Showing 51 of total 51 results (show query)
tidyverse
ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics
A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Maintained by Thomas Lin Pedersen. Last updated 8 days ago.
data-visualisationvisualisation
3.5 match 6.6k stars 25.10 score 645k scripts 7.5k dependents
ropensci
rvertnet:Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Retrieve, map and summarize data from the 'VertNet.org' archives (<https://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
Maintained by Dave Slager. Last updated 5 months ago.
speciesoccurrencesbiodiversitymapsvertnetmammalsmammaliaspecimensapi-wrapperspecimenspocc
10.0 match 7 stars 8.51 score 35 scripts 6 dependents
amices
mice:Multivariate Imputation by Chained Equations
Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.
Maintained by Stef van Buuren. Last updated 6 days ago.
chained-equationsfcsimputationmicemissing-datamissing-valuesmultiple-imputationmultivariate-datacpp
4.0 match 462 stars 16.50 score 10k scripts 154 dependents
paternogbc
sensiPhy:Sensitivity Analysis for Comparative Methods
An implementation of sensitivity analysis for phylogenetic comparative methods. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PCM: (i) Species Sampling uncertainty (sample size; influential species and clades). (ii) Phylogenetic uncertainty (different topologies and/or branch lengths). (iii) Data uncertainty (intraspecific variation and measurement error).
Maintained by Gustavo Paterno. Last updated 5 years ago.
comparative-methodsecologyevolutionphylogeneticssensitivity-analysis
10.3 match 13 stars 6.38 score 61 scripts
shimosan
scaleboot:Approximately Unbiased P-Values via Multiscale Bootstrap
Calculating approximately unbiased (AU) p-values from multiscale bootstrap probabilities. See Shimodaira (2004) <doi:10.1214/009053604000000823>, Shimodaira (2008) <doi:10.1016/j.jspi.2007.04.001>, Terada ans Shimodaira (2017) <arXiv:1711.00949>, and Shimodaira and Terada (2019) <doi.org/10.3389/fevo.2019.00174>.
Maintained by Hidetoshi Shimodaira. Last updated 5 years ago.
21.6 match 2.86 score 24 scripts
statistikat
VIM:Visualization and Imputation of Missing Values
New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.
Maintained by Matthias Templ. Last updated 7 months ago.
hotdeckimputation-methodsmodel-predictionsvisualizationcpp
4.0 match 85 stars 14.44 score 2.6k scripts 19 dependents
cran
flexclust:Flexible Cluster Algorithms
The main function kcca implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There are numerous visualization methods for cluster results (neighborhood graphs, convex cluster hulls, barcharts of centroids, ...), and bootstrap methods for the analysis of cluster stability.
Maintained by Bettina Grün. Last updated 16 days ago.
9.0 match 3 stars 5.81 score 52 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 2 months ago.
4.5 match 240 stars 11.39 score 6.0k scripts
weecology
portalr:Create Useful Summaries of the Portal Data
Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahuan desert. The raw data files can be found at <https://github.com/weecology/portaldata>.
Maintained by Glenda M. Yenni. Last updated 4 months ago.
community-ecologyecologysmall-mammal-trapping
6.7 match 11 stars 7.64 score 63 scripts
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 6 days ago.
3.5 match 18 stars 13.93 score 2.6k scripts 1.5k dependents
r-forge
Sleuth3:Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.
Maintained by Berwin A Turlach. Last updated 1 years ago.
7.5 match 6.38 score 522 scripts
b-cubed-eu
b3gbi:General Biodiversity Indicators for Biodiversity Data Cubes
Calculate general biodiversity indicators from GBIF data cubes. Includes many common indicators such as species richness and evenness, which can be calculated over time (trends) or space (maps).
Maintained by Shawn Dove. Last updated 12 days ago.
biodiversity-indicatorsdata-cubes
7.0 match 3 stars 6.26 score 34 scripts 1 dependentsr-forge
Sleuth2:Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.
Maintained by Berwin A Turlach. Last updated 1 years ago.
7.5 match 5.70 score 191 scripts
statmanrobin
Stat2Data:Datasets for Stat2
Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.
Maintained by Robin Lock. Last updated 6 years ago.
7.5 match 5 stars 4.94 score 544 scriptscran
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 15 days ago.
3.4 match 19 stars 10.53 score 11k dependentsropensci
phylotaR:Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
Maintained by Shixiang Wang. Last updated 8 months ago.
blastngenbankpeer-reviewedphylogeneticssequence-alignment
6.0 match 23 stars 5.86 score 156 scripts
alrobles
mddmaps:Download World Mammal Maps
Lightweight maps of mammals of the world. These maps are a comprehensive collection of maps aligned with the Mammal Diversity Database taxonomy of the American Society of Mammalogists. They are generated at low resolution for easy access, consultation and manipulation in shapefile format. The package connects to a binary backup hosted in the Digital Ocean cloud service and allows individual or batch download of any mammal species in the mdd taxonomy by providing the scientific species name.
Maintained by Angel Robles. Last updated 10 months ago.
20.1 match 1 stars 1.70 score
julianfaraway
faraway:Datasets and Functions for Books by Julian Faraway
Books are "Linear Models with R" published 1st Ed. August 2004, 2nd Ed. July 2014, 3rd Ed. February 2025 by CRC press, ISBN 9781439887332, and "Extending the Linear Model with R" published by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN 9781584884248 and "Practical Regression and ANOVA in R" contributed documentation on CRAN (now very dated).
Maintained by Julian Faraway. Last updated 1 months ago.
3.6 match 29 stars 9.43 score 1.7k scripts 1 dependents
rjknell
Biostatistics:Statistics Tutorials for Biologists
Tutorials for statistics, aimed at biological scientists. Subjects range from basic descriptive statistics through to complex linear modelling. The tutorials include text, videos, interactive coding exercises and multiple choice quizzes. The package also includes 19 datasets which are used in the tutorials.
Maintained by Rob Knell. Last updated 3 years ago.
6.9 match 4.54 score 5 scripts
animint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 27 days ago.
3.5 match 64 stars 8.87 score 173 scripts
sanfordweisberg
alr4:Data to Accompany Applied Linear Regression 4th Edition
Datasets to Accompany S. Weisberg (2014, ISBN: 978-1-118-38608-8), "Applied Linear Regression," 4th edition. Many data files in this package are included in the `alr3` package as well, so only one of them should be used.
Maintained by Sanford Weisberg. Last updated 7 years ago.
8.5 match 1 stars 3.45 score 306 scripts
mcomas
coda.base:A Basic Set of Functions for Compositional Data Analysis
A minimum set of functions to perform compositional data analysis using the log-ratio approach introduced by John Aitchison (1982). Main functions have been implemented in c++ for better performance.
Maintained by Marc Comas-Cufí. Last updated 1 years ago.
4.0 match 7 stars 6.93 score 81 scripts
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.
3.5 match 5 stars 7.09 score 310 scripts 3 dependents
mikemeredith
overlap:Estimates of Coefficient of Overlapping for Animal Activity Patterns
Provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.
Maintained by Liz Campbell. Last updated 2 years ago.
3.8 match 2 stars 6.42 score 265 scripts 1 dependentsr-forge
Gifi:Multivariate Analysis with Optimal Scaling
Implements categorical principal component analysis ('PRINCALS'), multiple correspondence analysis ('HOMALS'), monotone regression analysis ('MORALS'). It replaces the 'homals' package.
Maintained by Patrick Mair. Last updated 3 months ago.
4.5 match 4.90 score 37 scripts 1 dependents
daijiang
megatrees:Subsets of randomly selected phylogenies from existing mega-phylogenies
There are an increasing number of mega-phylogenies available nowadays, with many of them being sets of thousands of posterior distribution phylogenies. For ecological studies, we may need to randomly select many such posterior phylogeneies to conduct analyses. This data package serves this purpose by providing a small number (100) of randomly selected posterior phylogenies (if available) so that we can readily use them for our downstream analyses without repeating the downloading and selecting processes.
Maintained by Daijiang Li. Last updated 2 months ago.
6.8 match 4 stars 3.08 score 2 scripts 1 dependents
stibu81
ibawds:Functions and Datasets for the Data Science Course at IBAW
A collection of useful functions and datasets for the Data Science Course at IBAW.
Maintained by Stefan Lanz. Last updated 8 days ago.
data-science-learningeducational-resources
4.5 match 2 stars 4.26 score 8 scripts
hoehna
TESS:Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events
Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.
Maintained by Sebastian Hoehna. Last updated 3 years ago.
3.2 match 2 stars 5.93 score 95 scripts 1 dependentscran
psy:Various Procedures Used in Psychometrics
Kappa, ICC, reliability coefficient, parallel analysis, multi-traits multi-methods, spherical representation of a correlation matrix.
Maintained by Bruno Falissard. Last updated 3 years ago.
3.8 match 4.65 score 262 scripts 4 dependents
rdinnager
phyf:Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs
The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.
Maintained by Russell Dinnage. Last updated 7 months ago.
3.6 match 1 stars 4.20 score 53 scripts 1 dependents
frbcesab
popbayes:Bayesian Model to Estimate Population Trends from Counts Series
Infers the trends of one or several animal populations over time from series of counts. It does so by accounting for count precision (provided or inferred based on expert knowledge, e.g. guesstimates), smoothing the population rate of increase over time, and accounting for the maximum demographic potential of species. Inference is carried out in a Bayesian framework. This work is part of the FRB-CESAB working group AfroBioDrivers <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/afrobiodrivers/>.
Maintained by Nicolas Casajus. Last updated 1 years ago.
animalbayesiancountspopulationprecisiontemporal-trendjagscpp
3.5 match 1 stars 4.30 scorecran
cluster.datasets:Cluster Analysis Data Sets
A collection of data sets for teaching cluster analysis.
Maintained by Frederick Novomestky. Last updated 11 years ago.
7.5 match 2.00 scoredaijiang
neonDivData:Standardized NEON Organismal Data for Biodiversity Research
Cleaned, simplified, and standardized NEON organismal data for biodiversity research. The following taxonomic groups are included so far: algae, beetles, birds, fish, herptiles, macroinvertebrates, mosquitoes, plants, small_mammals, ticks, tick_pathogens, and zooplankton. NEON input data (<https://data.neonscience.org>) were processed and standardized using R package `ecocomDP` (<https://github.com/EDIorg/ecocomDP>).
Maintained by Daijiang Li. Last updated 10 months ago.
3.4 match 15 stars 4.36 score 17 scripts
puttickmacroevolution
motmot:Models of Trait Macroevolution on Trees
Functions for fitting models of trait evolution on phylogenies for continuous traits. The majority of functions described in Thomas and Freckleton (2012) <doi:10.1111/j.2041-210X.2011.00132.x> and include functions that allow for tests of variation in the rates of trait evolution.
Maintained by Mark Puttick. Last updated 5 years ago.
2.3 match 4 stars 6.05 score 35 scriptsstatmanrobin
Lock5Data:Datasets for "Statistics: UnLocking the Power of Data"
Datasets for the third edition of "Statistics: Unlocking the Power of Data" by Lock^5 Includes version of datasets from earlier editions.
Maintained by Robin Lock. Last updated 4 years ago.
4.5 match 2.90 score 322 scripts
prabhanjan-tattar
gpk:100 Data Sets for Statistics Education
Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India. With their permission, first letter of their names forms the name of this package, the package has been built by me and made available for the benefit of R users. This collection requires a rich class of models and can be a very useful building block for a beginner.
Maintained by Prabhanjan Tattar. Last updated 12 years ago.
7.3 match 1.69 score 49 scripts
biologicalrecordscentre
rYoutheria:Access to the YouTheria Mammal Trait Database
A programmatic interface to web-services of YouTheria. YouTheria is an online database of mammalian trait data <http://www.utheria.org.uk/>.
Maintained by Tom August. Last updated 6 years ago.
3.0 match 2 stars 4.00 score 10 scripts
lhvanegasp
glmtoolbox:Set of Tools to Data Analysis using Generalized Linear Models
Set of tools for the statistical analysis of data using: (1) normal linear models; (2) generalized linear models; (3) negative binomial regression models as alternative to the Poisson regression models under the presence of overdispersion; (4) beta-binomial and random-clumped binomial regression models as alternative to the binomial regression models under the presence of overdispersion; (5) Zero-inflated and zero-altered regression models to deal with zero-excess in count data; (6) generalized nonlinear models; (7) generalized estimating equations for cluster correlated data.
Maintained by Luis Hernando Vanegas. Last updated 8 months ago.
3.8 match 1 stars 3.00 score 149 scripts
agroscope-ch
OpenFoodTox:EFSA OpenFoodTox Data Made Accessible as an R Package
Provides convenient access to data extracted from some of the spreadsheet files made available by the chemical hazards database of the European Food Safety Authority (EFSA), accessible via <https://www.efsa.europa.eu/en/data-report/chemical-hazards-database-openfoodtox>.
Maintained by Johannes Ranke. Last updated 8 months ago.
3.0 match 1 stars 3.48 score 2 scripts
nschiett
fishualize:Color Palettes Based on Fish Species
Implementation of color palettes based on fish species.
Maintained by Nina M. D. Schiettekatte. Last updated 11 months ago.
1.1 match 155 stars 8.54 score 370 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.
3.6 match 2.28 score 38 scripts
pmair78
homals:Gifi Methods for Optimal Scaling
Performs a homogeneity analysis (multiple correspondence analysis) and various extensions. Rank restrictions on the category quantifications can be imposed (nonlinear PCA). The categories are transformed by means of optimal scaling with options for nominal, ordinal, and numerical scale levels (for rank-1 restrictions). Variables can be grouped into sets, in order to emulate regression analysis and canonical correlation analysis.
Maintained by Patrick Mair. Last updated 3 years ago.
4.5 match 1 stars 1.59 score 39 scripts
cseljatib
datana:Datasets and Functions to Accompany Analisis De Datos Con R
Datasets and functions to accompany the book 'Analisis de datos con el programa estadistico R: una introduccion aplicada' by Salas-Eljatib (2021, ISBN: 9789566086109). The package helps carry out data management, exploratory analyses, and model fitting.
Maintained by Christian Salas-Eljatib. Last updated 6 months ago.
3.2 match 1.30 score 1 scripts
swfsc
swfscAirDAS:Southwest Fisheries Science Center Aerial DAS Data Processing
Process and summarize aerial survey 'DAS' data (AirDAS) <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-185.PDF> collected using an aerial survey program from the Southwest Fisheries Science Center (SWFSC) <https://www.fisheries.noaa.gov/west-coast/science-data/california-current-marine-mammal-assessment-program>. PDF files detailing the relevant AirDAS data formats are included in this package.
Maintained by Sam Woodman. Last updated 5 months ago.
0.5 match 3.70 score 7 scriptscran
haploR:Query 'HaploReg', 'RegulomeDB'
A set of utilities for querying 'HaploReg' <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php>, 'RegulomeDB' <https://www.regulomedb.org/regulome-search/> web-based tools. The package connects to 'HaploReg', 'RegulomeDB' searches and downloads results, without opening web pages, directly from R environment. Results are stored in a data frame that can be directly used in various kinds of downstream analyses.
Maintained by Ilya Y. Zhbannikov. Last updated 1 years ago.
0.5 match 1 stars 3.24 score
dsjohnson
crawlUtils:Enhance And Integrate the {crawl} Package For Spatial Analysis Of Telemetry Output
Utility functions to augment the the {crawl} package and integrate it with the {sf} package for spatial analysis of telemetry model output. The additional function are targeted toward analysis of marine mammal telemetry, but can be used or easily modified for other situations.
Maintained by Devin S. Johnson. Last updated 6 months ago.
0.5 match 2 stars 2.60 score 1 scriptsdsjohnson
ctmmUtils:Auxillary functions for using the {ctmm} package efficiently
Utility functions to augment the the {ctmm} package. The additional function are targeted toward analysis of marine mammal telemetry, but can be used or easily modified for other situations.
Maintained by Devin S. Johnson. Last updated 3 months ago.
0.5 match 2.40 score
