# Peter Solymos

#### pbapply

cran
97th

Percentile

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.

#### dclone

cran
83th

Percentile

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 (R Journal 2(2):29--37). Sequential and parallel MCMC support for 'JAGS', 'WinBUGS' and 'OpenBUGS'.

#### mefa4

cran
82th

Percentile

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

#### detect

cran
77th

Percentile

Models for analyzing site occupancy and count data models with detection error, including single-visit based models, conditional distance sampling and time-removal models. Package development was supported by the Alberta Biodiversity Monitoring Institute (www.abmi.ca) and the Boreal Avian Modelling Project (borealbirds.ca).

#### dcmle

cran
66th

Percentile

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.

#### mefa

cran
66th

Percentile

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.

#### intrval

cran
57th

Percentile

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.

#### opticut

cran
47th

Percentile

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.

#### PVAClone

cran
47th

Percentile

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.

#### sharx

cran
35th

Percentile

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, Global Ecology and Biogeography 21, 109-120).

#### ResourceSelection

cran
18th

Percentile

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[3021:WDAEOR]2.0.CO;2>, Lele (2009) <doi:10.2193/2007-535>, and Solymos & Lele (2016) <doi:10.1111/2041-210X.12432>.

#### plotrix

cran
98th

Percentile

Lots of plots, various labeling, axis and color scaling functions.

#### vegan

cran
97th

Percentile

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