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.

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
http://matthewvavrek.com/programs-and-code/fossil/

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

Functions

ACE Man page
adj.rand.index Man page
aic.nest Man page
bootstrap Man page
braun.blanquet Man page
bray.curtis Man page
chao1 Man page
chao2 Man page
chao.jaccard Man page
chao.sorenson 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
ICE Man page
int.chao Man page
jaccard Man page
jack1 Man page
jack2 Man page
kulczynski Man page
lats2Shape Man page
localoptima Man page
loc.map Man page
manhattan Man page
morisita.horn Man page
msn2Shape Man page
msn.map 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
rclust.null Man page
rclust.weights Man page
relational.clustering Man page
sac Man page
sim.occ Man page
simpson Man page
sorenson Man page
spp.est Man page
tri.ineq Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.