 78-90. Hirabayashi S, Kroll CN, Nowak DJ (2015) i-Tree Eco Dry Deposition Model. Nowak DJ, Crane DE, Stevens JC (2006) <doi:10.1016/j.ufug.2006.01.007>. US EPA (1999) PCRAMMET User's Guide. EPA-454/B-96-001. Weiss A, Norman JM (1985) Agricultural and Forest Meteorology 34: 205—213.
Maintained by Silvestre Garcia de Jalon. Last updated 6 years ago.
11.3 match 1.69 score 49 scripts
goodsman
ICvectorfields:Vector Fields from Spatial Time Series of Population Abundance
Functions for converting time series of spatial abundance or density data in raster format to vector fields of population movement using the digital image correlation technique. More specifically, the functions in the package compute cross-covariance using discrete fast Fourier transforms for computational efficiency. Vectors in vector fields point in the direction of highest two dimensional cross-covariance. The package has a novel implementation of the digital image correlation algorithm that is designed to detect persistent directional movement when image time series extend beyond a sequence of two raster images.
Maintained by Devin Goodsman. Last updated 3 years ago.
5.1 match 1 stars 3.70 score 9 scripts
kharchenkolab
conos:Clustering on Network of Samples
Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Maintained by Evan Biederstedt. Last updated 1 years ago.
batch-correctionscrna-seqsingle-cell-rna-seqopenblascppopenmp
2.5 match 205 stars 7.33 score 258 scripts
antonio-pgarcia
evoper:Evolutionary Parameter Estimation for 'Repast Simphony' Models
The EvoPER, Evolutionary Parameter Estimation for Individual-based Models is an extensible package providing optimization driven parameter estimation methods using metaheuristics and evolutionary computation techniques (Particle Swarm Optimization, Simulated Annealing, Ant Colony Optimization for continuous domains, Tabu Search, Evolutionary Strategies, ...) which could be more efficient and require, in some cases, fewer model evaluations than alternatives relying on experimental design. Currently there are built in support for models developed with 'Repast Simphony' Agent-Based framework (<https://repast.github.io/>) and with NetLogo (<https://ccl.northwestern.edu/netlogo/>) which are the most used frameworks for Agent-based modeling.
Maintained by Antonio Prestes Garcia. Last updated 5 years ago.
4.5 match 6 stars 3.92 score 28 scripts
cneyens
raem:Analytic Element Modeling of Steady Single-Layer Groundwater Flow
A model of single-layer groundwater flow in steady-state under the Dupuit-Forchheimer assumption can be created by placing elements such as wells, area-sinks and line-sinks at arbitrary locations in the flow field. Output variables include hydraulic head and the discharge vector. Particle traces can be computed numerically in three dimensions. The underlying theory is described in Haitjema (1995) <doi:10.1016/B978-0-12-316550-3.X5000-4> and references therein.
Maintained by Cas Neyens. Last updated 7 months ago.
analytic-element-modelgroundwatergroundwater-modellinghydrogeologyhydrology
3.0 match 8 stars 5.68 score 6 scriptsgleon
rLakeAnalyzer:Lake Physics Tools
Standardized methods for calculating common important derived physical features of lakes including water density based based on temperature, thermal layers, thermocline depth, lake number, Wedderburn number, Schmidt stability and others.
Maintained by Luke Winslow. Last updated 4 years ago.
1.8 match 45 stars 9.05 score 280 scripts 1 dependents
rudjer
REBayes:Empirical Bayes Estimation and Inference
Kiefer-Wolfowitz maximum likelihood estimation for mixture models and some other density estimation and regression methods based on convex optimization. See Koenker and Gu (2017) REBayes: An R Package for Empirical Bayes Mixture Methods, Journal of Statistical Software, 82, 1--26, <DOI:10.18637/jss.v082.i08>.
Maintained by Roger Koenker. Last updated 9 months ago.
4.0 match 3 stars 3.89 score 27 scripts 1 dependents
karlines
OceanView:Visualisation of Oceanographic Data and Model Output
Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
Maintained by Karline Soetaert. Last updated 1 years ago.
3.8 match 4.08 score 60 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 7 days ago.
geologystructural-geologytectonics
2.0 match 7 stars 7.27 score 33 scripts
pdalgd
ISwR:Introductory Statistics with R
Data sets and scripts for text examples and exercises in P. Dalgaard (2008), `Introductory Statistics with R', 2nd ed., Springer Verlag, ISBN 978-0387790534.
Maintained by Peter Dalgaard. Last updated 9 days ago.
4.0 match 3.63 score 300 scripts
richardgeveritt
ggsmc:Visualising Output from Sequential Monte Carlo and Ensemble-Based Methods
Functions for plotting, and animating, the output of importance samplers, sequential Monte Carlo samplers (SMC) and ensemble-based methods. The package can be used to plot and animate histograms, densities, scatter plots and time series, and to plot the genealogy of an SMC or ensemble-based algorithm. These functions all rely on algorithm output to be supplied in tidy format. A function is provided to transform algorithm output from matrix format (one Monte Carlo point per row) to the tidy format required by the plotting and animating functions.
Maintained by Richard G Everitt. Last updated 2 months ago.
3.2 match 4.48 score 6 scripts
samhforbes
PupillometryR:A Unified Pipeline for Pupillometry Data
Provides a unified pipeline to clean, prepare, plot, and run basic analyses on pupillometry experiments.
Maintained by Samuel Forbes. Last updated 2 years ago.
1.9 match 44 stars 7.58 score 288 scripts 1 dependents
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 1 months ago.
bias-correctionbiogeographyecological-niche-modelingecological-niche-modellingniche-modelingniche-modellingspecies-distribution-modelingopenjdk
2.3 match 25 stars 5.57 score 37 scripts
pascalkieslich
mousetrap:Process and Analyze Mouse-Tracking Data
Mouse-tracking, the analysis of mouse movements in computerized experiments, is a method that is becoming increasingly popular in the cognitive sciences. The mousetrap package offers functions for importing, preprocessing, analyzing, aggregating, and visualizing mouse-tracking data. An introduction into mouse-tracking analyses using mousetrap can be found in Wulff, Kieslich, Henninger, Haslbeck, & Schulte-Mecklenbeck (2023) <doi:10.31234/osf.io/v685r> (preprint: <https://osf.io/preprints/psyarxiv/v685r>).
Maintained by Pascal J. Kieslich. Last updated 1 years ago.
analysisclusteringmouse-trackingvisualizationcpp
1.9 match 46 stars 6.66 score 124 scripts
deepankardatta
blandr:Bland-Altman Method Comparison
Carries out Bland Altman analyses (also known as a Tukey mean-difference plot) as described by JM Bland and DG Altman in 1986 <doi:10.1016/S0140-6736(86)90837-8>. This package was created in 2015 as existing Bland-Altman analysis functions did not calculate confidence intervals. This package was created to rectify this, and create reproducible plots. This package is also available as a module for the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more information).
Maintained by Deepankar Datta. Last updated 10 months ago.
bland-altmanggplot2method-comparisonstatistics
1.7 match 22 stars 7.22 score 75 scripts
dsjohnson
crawl:Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data
Fit continuous-time correlated random walk models with time indexed covariates to animal telemetry data. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.
Maintained by Devin S. Johnson. Last updated 6 months ago.
1.6 match 19 stars 6.29 score 63 scripts 3 dependents
thiagomini
WeibullFit:Fits and Plots a Dataset to the Weibull Probability Distribution Function
Provides a single function to fit data of an input data frame into one of the selected Weibull functions (w2, w3 and it's truncated versions), calculating the scale, location and shape parameters accordingly. The resulting plots and files are saved into the 'folder' parameter provided by the user. References: a) John C. Nash, Ravi Varadhan (2011). "Unifying Optimization Algorithms to Aid Software System Users: optimx for R" <doi:10.18637/jss.v043.i09>.
Maintained by Thiago Martins. Last updated 6 years ago.
3.8 match 2.70 score
mjg211
phaseR:Phase Plane Analysis of One- And Two-Dimensional Autonomous ODE Systems
Performs a qualitative analysis of one- and two-dimensional autonomous ordinary differential equation systems, using phase plane methods. Programs are available to identify and classify equilibrium points, plot the direction field, and plot trajectories for multiple initial conditions. In the one-dimensional case, a program is also available to plot the phase portrait. Whilst in the two-dimensional case, programs are additionally available to plot nullclines and stable/unstable manifolds of saddle points. Many example systems are provided for the user. For further details can be found in Grayling (2014) <doi:10.32614/RJ-2014-023>.
Maintained by Michael J Grayling. Last updated 3 years ago.
biological-modelingdifferential-equationsdynamical-systemsecological-modellinglotka-volterramanifoldsmodeling-dynamic-systemsmorris-lecarperturbation-analysisphase-planesir-modelspecies-interactionsvan-der-pol
1.5 match 15 stars 6.63 score 94 scripts 1 dependents
themisefth
duet:Analysing Non-Verbal Communication in Dyadic Interactions from Video Data
Analyzes non-verbal communication by processing data extracted from video recordings of dyadic interactions. It supports integration with open source tools, currently limited to 'OpenPose' (Cao et al. (2019) <doi:10.1109/TPAMI.2019.2929257>), converting its outputs into CSV format for further analysis. The package includes functions for data pre-processing, visualization, and computation of motion indices such as velocity, acceleration, and jerkiness (Cook et al. (2013) <doi:10.1093/brain/awt208>), facilitating the analysis of non-verbal cues in paired interactions and contributing to research on human communication dynamics.
Maintained by Themis Efthimiou. Last updated 1 months ago.
2.8 match 3.40 score
niccologalatioto
hydReng:Hydraulic Engineering Tools
The 'hydReng' package provides a set of functions for hydraulic engineering tasks and natural hazard assessments. It includes basic hydraulics (wetted area, wetted perimeter, flow, flow velocity, flow depth, and maximum flow) for open channels with arbitrary geometry under uniform flow conditions. For structures such as circular pipes, weirs, and gates, the package includes calculations for pressure flow, backwater depth, and overflow over a weir crest. Additionally, it provides formulas for calculating bedload transport. The formulas used can be found in standard literature on hydraulics, such as Bollrich (2019, ISBN:978-3-410-29169-5) or Hager (2011, ISBN:978-3-642-77430-0).
Maintained by Galatioto Niccolo. Last updated 2 months ago.
2.8 match 3.40 scorecran
radar:Fundamental Formulas for Radar
Fundamental formulas for Radar, for attenuation, range, velocity, effectiveness, power, scatter, doppler, geometry, radar equations, etc. Based on Nick Guy's Python package PyRadarMet
Maintained by Jose Gama. Last updated 10 years ago.
9.3 match 1 stars 1.00 score
parkerholzer
rvmethod:Radial Velocity Method for Detecting Exoplanets
Has various functions designed to implement the Hermite-Gaussian Radial Velocity (HGRV) estimation approach of Holzer et al. (2020) <arXiv:2005.14083>, which is a particular application of the radial velocity method for detecting exoplanets. The overall approach consists of four sequential steps, each of which has a function in this package: (1) estimate the template spectrum with the function estimate_template(), (2) find absorption features in the estimated template with the function findabsorptionfeatures(), (3) fit Gaussians to the absorption features with the function Gaussfit(), (4) apply the HGRV with simple linear regression by calling the function hgrv(). This package is meant to be open source. But please cite the paper Holzer et al. (2020) <arXiv:2005.14083> when publishing results that use this package.
Maintained by Parker Holzer. Last updated 5 years ago.
5.5 match 1 stars 1.70 score 8 scriptskarlines
marelac:Tools for Aquatic Sciences
Datasets, constants, conversion factors, and utilities for 'MArine', 'Riverine', 'Estuarine', 'LAcustrine' and 'Coastal' science. The package contains among others: (1) chemical and physical constants and datasets, e.g. atomic weights, gas constants, the earths bathymetry; (2) conversion factors (e.g. gram to mol to liter, barometric units, temperature, salinity); (3) physical functions, e.g. to estimate concentrations of conservative substances, gas transfer and diffusion coefficients, the Coriolis force and gravity; (4) thermophysical properties of the seawater, as from the UNESCO polynomial or from the more recent derivation based on a Gibbs function.
Maintained by Karline Soetaert. Last updated 2 years ago.
2.0 match 4.63 score 119 scripts 4 dependents
cran
Rlab:Functions and Datasets Required for ST370 Class
Provides functions and datasets required for the ST 370 course at North Carolina State University.
Maintained by Dennis Boos. Last updated 3 years ago.
3.5 match 2.38 score 8 dependents
coffeemuggler
eseis:Environmental Seismology Toolbox
Environmental seismology is a scientific field that studies the seismic signals, emitted by Earth surface processes. This package provides all relevant functions to read/write seismic data files, prepare, analyse and visualise seismic data, and generate reports of the processing history.
Maintained by Michael Dietze. Last updated 7 days ago.
1.7 match 9 stars 4.72 score 58 scripts
bogdanpotanin
gena:Genetic Algorithm and Particle Swarm Optimization
Implements genetic algorithm and particle swarm algorithm for real-valued functions. Various modifications (including hybridization and elitism) of these algorithms are provided. Implemented functions are based on ideas described in S. Katoch, S. Chauhan, V. Kumar (2020) <doi:10.1007/s11042-020-10139-6> and M. Clerc (2012) <https://hal.archives-ouvertes.fr/hal-00764996>.
Maintained by Bogdan Potanin. Last updated 3 years ago.
5.3 match 1.48 score 1 dependents
schw4b
emov:Eye Movement Analysis Package for Fixation and Saccade Detection
Fixation and saccade detection in eye movement recordings. This package implements a dispersion-based algorithm (I-DT) proposed by Salvucci & Goldberg (2000) which detects fixation duration and position.
Maintained by Simon Schwab. Last updated 9 years ago.
2.0 match 14 stars 3.85 score 4 scripts
mc-schaaf
mousetRajectory:Mouse Trajectory Analyses for Behavioural Scientists
Helping psychologists and other behavioural scientists to analyze mouse movement (and other 2-D trajectory) data. Bundles together several functions that compute spatial measures (e.g., maximum absolute deviation, area under the curve, sample entropy) or provide a shorthand for procedures that are frequently used (e.g., time normalization, linear interpolation, extracting initiation and movement times). For more informationsee Pfister et al. (2024) <doi:10.20982/tqmp.20.3.p217>.
Maintained by Roland Pfister. Last updated 7 months ago.
1.9 match 2 stars 4.00 score 5 scriptscran
growthrate:Bayesian reconstruction of growth velocity
A nonparametric empirical Bayes method for recovering gradients (or growth velocities) from observations of smooth functions (e.g., growth curves) at isolated time points.
Maintained by Ian W. McKeague. Last updated 11 years ago.
7.5 match 1.00 scorekarlines
ReacTran:Reactive Transport Modelling in 1d, 2d and 3d
Routines for developing models that describe reaction and advective-diffusive transport in one, two or three dimensions. Includes transport routines in porous media, in estuaries, and in bodies with variable shape.
Maintained by Karline Soetaert. Last updated 8 years ago.
1.6 match 6 stars 4.57 score 52 scriptscran
airGR:Suite of GR Hydrological Models for Precipitation-Runoff Modelling
Hydrological modelling tools developed at INRAE-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR5H, GR4J, GR5J, GR6J, GR2M, GR1A) that can be applied either on a lumped or semi-distributed way. A snow accumulation and melt model (CemaNeige) and the associated functions for the calibration and evaluation of models are also included. Use help(airGR) for package description and references.
Maintained by Olivier Delaigue. Last updated 1 years ago.
1.3 match 4 stars 5.39 score 4 dependents
kjetil1001
SenSrivastava:Datasets from Sen & Srivastava
Collection of datasets from Sen & Srivastava: "Regression Analysis, Theory, Methods and Applications", Springer. Sources for individual data files are more fully documented in the book.
Maintained by Kjetil B Halvorsen. Last updated 1 years ago.
4.0 match 1.76 score 57 scripts
chicozo1989
ThermIndex:Calculate Thermal Indexes
Calculates several thermal comfort indexes using temperature, wind speed and relative humidity values, calculating indexes such as Humidex, windchill, Discomfort Index and others.
Maintained by Francisco Jablinski Castelhano. Last updated 8 years ago.
7.0 match 1.00 score 10 scripts
jgarriga65
EMbC:Expectation-Maximization Binary Clustering
Unsupervised, multivariate, binary clustering for meaningful annotation of data, taking into account the uncertainty in the data. A specific constructor for trajectory analysis in movement ecology yields behavioural annotation of trajectories based on estimated local measures of velocity and turning angle, eventually with solar position covariate as a daytime indicator, ("Expectation-Maximization Binary Clustering for Behavioural Annotation").
Maintained by Joan Garriga. Last updated 1 years ago.
1.8 match 3.63 score 43 scripts
fawda123
WtRegDO:Implement Weighted Regression on Dissolved Oxygen Time Series
A sample dataset and functions to implement weighted regression on dissolved oxygen time series are included as a simple example to reduce the effects of tidal advection. Functions are also available to estimate net ecosystem metabolism using the open-water method.
Maintained by Marcus W. Beck. Last updated 10 months ago.
detidingmetabolismweighted-regression
1.8 match 5 stars 3.50 score 42 scriptscran
SMPracticals:Practicals for Use with Davison (2003) Statistical Models
Contains the datasets and a few functions for use with the practicals outlined in Appendix A of the book Statistical Models (Davison, 2003, Cambridge University Press), which can be found at <doi:10.1017/CBO9780511815850>.
Maintained by Alessandra R. Brazzale. Last updated 1 years ago.
4.0 match 1.48 score 1 dependents
vinhdizzo
IRexamples:Collection of Practical Institutional Research Examples and Tutorials
Provides examples of code for analyzing data or accomplishing tasks that may be useful to institutional or educational researchers.
Maintained by Vinh Nguyen. Last updated 2 years ago.
1.1 match 4 stars 5.00 score 4 scripts
josemaga
stabilo:Stabilometric Signal Quantification
Functions for stabilometric signal quantification. The input is a data frame containing the x, y coordinates of the center-of-pressure displacement. Jose Magalhaes de Oliveira (2017) <doi:10.3758/s13428-016-0706-4> "Statokinesigram normalization method"; T E Prieto, J B Myklebust, R G Hoffmann, E G Lovett, B M Myklebust (1996) <doi:10.1109/10.532130> "Measures of postural steadiness: Differences between healthy young and elderly adults"; L F Oliveira et al (1996) <doi:10.1088/0967-3334/17/4/008> "Calculation of area of stabilometric signals using principal component analisys".
Maintained by Jose Oliveira. Last updated 2 years ago.
5.3 match 1.00 score
tuomaseerola
movementsync:Analysis and Visualisation of Musical Audio and Video Movement Synchrony Data
Analysis and visualisation of synchrony, interaction, and joint movements from audio and video movement data of a group of music performers. The demo is data described in Clayton, Leante, and Tarsitani (2021) <doi:10.17605/OSF.IO/KS325>, while example analyses can be found in Clayton, Jakubowski, and Eerola (2019) <doi:10.1177/1029864919844809>. Additionally, wavelet analysis techniques have been applied to examine movement-related musical interactions, as shown in Eerola et al. (2018) <doi:10.1098/rsos.171520>.
Maintained by Tuomas Eerola. Last updated 1 years ago.
1.9 match 1 stars 2.85 score 14 scripts
lmjl-alea
squat:Statistics for Quaternion Temporal Data
An implementation of statistical tools for the analysis of rotation-valued time series and functional data. It relies on pre-existing quaternion data structure provided by the 'Eigen' 'C++' library.
Maintained by Aymeric Stamm. Last updated 1 years ago.
1.8 match 2 stars 3.00 score 6 scriptscran
pMEM:Predictive Moran's Eigenvector Maps
Calculation of Predictive Moran's eigenvector maps (pMEM), as defined by Guénard and Legendre (In Press) "Spatially-explicit predictions using spatial eigenvector maps" <doi:10.5281/zenodo.13356457>. Methods in Ecology and Evolution. This method enables scientists to predict the values of spatially-structured environmental variables. Multiple types of pMEM are defined, each one implemented on the basis of spatial weighting function taking a range parameter, and sometimes also a shape parameter. The code's modular nature enables programers to implement new pMEM by defining new spatial weighting functions.
Maintained by Guillaume Guénard. Last updated 6 months ago.
2.6 match 2.00 scorecran
TrendSLR:Estimating Trend, Velocity and Acceleration from Sea Level Records
Analysis of annual average ocean water level time series, providing improved estimates of trend (mean sea level) and associated real-time velocities and accelerations. Improved trend estimates are based on singular spectrum analysis methods. Various gap-filling options are included to accommodate incomplete time series records. The package also includes a range of diagnostic tools to inspect the components comprising the original time series which enables expert interpretation and selection of likely trend components. A wide range of screen and plot to file options are available in the package.
Maintained by Phil J Watson. Last updated 6 years ago.
5.0 match 1.00 score
drjohanlk
kollaR:Filtering, Visualization and Analysis of Eye Tracking Data
Functions for analysing eye tracking data, including event detection (I-VT, I-DT and two means clustering), visualizations and area of interest (AOI) based analyses. See separate documentation for each function. The principles underlying I-VT and I-DT filters are described in Salvucci & Goldberg (2000,\doi{10.1145/355017.355028}). Two-means clustering is described in Hessels et al. (2017, \doi{10.3758/s13428-016-0822-1}).
Maintained by Johan Lundin Kleberg. Last updated 1 months ago.
3.5 match 1.30 score
ek-lee
EMSaov:The Analysis of Variance with EMS
Provides the analysis of variance table including the expected mean squares (EMS) for various types of experimental design. When some variables are random effects or we use special experimental design such as nested design, repeated-measures design, or split-plot design, it is not easy to find the appropriate test, especially denominator for F-statistic which depends on EMS.
Maintained by Eun-Kyung Lee. Last updated 7 years ago.
3.6 match 1 stars 1.26 score 18 scriptscran
astrodatR:Astronomical Data
A collection of 19 datasets from contemporary astronomical research. They are described the textbook `Modern Statistical Methods for Astronomy with R Applications' by Eric D. Feigelson and G. Jogesh Babu (Cambridge University Press, 2012, Appendix C) or on the website of Penn State's Center for Astrostatistics (http://astrostatistics.psu.edu/datasets). These datasets can be used to exercise methodology involving: density estimation; heteroscedastic measurement errors; contingency tables; two-sample hypothesis tests; spatial point processes; nonlinear regression; mixture models; censoring and truncation; multivariate analysis; classification and clustering; inhomogeneous Poisson processes; periodic and stochastic time series analysis.
Maintained by "Eric D., Feigelson". Last updated 11 years ago.
4.0 match 1 stars 1.00 score
laerciojuniosilva
SeedCalc:Seed Germination and Seedling Growth Indexes
Functions to calculate seed germination and seedling emergence and growth indexes. The main indexes for germination and seedling emergence, considering the time for seed germinate are: T10, T50 and T90, in Farooq et al. (2005) <10.1111/j.1744-7909.2005.00031.x>; and MGT, in Labouriau (1983). Considering the germination speed are: Germination Speed Index, in Maguire (1962), Mean Germination Rate, in Labouriau (1983); considering the homogeneity of germination are: Coefficient of Variation of the Germination Time, in Carvalho et al. (2005) <10.1590/S0100-84042005000300018>, and Variance of Germination, in Labouriau (1983); Uncertainty, in Labouriau and Valadares (1976) <ISSN:0001-3765>; and Synchrony, in Primack (1980). The main seedling indexes are Growth, in Sako (2001), Uniformity, in Sako (2001) and Castan et al. (2018) <doi:10.1590/1678-992x-2016-0401>; and Vigour, in Medeiros and Pereira (2018) <doi:10.1590/1983-40632018v4852340>.
Maintained by Laercio Junio da Silva. Last updated 6 years ago.
2.0 match 1.68 score 24 scripts
vtrevino
valorate:Velocity and Accuracy of the LOg-RAnk TEst
The algorithm implemented in this package was designed to quickly estimates the distribution of the log-rank especially for heavy unbalanced groups. VALORATE estimates the null distribution and the p-value of the log-rank test based on a recent formulation. For a given number of alterations that define the size of survival groups, the estimation involves a weighted sum of distributions that are conditional on a co-occurrence term where mutations and events are both present. The estimation of conditional distributions is quite fast allowing the analysis of large datasets in few minutes <https://bioinformatics.mx/index.php/bioinfo-tools/>.
Maintained by Victor Trevino. Last updated 5 days ago.
3.0 match 1.00 score 9 scripts
darkeyes
VLTimeCausality:Variable-Lag Time Series Causality Inference Framework
A framework to infer causality on a pair of time series of real numbers based on variable-lag Granger causality and transfer entropy. Typically, Granger causality and transfer entropy have an assumption of a fixed and constant time delay between the cause and effect. However, for a non-stationary time series, this assumption is not true. For example, considering two time series of velocity of person A and person B where B follows A. At some time, B stops tying his shoes, then running to catch up A. The fixed-lag assumption is not true in this case. We propose a framework that allows variable-lags between cause and effect in Granger causality and transfer entropy to allow them to deal with variable-lag non-stationary time series. Please see Chainarong Amornbunchornvej, Elena Zheleva, and Tanya Berger-Wolf (2021) <doi:10.1145/3441452> when referring to this package in publications.
Maintained by Chainarong Amornbunchornvej. Last updated 10 months ago.
causal-inferencegranger-causalitytime-seriestime-series-analysistransfer-entropy
0.5 match 54 stars 5.77 score 11 scripts
eligurarie
bcpa:Behavioral Change Point Analysis of Animal Movement
The Behavioral Change Point Analysis (BCPA) is a method of identifying hidden shifts in the underlying parameters of a time series, developed specifically to be applied to animal movement data which is irregularly sampled. The method is based on: E. Gurarie, R. Andrews and K. Laidre A novel method for identifying behavioural changes in animal movement data (2009) Ecology Letters 12:5 395-408. A development version is on <https://github.com/EliGurarie/bcpa>. NOTE: the BCPA method may be useful for any univariate, irregularly sampled Gaussian time-series, but animal movement analysts are encouraged to apply correlated velocity change point analysis as implemented in the smoove package, as of this writing on GitHub at <https://github.com/EliGurarie/smoove>. An example of a univariate analysis is provided in the UnivariateBCPA vignette.
Maintained by Eliezer Gurarie. Last updated 3 years ago.
0.5 match 3 stars 5.26 score 30 scriptsbioc
rifi:'rifi' analyses data from rifampicin time series created by microarray or RNAseq
'rifi' analyses data from rifampicin time series created by microarray or RNAseq. 'rifi' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, 'rifi' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.
Maintained by Jens Georg. Last updated 5 months ago.
rnaseqdifferentialexpressiongeneregulationtranscriptomicsregressionmicroarraysoftware
0.5 match 4.60 score 1 scripts
liumiguo
simET:Tools for Simulation of Evapotranspiration of Field Crops and Soil Water Balance
Supports the calculation of meteorological characteristics in evapotranspiration research and reference crop evapotranspiration, and offers three models to simulate crop evapotranspiration and soil water balance in the field, including single crop coefficient and dual crop coefficient, as well as the Shuttleworth-Wallace model. These calculations main refer to Allen et al.(1998, ISBN:92-5-104219-5), Teh (2006, ISBN:1-58-112-998-X), and Liu et al.(2006) <doi:10.1016/j.agwat.2006.01.018>.
Maintained by Minguo Liu. Last updated 2 years ago.
2.0 match 1.00 score 9 scripts
kybak90
spheresmooth:Piecewise Geodesic Smoothing for Spherical Data
Fitting a smooth path to a given set of noisy spherical data observed at known time points. It implements a piecewise geodesic curve fitting method on the unit sphere based on a velocity-based penalization scheme. The proposed approach is implemented using the Riemannian block coordinate descent algorithm. To understand the method and algorithm, one can refer to Bak, K. Y., Shin, J. K., & Koo, J. Y. (2023) <doi:10.1080/02664763.2022.2054962> for the case of order 1. Additionally, this package includes various functions necessary for handling spherical data.
Maintained by Kwan-Young Bak. Last updated 4 months ago.
0.5 match 3.18 score 2 scripts
steyerli
elasdics:Elastic Analysis of Sparse, Dense and Irregular Curves
Provides functions to align curves and to compute mean curves based on the elastic distance defined in the square-root-velocity framework. For more details on this framework see Srivastava and Klassen (2016, <doi:10.1007/978-1-4939-4020-2>). For more theoretical details on our methods and algorithms see Steyer et al. (2023, <doi:10.1111/biom.13706>) and Steyer et al. (2023, <arXiv:2305.02075>).
Maintained by Lisa Steyer. Last updated 1 years ago.
0.5 match 1.48 score 1 scripts 1 dependentscran
swash:Swash-Backwash Model for the Single Epidemic Wave
The Swash-Backwash Model for the Single Epidemic Wave was developed by Cliff and Haggett (2006) <doi:10.1007/s10109-006-0027-8> to model the velocity of spread of infectious diseases across space. This package enables the calculation of the Swash-Backwash Model for user-supplied panel data on regional infections. The package also provides additional functions for bootstrap confidence intervals, country comparison, visualization of results, and data management.
Maintained by Thomas Wieland. Last updated 1 months ago.
0.5 match 1.30 scorecran
sonar:Fundamental Formulas for Sonar
Formulas for calculating sound velocity, water pressure, depth, density, absorption and sonar equations.
Maintained by Jose Gama. Last updated 9 years ago.
0.5 match 1.00 score
drjphughesjr
pearson7:Maximum Likelihood Inference for the Pearson VII Distribution with Shape Parameter 3/2
Supports maximum likelihood inference for the Pearson VII distribution with shape parameter 3/2 and free location and scale parameters. This distribution is relevant when estimating the velocity of processive motor proteins with random detachment.
Maintained by John Hughes. Last updated 5 years ago.
0.5 match 1.00 score 6 scripts