R: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

# Tools for Ecological Niche Evolution Assessment Considering Uncertainty

## Documentation for package ‘nichevol’ version 0.1.20

- DESCRIPTION file
- Package NEWS
- Package README

## 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