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fossil (version 0.4.0)

Palaeoecological and Palaeogeographical Analysis Tools

Description

A set of analytical tools useful in analysing ecological and geographical data sets, both ancient and modern. The package includes functions for estimating species richness (Chao 1 and 2, ACE, ICE, Jacknife), shared species/beta diversity, species area curves and geographic distances and areas.

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Version

Install

install.packages('fossil')

Monthly Downloads

1,443

Version

0.4.0

License

GPL (>= 2)

Maintainer

Matthew J Vavrek

Last Published

March 23rd, 2020

Functions in fossil (0.4.0)

bootstrap

Bootstrap Species Richness Estimator
similarity

Similarity/Dissimilarity Indices
earth.poly

Calculating a Minimum Convex Polygon
loc.map

Mapping Points on a Global Map
sim.occ

Simulated Species Occurrence data
lats2Shape

Converting a Table of Latitudes and Longitudes to a Shapefile
sac

Calculate Species Area Curves
chao1

Chao's Species Estimators
ACE

Abundance- and Incidence-based Coverage Estimators
coi

Cohesiveness Index for Relational Clustering
dino.mst

Calculate a Minimum Spanning Tree or Network
euler.rot

Calculate the Euler Rotation of a Point
new.lat.long

Find a New Latitude and Longitude
earth.bear

Bearings Between Geographic Locations
earth.tri

Calculating the Surface Area Enclosed by Three Geographic Points
spp.est

Estimating Species Diversity
tri.ineq

Testing for the Triangle Inequality
aic.nest

Nestedness of samples using AIC
rclust.dist

Relational Clustering
nmds.mst

Creating NMDS plots with overlain Minimum Spanning Trees
rclust.null

Relational Clustering
int.chao

Internal function for chao estimators
create.lats

Creating a table of Latitudes and Longitudes
create.matrix

Creating species locality matrices
jack1

First- and second-order jacknife estimators
fdata

A Sample Species Abundance Dataset
chao.sorenson

Chao's Jaccard and Sorenson Estimators of Shared Species
fossil-package

fossil: Palaeoecological and Palaeogeographical Analysis Tools
chao.sd

Chao's estimation of standard error
deg.dist

Haversine Distance Formula
rand.index

Rand Index and Adjusted Rand Index
localoptima

Function to Find Local Optimization for clustering
ecol.dist

Creating a Distance Matrix
msn.map

Mapping a Minimum Spanning Tree
msn2Shape

Convert a Minimum spanning Network or Tree to Shapefile
rclust

Relational Clustering
relational.clustering

Relational Clustering
rclust.weights

Relational Clustering
mstlines

Display a Minimum Spanning Tree or Network
earth.dist

Calculating Geographic Distances