Package: fossil 0.4.0

Matthew J. Vavrek

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.

Authors:Matthew J. Vavrek <[email protected]>

fossil_0.4.0.tar.gz
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fossil.pdf |fossil.html✨
fossil/json (API)

# Install 'fossil' in R:
install.packages('fossil', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

5.23 score 1 stars 7 packages 550 scripts 1.5k downloads 44 mentions 54 exports 5 dependencies

Last updated 5 years agofrom:f139d41cea. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-linuxOKDec 18 2024

Exports:ACEadj.rand.indexaic.nestbootstrapbraun.blanquetbray.curtischao.jaccardchao.sdchao.sorensonchao1chao2coicreate.latscreate.matrixdeg.distdino.distdino.msndino.mstearth.bearearth.distearth.polyearth.triecol.disteuclideaneuler.rotICEint.chaojaccardjack1jack2kulczynskilats2Shapeloc.maplocaloptimamanhattanmorisita.hornmsn.mapmsn2Shapemstlinesnew.lat.longnmds.mstochiairand.indexrclustrclust.distrclust.nullrclust.weightsrelational.clusteringsacsim.occsimpsonsorensonspp.esttri.ineq

Dependencies:foreignlatticemapsshapefilessp

Readme and manuals

Help Manual

Help pageTopics
fossil: Palaeoecological and Palaeogeographical Analysis Toolsfossil-package fossil
Abundance- and Incidence-based Coverage EstimatorsACE ICE
Nestedness of samples using AICaic.nest
Bootstrap Species Richness Estimatorbootstrap
Chao's estimation of standard errorchao.sd
Chao's Jaccard and Sorenson Estimators of Shared Specieschao.jaccard chao.sorenson
Chao's Species Estimatorschao1 chao2
Cohesiveness Index for Relational Clusteringcoi
Creating a table of Latitudes and Longitudescreate.lats
Creating species locality matricescreate.matrix
Haversine Distance Formuladeg.dist
Calculate a Minimum Spanning Tree or Networkdino.msn dino.mst
Bearings Between Geographic Locationsearth.bear
Calculating Geographic Distancesearth.dist
Calculating a Minimum Convex Polygonearth.poly
Calculating the Surface Area Enclosed by Three Geographic Pointsearth.tri
Creating a Distance Matrixdino.dist ecol.dist
Calculate the Euler Rotation of a Pointeuler.rot
A Sample Species Abundance Datasetfdata.lats fdata.list fdata.mat
Internal function for chao estimatorsint.chao
First- and second-order jacknife estimatorsjack1 jack2
Converting a Table of Latitudes and Longitudes to a Shapefilelats2Shape
Mapping Points on a Global Maploc.map
Function to Find Local Optimization for clusteringlocaloptima
Mapping a Minimum Spanning Treemsn.map
Convert a Minimum spanning Network or Tree to Shapefilemsn2Shape
Display a Minimum Spanning Tree or Networkmstlines
Find a New Latitude and Longitudenew.lat.long
Creating NMDS plots with overlain Minimum Spanning Treesnmds.mst
Rand Index and Adjusted Rand Indexadj.rand.index rand.index
Relational Clusteringrclust
Relational Clusteringrclust.dist
Relational Clusteringrclust.null
Relational Clusteringrclust.weights
Relational Clusteringrelational.clustering
Calculate Species Area Curvessac
Simulated Species Occurrence datasim.occ
Similarity/Dissimilarity Indicesbraun.blanquet bray.curtis euclidean jaccard kulczynski manhattan morisita.horn ochiai simpson sorenson
Estimating Species Diversityspp.est
Testing for the Triangle Inequalitytri.ineq