Package MBI. February 19, 2015
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1 Type Package Package MBI February 19, 2015 Title (M)ultiple-site (B)iodiversity (I)ndices Calculator Version 1.0 Date Author Youhua Chen Maintainer Over 20 multiple-site diversity indices can be calculated. Later versions will include phylogenetic diversity License GPL-2 Repository CRAN Date/Publication :45:03 NeedsCompilation no R topics documented: MBI-package batch.calculation cfull cl cn crep crich ct do harrison ht mjaccard ml mn mrep mrich msorensen
2 2 MBI-package mt rarity wbeta wnodf wt Index 24 MBI-package MBI: (M)ultiple-site (B)iodiversity (I)ndices Calculator Details Over 20 multiple-site beta diversity indices can be calculated. Later versions will include phylogenetic diversity Package: MBI Type: Package Version: 1.0 Date: License: GPL-2 Author: Youhua Chen Maintainer:
3 batch.calculation 3 batch.calculation(test) batch.calculation calculate all diversity indices at the same time calculate all diversity indices at the same time,will return a table, each column indicates one index batch.calculation(mat) mat mat can be in a form of a single matrix, or a list of matrices for batch handling. Details will return a table, each column indicates one index batch.calculation(test)
4 4 cfull cfull calculate Baselga s biodiversity index (nestdness+turnover) calculate Baselga s biodiversity index (nestdness+turnover) cfull() cn, ct, batch.calculation cfull(test)
5 cl 5 cl calculate Lennon s multiple-site richness index this is a multiple-site version without calculating pairwise Lennon s richness index, see the average version of pairwise Lennon s richness index for comparison: ml() cl() Lennon J, Koleff P, Greenwood J, Gaston K (2001) The geographical structure of British bird distributions: diversity, spatial turnover and scale. Journal of Animal Ecology, 70, ml cl(test)
6 6 cn cn Calculate Baselga s multiple-site nestedness index another version is the average of Baselga s pairwise-site nestedness index, see the function of mn() cn() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, ct, cfull, mn cn(test)
7 crep 7 crep Calculate Carvalho s multiple-site replacement index Another version is the average of Carvalho s pairwise-site replacement index across all pairs of sites, see the function of mrep() crep() Carvalho J, Cardoso P, Gomes P (2012) Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. Global Ecology and Biogeography, 21, crich, mrep crep(test)
8 8 crich crich Calculate Carvalho s multiple-site richness difference index Another version is the average of Carvalho s pairwise-site richness difference index across all pairs of sites, see the function of mrich() crich() Carvalho J, Cardoso P, Gomes P (2012) Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. Global Ecology and Biogeography, 21, crep, mrich crich(test)
9 ct 9 ct Calculate Baselga s multiple-site turnover index another version is the average of Baselga s pairwise-site turnover index, see the function of mt() ct() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, cn, cfull, mt ct(test)
10 10 do do Calculate Diserud-Odegaard s index See Chen (2012),or Baselga (2010) Diserud and Odegaard (2007) for introduction of the index do() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, Diserud O, Odegaard F (2007) A multiple-site similarity measure. Biology Letters, 3, batch.calculation do(test)
11 harrison 11 harrison Calculate Harrison s dissimilarity index See Chen (2012) or Baselga (2010) for introduction of the index harrison() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, batch.calculation harrison(test)
12 12 ht ht Calculate Harrison s turnover index See Chen (2012) or Baselga (2010) for introduction of the index ht() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, batch.calculation ht(test)
13 mjaccard 13 mjaccard Calculate the average of Jaccard pairwise-site dissimilarity index across all pairs of sites Calculate the average of Jaccard pairwise-site dissimilarity index across all pairs of sites mjaccard() batch.calculation mjaccard(test)
14 14 ml ml calculate the average Lennon s pairwise-site richness index this is the average version of pairwise Lennon s richness index, see a multiple-site version without calculating pairwise Lennon s richness index for comparison: cl() ml() Lennon J, Koleff P, Greenwood J, Gaston K (2001) The geographical structure of British bird distributions: diversity, spatial turnover and scale. Journal of Animal Ecology, 70, cl ml(test)
15 mn 15 mn Calculate the average of Baselga s pairwise-site nestedness index across all pairs of sites Another version is Baselga s multiple-site nestedness index across all pairs of sites, see the function of cn() mn() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, cn, cfull, mt mn(test)
16 16 mrep mrep Calculate the average of Carvalho s pairwise-site replacement index across all pairs of sites Another version is Carvalho s multiple-site replacement index, see the function of crep() mrep() Carvalho J, Cardoso P, Gomes P (2012) Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. Global Ecology and Biogeography, 21, crep, mrich mrep(test)
17 mrich 17 mrich Calculate the average of Carvalho s pairwise-site richness difference index across all pairs of sites Another version is Carvalho s multiple-site richness difference index, see the function of crich() mrich() Carvalho J, Cardoso P, Gomes P (2012) Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. Global Ecology and Biogeography, 21, crich, mrep mrich(test)
18 18 msorensen msorensen Calculate the average of Sorensen pairwise-site dissimilarity index across all pairs of sites Calculate the average of Sorensen pairwise-site dissimilarity index across all pairs of sites msorensen() batch.calculation msorensen(test)
19 mt 19 mt Calculate the average of Baselga s pairwise-site turnover index across all pairs of sites Another version is Baselga s multiple-site turnover index across all pairs of sites, see the function of ct() mt() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, ct, cfull, mn mt(test)
20 20 rarity rarity Calculate rarity degrees (decided by the argument "percent") based on distributional ranges of species and abundance of species argument "percent" determines the rarity degree you want to calculate rarity(, percent = 0.3) percent determines the rarity degree you want to calculate. default is.3, meaning that species have distributional sites less than 30 Details Value This index is not beta diversity index, thus not being included in the batch.calculation() function return two percentage values, one denotes the range rarity percentage, another denotes the abundance rarity percentage rarity(test,percent=.3)
21 wbeta 21 wbeta Calculate Whittaker s beta diversity index See Chen (2012) and Baselga (2010) for introduction of the index, this index can have value larger than 1. wbeta() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, batch.calculation wbeta(test)
22 22 wnodf wnodf Calculate Almeida-Neto and Ulrich s nestedness index Calculate Almeida-Neto and Ulrich s nestedness index, can handle both abundance and occurrence situations automatically wnodf() Almeida-Neto M, Ulrich W (2011) A straightforward computational approach for measuring nestedness using quantitative matrices. Environmental Modelling and Software, 26, Almeida-Neto M, Guimaraes P, Guimaraes P, Loyola R, Ulrich W (2008) A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos, 117, batch.calculation wnodf(test)
23 wt 23 wt Calculate Williams s turnover index See Chen (2012) or Baselga (2010) for introduction of the index wt() Baselga A (2010) Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, batch.calculation wt(test)
24 Index batch.calculation, 3, 4, 10 13, 18, cfull, 4, 6, 9, 15, 19 cl, 5, 14 cn, 4, 6, 9, 15 crep, 7, 8, 16 crich, 7, 8, 17 ct, 4, 6, 9, 19 do, 10 harrison, 11 ht, 12 MBI (MBI-package), 2 MBI-package, 2 mjaccard, 13 ml, 5, 14 mn, 6, 15, 19 mrep, 7, 16, 17 mrich, 8, 16, 17 msorensen, 18 mt, 9, 15, 19 rarity, 20 wbeta, 21 wnodf, 22 wt, 23 24
Appendix S1 Replacement, richness difference and nestedness indices
Appendix to: Legendre, P. (2014) Interpreting the replacement and richness difference components of beta diversity. Global Ecology and Biogeography, 23, 1324-1334. Appendix S1 Replacement, richness difference
BAT Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity
Methods in Ecology and Evolution 2015, 6, 232 236 doi: 10.1111/2041-210X.12310 APPLICATION BAT Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic
ecological area-network relations: methodology Christopher Moore cs765: complex networks 16 November 2011
ecological area-network relations: methodology Christopher Moore cs765: complex networks 16 November 2011 ecology: the study of the spatial and temporal patterns of the distribution and abundance of organisms,
betapart: an R package for the study of beta diversity Andre s Baselga 1 * and C. David L. Orme 2
Methods in Ecology and Evolution 2012, 3, 808 812 doi: 10.1111/j.2041-210X.2012.00224.x APPLICATION betapart: an R package for the study of beta diversity Andre s Baselga 1 * and C. David L. Orme 2 1 Departamento
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Measuring fractions of beta diversity and their relationships to. nestedness: a theoretical and empirical comparison of novel
1 Oikos 122: 825-834 (2013) 2 3 4 5 Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches 6 7 8 José C. Carvalho 1,2,*,
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Comparing methods to separate components of beta diversity
Methods in Ecology and Evolution 2015, 6, 1069 1079 doi: 10.1111/2041-210X.12388 Comparing methods to separate components of beta diversity Andres Baselga 1 * and Fabien Leprieur 2 1 Departamento de Zoologıa,
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Global Ecology and Biogeography, (Global Ecol. Biogeogr.) (2017) 26, 1 5 ECOLOGICAL SOUNDINGS The tangled link between b- and c-diversity: a Narcissus effect weakens statistical inferences in null model
MBI: an R package for calculating multiple-site beta diversity indices
Artcle MBI: an R package for calculatng multple-ste beta dversty ndces YouHua Chen Department of Zoology, Unversty of Brtsh Columba, Vancouver, V6T Z4, Canada E-mal: yhchen@zoology.ubc.ca, hayd@26.com
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Package GORCure January 13, 2017 Type Package Title Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data Version 2.0 Date 2017-01-12 Author Jie Zhou, Jiajia Zhang, Wenbin Lu Maintainer
Package factorqr. R topics documented: February 19, 2015
Package factorqr February 19, 2015 Version 0.1-4 Date 2010-09-28 Title Bayesian quantile regression factor models Author Lane Burgette , Maintainer Lane Burgette
Package SPECIES. R topics documented: April 23, Type Package. Title Statistical package for species richness estimation. Version 1.
Package SPECIES April 23, 2011 Type Package Title Statistical package for species richness estimation Version 1.0 Date 2010-01-24 Author Ji-Ping Wang, Maintainer Ji-Ping Wang
Package GD. January 12, 2018
Tpe Package Title Geographical Detectors Date 2017-12-22 Version 1.1 Package GD Januar 12, 2018 Maintainer Yongze Song Geographical detectors for measuring spatial stratified
Package flora. R topics documented: August 29, Type Package. Title flora: taxonomical information on flowering species that occur in Brazil
Package flora August 29, 2013 Type Package Title flora: taxonomical information on flowering species that occur in Brazil Version 0.1 Date 2013-07-03 Author Gustavo Carvalho Maintainer Gustavo Carvalho
Package crossreg. February 19, 2015
Package crossreg February 19, 2015 Type Package Title Confidence intervals for crossover points of two simple regression lines Version 1.0 Date 2014-07-08 Author Maintainer This package
Package IsingFit. September 7, 2016
Type Package Package IsingFit September 7, 2016 Title Fitting Ising Models Using the ELasso Method Version 0.3.1 Date 2016-9-6 Depends R (>= 3.0.0) Imports qgraph, Matrix, glmnet Suggests IsingSampler
Package pfa. July 4, 2016
Type Package Package pfa July 4, 2016 Title Estimates False Discovery Proportion Under Arbitrary Covariance Dependence Version 1.1 Date 2016-06-24 Author Jianqing Fan, Tracy Ke, Sydney Li and Lucy Xia
Package jaccard. R topics documented: June 14, Type Package
Tpe Package Package jaccard June 14, 2018 Title Test Similarit Between Binar Data using Jaccard/Tanimoto Coefficients Version 0.1.0 Date 2018-06-06 Author Neo Christopher Chung , Błażej
Package sscor. January 28, 2016
Type Package Package sscor January 28, 2016 Title Robust Correlation Estimation and Testing Based on Spatial Signs Version 0.2 Date 2016-01-19 Depends pcapp, robustbase, mvtnorm Provides the spatial sign