Showing 104 of total 104 results (show query)
hehta
RESIDE:Rapid Easy Synthesis to Inform Data Extraction
Developed to assist researchers with planning analysis, prior to obtaining data from Trusted Research Environments (TREs) also known as safe havens. With functionality to export and import marginal distributions as well as synthesise data, both with and without correlations from these marginal distributions. Using a multivariate cumulative distribution (COPULA). Additionally the International Stroke Trial (IST) is included as an example dataset under ODC-By licence Sandercock et al. (2011) <doi:10.7488/ds/104>, Sandercock et al. (2011) <doi:10.1186/1745-6215-12-101>.
Maintained by Ryan Field. Last updated 12 days ago.
57.7 match 5.44 score 5 scripts
reside-ic
ids:Generate Random Identifiers
Generate random or human readable and pronounceable identifiers.
Maintained by Rich FitzJohn. Last updated 3 years ago.
15.0 match 94 stars 13.27 score 175 scripts 165 dependents
rosieluain
mort:Identifying Potential Mortalities and Expelled Tags in Aquatic Acoustic Telemetry Arrays
A toolkit for identifying potential mortalities and expelled tags in aquatic acoustic telemetry arrays. Designed for arrays with non-overlapping receivers.
Maintained by Rosie Smith. Last updated 6 months ago.
acoustic-telemetryaquaticmortality-estimation
20.6 match 4 stars 5.35 score 16 scripts
r-spatial
RSAGA:SAGA Geoprocessing and Terrain Analysis
Provides access to geocomputing and terrain analysis functions of the geographical information system (GIS) 'SAGA' (System for Automated Geoscientific Analyses) from within R by running the command line version of SAGA. This package furthermore provides several R functions for handling ASCII grids, including a flexible framework for applying local functions (including predict methods of fitted models) and focal functions to multiple grids. SAGA GIS is available under GPL-2 / LGPL-2 licences from <https://sourceforge.net/projects/saga-gis/>.
Maintained by Alexander Brenning. Last updated 1 months ago.
9.0 match 23 stars 8.72 score 275 scripts
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.
6.6 match 240 stars 11.39 score 6.0k scripts
hugomflavio
actel:Acoustic Telemetry Data Analysis
Designed for studies where animals tagged with acoustic tags are expected to move through receiver arrays. This package combines the advantages of automatic sorting and checking of animal movements with the possibility for user intervention on tags that deviate from expected behaviour. The three analysis functions (explore(), migration() and residency()) allow the users to analyse their data in a systematic way, making it easy to compare results from different studies. CJS calculations are based on Perry et al. (2012) <https://www.researchgate.net/publication/256443823_Using_mark-recapture_models_to_estimate_survival_from_telemetry_data>.
Maintained by Hugo Flávio. Last updated 26 days ago.
acoustic-telemetryfish-packagestelemetry-data
11.5 match 26 stars 6.49 score 16 scripts
simondedman
movegroup:Visualizing and Quantifying Space Use Data for Groups of Animals
Offers an easy and automated way to scale up individual-level space use analysis to that of groups. Contains a function from the 'move' package to calculate a dynamic Brownian bridge movement model from movement data for individual animals, as well as functions to visualize and quantify space use for individuals aggregated in groups. Originally written with passive acoustic telemetry in mind, this package also provides functionality to account for unbalanced acoustic receiver array designs, and satellite tag data.
Maintained by Simon Dedman. Last updated 2 months ago.
brownian-bridgehome-rangehome-range-analysismigrationresidencyspace-usetracking
10.0 match 17 stars 5.63 score 4 scripts
yrosseel
lavaan:Latent Variable Analysis
Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.
Maintained by Yves Rosseel. Last updated 16 hours ago.
factor-analysisgrowth-curve-modelslatent-variablesmissing-datamultilevel-modelsmultivariate-analysispath-analysispsychometricsstatistical-modelingstructural-equation-modeling
3.3 match 453 stars 16.85 score 8.4k scripts 216 dependents
lme4
lme4:Linear Mixed-Effects Models using 'Eigen' and S4
Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Maintained by Ben Bolker. Last updated 4 days ago.
2.3 match 647 stars 20.69 score 35k scripts 1.5k dependents
bioc
affyPLM:Methods for fitting probe-level models
A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.
Maintained by Ben Bolstad. Last updated 2 months ago.
microarrayonechannelpreprocessingqualitycontrolopenblaszlib
6.3 match 6.99 score 206 scripts 4 dependents
schochastics
networkdata:Repository of Network Datasets
The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.
Maintained by David Schoch. Last updated 12 months ago.
8.5 match 143 stars 5.01 score 143 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 18 days ago.
ncanoncompartmental-analysispharmacokinetics
3.3 match 73 stars 12.61 score 214 scripts 4 dependents
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 8 days ago.
2.3 match 1 stars 17.23 score 33k scripts 12k dependents
thiyangt
denguedatahub:A Tidy Format Datasets of Dengue by Country
Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country.
Maintained by Thiyanga S. Talagala. Last updated 1 months ago.
6.7 match 11 stars 5.12 score 34 scripts
humaniverse
healthyr:R package for mapping UK health data
A package to distribute and summarise on UK health data.
Maintained by Mike Page. Last updated 1 months ago.
7.0 match 4 stars 4.86 score 90 scripts
mages
ChainLadder:Statistical Methods and Models for Claims Reserving in General Insurance
Various statistical methods and models which are typically used for the estimation of outstanding claims reserves in general insurance, including those to estimate the claims development result as required under Solvency II.
Maintained by Markus Gesmann. Last updated 1 months ago.
3.3 match 82 stars 10.04 score 196 scripts 2 dependents
rmheiberger
HH:Statistical Analysis and Data Display: Heiberger and Holland
Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Maintained by Richard M. Heiberger. Last updated 1 months ago.
4.9 match 3 stars 6.42 score 752 scripts 5 dependents
rkoenker
quantreg:Quantile Regression
Estimation and inference methods for models for conditional quantile functions: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included. See Koenker, R. (2005) Quantile Regression, Cambridge U. Press, <doi:10.1017/CBO9780511754098> and Koenker, R. et al. (2017) Handbook of Quantile Regression, CRC Press, <doi:10.1201/9781315120256>.
Maintained by Roger Koenker. Last updated 8 days ago.
2.3 match 18 stars 13.93 score 2.6k scripts 1.5k dependents
ebird
ebirdst:Access and Analyze eBird Status and Trends Data Products
Tools for accessing and analyzing eBird Status and Trends Data Products (<https://science.ebird.org/en/status-and-trends>). eBird (<https://ebird.org/home>) is a global database of bird observations collected by member of the public. eBird Status and Trends uses these data to model global bird distributions, abundances, and population trends at a high spatial and temporal resolution.
Maintained by Matthew Strimas-Mackey. Last updated 21 days ago.
3.5 match 26 stars 8.85 score 228 scripts
alanarnholt
BSDA:Basic Statistics and Data Analysis
Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.
Maintained by Alan T. Arnholt. Last updated 2 years ago.
3.4 match 7 stars 9.11 score 1.3k scripts 6 dependents
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.
4.8 match 10 stars 6.38 score 112 scripts
koalaverse
sure:Surrogate Residuals for Ordinal and General Regression Models
An implementation of the surrogate approach to residuals and diagnostics for ordinal and general regression models; for details, see Liu and Zhang (2017, <doi:https://doi.org/10.1080/01621459.2017.1292915>) and Greenwell et al. (2017, <https://journal.r-project.org/archive/2018/RJ-2018-004/index.html>). These residuals can be used to construct standard residual plots for model diagnostics (e.g., residual-vs-fitted value plots, residual-vs-covariate plots, Q-Q plots, etc.). The package also provides an 'autoplot' function for producing standard diagnostic plots using 'ggplot2' graphics. The package currently supports cumulative link models from packages 'MASS', 'ordinal', 'rms', and 'VGAM'. Support for binary regression models using the standard 'glm' function is also available.
Maintained by Brandon Greenwell. Last updated 15 days ago.
categorical-datadiagnosticsordinal-regressionresiduals
5.3 match 9 stars 5.58 score 47 scripts 1 dependents
robjhyndman
fpp3:Data for "Forecasting: Principles and Practice" (3rd Edition)
All data sets required for the examples and exercises in the book "Forecasting: principles and practice" by Rob J Hyndman and George Athanasopoulos <https://OTexts.com/fpp3/>. All packages required to run the examples are also loaded. Additional data sets not used in the book are also included.
Maintained by Rob Hyndman. Last updated 6 months ago.
3.4 match 142 stars 8.54 score 2.5k scripts
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.
12.4 match 2.28 score 38 scripts
actuaryzhang
cplm:Compound Poisson Linear Models
Likelihood-based and Bayesian methods for various compound Poisson linear models based on Zhang, Yanwei (2013) <doi:10.1007/s11222-012-9343-7>.
Maintained by Yanwei (Wayne) Zhang. Last updated 1 years ago.
3.3 match 16 stars 8.55 score 75 scripts 10 dependents
suyusung
arm:Data Analysis Using Regression and Multilevel/Hierarchical Models
Functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.
Maintained by Yu-Sung Su. Last updated 5 months ago.
2.3 match 25 stars 12.38 score 3.3k scripts 89 dependents
thiloklein
matchingMarkets:Analysis of Stable Matchings
Implements structural estimators to correct for the sample selection bias from observed outcomes in matching markets. This includes one-sided matching of agents into groups as well as two-sided matching of students to schools. The package also contains algorithms to find stable matchings in the three most common matching problems: the stable roommates problem, the college admissions problem, and the house allocation problem.
Maintained by Thilo Klein. Last updated 5 years ago.
4.6 match 40 stars 5.99 score 49 scripts
danlwarren
ENMTools:Analysis of Niche Evolution using Niche and Distribution Models
Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Maintained by Dan Warren. Last updated 2 months ago.
3.9 match 105 stars 6.91 score 126 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.
3.5 match 16 stars 7.48 score 159 scripts 1 dependents
sachaepskamp
psychonetrics:Structural Equation Modeling and Confirmatory Network Analysis
Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Maintained by Sacha Epskamp. Last updated 14 days ago.
3.3 match 51 stars 6.82 score 41 scripts 1 dependents
elvanceyhan
pcds:Proximity Catch Digraphs and Their Applications
Contains the functions for construction and visualization of various families of the proximity catch digraphs (PCDs) (see (Ceyhan (2005) ISBN:978-3-639-19063-2), for computing the graph invariants for testing the patterns of segregation and association against complete spatial randomness (CSR) or uniformity in one, two and three dimensional cases. The package also has tools for generating points from these spatial patterns. The graph invariants used in testing spatial point data are the domination number (Ceyhan (2011) <doi:10.1080/03610921003597211>) and arc density (Ceyhan et al. (2006) <doi:10.1016/j.csda.2005.03.002>; Ceyhan et al. (2007) <doi:10.1002/cjs.5550350106>). The PCD families considered are Arc-Slice PCDs, Proportional-Edge PCDs, and Central Similarity PCDs.
Maintained by Elvan Ceyhan. Last updated 2 years ago.
3.5 match 5.80 score 21 scripts 2 dependents
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.
2.3 match 1 stars 8.62 score 356 scripts 7 dependents
guyabel
migest:Methods for the Indirect Estimation of Bilateral Migration
Tools for estimating, measuring and working with migration data.
Maintained by Guy J. Abel. Last updated 1 months ago.
3.3 match 32 stars 5.80 score 86 scripts
cbracis
recurse:Computes Revisitation Metrics for Trajectory Data
Computes revisitation metrics for trajectory data, such as the number of revisitations for each location as well as the time spent for that visit and the time since the previous visit. Also includes functions to plot data.
Maintained by Chloe Bracis. Last updated 8 months ago.
3.0 match 10 stars 6.24 score 43 scripts
ajmcneil
tscopula:Time Series Copula Models
Functions for the analysis of time series using copula models. The package is based on methodology described in the following references. McNeil, A.J. (2021) <doi:10.3390/risks9010014>, Bladt, M., & McNeil, A.J. (2021) <doi:10.1016/j.ecosta.2021.07.004>, Bladt, M., & McNeil, A.J. (2022) <doi:10.1515/demo-2022-0105>.
Maintained by Alexander McNeil. Last updated 26 days ago.
3.3 match 2 stars 5.53 score 12 scripts
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-connectivitybrain-imagingcomplex-networksconnectomeconnectomicsfmrigraph-theorymrinetwork-analysisneuroimagingneurosciencestatisticstractography
2.3 match 188 stars 7.86 score 107 scripts 3 dependents
fmmgroupva
FMM:Rhythmic Patterns Modeling by FMM Models
Provides a collection of functions to fit and explore single, multi-component and restricted Frequency Modulated Moebius (FMM) models. 'FMM' is a nonlinear parametric regression model capable of fitting non-sinusoidal shapes in rhythmic patterns. Details about the mathematical formulation of 'FMM' models can be found in Rueda et al. (2019) <doi:10.1038/s41598-019-54569-1>.
Maintained by Itziar Fernandez. Last updated 25 days ago.
3.3 match 2 stars 5.30 score
jalilian
ETAS:Modeling Earthquake Data Using 'ETAS' Model
Fits the space-time Epidemic Type Aftershock Sequence ('ETAS') model to earthquake catalogs using a stochastic 'declustering' approach. The 'ETAS' model is a 'spatio-temporal' marked point process model and a special case of the 'Hawkes' process. The package is based on a Fortran program by 'Jiancang Zhuang' (available at <http://bemlar.ism.ac.jp/zhuang/software.html>), which is modified and translated into C++ and C such that it can be called from R. Parallel computing with 'OpenMP' is possible on supported platforms.
Maintained by Abdollah Jalilian. Last updated 6 months ago.
2.3 match 24 stars 7.18 score 21 scripts 1 dependents
kjakobse
EpiForsk:Code Sharing at the Department of Epidemiological Research at Statens Serum Institut
This is a collection of assorted functions and examples collected from various projects. Currently we have functionalities for simplifying overlapping time intervals, Charlson comorbidity score constructors for Danish data, getting frequency for multiple variables, getting standardized output from logistic and log-linear regressions, sibling design linear regression functionalities a method for calculating the confidence intervals for functions of parameters from a GLM, Bayes equivalent for hypothesis testing with asymptotic Bayes factor, and several help functions for generalized random forest analysis using 'grf'.
Maintained by Kim Daniel Jakobsen. Last updated 1 years ago.
3.6 match 4.48 score 8 scriptsbioc
TFutils:TFutils
This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.
Maintained by Vincent Carey. Last updated 4 months ago.
3.3 match 4.80 score 21 scripts
nashjc
nlsr:Functions for Nonlinear Least Squares Solutions - Updated 2022
Provides tools for working with nonlinear least squares problems. For the estimation of models reliable and robust tools than nls(), where the the Gauss-Newton method frequently stops with 'singular gradient' messages. This is accomplished by using, where possible, analytic derivatives to compute the matrix of derivatives and a stabilization of the solution of the estimation equations. Tools for approximate or externally supplied derivative matrices are included. Bounds and masks on parameters are handled properly.
Maintained by John C Nash. Last updated 29 days ago.
2.3 match 7.02 score 94 scripts 5 dependents
clementcalenge
adehabitatLT:Analysis of Animal Movements
A collection of tools for the analysis of animal movements.
Maintained by Clement Calenge. Last updated 6 months ago.
1.8 match 6 stars 8.60 score 370 scripts 12 dependents
kenaho1
asbio:A Collection of Statistical Tools for Biologists
Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Maintained by Ken Aho. Last updated 2 months ago.
2.0 match 5 stars 7.32 score 310 scripts 3 dependents
brockk
trialr:Clinical Trial Designs in 'rstan'
A collection of clinical trial designs and methods, implemented in 'rstan' and R, including: the Continual Reassessment Method by O'Quigley et al. (1990) <doi:10.2307/2531628>; EffTox by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the two-parameter logistic method of Neuenschwander, Branson & Sponer (2008) <doi:10.1002/sim.3230>; and the Augmented Binary method by Wason & Seaman (2013) <doi:10.1002/sim.5867>; and more. We provide functions to aid model-fitting and analysis. The 'rstan' implementations may also serve as a cookbook to anyone looking to extend or embellish these models. We hope that this package encourages the use of Bayesian methods in clinical trials. There is a preponderance of early phase trial designs because this is where Bayesian methods are used most. If there is a method you would like implemented, please get in touch.
Maintained by Kristian Brock. Last updated 1 years ago.
1.7 match 41 stars 8.55 score 106 scripts 3 dependents
geobosh
gbutils:Utilities for Simulation, Plots, Quantile Functions and Programming
Plot density and distribution functions with automatic selection of suitable regions. Numerically invert (compute quantiles) distribution functions. Simulate real and complex numbers from distributions of their magnitude and arguments. Optionally, the magnitudes and/or arguments may be fixed in almost arbitrary ways. Create polynomials from roots given in Cartesian or polar form. Small programming utilities: check if an object is identical to NA, count positional arguments in a call, set intersection of more than two sets, check if an argument is unnamed, compute the graph of S4 classes in packages.
Maintained by Georgi N. Boshnakov. Last updated 3 years ago.
adjacency-matrixcomplex-numbersplotting-functionss4s4classsimulation
1.8 match 1 stars 7.32 score 29 scripts 56 dependents
tspaulding-esa
telemetR:Filter and Analyze Generalised Telemetry Data from Organisms
Analyze telemetry datasets generalized to allow any technology. The filtering steps check for false positives caused by reflected transmissions from surfaces and false pings from other noise generating equipment. The filters are based on JSATS filtering algorithms found in package 'filteRjsats' <https://CRAN.R-project.org/package=filteRjsats> but have been generalized to allow the user to define many of the filtering variables. Additionally, this package contains scripts used to help identify an optimal maximum blanking period as defined in Capello et al (2015) <doi:10.1371/journal.pone.0134002>. The functions were written according to their manuscript description, but have not been reviewed by the authors for accuracy. It is included here as is, without warranty.
Maintained by Taylor Spaulding. Last updated 1 years ago.
3.9 match 2 stars 3.30 score 3 scriptsbioc
lmdme:Linear Model decomposition for Designed Multivariate Experiments
linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.
Maintained by Cristobal Fresno. Last updated 5 months ago.
microarrayonechanneltwochannelvisualizationdifferentialexpressionexperimentdatacancer
3.3 match 3.78 score 1 scripts
maximeherve
RVAideMemoire:Testing and Plotting Procedures for Biostatistics
Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Maintained by Maxime HERVE. Last updated 1 years ago.
2.3 match 8 stars 5.31 score 632 scripts
wjbraun
MPV:Data Sets from Montgomery, Peck and Vining
Most of this package consists of data sets from the textbook Introduction to Linear Regression Analysis, by Montgomery, Peck and Vining. All data sets from the 3rd edition are included and many from the 6th edition are also included. The package also contains some additional data sets and functions.
Maintained by W.J. Braun. Last updated 7 months ago.
3.5 match 3.36 score 193 scripts 1 dependents
sjuhl
spfilteR:Semiparametric Spatial Filtering with Eigenvectors in (Generalized) Linear Models
Tools to decompose (transformed) spatial connectivity matrices and perform supervised or unsupervised semiparametric spatial filtering in a regression framework. The package supports unsupervised spatial filtering in standard linear as well as some generalized linear regression models.
Maintained by Sebastian Juhl. Last updated 25 days ago.
2.3 match 7 stars 5.15 score 10 scripts
hughparsonage
grattan:Australian Tax Policy Analysis
Utilities to cost and evaluate Australian tax policy, including fast projections of personal income tax collections, high-performance tax and transfer calculators, and an interface to common indices from the Australian Bureau of Statistics. Written to support Grattan Institute's Australian Perspectives program, and related projects. Access to the Australian Taxation Office's sample files of personal income tax returns is assumed.
Maintained by Hugh Parsonage. Last updated 12 months ago.
1.8 match 25 stars 6.34 score 124 scripts
pcarbo
varbvs:Large-Scale Bayesian Variable Selection Using Variational Methods
Fast algorithms for fitting Bayesian variable selection models and computing Bayes factors, in which the outcome (or response variable) is modeled using a linear regression or a logistic regression. The algorithms are based on the variational approximations described in "Scalable variational inference for Bayesian variable selection in regression, and its accuracy in genetic association studies" (P. Carbonetto & M. Stephens, 2012, <DOI:10.1214/12-BA703>). This software has been applied to large data sets with over a million variables and thousands of samples.
Maintained by Peter Carbonetto. Last updated 2 years ago.
2.3 match 4.85 score 146 scripts 2 dependents
hyunseungkang
ivmodel:Statistical Inference and Sensitivity Analysis for Instrumental Variables Model
Carries out instrumental variable estimation of causal effects, including power analysis, sensitivity analysis, and diagnostics. See Kang, Jiang, Zhao, and Small (2021) <https://muse.jhu.edu/article/804372> for details.
Maintained by Hyunseung Kang. Last updated 2 years ago.
2.3 match 10 stars 4.69 score 97 scripts
cran
support.CEs:Basic Functions for Supporting an Implementation of Choice Experiments
Provides basic functions that support an implementation of (discrete) choice experiments (CEs). CEs is a question-based survey method measuring people's preferences for goods/services and their characteristics. Refer to Louviere et al. (2000) <doi:10.1017/CBO9780511753831> for details on CEs, and Aizaki (2012) <doi:10.18637/jss.v050.c02> for the package.
Maintained by Hideo Aizaki. Last updated 1 years ago.
3.3 match 3 stars 3.06 score 4 dependents
mountainmath
cancensus:Access, Retrieve, and Work with Canadian Census Data and Geography
Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016; 2021).
Maintained by Dmitry Shkolnik. Last updated 1 years ago.
1.1 match 82 stars 8.80 score 414 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.
0.5 match 127 stars 18.63 score 35k scripts 1.3k dependents
lukece
CoDaImpact:Interpreting CoDa Regression Models
Provides methods for interpreting CoDa (Compositional Data) regression models along the lines of "Pairwise share ratio interpretations of compositional regression models" (Dargel and Thomas-Agnan 2024) <doi:10.1016/j.csda.2024.107945>. The new methods include variation scenarios, elasticities, elasticity differences and share ratio elasticities. These tools are independent of log-ratio transformations and allow an interpretation in the original space of shares. 'CoDaImpact' is designed to be used with the 'compositions' package and its ecosystem.
Maintained by Lukas Dargel. Last updated 12 months ago.
2.2 match 4.30 score
sahilseth
funr:Simple Utility Providing Terminal Access to all R Functions
A small utility which wraps Rscript and provides access to all R functions from the shell.
Maintained by Sahil Seth. Last updated 4 years ago.
1.7 match 34 stars 5.25 score 104 scripts
cran
MCI:Multiplicative Competitive Interaction (MCI) Model
Market area models are used to analyze and predict store choices and market areas concerning retail and service locations. This package implements two market area models (Huff Model, Multiplicative Competitive Interaction Model) into R, while the emphases lie on 1.) fitting these models based on empirical data via OLS regression and nonlinear techniques and 2.) data preparation and processing (esp. interaction matrices and data preparation for the MCI Model).
Maintained by Thomas Wieland. Last updated 7 years ago.
3.4 match 2.53 score 42 scripts
philchalmers
faoutlier:Influential Case Detection Methods for Factor Analysis and Structural Equation Models
Tools for detecting and summarize influential cases that can affect exploratory and confirmatory factor analysis models as well as structural equation models more generally (Chalmers, 2015, <doi:10.1177/0146621615597894>; Flora, D. B., LaBrish, C. & Chalmers, R. P., 2012, <doi:10.3389/fpsyg.2012.00055>).
Maintained by Phil Chalmers. Last updated 2 years ago.
2.3 match 7 stars 3.80 score 18 scripts
georgeweigt
itsmr:Time Series Analysis Using the Innovations Algorithm
Provides functions for modeling and forecasting time series data. Forecasting is based on the innovations algorithm. A description of the innovations algorithm can be found in the textbook "Introduction to Time Series and Forecasting" by Peter J. Brockwell and Richard A. Davis. <https://link.springer.com/book/10.1007/b97391>.
Maintained by George Weigt. Last updated 3 years ago.
3.3 match 2.34 score 218 scriptsbioc
flowGraph:Identifying differential cell populations in flow cytometry data accounting for marker frequency
Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.
Maintained by Alice Yue. Last updated 5 months ago.
flowcytometrystatisticalmethodimmunooncologysoftwarecellbasedassaysvisualization
1.9 match 4.00 score 10 scriptscran
FertBoot:Fertilizer Response Curve Analysis by Bootstrapping Residuals
Quantify variability (such as confidence interval) of fertilizer response curves and optimum fertilizer rates using bootstrapping residuals with several popular non-linear and linear models.
Maintained by Ting Fung (Ralph) Ma. Last updated 4 years ago.
5.8 match 2 stars 1.30 score
ubclxing
MTPS:Multi-Task Prediction using Stacking Algorithms
Simultaneous multiple outcomes prediction based on revised stacking algorithms, which enables the integration of information from predictions of individual models. An implementation of methodologies proposed in our paper: Li Xing, Mary L Lesperance, Xuekui Zhang. (2019) Bioinformatics, "Simultaneous prediction of multiple outcomes using revised stacking algorithms" <doi:10.1093/bioinformatics/btz531>.
Maintained by Li Xing. Last updated 2 years ago.
2.3 match 3.18 score 8 scripts 1 dependents
dragosmg
rocnp:Work with Romanian Personal Numeric Codes PNC / CNP
A set of tools for working with Romanian personal numeric codes. The core is a validation function which applies several verification criteria to assess the validity of numeric codes. This is accompanied by functionality for extracting the different components of a personal numeric code. A personal numeric code is issued to all Romanian residents either at birth or when they obtain a residence permit.
Maintained by Dragoș Moldovan-Grünfeld. Last updated 3 years ago.
2.5 match 2.70 score 2 scripts
crlsierra
SoilR:Models of Soil Organic Matter Decomposition
Functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems with linear and nonlinear systems of differential equations. The package implements models according to the compartmental system representation described in Sierra and others (2012) <doi:10.5194/gmd-5-1045-2012> and Sierra and others (2014) <doi:10.5194/gmd-7-1919-2014>.
Maintained by Carlos A. Sierra. Last updated 1 years ago.
2.0 match 5 stars 2.88 score 153 scripts
benowell
regspec:Non-Parametric Bayesian Spectrum Estimation for Multirate Data
Computes linear Bayesian spectral estimates from multirate data for second-order stationary time series. Provides credible intervals and methods for plotting various spectral estimates. Please see the paper `Should we sample a time series more frequently?' (doi below) for a full description of and motivation for the methodology.
Maintained by Ben Powell. Last updated 1 years ago.
5.6 match 1.00 score 6 scriptsbioc
ldblock:data structures for linkage disequilibrium measures in populations
Define data structures for linkage disequilibrium measures in populations.
Maintained by VJ Carey. Last updated 5 months ago.
1.6 match 3.30 score 10 scripts
skoval
blm:Binomial Linear Regression
Implements regression models for binary data on the absolute risk scale. These models are applicable to cohort and population-based case-control data.
Maintained by S.Kovalchik. Last updated 3 years ago.
3.3 match 1.41 score 26 scripts
fchenunswms
IHSEP:Inhomogeneous Self-Exciting Process
Simulate an inhomogeneous self-exciting process (IHSEP), or Hawkes process, with a given (possibly time-varying) baseline intensity and an excitation function. Calculate the likelihood of an IHSEP with given baseline intensity and excitation functions for an (increasing) sequence of event times. Calculate the point process residuals (integral transforms of the original event times). Calculate the mean intensity process.
Maintained by Feng Chen. Last updated 3 years ago.
2.3 match 1.98 score 16 scripts 2 dependents
bpfaff
gogarch:Generalized Orthogonal GARCH (GO-GARCH) Models
Provision of classes and methods for estimating generalized orthogonal GARCH models. This is an alternative approach to CC-GARCH models in the context of multivariate volatility modeling.
Maintained by Bernhard Pfaff. Last updated 3 years ago.
3.3 match 1.26 score 18 scripts
wasquith
lmomco:L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments, and Many Distributions
Extensive functions for Lmoments (LMs) and probability-weighted moments (PWMs), distribution parameter estimation, LMs for distributions, LM ratio diagrams, multivariate Lcomoments, and asymmetric (asy) trimmed LMs (TLMs). Maximum likelihood and maximum product spacings estimation are available. Right-tail and left-tail LM censoring by threshold or indicator variable are available. LMs of residual (resid) and reversed (rev) residual life are implemented along with 13 quantile operators for reliability analyses. Exact analytical bootstrap estimates of order statistics, LMs, and LM var-covars are available. Harri-Coble Tau34-squared Normality Test is available. Distributions with L, TL, and added (+) support for right-tail censoring (RC) encompass: Asy Exponential (Exp) Power [L], Asy Triangular [L], Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen) Exp Poisson [L], Gen Extreme Value [L], Gen Lambda [L, TL], Gen Logistic [L], Gen Normal [L], Gen Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L], Kumaraswamy [L], Laplace [L], Linear Mean Residual Quantile Function [L], Normal [L], 3p log-Normal [L], Pearson Type III [L], Polynomial Density-Quantile 3 and 4 [L], Rayleigh [L], Rev-Gumbel [L+RC], Rice [L], Singh Maddala [L], Slash [TL], 3p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L].
Maintained by William Asquith. Last updated 1 months ago.
flood-frequency-analysisl-momentsmle-estimationmps-estimationprobability-distributionrainfall-frequency-analysisreliability-analysisrisk-analysissurvival-analysis
0.5 match 2 stars 8.06 score 458 scripts 38 dependents
dusadrian
admisc:Adrian Dusa's Miscellaneous
Contains functions used across packages 'DDIwR', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly versatile recoding routine and some more flexible alternatives to the base functions 'with()' and 'within()'. SOP simplification functions in this package use related minimization from package 'QCA', which is recommended to be installed despite not being listed in the Imports field, due to circular dependency issues.
Maintained by Adrian Dusa. Last updated 5 days ago.
0.5 match 2 stars 7.61 score 20 scripts 92 dependents
arbrazzale
nlreg:Higher Order Inference for Nonlinear Heteroscedastic Models
Likelihood inference based on higher order approximations for nonlinear models with possibly non constant variance.
Maintained by Alessandra R. Brazzale. Last updated 6 years ago.
2.3 match 1.67 score 47 scripts
jonaspet
GeneralisedCovarianceMeasure:Test for Conditional Independence Based on the Generalized Covariance Measure (GCM)
A statistical hypothesis test for conditional independence. It performs nonlinear regressions on the conditioning variable and then tests for a vanishing covariance between the resulting residuals. It can be applied to both univariate random variables and multivariate random vectors. Details of the method can be found in Rajen D. Shah and Jonas Peters: The Hardness of Conditional Independence Testing and the Generalised Covariance Measure, Annals of Statistics 48(3), 1514--1538, 2020.
Maintained by Jonas Peters. Last updated 3 years ago.
2.3 match 1 stars 1.62 score 14 scripts 1 dependentscran
cold:Count Longitudinal Data
Performs regression analysis for longitudinal count data, allowing for serial dependence among observations from a given individual and two dimensional random effects on the linear predictor. Estimation is via maximization of the exact likelihood of a suitably defined model. Missing values and unbalanced data are allowed. Details can be found in the accompanying scientific papers: Goncalves & Cabral (2021, Journal of Statistical Software, <doi:10.18637/jss.v099.i03>) and Goncalves et al. (2007, Computational Statistics & Data Analysis, <doi:10.1016/j.csda.2007.03.002>).
Maintained by M. Helena Goncalves. Last updated 4 years ago.
3.3 match 1.00 score
richelbilderbeek
pureseqtmr:Predict Transmembrane Protein Topology
Proteins reside in either the cell plasma or in the cell membrane. A membrane protein goes through the membrane at least once. Given the amino acid sequence of a membrane protein, the tool 'PureseqTM' (<https://github.com/PureseqTM/pureseqTM_package>, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), <doi:10.1101/627307>), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.
Maintained by Richèl J.C. Bilderbeek. Last updated 2 years ago.
0.5 match 1 stars 3.90 score 16 scriptsbioc
Streamer:Enabling stream processing of large files
Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is 'streamed' from disk into R via a `producer' and through a series of `consumers' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details.
Maintained by Martin Morgan. Last updated 5 months ago.
0.5 match 3.30 score 2 scripts
mrc-ide
demogsurv:Demographic analysis of DHS and other household surveys
This package includes tools for calculating demographic indicators from household survey data. Initially developed for for processing and analysis from Demographic and Health Surveys (DHS) and Multiple Indicator Cluster Surveys (MICS). The package provides tools to calculate standard child mortality, adult mortality, and fertility indicators stratified arbitrarily by age group, calendar period, pre-survey time periods, birth cohorts and other survey variables (e.g. residence, region, wealth status, education, etc.). Design-based standard errors and sample correlations are available for all indicators via Taylor linearisation or jackknife.
Maintained by Jeff Eaton. Last updated 3 years ago.
0.5 match 6 stars 2.92 score 28 scripts
tverbeke
helloJavaWorld:Hello Java World
A dummy package to demonstrate how to interface to a jar file that resides inside an R package.
Maintained by Tobias Verbeke. Last updated 11 years ago.
0.6 match 2.00 score 7 scriptscran
MigrationDetectR:Segment-Based Migration Detection Algorithm
Detection of migration events and segments of continuous residence based on irregular time series of location data as published in Chi et al. (2020) <doi:10.1371/journal.pone.0239408>.
Maintained by Johannes Mast. Last updated 1 years ago.
0.5 match 1.70 scorecran
IGC.CSM:Simulate Impact of Different Urban Policies Through a General Equilibrium Model
Develops a General Equilibrium (GE) Model, which estimates key variables such as wages, the number of residents and workers, the prices of the floor space, and its distribution between commercial and residential use, as in Ahlfeldt et al., (2015) <doi:10.3982/ECTA10876>. By doing so, the model allows understanding the economic influence of different urban policies.
Maintained by Roman Zarate. Last updated 6 months ago.
0.5 match 1.70 score
davidzarruk
IGCities:Simulate Impact of Different Urban Policies Through a General Equilibrium Model
Develops a General Equilibrium (GE) Model, which estimates key variables such as wages, the number of residents and workers, the prices of the floor space, and its distribution between commercial and residential use, as in Ahlfeldt et al., (2015) <https://onlinelibrary.wiley.com/doi/abs/10.3982/ECTA10876>. By doing so, the model allows understanding the economic influence of different urban policies.
Maintained by David Zarruk. Last updated 2 years ago.
0.5 match 1 stars 1.70 scorecran
rtape:Manage and manipulate large collections of R objects stored as tape-like files
Storing huge data in RData format causes problems because of the necessity to load the whole file to the memory in order to access and manipulate objects inside such file; rtape is a simple solution to this problem. The package contains several wrappers of R built-in serialize/unserialize mechanism allowing user to quickly append objects to a tape-like file and later iterate over them requiring only one copy of each stored object to reside in memory a time.
Maintained by Miron B. Kursa. Last updated 14 years ago.
0.5 match 1.00 score