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BiodiversityR - Package for Community Ecology and Suitability Analysis

Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.

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6.97 score 18 stars 2 dependents 374 scripts 2.3k downloads

WorldFlora - Standardize Plant Names According to World Flora Online Taxonomic Backbone

World Flora Online is an online flora of all known plants, available from <https://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013.

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2.64 score 3 stars 1 dependents 48 scripts 583 downloads

maxlike - Model Species Distributions by Estimating the Probability of Occurrence Using Presence-Only Data

Provides a likelihood-based approach to modeling species distributions using presence-only data. In contrast to the popular software program MAXENT, this approach yields estimates of the probability of occurrence, which is a natural descriptor of a species' distribution.

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2.46 score 27 scripts 3.5k downloads

AlleleShift - Predict and Visualize Population-Level Changes in Allele Frequencies in Response to Climate Change

Methods (<doi:10.7717/peerj.11534>) are provided of calibrating and predicting shifts in allele frequencies through redundancy analysis ('vegan::rda()') and generalized additive models ('mgcv::gam()'). Visualization functions for predicted changes in allele frequencies include 'shift.dot.ggplot()', 'shift.pie.ggplot()', 'shift.moon.ggplot()', 'shift.waffle.ggplot()' and 'shift.surf.ggplot()' that are made with input data sets that are prepared by helper functions for each visualization method. Examples in the documentation show how to prepare animated climate change graphics through a time series with the 'gganimate' package. Function 'amova.rda()' shows how Analysis of Molecular Variance can be directly conducted with the results from redundancy analysis.

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1.70 score 1 stars 5 scripts 267 downloads

RcmdrPlugin.WorldFlora - R Commander Plug-in for the 'WorldFlora' Package

An R Commander plug-in for the 'WorldFlora' package. It was mainly developed to show work flows and scripts for first-time users.

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1.00 score 1 stars 1 scripts 422 downloads