vegan - Community Ecology Package

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

Last updated

ecological-modellingecologyordinationopenblasfortran

19.86 score 533 stars 504 dependents 25k scripts 147k downloads

pbapply - Adding Progress Bar to '*apply' Functions

A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where showing the progress is useful (e.g. bootstrap). The type and style of the progress bar (with percentages or remaining time) can be set through options. Supports several parallel processing backends including mirai and future.

Last updated

progress-bar

14.70 score 163 stars 722 dependents 4.5k scripts 133k downloads

ResourceSelection - Resource Selection (Probability) Functions for Use-Availability Data

Resource Selection (Probability) Functions for use-availability wildlife data based on weighted distributions as described in Lele and Keim (2006) <doi:10.1890/0012-9658(2006)87%5B3021:WDAEOR%5D2.0.CO;2>, Lele (2009) <doi:10.2193/2007-535>, and Solymos & Lele (2016) <doi:10.1111/2041-210X.12432>.

Last updated

ecologyestimationlelersfrspfsolymosweighted-distributions

8.91 score 9 stars 4 dependents 1.2k scripts 12k downloads

dclone - Data Cloning and MCMC Tools for Maximum Likelihood Methods

Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods as described in Solymos 2010 <doi:10.32614/RJ-2010-011>. Sequential and parallel MCMC support for 'JAGS', 'WinBUGS', 'OpenBUGS', and 'Stan'.

Last updated

jagscpp

7.01 score 7 stars 4 dependents 273 scripts 449 downloads

bSims - Agent-Based Bird Point Count Simulator

A highly scientific and utterly addictive bird point count simulator to test statistical assumptions, aid survey design, and have fun while doing it (Solymos 2024 <doi:10.1007/s42977-023-00183-2>). The simulations follow time-removal and distance sampling models based on Matsuoka et al. (2012) <doi:10.1525/auk.2012.11190>, Solymos et al. (2013) <doi:10.1111/2041-210X.12106>, and Solymos et al. (2018) <doi:10.1650/CONDOR-18-32.1>, and sound attenuation experiments by Yip et al. (2017) <doi:10.1650/CONDOR-16-93.1>.

Last updated

biasbirdsdetectabilityshinysimulationsurvey-design

6.43 score 4 stars 56 scripts 259 downloads

intrval - Relational Operators for Intervals

Evaluating if values of vectors are within different open/closed intervals (`x %[]% c(a, b)`), or if two closed intervals overlap (`c(a1, b1) %[]o[]% c(a2, b2)`). Operators for negation and directional relations also implemented.

Last updated

closed-intervalsinterval-endpointsinterval-operatorsnegationopen-intervals

6.18 score 40 stars 1 dependents 127 scripts 276 downloads

detect - Analyzing Wildlife Data with Detection Error

Models for analyzing site occupancy and count data models with detection error, including single-visit based models (Lele et al. 2012 <doi:10.1093/jpe/rtr042>, Moreno et al. 2010 <doi:10.1890/09-1073.1>, Solymos et al. 2012 <doi:10.1002/env.1149>, Denes et al. 2016 <doi:10.1111/1365-2664.12818>), conditional distance sampling and time-removal models (QPAD) (Solymos et al. 2013 <doi:10.1111/2041-210X.12106>, Solymos et al. 2018 <doi:10.1650/CONDOR-18-32.1>), and single bin QPAD (SQPAD) models (Lele & Solymos 2025 <doi:10.1093/ornithapp/duaf078>). Package development was supported by the Alberta Biodiversity Monitoring Institute and the Boreal Avian Modelling Project.

Last updated

6.13 score 6 stars 150 scripts 582 downloads

dclone - Data Cloning and MCMC Tools for Maximum Likelihood Methods

Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods as described in Solymos 2010 <doi:10.32614/RJ-2010-011>. Sequential and parallel MCMC support for 'JAGS', 'WinBUGS', 'OpenBUGS', and 'Stan'.

Last updated

jagscpp

6.06 score 7 stars 4 dependents 273 scripts 449 downloads

mefa4 - Multivariate Data Handling with S4 Classes and Sparse Matrices

An S4 update of the 'mefa' package using sparse matrices for enhanced efficiency. Sparse array-like objects are supported via lists of sparse matrices.

Last updated

data-manipulationecologysparse-matrices

5.41 score 2 dependents 432 scripts 311 downloads

mefa - Multivariate Data Handling in Ecology and Biogeography

A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.

Last updated

4.86 score 2 stars 1 dependents 120 scripts 806 downloads

deps - Dependency Management with 'roxygen'-Style Comments

Manage your source code dependencies by decorating your existing R code with special, 'roxygen'-style comments.

Last updated

dependenciespackagesreproducibility

4.49 score 34 stars 18 scripts 664 downloads

deps - Dependency Management with 'roxygen'-Style Comments

Manage your source code dependencies by decorating your existing R code with special, 'roxygen'-style comments.

Last updated

dependenciespackagesreproducibility

4.49 score 34 stars 18 scripts 664 downloads

rconfig - Manage R Configuration at the Command Line

Configuration management using files (YAML, JSON, INI, TXT), JSON strings, and command line arguments. Command line arguments can be used to override configuration. Period-separated command line flags are parsed as hierarchical lists. Environment variables, R global variables, and configuration values can be substituted.

Last updated

cliconfigjsonyaml

4.43 score 27 stars 9 scripts 216 downloads

rconfig - Manage R Configuration at the Command Line

Configuration management using files (YAML, JSON, INI, TXT), JSON strings, and command line arguments. Command line arguments can be used to override configuration. Period-separated command line flags are parsed as hierarchical lists. Environment variables, R global variables, and configuration values can be substituted.

Last updated

cliconfigjsonyaml

4.43 score 27 stars 9 scripts 216 downloads

dcmle - Hierarchical Models Made Easy with Data Cloning

S4 classes around infrastructure provided by the 'coda' and 'dclone' packages to make package development easy as a breeze with data cloning for hierarchical models.

Last updated

jagscpp

4.30 score 2 dependents 66 scripts 266 downloads

dcmle - Hierarchical Models Made Easy with Data Cloning

S4 classes around infrastructure provided by the 'coda' and 'dclone' packages to make package development easy as a breeze with data cloning for hierarchical models.

Last updated

jagscpp

4.30 score 2 dependents 66 scripts 267 downloads

opticut - Likelihood Based Optimal Partitioning and Indicator Species Analysis

Likelihood based optimal partitioning and indicator species analysis. Finding the best binary partition for each species based on model selection, with the possibility to take into account modifying/confounding variables as described in Kemencei et al. (2014) <doi:10.1556/ComEc.15.2014.2.6>. The package implements binary and multi-level response models, various measures of uncertainty, Lorenz-curve based thresholding, with native support for parallel computations.

Last updated

ecologyindicator-species-analysislikelihoodoptimal-partitioningspecies

4.18 score 2 stars 76 scripts 187 downloads

multibiasmeta - Sensitivity Analysis for Multiple Biases in Meta-Analyses

Meta-analyses can be compromised by studies' internal biases (e.g., confounding in nonrandomized studies) as well as by publication bias. This package conducts sensitivity analyses for the joint effects of these biases (per Mathur (2022) <doi:10.31219/osf.io/u7vcb>). These sensitivity analyses address two questions: (1) For a given severity of internal bias across studies and of publication bias, how much could the results change?; and (2) For a given severity of publication bias, how severe would internal bias have to be, hypothetically, to attenuate the results to the null or by a given amount?

Last updated

4.00 score 6 scripts 161 downloads

EDMAinR - Euclidean Distance Matrix Analysis in R

A coordinate-free approach for comparing biological shapes using landmark data based on Lele and Richtsmeier (1991) <doi:10.1002/ajpa.1330860307>.

Last updated

comparing-biological-shapescoordinate-freelandmark-datamorphometricsmultivariate-statistics

3.90 score 4 stars 9 scripts

PublicationBias - Sensitivity Analysis for Publication Bias in Meta-Analyses

Performs sensitivity analysis for publication bias in meta-analyses (per Mathur & VanderWeele, 2020 [<doi:10.31219/osf.io/s9dp6>]). These analyses enable statements such as: "For publication bias to shift the observed point estimate to the null, 'significant' results would need to be at least 30-fold more likely to be published than negative or 'nonsignificant' results." Comparable statements can be made regarding shifting to a chosen non-null value or shifting the confidence interval. Provides a worst-case meta-analytic point estimate under maximal publication bias obtained simply by conducting a standard meta-analysis of only the negative and "nonsignificant" studies.

Last updated

3.68 score 16 scripts 326 downloads

metabias - Meta-Analysis for Within-Study and/or Across-Study Biases

Provides common components (classes, methods, documentation) for packages that conduct meta-analytic corrections and sensitivity analyses for within-study and/or across-study biases in meta-analysis. See the packages 'PublicationBias', 'phacking', and 'multibiasmeta'. These package implement methods described in, respectively: Mathur & VanderWeele (2020) <doi:10.31219/osf.io/s9dp6>; Mathur (2022) <doi:10.31219/osf.io/ezjsx>; Mathur (2022) <doi:10.31219/osf.io/u7vcb>.

Last updated

3.65 score 3 dependents 331 downloads

clickrup - Interacting with the ClickUp v2 API from R

Work with the ClickUp productivity app from R to manage tasks, goals, time tracking, and more.

Last updated

apiclickupclickup-apiproject-management

3.26 score 18 stars 7 scripts

tryr - Client/Server Error Handling for HTTP API Frameworks

Differentiate client errors (4xx) from server errors (5xx) for the 'plumber' and 'RestRserve' HTTP API frameworks. The package also includes a built-in logging mechanism to standard output (STDOUT) or standard error (STDERR) depending on the log level.

Last updated

3.18 score 3 stars 2 scripts 211 downloads

truncnormbayes - Estimates Moments for a Truncated Normal Distribution using 'Stan'

Finds the posterior modes for the mean and standard deviation for a truncated normal distribution with one or two known truncation points. The method used extends Bayesian methods for parameter estimation for a singly truncated normal distribution under the Jeffreys prior (see Zhou X, Giacometti R, Fabozzi FJ, Tucker AH (2014). "Bayesian estimation of truncated data with applications to operational risk measurement". <doi:10.1080/14697688.2012.752103>). This package additionally allows for a doubly truncated normal distribution.

Last updated

cpp

3.18 score 3 scripts 227 downloads

cure4insect - Custom Reporting for Intactness and Sector Effects

Decision support tool that provides an interface to enable custom reporting for intactness and sector effects based on estimates and predictions created by the Alberta Biodiversity Monitoring Institute (ABMI) in collaboration with the Boreal Avian Modelling (BAM) Project.

Last updated

3.09 score 4 stars 62 scripts

PVAClone - Population Viability Analysis with Data Cloning

Likelihood based population viability analysis in the presence of observation error and missing data. The package can be used to fit, compare, predict, and forecast various growth model types using data cloning.

Last updated

jagscpp

3.02 score 1 stars 21 scripts 280 downloads

phacking - Sensitivity Analysis for p-Hacking in Meta-Analyses

Fits right-truncated meta-analysis (RTMA), a bias correction for the joint effects of p-hacking (i.e., manipulation of results within studies to obtain significant, positive estimates) and traditional publication bias (i.e., the selective publication of studies with significant, positive results) in meta-analyses [see Mathur MB (2022). "Sensitivity analysis for p-hacking in meta-analyses." <doi:10.31219/osf.io/ezjsx>.]. Unlike publication bias alone, p-hacking that favors significant, positive results (termed "affirmative") can distort the distribution of affirmative results. To bias-correct results from affirmative studies would require strong assumptions on the exact nature of p-hacking. In contrast, joint p-hacking and publication bias do not distort the distribution of published nonaffirmative results when there is stringent p-hacking (e.g., investigators who hack always eventually obtain an affirmative result) or when there is stringent publication bias (e.g., nonaffirmative results from hacked studies are never published). This means that any published nonaffirmative results are from unhacked studies. Under these assumptions, RTMA involves analyzing only the published nonaffirmative results to essentially impute the full underlying distribution of all results prior to selection due to p-hacking and/or publication bias. The package also provides diagnostic plots described in Mathur (2022).

Last updated

cpp

3.00 score 1 stars 7 scripts 284 downloads

lhreg - Phylogeny and Species Trait Effects on Detectability

Phylogeny and species trait effects on detectability, supporting material for the manuscript entitled 'Phylogeny and species traits predict songbird detectability' by Solymos, Matsuoka, Stralberg, Bayne, and Barker.

Last updated

birdsborealdetectabilityecologyphylogenyspecies-trait-effects

2.81 score 1 stars 13 scripts

sharx - Models and Data Sets for the Study of Species-Area Relationships

Hierarchical models for the analysis of species-area relationships (SARs) by combining several data sets and covariates; with a global data set combining individual SAR studies; as described in Solymos and Lele (2012) <doi:10.1111/j.1466-8238.2011.00655.x>.

Last updated

jagscpp

2.70 score 1 stars 4 scripts 226 downloads

QPAD - QPAD estimates

QPAD.

Last updated

2.36 score 46 scripts

moosecounter - Adaptive Moose Surveys

Adaptive Moose surveys.

Last updated

shiny

2.18 score 3 stars 4 scripts

paired - Example point count data set with paired human and ARU data

Data set from Van Wilgenburg et al. 2016 <doi:10.5751/ACE-00975-120113>.

Last updated

1.70 score 7 scripts

bananas - Data Set of Ripening Bananas

Color information about ripening bananas over 21 days.

Last updated

1.70 score 4 scripts

allinone - All-in-on Model Based Custom Predictions for Alberta

Decision support tool that provides an interface to enable custom predictions based on estimates created by the Alberta Biodiversity Monitoring Institute (ABMI) in collaboration with the Boreal Avian Modelling (BAM) Project.

Last updated

species-distribution-models

1.70 score 1 stars 4 scripts

WildLift - An Open-source Tool to Guide Decisions for Wildlife Conservation

Compare alternative recovery actions: Linear Feature Restoration, Linear Feature Deactivation, Maternal Penning, Conservation Breeding, Predator Exclosure, Wolf Reduction, and Moose Reduction. Quantifying the trade-offs associated with alternative recovery actions for threatened species. The tool consists of a generalized matrix population model that is parametrized based on information from the published literature or ongoing experiments. Users can input population parameters (e.g., population size and survival rates) or choose from pre-set caribou subpopulations to estimate changes to populations from implementing recovery actions as described in Nagy-Reis et al. (2020) <doi:10.3389/fevo.2020.564508>.

Last updated

1.70 score 5 scripts

KnockKnockJokes - Knock-Knock Jokes

An S4 exercise for Knock-Knock Joke lovers.

Last updated

1.70 score 1 stars 3 scripts