Tools for Ecological Niche Evolution Assessment Considering Uncertainty

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Documentation for package ‘nichevol’ version 0.1.20

Help Pages

bin_env Helper function to prepare bin tables
bin_ml_rec Maximum likelihood reconstruction of ancestral character states
bin_par_rec Maximum parsimony reconstruction of ancestral character states
bin_table Bin table of environmental conditions in M and for occurrences
bin_tables Bin tables of environmental conditions in M and for occurrences from objects
bin_tables0 Bin tables of environmental conditions in M and for occurrences from data
character_table Example of character table for six species
histograms_env Histograms of environmental conditions in M and for occurrences
hist_evalues Histograms of environmental conditions in M and for occurrences (one species)
m Example of accessible areas for a species
m1 Example of accessible areas for a species
m2 Example of accessible areas for a species
m3 Example of accessible areas for a species
m4 Example of accessible areas for a species
m5 Example of accessible areas for a species
m6 Example of accessible areas for a species
map_nichevol Maps of niche reconstructions and changes detected
nichevol nichevol: Assessment of Species’ Ecological Niche Evolution Considering Uncertainty in Reconstructions
nichevol_bars PNG bar figures for representing niche evolution
nichevol_labels Labels to represent changes of niche characteristics between ancestors and descendants
nichevol_legend Legends for niche evolution labels in phylogenetic trees
niche_bars PNG bar figures to represent ecological niches of distinct taxa
niche_labels Labels to represent niches of tips and ancestors
niche_legend Legends for niche labels in phylogenetic trees
occ_list Example of occurrence records for six species
par_rec_table Example of table with results from parsimony reconstructions
pdf_histograms Helper function to create PDF files with histograms
read_bin_table Read tables of binary niche characters from directory
read_bin_tables Read tables of binary niche characters from directory
rename_tips Helper function to rename tips of trees for simulations
score_tip Helper function to calculate the median bin score for a given species
score_tree Helper function to assign bin scores to every tip in a given tree
set_uncertainty Set values of uncertainty towards one or both ends of the variable
sig_sq Helper function to get sigma squared values for a given dataset
smooth_rec Smooth character table values resulted from ancestral character state reconstructions
stats_eval Statistics of environmental conditions in M and for occurrences (one variable)
stats_evalues Statistics of environmental conditions in M and for occurrences (multiple variables)
temp Example of an environmental variable used in analysis
tree Example of a phylogenetic tree for six species
tree5 Example of a phylogenetic tree for five species
tree_data Example of a list containing a tree and a table of characters for six species