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Converte EndNote exports as BibTex using R
##从Endnote导出BibTex格式的文本文档后,由于缺少BibTex的文献标签(key)。
##以下R程序就是给导出的文本文档给每条文献逐条加上BibTex所需要的标签。
##标签的格式是'James:2010'。如果是两位作者,则为'James-White:2010'。如果是
##三位及其以上作者,则为'James-etal:2010'。
##若刚好碰到文献的标签有重复,如某一作者在同一年不同杂志上发表了多篇
##论文,则用a,b,c...来区分标记,即'James:2010a','James:2010b','James:2010c'。
##
## 斯幸峰(http://www.sixf.org) 2014年3月28日
##
oldbib.ori = read.delim(file.choose(),h=F,stringsAsFactors=F) # load the file "oldbib.txt"
oldbib=oldbib.ori[,1]
# check '@' for each line
at.f=function(test){
test=as.character(test)
ntest=nchar(test)
testsplit=strsplit(test,NULL)[[1]]
en.res=paste(testsplit[testsplit%in%c("@")],collapse="")
en.res
}
# retrive English letters
en.f=function(test){
test=as.character(test)
ntest=nchar(test)
testsplit=strsplit(test,NULL)[[1]]
en.res=paste(testsplit[testsplit%in%c(LETTERS,letters)],collapse="")
en.res
}
# retrive Chinese letter
marknotes=c(" ","-","‐",".","(",")",",","’","=","{","}")
specialletters=c("ç","ó","á","é","í","ø","ä","ú","ñ","å","Ø","ï","ã","š","ü")
zh.f=function(test){
test=as.character(test)
ntest=nchar(test)
testsplit=strsplit(test,NULL)[[1]]
zh.res=paste(testsplit[!testsplit%in%c(LETTERS,letters,marknotes,specialletters)],collapse="")
zh.res
}
# Number of authors
author.f=function(test){
test=as.character(test)
if (length(strsplit(test,"author =")[[1]])>1) {
author.no=length(strsplit(test," and ")[[1]])
} else {
author.no=0
}
author.no
}
# retrive the year
number.f=function(test){
test=as.character(test)
ntest=nchar(test)
if (length(strsplit(test,"year =")[[1]])>1) {
testsplit=strsplit(test,NULL)[[1]]
number.res=paste(testsplit[testsplit%in%c(0:9)],collapse="")
} else {number.res="NA"}
number.res
}
# create a blank matrix to store the line number of each reference with
# corresponding line numbers of author and year.
idx.mat=matrix(NA,ncol=3,nrow=length(oldbib),dimnames=list(1:length(oldbib),c("ref","author","year")))
for (i in 1:1:length(oldbib)) {
if (at.f(oldbib[i])=="@") idx.mat[i,1]=i
if (author.f(oldbib[i])!=0) idx.mat[i,2]=i
if (number.f(oldbib[i])!="NA") idx.mat[i,3]=i
}
# exclude the 'NA' in the 'idx.mat'
# so the rownumber of 'idx.ref' is the total number of reference.
idx.ref=idx.mat[!is.na(idx.mat[,1]),]
rownames(idx.ref)=1:dim(idx.ref)[1]
idx.ref[,2]=idx.mat[!is.na(idx.mat[,2]),2]
idx.ref[,3]=idx.mat[!is.na(idx.mat[,3]),3]
# function of creating the key for each reference
key.f=function(idx.ref){
test=oldbib[idx.ref[2]]
left.no = which(strsplit(test,NULL)[[1]]=="{")
right.no = which(strsplit(test,NULL)[[1]]=="}")
comma.no = which(strsplit(test,NULL)[[1]]==",")
new.name.line=substr(test,left.no+1,right.no-1)
author.no = length(strsplit(new.name.line," and ")[[1]])
if (author.no==1) { # only one author in the reference
if (zh.f(test)!="") { # check whether this is a Chinese reference
author=zh.f(strsplit(new.name.line," and ")[[1]][1])
year=number.f(oldbib[idx.ref[3]])
key=paste(author,":",year,sep="")
} else { # or else considering as English. Similar as below.
author=en.f(substr(test,left.no+1,comma.no[1]-1))
year=number.f(oldbib[idx.ref[3]])
key=paste(author,":",year,sep="")
}
}
if (author.no==2) { # two authors in the reference
if (nchar(en.f(test))<12) { # or use: zh.f(test)!=""
author1=zh.f(strsplit(new.name.line," and ")[[1]][1])
author2=zh.f(strsplit(new.name.line," and ")[[1]][2])
year=number.f(oldbib[idx.ref[3]])
key=paste(author1,"-",author2,":",year,sep="")
} else {
author1=en.f(substr(test,left.no+1,comma.no[1]-1))
fullname2=strsplit(new.name.line," and ")[[1]][2]
comma.no2=which(strsplit(fullname2,NULL)[[1]]==",")
author2=substr(fullname2,1,comma.no2-1)
year=number.f(oldbib[idx.ref[3]])
key=paste(author1,"-",author2,":",year,sep="")
}
}
if (author.no>2) { # three or more authors in the reference
if (nchar(en.f(test))<20) { # or use: zh.f(test)!=""
author=zh.f(strsplit(new.name.line," and ")[[1]][1])
year=number.f(oldbib[idx.ref[3]])
key=paste(author,"-etal:",year,sep="")
} else {
author=en.f(substr(test,left.no+1,comma.no[1]-1))
year=number.f(oldbib[idx.ref[3]])
key=paste(author,"-etal:",year,sep="")
}
}
key
}
# create the key
key.df=as.data.frame(idx.ref)
key.df$key=apply(idx.ref,1,key.f)
# add 'a','b','c'... as a suffix for the same keys
for (i in 1:dim(key.df)[1]) {
key.rep=which(key.df$key%in%key.df$key[i])
key.no=length(key.rep)
if (key.no>1) {
for (j in 1:key.no) {
key.df[key.rep[j],"key"]=paste(key.df[key.rep[j],"key"],letters[j],sep="")
}
}
}
# check whether each key is unique.
max(table(key.df$key)) # if the result is 1, then continue
# create the new bibliography as 'newbib'
newbib=oldbib.ori[,1]
for (i in 1:dim(key.df)[1]) {
newbib[key.df[i,"ref"]]=paste(oldbib[key.df[i,"ref"]],key.df[i,"key"],",",sep="")
}
# write the new bibliography 'newbib' as 'newbib.bib' in the console
write.table(newbib,"newbib.bib",row.names=F,col.names=F,quote=FALSE)
@article{斯幸峰-丁平:2011,
author = {斯幸峰 and 丁平},
title = {欧美陆地鸟类监测的历史, 现状与我国的对策},
journal = {生物多样性},
volume = {19},
pages = {303-310},
year = {2011},
type = {Journal Article}
}
@article{Abbott:1983,
author = {Abbott, Ian},
title = {The Meaning of z in Species/Area Regressions and the Study of Species Turnover in Island Biogeography},
journal = {Oikos},
volume = {41},
pages = {385-390},
year = {1983},
type = {Journal Article}
}
@article{Aguirre-etal:2003,
author = {Aguirre, Luis F and Lens, Luc and van Damme, Raoul and Matthysen, Erik},
title = {Consistency and variation in the bat assemblages inhabiting two forest islands within a neotropical savanna in Bolivia},
journal = {Journal of Tropical Ecology},
volume = {19},
pages = {367-374},
year = {2003},
type = {Journal Article}
}
@article{AlmeidaNeto-etal:2012,
author = {Almeida‐Neto, Mário and Frensel, Daniella and Ulrich, Werner},
title = {Rethinking the relationship between nestedness and beta diversity: a comment on Baselga (2010)},
journal = {Global Ecology and Biogeography},
volume = {21},
pages = {772-777},
year = {2012},
type = {Journal Article}
}
@book{Anderson:2008,
author = {Anderson, David Raymond},
title = {Model based inference in the life sciences: a primer on evidence},
publisher = {Springer},
address = {New York, NY},
ISBN = {0387740759},
year = {2008},
type = {Book}
}
@article{Azeria:2004,
author = {Azeria, Ermias T},
title = {Terrestrial bird community patterns on the coralline islands of the Dahlak Archipelago, Red Sea, Eritrea},
journal = {Global Ecology and Biogeography},
volume = {13},
pages = {177-187},
year = {2004},
type = {Journal Article}
}
@article{Azeria-etal:2006,
author = {Azeria, Ermias T. and Carlson, Allan and Pärt, Tomas and Wiklund, Christer G.},
title = {Temporal dynamics and nestedness of an oceanic island bird fauna},
journal = {Global Ecology and Biogeography},
volume = {15},
pages = {328-338},
year = {2006},
type = {Journal Article}
}
@article{Bach-etal:2007,
author = {Bach, K and Kessler, M and Gradstein, SR},
title = {A simulation approach to determine statistical significance of species turnover peaks in a species‐rich tropical cloud forest},
journal = {Diversity and Distributions},
volume = {13},
pages = {863-870},
year = {2007},
type = {Journal Article}
}
@article{Baeten-etal:2012a,
author = {Baeten, Lander and Vangansbeke, Pieter and Hermy, Martin and Peterken, George and Vanhuyse, Kathleen and Verheyen, Kris},
title = {Distinguishing between turnover and nestedness in the quantification of biotic homogenization},
journal = {Biodiversity and Conservation},
volume = {21},
pages = {1399-1409},
year = {2012},
type = {Journal Article}
}
@article{Baeten-etal:2012b,
author = {Baeten, Lander and Vangansbeke, Pieter and Hermy, Martin and Peterken, George and Vanhuyse, Kathleen and Verheyen, Kris},
title = {Distinguishing between turnover and nestedness in the quantification of biotic homogenization},
journal = {Biodiversity and Conservation},
volume = {21},
pages = {1399-1409},
year = {2012},
type = {Journal Article}
}
@article{Bahn-McGill:2013,
author = {Bahn, Volker and McGill, Brian J.},
title = {Testing the predictive performance of distribution models},
journal = {Oikos},
pages = {no-no},
year = {2013},
type = {Journal Article}
}
@article{Baiser-Lockwood:2011,
author = {Baiser, Benjamin and Lockwood, Julie L.},
title = {The relationship between functional and taxonomic homogenization},
journal = {Global Ecology and Biogeography},
volume = {20},
pages = {134-144},
year = {2011},
type = {Journal Article}
}
@article{Baiser-etal:2012,
author = {Baiser, Benjamin and Olden, Julian D. and Record, Sydne and Lockwood, Julie L. and McKinney, Michael L.},
title = {Pattern and process of biotic homogenization in the New Pangaea},
journal = {Proceedings of the Royal Society B: Biological Sciences},
volume = {279},
pages = {4772-4777},
year = {2012},
type = {Journal Article}
}
@article{Barbaro-etal:2014,
author = {Barbaro, Luc and Giffard, Brice and Charbonnier, Yohan and van Halder, Inge and Brockerhoff, Eckehard G.},
title = {Bird functional diversity enhances insectivory at forest edges: a transcontinental experiment},
journal = {Diversity and Distributions},
volume = {20},
pages = {149-159},
year = {2014},
type = {Journal Article}
}
@article{Barton-etal:2013,
author = {Barton, Philip S. and Cunningham, Saul A. and Manning, Adrian D. and Gibb, Heloise and Lindenmayer, David B. and Didham, Raphael K.},
title = {The spatial scaling of beta diversity},
journal = {Global Ecology and Biogeography},
volume = {22},
pages = {639-647},
year = {2013},
type = {Journal Article}
}
@article{Baselga:2008,
author = {Baselga, Andrés},
title = {Determinants of species richness, endemism and turnover in European longhorn beetles},
journal = {Ecography},
volume = {31},
pages = {263-271},
year = {2008},
type = {Journal Article}
}
@article{Baselga:2010,
author = {Baselga, Andrés},
title = {Partitioning the turnover and nestedness components of beta diversity},
journal = {Global Ecology and Biogeography},
volume = {19},
pages = {134-143},
year = {2010},
type = {Journal Article}
}
@article{Baselga:2012,
author = {Baselga, Andrés},
title = {The relationship between species replacement, dissimilarity derived from nestedness, and nestedness},
journal = {Global Ecology and Biogeography},
volume = {21},
pages = {1223-1232},
year = {2012},
type = {Journal Article}
}
@article{Baselga:2013a,
author = {Baselga, Andrés},
title = {Separating the two components of abundance-based dissimilarity: balanced changes in abundance vs. abundance gradients},
journal = {Methods in Ecology and Evolution},
volume = {4},
pages = {552-557},
year = {2013},
type = {Journal Article}
}
@article{Baselga:2013b,
author = {Baselga, Andrés},
title = {Multiple site dissimilarity quantifies compositional heterogeneity among several sites, while average pairwise dissimilarity may be misleading},
journal = {Ecography},
volume = {36},
pages = {124-128},
year = {2013},
type = {Journal Article}
}
@article{Baselga-etal:2012a,
author = {Baselga, Andrés and Gómez-Rodríguez, Carola and Lobo, Jorge M},
title = {Historical legacies in world amphibian diversity revealed by the turnover and nestedness components of beta diversity},
journal = {PloS one},
volume = {7},
pages = {e32341},
year = {2012},
type = {Journal Article}
}
@article{Baselga-etal:2007,
author = {Baselga, Andrés and Jiménez-Valverde, Alberto and Niccolini, Gilles},
title = {A multiple-site similarity measure independent of richness},
journal = {Biology Letters},
volume = {3},
pages = {642-645},
year = {2007},
type = {Journal Article}
}
@article{Baselga-etal:2012b,
author = {Baselga, Andrés and Lobo, Jorge M and Svenning, Jens‐Christian and Aragón, Pedro and Araújo, Miguel B},
title = {Dispersal ability modulates the strength of the latitudinal richness gradient in European beetles},
journal = {Global Ecology and Biogeography},
volume = {21},
pages = {1106-1113},
year = {2012},
type = {Journal Article}
}
@article{Baselga-Orme:2012,
author = {Baselga, Andrés and Orme, C. David L.},
title = {betapart: an R package for the study of beta diversity},
journal = {Methods in Ecology and Evolution},
volume = {3},
pages = {808-812},
year = {2012},
type = {Journal Article}
}
@article{Beck-etal:2013,
author = {Beck, Jan and Holloway, Jeremy D. and Schwanghart, Wolfgang},
title = {Undersampling and the measurement of beta diversity},
journal = {Methods in Ecology and Evolution},
volume = {4},
pages = {370-382},
year = {2013},
type = {Journal Article}
}
@article{Bellemain-Ricklefs:2008,
author = {Bellemain, Eva and Ricklefs, Robert E},
title = {Are islands the end of the colonization road?},
journal = {Trends in Ecology & Evolution},
volume = {23},
pages = {461-468},
year = {2008},
type = {Journal Article}
}
@article{Bellier-etal:2014,
author = {Bellier, Edwige and Grøtan, Vidar and Engen, Steinar and Schartau, Ann Kristin and Herfindal, Ivar and Finstad, Anders G},
title = {Distance decay of similarity, effects of environmental noise and ecological heterogeneity among species in the spatio‐temporal dynamics of a dispersal‐limited community},
journal = {Ecography},
volume = {37},
pages = {172-182},
year = {2014},
type = {Journal Article}
}
@article{Berg-etal:2011,
author = {Berg, Sofia and Christianou, Maria and Jonsson, Tomas and Ebenman, Bo},
title = {Using sensitivity analysis to identify keystone species and keystone links in size-based food webs},
journal = {Oikos},
volume = {120},
pages = {510-519},
year = {2011},
type = {Journal Article}
}
@book{Bibby-etal:2000,
author = {Bibby, Colin J. and Burgess, N. D. and Hill, D. A. and Mustoe, S.},
title = {Bird Census Techniques},
publisher = {Academic Press},
address = {London},
edition = {2nd},
year = {2000},
type = {Book}
}
@article{Blackburn-Gaston:1996,
author = {Blackburn, Tim M. and Gaston, Kevin J.},
title = {The Distribution of Bird Species in the New World: Patterns in Species Turnover},
journal = {Oikos},
volume = {77},
pages = {146-152},
year = {1996},
type = {Journal Article}
}
@inbook{Boecklen-Simberloff:1986,
author = {Boecklen, WILLIAM J and Simberloff, DANIEL},
title = {Area-based extinction models in conservation},
booktitle = {Dynamics of extinction},
editor = {Elliott, D K},
publisher = {John Wiley & Sons},
address = {New York, NY},
pages = {247-276},
year = {1986},
type = {Book Section}
}
@book{Burnham-Anderson:2002,
author = {Burnham, Kenneth P and Anderson, David R},
title = {Model Selection and Multi-model Inference: a Practical Information-theoretic Approach},
publisher = {Springer Verlag},
address = {New York, NY},
edition = {2nd},
ISBN = {0387953647},
year = {2002},
type = {Book}
}
@article{Burns-Neufeld:2009,
author = {Burns, Kevin C. and Neufeld, Christopher J.},
title = {Plant extinction dynamics in an insular metacommunity},
journal = {Oikos},
volume = {118},
pages = {191-198},
year = {2009},
type = {Journal Article}
}
@article{Bush-Whittaker:1993,
author = {Bush, Mark B and Whittaker, Robert J},
title = {Non-equilibration in island theory of Krakatau},
journal = {Journal of Biogeography},
pages = {453-457},
year = {1993},
type = {Journal Article}
}
@article{CaldernPatrn-etal:2013,
author = {Calderón-Patrón, Jaime M and Moreno, Claudia E and Pineda-López, Rubén and Sánchez-Rojas, Gerardo and Zuria, Iriana},
title = {Vertebrate Dissimilarity Due to Turnover and Richness Differences in a Highly Beta-Diverse Region: The Role of Spatial Grain Size, Dispersal Ability and Distance},
journal = {PloS one},
volume = {8},
pages = {e82905},
year = {2013},
type = {Journal Article}
}
@article{Carstensen-etal:2013,
author = {Carstensen, Daniel W. and Dalsgaard, Bo and Svenning, Jens-Christian and Rahbek, Carsten and Fjeldså, Jon and Sutherland, William J. and Olesen, Jens M.},
title = {The functional biogeography of species: biogeographical species roles of birds in Wallacea and the West Indies},
journal = {Ecography},
pages = {no-no},
year = {2013},
type = {Journal Article}
}
@article{Carvalho-etal:2012,
author = {Carvalho, José C and Cardoso, Pedro and Gomes, Pedro},
title = {Determining the relative roles of species replacement and species richness differences in generating beta‐diversity patterns},
journal = {Global Ecology and Biogeography},
volume = {21},
pages = {760-771},
year = {2012},
type = {Journal Article}
}
@article{Ferraz-etal:2003,
author = {Ferraz, G. and Russell, G. J. and Stouffer, P. C. and Bierregaard, R. O. and Pimm, S. L. and Lovejoy, T. E.},
title = {Rates of species loss from Amazonian forest fragments},
journal = {Proceedings of the National Academy of Sciences USA},
volume = {100},
pages = {14069-14073},
year = {2003},
type = {Journal Article}
}
@article{Ficetola-etal:2012,
author = {Ficetola, Gentile Francesco and Bonardi, Anna and Sindaco, Roberto and Padoa-Schioppa, Emilio},
title = {Estimating patterns of reptile biodiversity in remote regions},
journal = {Journal of Biogeography},
pages = {n/a-n/a},
year = {2012},
type = {Journal Article}
}
@article{Fischer-Lindenmayer:2007,
author = {Fischer, Joern and Lindenmayer, David B},
title = {Landscape modification and habitat fragmentation: a synthesis},
journal = {Global Ecology and Biogeography},
volume = {16},
pages = {265-280},
year = {2007},
type = {Journal Article}
}
@article{McKnight-etal:2007,
author = {McKnight, Meghan W and White, Peter S and McDonald, Robert I and Lamoreux, John F and Sechrest, Wes and Ridgely, Robert S and Stuart, Simon N},
title = {Putting beta-diversity on the map: broad-scale congruence and coincidence in the extremes},
journal = {PLoS biology},
volume = {5},
pages = {e272},
year = {2007},
type = {Journal Article}
}
@article{McNaughton:1977,
author = {McNaughton, S. J.},
title = {Diversity and Stability of Ecological Communities: A Comment on the Role of Empiricism in Ecology},
journal = {The American Naturalist},
volume = {111},
pages = {515-525},
year = {1977},
type = {Journal Article}
}
@article{Morrison:1998,
author = {Morrison, Lloyd W.},
title = {The spatiotemporal dynamics of insular ant metapopulations},
journal = {Ecology},
volume = {79},
pages = {1135-1146},
year = {1998},
type = {Journal Article}
}
@article{Morrison:2002a,
author = {Morrison, Lloyd W.},
title = {Determinants of plant species richness on small Bahamian islands},
journal = {Journal of Biogeography},
volume = {29},
pages = {931-941},
year = {2002},
type = {Journal Article}
}
@article{Morrison:2002b,
author = {Morrison, Lloyd W.},
title = {Island biogeography and metapopulation dynamics of Bahamian ants},
journal = {Journal of Biogeography},
volume = {29},
pages = {387-394},
year = {2002},
type = {Journal Article}
}
@article{Morrison:2010a,
author = {Morrison, Lloyd W.},
title = {Disequilibrial island turnover dynamics: a 17-year record of Bahamian ants},
journal = {Journal of Biogeography},
volume = {37},
pages = {2148-2157},
year = {2010},
type = {Journal Article}
}
@article{Morrison:2010b,
author = {Morrison, Lloyd W.},
title = {Long-term non-equilibrium dynamics of insular floras: a 17-year record},
journal = {Global Ecology and Biogeography},
volume = {19},
pages = {663-672},
year = {2010},
type = {Journal Article}
}
@article{Morrison:2010c,
author = {Morrison, Lloyd W.},
title = {Disequilibrial island turnover dynamics: a 17-year record of Bahamian ants},
journal = {Journal of Biogeography},
volume = {37},
pages = {2148-2157},
year = {2010},
type = {Journal Article}
}
@article{Morrison:2011,
author = {Morrison, Lloyd W.},
title = {Why do some small islands lack vegetation? Evidence from long-term introduction experiments},
journal = {Ecography},
volume = {34},
pages = {384-391},
year = {2011},
type = {Journal Article}
}
@article{Schoener:1983a,
author = {Schoener, Thomas W.},
title = {Rate of Species Turnover Decreases from Lower to Higher Organisms: A Review of the Data},
journal = {Oikos},
volume = {41},
pages = {372-377},
year = {1983},
type = {Journal Article}
}
@article{Schoener:1983b,
author = {Schoener, Thomas W},
title = {Field experiments on interspecific competition},
journal = {American naturalist},
pages = {240-285},
year = {1983},
type = {Journal Article}
}
@article{Schoener:1983c,
author = {Schoener, Thomas W.},
title = {Rate of species turnover decreases from lower to higher organisms: a review of the data},
journal = {Oikos},
pages = {372-377},
year = {1983},
type = {Journal Article}
}
@inbook{Schoener:2010,
author = {Schoener, Thomas W},
title = {The MacArthur-Wilson equilibrium model: a chronicle of what it said and how it was tested},
booktitle = {The Theory of Island Biogeography Revisited},
editor = {Losos, Jonathan B and Ricklefs, Robert E},
publisher = {Princeton University Press},
address = {Princeton},
pages = {52-87},
ISBN = {069113653X},
year = {2010},
type = {Book Section}
}
@article{Schoereder-etal:2004,
author = {Schoereder, José H. and Galbiati, Carla and Ribas, Carla R. and Sobrinho, Tathiana G. and Sperber, Carlos F. and DeSouza, Og and Lopes-Andrade, Cristiano},
title = {Should we use proportional sampling for species–area studies?},
journal = {Journal of Biogeography},
volume = {31},
pages = {1219-1226},
year = {2004b},
type = {Journal Article}
}
@article{Simberloff:1976,
author = {Simberloff, Daniel},
title = {Species turnover and equilibrium island biogeography},
journal = {Science},
volume = {194},
pages = {572-578},
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author = {Villéger, Sébastien and Mason, Norman WH and Mouillot, David},
title = {New multidimensional functional diversity indices for a multifaceted framework in functional ecology},
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pages = {2290-2301},
year = {2008},
type = {Journal Article}
}
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author = {Villéger, Sébastien and Miranda, Julia Ramos and Hernandez, Domingo Flores and Mouillot, David},
title = {Low functional β-diversity despite high taxonomic β-diversity among tropical estuarine fish communities},
journal = {PloS ONE},
volume = {7},
pages = {e40679},
year = {2012},
type = {Journal Article}
}
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author = {Villéger, Sébastien and Novack‐Gottshall, Philip M and Mouillot, David},
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pages = {561-568},
year = {2011},
type = {Journal Article}
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author = {Wolfram Research Inc},
title = {Mathematica Edition Version 9.0},
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