fossil: Palaeoecological and Palaeogeographical Analysis Tools
Version 0.3.7

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.

Browse man pages Browse package API and functions Browse package files

AuthorMatthew J. Vavrek <matthew@matthewvavrek.com>
Date of publication2012-03-30 07:54:11
MaintainerMatthew J. Vavrek <matthew@matthewvavrek.com>
LicenseGPL (>= 2)
Version0.3.7
URL http://matthewvavrek.com/programs-and-code/fossil/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("fossil")

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.sd: Chao's estimation of standard error
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

Functions

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

Files

MD5
inst
inst/CITATION
man
man/relational.clustering.Rd
man/rclust.Rd
man/new.lat.long.Rd
man/dino.mst.Rd
man/create.lats.Rd
man/bootstrap.Rd
man/mstlines.Rd
man/rclust.weights.Rd
man/aic.nest.Rd
man/create.matrix.Rd
man/rand.index.Rd
man/earth.tri.Rd
man/tri.ineq.Rd
man/sac.Rd
man/localoptima.Rd
man/chao.sd.rd
man/msn2Shape.Rd
man/chao1.Rd
man/rclust.dist.Rd
man/fdata.Rd
man/lats2Shape.Rd
man/dino.dist.Rd
man/int.chao.Rd
man/coi.Rd
man/earth.poly.Rd
man/sim.occ.Rd
man/deg.dist.Rd
man/ace.Rd
man/earth.bear.Rd
man/spp.est.Rd
man/jack1.Rd
man/loc.map.Rd
man/nmds.mst.Rd
man/msn.map.Rd
man/bray.curtis.Rd
man/fossil-package.Rd
man/rclust.null.Rd
man/earth.dist.Rd
man/chao.sorenson.Rd
NAMESPACE
DESCRIPTION
R
R/sorenson.R
R/bray.curtis.R
R/coi.R
R/manhattan.R
R/dino.mst.R
R/rclust.weights.R
R/earth.bear.R
R/mstlines.R
R/aic.nest.R
R/morisita.horn.R
R/deg.dist.R
R/euclidean.R
R/jaccard.R
R/nmds.mst.R
R/earth.tri.R
R/relational.clustering.R
R/rclust.null.R
R/dino.dist.R
R/new.lat.long.R
R/rclust.R
R/adj.rand.index.R
R/chao.jaccard.R
R/localoptima.R
R/bootstrap.R
R/sac.R
R/earth.poly.R
R/jack1.R
R/ecol.dist.R
R/jack2.R
R/loc.map.R
R/msn2Shape.R
R/ACE.R
R/chao2.R
R/kulczynski.R
R/rand.index.R
R/ochiai.R
R/earth.dist.R
R/rclust.dist.R
R/chao.sd.R
R/simpson.R
R/create.lats.R
R/create.matrix.R
R/spp.est.R
R/sim.occ.R
R/int.chao.R
R/lats2Shape.R
R/dino.msn.R
R/braun.blanquet.R
R/chao.sorenson.R
R/tri.ineq.R
R/ICE.R
R/msn.map.R
R/chao1.R
data
data/fdata.list.rda
data/fdata.lats.rda
data/fdata.mat.rda
fossil documentation built on May 19, 2017, 8:26 p.m.