fossil: Palaeoecological and Palaeogeographical Analysis Tools

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.

Author
Matthew J. Vavrek <matthew@matthewvavrek.com>
Date of publication
2012-03-30 07:54:11
Maintainer
Matthew J. Vavrek <matthew@matthewvavrek.com>
License
GPL (>= 2)
Version
0.3.7
URLs

View on CRAN

Man pages

ace
Abundance- and Incidence-based Coverage Estimators
aic.nest
Nestedness of samples using AIC
bootstrap
Bootstrap Species Richness Estimator
bray.curtis
Similarity/Dissimilarity Indices
chao1
Chao's Species Estimators
chao.sorenson
Chao's Jaccard and Sorenson Estimators of Shared Species
coi
Cohesiveness Index for Relational Clustering
create.lats
Creating a table of Latitudes and Longitudes
create.matrix
Creating species locality matrices
deg.dist
Haversine Distance Formula
dino.dist
Creating a Distance Matrix
dino.mst
Calculate a Minimum Spanning Tree or Network
earth.bear
Bearings Between Geographic Locations
earth.dist
Calculating Geographic Distances
earth.poly
Calculating a Minimum Convex Polygon
earth.tri
Calculating the Surface Area Enclosed by Three Geographic...
fdata
A Sample Species Abundance Dataset
fossil-package
fossil: Palaeoecological and Palaeogeographical Analysis...
int.chao
Internal function for chao estimators
jack1
First- and second-order jacknife estimators
lats2Shape
Converting a Table of Latitudes and Longitudes to a Shapefile
localoptima
Function to Find Local Optimization for clustering
loc.map
Mapping Points on a Global Map
msn2Shape
Convert a Minimum spanning Network or Tree to Shapefile
msn.map
Mapping a Minimum Spanning Tree
mstlines
Display a Minimum Spanning Tree or Network
new.lat.long
Find a New Latitude and Longitude
nmds.mst
Creating NMDS plots with overlain Minimum Spanning Trees
rand.index
Rand Index and Adjusted Rand Index
rclust
Relational Clustering
rclust.dist
Relational Clustering
rclust.null
Relational Clustering
rclust.weights
Relational Clustering
relational.clustering
Relational Clustering
sac
Calculate Species Area Curves
sim.occ
Simulated Species Occurrence data
spp.est
Estimating Species Diversity
tri.ineq
Testing for the Triangle Inequality

Files in this package

fossil
fossil/MD5
fossil/inst
fossil/inst/CITATION
fossil/man
fossil/man/relational.clustering.Rd
fossil/man/rclust.Rd
fossil/man/new.lat.long.Rd
fossil/man/dino.mst.Rd
fossil/man/create.lats.Rd
fossil/man/bootstrap.Rd
fossil/man/mstlines.Rd
fossil/man/rclust.weights.Rd
fossil/man/aic.nest.Rd
fossil/man/create.matrix.Rd
fossil/man/rand.index.Rd
fossil/man/earth.tri.Rd
fossil/man/tri.ineq.Rd
fossil/man/sac.Rd
fossil/man/localoptima.Rd
fossil/man/chao.sd.rd
fossil/man/msn2Shape.Rd
fossil/man/chao1.Rd
fossil/man/rclust.dist.Rd
fossil/man/fdata.Rd
fossil/man/lats2Shape.Rd
fossil/man/dino.dist.Rd
fossil/man/int.chao.Rd
fossil/man/coi.Rd
fossil/man/earth.poly.Rd
fossil/man/sim.occ.Rd
fossil/man/deg.dist.Rd
fossil/man/ace.Rd
fossil/man/earth.bear.Rd
fossil/man/spp.est.Rd
fossil/man/jack1.Rd
fossil/man/loc.map.Rd
fossil/man/nmds.mst.Rd
fossil/man/msn.map.Rd
fossil/man/bray.curtis.Rd
fossil/man/fossil-package.Rd
fossil/man/rclust.null.Rd
fossil/man/earth.dist.Rd
fossil/man/chao.sorenson.Rd
fossil/NAMESPACE
fossil/DESCRIPTION
fossil/R
fossil/R/sorenson.R
fossil/R/bray.curtis.R
fossil/R/coi.R
fossil/R/manhattan.R
fossil/R/dino.mst.R
fossil/R/rclust.weights.R
fossil/R/earth.bear.R
fossil/R/mstlines.R
fossil/R/aic.nest.R
fossil/R/morisita.horn.R
fossil/R/deg.dist.R
fossil/R/euclidean.R
fossil/R/jaccard.R
fossil/R/nmds.mst.R
fossil/R/earth.tri.R
fossil/R/relational.clustering.R
fossil/R/rclust.null.R
fossil/R/dino.dist.R
fossil/R/new.lat.long.R
fossil/R/rclust.R
fossil/R/adj.rand.index.R
fossil/R/chao.jaccard.R
fossil/R/localoptima.R
fossil/R/bootstrap.R
fossil/R/sac.R
fossil/R/earth.poly.R
fossil/R/jack1.R
fossil/R/ecol.dist.R
fossil/R/jack2.R
fossil/R/loc.map.R
fossil/R/msn2Shape.R
fossil/R/ACE.R
fossil/R/chao2.R
fossil/R/kulczynski.R
fossil/R/rand.index.R
fossil/R/ochiai.R
fossil/R/earth.dist.R
fossil/R/rclust.dist.R
fossil/R/chao.sd.R
fossil/R/simpson.R
fossil/R/create.lats.R
fossil/R/create.matrix.R
fossil/R/spp.est.R
fossil/R/sim.occ.R
fossil/R/int.chao.R
fossil/R/lats2Shape.R
fossil/R/dino.msn.R
fossil/R/braun.blanquet.R
fossil/R/chao.sorenson.R
fossil/R/tri.ineq.R
fossil/R/ICE.R
fossil/R/msn.map.R
fossil/R/chao1.R
fossil/data
fossil/data/fdata.list.rda
fossil/data/fdata.lats.rda
fossil/data/fdata.mat.rda