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

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

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

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