Learn R Programming
⚠️There's a newer version (0.4.0) of this package.Take me there.

fossil (version 0.3.7)

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.

Copy Link

Version

Install

install.packages('fossil')

Monthly Downloads

1,546

Version

0.3.7

License

GPL (>= 2)

Maintainer

Matthew J Vavrek

Last Published

March 30th, 2012

Functions in fossil (0.3.7)

bootstrap

Bootstrap Species Richness Estimator
earth.bear

Bearings Between Geographic Locations
sac

Calculate Species Area Curves
earth.poly

Calculating a Minimum Convex Polygon
rclust.null

Relational Clustering
fdata

A Sample Species Abundance Dataset
spp.est

Estimating Species Diversity
loc.map

Mapping Points on a Global Map
mstlines

Display a Minimum Spanning Tree or Network
rclust.weights

Relational Clustering
rclust.dist

Relational Clustering
chao1

Chao's Species Estimators
int.chao

Internal function for chao estimators
fossil-package

fossil: Palaeoecological and Palaeogeographical Analysis Tools
sim.occ

Simulated Species Occurrence data
lats2Shape

Converting a Table of Latitudes and Longitudes to a Shapefile
create.matrix

Creating species locality matrices
dino.mst

Calculate a Minimum Spanning Tree or Network
new.lat.long

Find a New Latitude and Longitude
jack1

First- and second-order jacknife estimators
localoptima

Function to Find Local Optimization for clustering
similarity

Similarity/Dissimilarity Indices
relational.clustering

Relational Clustering
rclust

Relational Clustering
coi

Cohesiveness Index for Relational Clustering
aic.nest

Nestedness of samples using AIC
rand.index

Rand Index and Adjusted Rand Index
tri.ineq

Testing for the Triangle Inequality
msn2Shape

Convert a Minimum spanning Network or Tree to Shapefile
deg.dist

Haversine Distance Formula
ACE

Abundance- and Incidence-based Coverage Estimators
ecol.dist

Creating a Distance Matrix
nmds.mst

Creating NMDS plots with overlain Minimum Spanning Trees
chao.sorenson

Chao's Jaccard and Sorenson Estimators of Shared Species
msn.map

Mapping a Minimum Spanning Tree
earth.dist

Calculating Geographic Distances
earth.tri

Calculating the Surface Area Enclosed by Three Geographic Points
create.lats

Creating a table of Latitudes and Longitudes
chao.sd

Chao's estimation of standard error