├── main.pdf ├── ecobiblatex.pdf ├── ELE ├── ele.cbx └── ele.bbx ├── GEB ├── geb.cbx └── geb.bbx ├── TREE ├── tree.cbx └── tree.bbx ├── BES ├── bes.cbx └── bes.bbx ├── ICB ├── icb.cbx └── icb.bbx ├── main-blx.bib ├── README.md ├── main.tex ├── main.blg ├── main.aux ├── main.run.xml ├── main.bbl └── main.log /main.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tpoisot/ecobiblatex/HEAD/main.pdf -------------------------------------------------------------------------------- /ecobiblatex.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tpoisot/ecobiblatex/HEAD/ecobiblatex.pdf -------------------------------------------------------------------------------- /ELE/ele.cbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{ele.cbx}[biblatex style for Ecology Letters] 2 | 3 | \RequireCitationStyle{authoryear-comp} 4 | 5 | \endinput -------------------------------------------------------------------------------- /GEB/geb.cbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{geb.cbx}[biblatex style for Global Ecology and Biogegraphy] 2 | 3 | \RequireCitationStyle{authoryear-comp} 4 | 5 | \endinput -------------------------------------------------------------------------------- /TREE/tree.cbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{tree.cbx}[biblatex style for Trends in Ecology and Evolution] 2 | 3 | \RequireCitationStyle{numeric-comp} 4 | 5 | \endinput -------------------------------------------------------------------------------- /BES/bes.cbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{bes.cbx}[biblatex style for British Ecological Society journals] 2 | 3 | \RequireCitationStyle{authoryear-comp} 4 | 5 | \endinput -------------------------------------------------------------------------------- /ICB/icb.cbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{icb.cbx}[biblatex style for Integrative and Comparative Biology] 2 | 3 | \RequireCitationStyle{authoryear-comp} 4 | 5 | \endinput -------------------------------------------------------------------------------- /main-blx.bib: -------------------------------------------------------------------------------- 1 | @Comment{$ biblatex control file $} 2 | @Comment{$ biblatex version 1.7 $} 3 | Do not modify this file! 4 | 5 | This is an auxiliary file used by the 'biblatex' package. 6 | This file may safely be deleted. It will be recreated as 7 | required. 8 | 9 | @Control{biblatex-control, 10 | options = {1.7:0:0:1:0:0:1:1:0:0:1:0:2:1:2:1:79:+}, 11 | } 12 | -------------------------------------------------------------------------------- /TREE/tree.bbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{tree.bbx}[biblatex style for Trends in Ecology and Evolution] 2 | 3 | %% We build on the original author-year comp 4 | \RequireBibliographyStyle{standard} 5 | \RequireBibliographyStyle{numeric-comp} 6 | 7 | %% General options to match the ELE requirements 8 | \ExecuteBibliographyOptions 9 | { 10 | doi = false , 11 | eprint = false , 12 | firstinits = true , 13 | isbn = false , 14 | maxnames = 2 , 15 | minnames = 1 , 16 | url = false , 17 | dashed = false , 18 | sorting = none 19 | } 20 | 21 | %% Only the year is important 22 | \AtEveryBibitem{% 23 | \clearfield{day}% 24 | \clearfield{month}% 25 | \clearfield{endday}% 26 | \clearfield{endmonth}% 27 | } 28 | 29 | %% References are not spaced in the bibliography 30 | \setlength{\bibitemsep}{0px}% 31 | \setlength{\itemsep}{\bibitemsep}% 32 | 33 | \endinput -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # ecobiblatex 2 | 3 | A collaborative effort to provide biblatex files for most ecological journals. 4 | 5 | [Biblatex](https://github.com/plk/biblatex) is a set of LaTeX macros to handle the printing of citations and references, designed to work with [biber](http://biblatex-biber.sourceforge.net/). 6 | While it's really impressive and easy to use, there are not a lot of citation styles currently available, and this project aims to provide some for the most common ecological journals. 7 | 8 | The list below indicates which styles are implemented in the current release. 9 | The link refers to the instruction for authors pages. 10 | However, the correct format was taken from the list of references in a PDF of the latest issue at the time of the commit. 11 | 12 | ## Styles currently implemented 13 | 14 | [*Ecol. Lett.*](http://bit.ly/IdEIY5) 15 | [*Glob. Ecol. Biogeogr.*](http://bit.ly/JoUgbk) 16 | *British Ecological Society* 17 | [*Trends Ecol. Evol.*](http://bit.ly/ItbUrh) - in progress 18 | *Am. Nat.* - coming soon 19 | *Integr. Comp. Biol.* - in progress 20 | -------------------------------------------------------------------------------- /main.tex: -------------------------------------------------------------------------------- 1 | \documentclass[12pt]{article} 2 | 3 | 4 | 5 | \usepackage{geometry} 6 | \usepackage{setspace} 7 | \geometry{letterpaper} 8 | 9 | \usepackage[T1]{fontenc} 10 | \usepackage{kpfonts} 11 | 12 | \usepackage[style=BES/bes]{biblatex} 13 | \bibliography{library} 14 | 15 | \begin{document}\doublespacing 16 | 17 | \section*{EcoBib\LaTeX test file} 18 | 19 | This is a book as \texttt{parencite} \parencite{Darwin1859}, and as \texttt{textcite} 20 | \textcite{Elton1927}. This is a citation from a book chapter \parencite{Dunne2006}. 21 | 22 | This is a paper as \texttt{parencite} \parencite{Holt1996}, and as \texttt{textcite} 23 | \textcite{Anderson2011}. 24 | 25 | This is a citation command with two papers by the same author \parencite{Tuomisto2010,Tuomisto2011}. 26 | This is a citation command with more than two papers by the same author, on the same year 27 | \parencite{Frank1993,Frank1993a,Frank1993b}. 28 | 29 | This is a citation of a paper with only two authors in \texttt{parencite} 30 | \parencite{PoisotBJLS2010}, and another one in \texttt{textcite} \textcite{Yang2012}. 31 | 32 | This is a reference to R \parencite{R-Development-Core-Team2008}. This is a reference to 33 | non-consecutive entries \parencite{Yang2012,Dunne2006,Frank1993,Frank1993a,Frank1993b}. 34 | 35 | \printbibliography 36 | 37 | \end{document} -------------------------------------------------------------------------------- /main.blg: -------------------------------------------------------------------------------- 1 | This is BibTeX, Version 0.99c (TeX Live 2009/Debian) 2 | The top-level auxiliary file: main.aux 3 | The style file: biblatex.bst 4 | Reallocated wiz_functions (elt_size=4) to 6000 items from 3000. 5 | Database file #1: main-blx.bib 6 | Database file #2: library.bib 7 | Repeated entry---line 40963 of file library.bib 8 | : @article{Tuomisto2011 9 | : , 10 | I'm skipping whatever remains of this entry 11 | Biblatex version: 1.7 12 | Reallocated wiz_functions (elt_size=4) to 9000 items from 6000. 13 | You've used 14 entries, 14 | 6019 wiz_defined-function locations, 15 | 1251 strings with 16509 characters, 16 | and the built_in function-call counts, 49720 in all, are: 17 | = -- 2261 18 | > -- 1560 19 | < -- 551 20 | + -- 577 21 | - -- 535 22 | * -- 3588 23 | := -- 2928 24 | add.period$ -- 0 25 | call.type$ -- 14 26 | change.case$ -- 370 27 | chr.to.int$ -- 64 28 | cite$ -- 26 29 | duplicate$ -- 5504 30 | empty$ -- 5177 31 | format.name$ -- 870 32 | if$ -- 11326 33 | int.to.chr$ -- 0 34 | int.to.str$ -- 48 35 | missing$ -- 0 36 | newline$ -- 502 37 | num.names$ -- 810 38 | pop$ -- 4083 39 | preamble$ -- 1 40 | purify$ -- 400 41 | quote$ -- 0 42 | skip$ -- 2991 43 | stack$ -- 0 44 | substring$ -- 1752 45 | swap$ -- 2064 46 | text.length$ -- 355 47 | text.prefix$ -- 13 48 | top$ -- 1 49 | type$ -- 520 50 | warning$ -- 0 51 | while$ -- 342 52 | width$ -- 0 53 | write$ -- 487 54 | (There was 1 error message) 55 | -------------------------------------------------------------------------------- /main.aux: -------------------------------------------------------------------------------- 1 | \relax 2 | \bibstyle{biblatex} 3 | \bibdata{main-blx,library} 4 | \citation{biblatex-control} 5 | \citation{Darwin1859} 6 | \citation{Elton1927} 7 | \citation{Dunne2006} 8 | \citation{Holt1996} 9 | \citation{Anderson2011} 10 | \citation{Tuomisto2010} 11 | \citation{Tuomisto2011} 12 | \citation{Frank1993} 13 | \citation{Frank1993a} 14 | \citation{Frank1993b} 15 | \citation{PoisotBJLS2010} 16 | \citation{Yang2012} 17 | \citation{R-Development-Core-Team2008} 18 | \citation{Yang2012} 19 | \citation{Dunne2006} 20 | \citation{Frank1993} 21 | \citation{Frank1993a} 22 | \citation{Frank1993b} 23 | \@writefile{toc}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax } 24 | \@writefile{lof}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax } 25 | \@writefile{lot}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax } 26 | \abx@aux@page{1}{1} 27 | \abx@aux@page{2}{1} 28 | \abx@aux@page{3}{1} 29 | \abx@aux@page{4}{1} 30 | \abx@aux@page{5}{1} 31 | \abx@aux@page{6}{1} 32 | \abx@aux@page{7}{1} 33 | \abx@aux@page{8}{1} 34 | \abx@aux@page{9}{1} 35 | \abx@aux@page{10}{1} 36 | \abx@aux@page{11}{1} 37 | \abx@aux@page{12}{1} 38 | \abx@aux@page{13}{1} 39 | \abx@aux@page{14}{1} 40 | \abx@aux@page{15}{1} 41 | \abx@aux@page{16}{1} 42 | \abx@aux@page{17}{1} 43 | \abx@aux@page{18}{1} 44 | \abx@aux@page{19}{1} 45 | \abx@aux@page{20}{1} 46 | \abx@aux@page{21}{1} 47 | \abx@aux@page{22}{1} 48 | \abx@aux@page{23}{2} 49 | \abx@aux@page{24}{2} 50 | \abx@aux@page{25}{2} 51 | \abx@aux@page{26}{2} 52 | \abx@aux@page{27}{2} 53 | \abx@aux@page{28}{2} 54 | \abx@aux@page{29}{2} 55 | \abx@aux@page{30}{2} 56 | \abx@aux@page{31}{2} 57 | -------------------------------------------------------------------------------- /main.run.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 23 | 28 | 33 | 36 | 39 | 42 | ]> 43 | 44 | 45 | latex 46 | 47 | main.aux 48 | main-blx.bib 49 | 50 | 51 | main.bbl 52 | 53 | 54 | blx-compat.def 55 | biblatex.def 56 | BES/bes.bbx 57 | standard.bbx 58 | authoryear-comp.bbx 59 | authoryear.bbx 60 | BES/bes.cbx 61 | authoryear-comp.cbx 62 | biblatex.cfg 63 | english.lbx 64 | 65 | 66 | 67 | bibtex 68 | 69 | bibtex 70 | 71 | main 72 | 73 | 74 | main.aux 75 | 76 | 77 | main.bbl 78 | 79 | 80 | main.bbl 81 | 82 | 83 | main.aux 84 | main-blx.bib 85 | 86 | 87 | library.bib 88 | 89 | 90 | biblatex.bst 91 | 92 | 93 | 94 | -------------------------------------------------------------------------------- /GEB/geb.bbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{geb.bbx}[biblatex style for Global Ecology and Biogeography] 2 | 3 | %% We build on the original author-year comp 4 | \RequireBibliographyStyle{authoryear-comp} 5 | 6 | %% General options to match the ELE requirements 7 | \ExecuteBibliographyOptions 8 | { 9 | doi = false , 10 | eprint = false , 11 | firstinits = true , 12 | isbn = false , 13 | maxcitenames = 2 , 14 | mincitenames = 1 , 15 | url = false , 16 | dashed = false , 17 | sorting = nyt 18 | } 19 | 20 | %% Only the year is important 21 | \AtEveryBibitem{% 22 | \clearfield{day}% 23 | \clearfield{month}% 24 | \clearfield{endday}% 25 | \clearfield{endmonth}% 26 | } 27 | 28 | %% Titles are in upright, no quotes 29 | \DeclareFieldFormat[article,inbook,incollection,inproceedings,patent,thesis,unpublished]{title}{#1\isdot} 30 | 31 | %% Articles have no page number indication 32 | \DeclareFieldFormat[article]{pages}{#1} 33 | \DeclareFieldFormat[article]{volume}{\mkbibbold{#1}} 34 | \DeclareFieldFormat{journaltitle}{\mkbibemph{#1\isdot}} 35 | 36 | %% Last author is separated by an ampersand 37 | \renewcommand*{\finalnamedelim}{\addspace\&\space} 38 | 39 | %% Authors are Name, F.S. 40 | \DeclareNameAlias{sortname}{last-first} 41 | 42 | %% The initials are separated by a thin space, as per Bringhurst 43 | \renewrobustcmd*{\bibinitdelim}{\addnbthinspace} 44 | 45 | \DeclareNameAlias{default}{last-first} 46 | 47 | \renewcommand*{\labelnamepunct}{\addspace} 48 | 49 | \DeclareFieldFormat{editortype}{\mkbibparens{#1}} 50 | \renewbibmacro*{bbx:editor}[1]{% 51 | \ifboolexpr{ 52 | test \ifuseeditor 53 | and 54 | not test {\ifnameundef{editor}} 55 | } 56 | {\usebibmacro{bbx:dashcheck} 57 | {\bibnamedash} 58 | {\printnames{editor}% 59 | \setunit{\addspace}% 60 | \usebibmacro{bbx:savehash}}% 61 | \usebibmacro{#1}% 62 | \clearname{editor}% 63 | \setunit{\addspace}}% 64 | {\global\undef\bbx@lasthash 65 | \usebibmacro{labeltitle}% 66 | \setunit*{\addspace}}% 67 | \usebibmacro{date+extrayear}} 68 | 69 | \renewbibmacro{in:}{} 70 | 71 | \renewbibmacro*{journal+issuetitle}{% 72 | \usebibmacro{journal}% 73 | \setunit*{\addcomma\space}% 74 | \usebibmacro{volume+number+eid}% 75 | \newunit 76 | } 77 | 78 | \renewbibmacro*{volume+number+eid}{% 79 | \printfield{volume}% 80 | \setunit*{\addspace}% 81 | \printfield{eid}% 82 | } 83 | 84 | \renewbibmacro*{publisher+location+date}{% 85 | \restorefield{edition}{\bbx@savededit} 86 | \printfield{edition}% 87 | \setunit*{\addcomma\space}% 88 | \printlist{publisher}% 89 | \setunit{\addcomma\space}% 90 | \printlist{location}% 91 | } 92 | 93 | \renewbibmacro{begentry}{% 94 | \savefield{edition}{\bbx@savededit}% 95 | \clearfield{edition}} 96 | 97 | 98 | \DeclareBibliographyDriver{incollection}{% 99 | \usebibmacro{bibindex}% 100 | \usebibmacro{begentry}% 101 | \usebibmacro{author/translator+others}% 102 | \setunit{\labelnamepunct}\newblock 103 | \usebibmacro{title}% 104 | \newunit 105 | \printlist{language}% 106 | \newunit\newblock 107 | \usebibmacro{byauthor}% 108 | \newunit\newblock 109 | \usebibmacro{in:}% 110 | \usebibmacro{maintitle+booktitle}% 111 | \setunit{\addspace}% 112 | \printtext[parens]{% 113 | \usebibmacro{byeditor+others}}% 114 | \newunit\newblock 115 | \printfield{edition}% 116 | \newunit 117 | \iffieldundef{maintitle} 118 | {\printfield{volume}% 119 | \printfield{part}} 120 | {}% 121 | \newunit 122 | \printfield{volumes}% 123 | \newunit\newblock 124 | \usebibmacro{series+number}% 125 | \newunit\newblock 126 | \printfield{note}% 127 | \newunit\newblock 128 | \usebibmacro{chapter+pages}% 129 | \newunit\newblock 130 | \usebibmacro{publisher+location+date}% 131 | \newunit\newblock 132 | \iftoggle{bbx:isbn} 133 | {\printfield{isbn}} 134 | {}% 135 | \newunit\newblock 136 | \usebibmacro{doi+eprint+url}% 137 | \newunit\newblock 138 | \usebibmacro{addendum+pubstate}% 139 | \setunit{\bibpagerefpunct}\newblock 140 | \usebibmacro{pageref}% 141 | \newunit\newblock 142 | \iftoggle{bbx:related} 143 | {\usebibmacro{related:init}% 144 | \usebibmacro{related}} 145 | {}% 146 | \usebibmacro{finentry}} 147 | 148 | \endinput 149 | -------------------------------------------------------------------------------- /ELE/ele.bbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{ele.bbx}[biblatex style for Ecology Letters] 2 | 3 | %% We build on the original author-year comp 4 | \RequireBibliographyStyle{standard} 5 | \RequireBibliographyStyle{authoryear-comp} 6 | 7 | %% General options to match the ELE requirements 8 | \ExecuteBibliographyOptions 9 | { 10 | doi = false , 11 | eprint = false , 12 | firstinits = true , 13 | isbn = false , 14 | maxcitenames = 2 , 15 | mincitenames = 1 , 16 | maxbibnames = 7 , 17 | minbibnames = 6 , 18 | url = false , 19 | dashed = false , 20 | sorting = nyt 21 | } 22 | 23 | %% Only the year is important 24 | \AtEveryBibitem{% 25 | \clearfield{day}% 26 | \clearfield{month}% 27 | \clearfield{endday}% 28 | \clearfield{endmonth}% 29 | } 30 | 31 | %% Titles are in upright, no quotes 32 | \DeclareFieldFormat[article,inbook,incollection,inproceedings,patent,thesis,unpublished]{title}{#1\isdot} 33 | 34 | %% Articles have no page number indication 35 | \DeclareFieldFormat[article]{pages}{#1} 36 | 37 | %% Last author is separated by an ampersand 38 | \renewcommand*{\finalnamedelim}{\addspace\&\space} 39 | 40 | %% Authors are Name, F.S. 41 | \DeclareNameAlias{sortname}{last-first} 42 | 43 | %% The initials are separated by a thin space, as per Bringhurst 44 | \renewcommand*{\mkbibnamefirst}[1]{{\let~\,#1}} 45 | 46 | 47 | \DeclareNameFormat{default}{% 48 | \renewcommand*{\multinamedelim}{\addsemicolon\addspace}% 49 | \usebibmacro{name:last-first}{#1}{#4}{#5}{#7}% 50 | \usebibmacro{name:andothers}% 51 | } 52 | 53 | \DeclareBibliographyDriver{article}{% 54 | \usebibmacro{bibindex}% 55 | \usebibmacro{begentry}% 56 | \usebibmacro{author/translator+others}% 57 | \setunit{\labelnamepunct}\newblock 58 | \usebibmacro{title}% 59 | \newunit 60 | \printlist{language}% 61 | \newunit\newblock 62 | \usebibmacro{byauthor}% 63 | \newunit\newblock 64 | \usebibmacro{bytranslator+others}% 65 | \newunit\newblock 66 | \printfield{version}% 67 | \newunit\newblock% 68 | \usebibmacro{journal+issuetitle}% 69 | \newunit 70 | \usebibmacro{byeditor+others}% 71 | \newunit 72 | \usebibmacro{note+pages}% 73 | \newunit\newblock 74 | \usebibmacro{addendum+pubstate}% 75 | \setunit{\bibpagerefpunct}\newblock 76 | \usebibmacro{pageref}% 77 | \usebibmacro{finentry}} 78 | 79 | \renewbibmacro*{journal+issuetitle}{% 80 | \usebibmacro{journal},% 81 | \setunit*{\addspace}% 82 | \usebibmacro{volume+number+eid}% 83 | \newunit 84 | } 85 | 86 | \renewbibmacro*{volume+number+eid}{% 87 | \printfield{volume}% 88 | \setunit*{\addspace}% 89 | \printfield{eid}% 90 | } 91 | 92 | \renewbibmacro*{name:andothers}{ 93 | \ifboolexpr{ 94 | test {\ifnumequal{\value{listcount}}{\value{liststop}}} 95 | and 96 | test \ifmorenames 97 | } 98 | {\ifnumgreater{\value{liststop}}{1} 99 | {\finalandcomma} 100 | {}% 101 | \andothersdelim\bibstring[\emph]{andothers}} 102 | {}% 103 | } 104 | 105 | \DeclareFieldFormat[incollection]{booktitle}{\emph{#1}} 106 | 107 | \renewbibmacro*{publisher+location+date}{% 108 | \printlist{publisher}% 109 | \newunit 110 | \printlist{location}% 111 | \newunit 112 | \printfield{edition}% 113 | \newunit 114 | } 115 | 116 | \DeclareBibliographyDriver{incollection}{% 117 | \usebibmacro{bibindex}% 118 | \usebibmacro{begentry}% 119 | \usebibmacro{author/translator+others}% 120 | \setunit{\labelnamepunct}\newblock 121 | \printlist{language}% 122 | \newunit\newblock 123 | \usebibmacro{byauthor}% 124 | \newunit 125 | \usebibmacro{title} 126 | \newunit\newblock 127 | \usebibmacro{in:}% 128 | \newunit 129 | \usebibmacro{bybookauthor}% 130 | \newunit\newblock 131 | \printfield{booktitle}\addspace% 132 | \printtext[parens]{% 133 | \usebibmacro{editorstrg}% 134 | \addspace% 135 | \printnames[byeditor]{editor}% 136 | \clearname{editor}% 137 | }% 138 | \newunit\newblock 139 | \printfield{volumes}% 140 | \newunit\newblock 141 | \usebibmacro{series+number}% 142 | \newunit\newblock 143 | \printfield{note}% 144 | \newunit\newblock 145 | \usebibmacro{publisher+location+date}% 146 | \newunit\newblock 147 | \usebibmacro{chapter+pages}% 148 | \newunit\newblock 149 | \usebibmacro{addendum+pubstate}% 150 | \setunit{\bibpagerefpunct}\newblock 151 | \usebibmacro{pageref}% 152 | \usebibmacro{finentry}% 153 | } 154 | 155 | \endinput -------------------------------------------------------------------------------- /ICB/icb.bbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{icb.bbx}[biblatex style for Integrative and Comparative Biology] 2 | 3 | % Build from authoryear-comp style 4 | \RequireBibliographyStyle{authoryear-comp} 5 | 6 | %% General options 7 | \ExecuteBibliographyOptions 8 | { 9 | doi = false, 10 | eprint = false, 11 | giveninits = true, 12 | terseinits = true, 13 | isbn = false, 14 | maxcitenames = 2, 15 | mincitenames = 1, 16 | maxbibnames = 10, 17 | minbibnames = 10, 18 | url = false, 19 | dashed = false, 20 | abbreviate = false, 21 | sorting = nyt 22 | } 23 | 24 | %% Clear unnecessary fields in case 25 | \AtEveryBibitem{% 26 | \clearfield{day}% 27 | \clearfield{month}% 28 | \clearfield{endday}% 29 | \clearfield{endmonth}% 30 | } 31 | 32 | %% Titles are upright, no quotes 33 | \DeclareFieldFormat[article,book,inbook,incollection,inproceedings,patent,thesis,unpublished]{title}{#1\isdot} 34 | 35 | %% Plain journal and book titles 36 | \DeclareFieldFormat{journaltitle}{#1} 37 | \DeclareFieldFormat{booktitle}{#1} 38 | 39 | %% Articles have no page number indication but collections do have a "p." 40 | \DeclareFieldFormat{pages}{#1} 41 | \DeclareFieldFormat[incollection]{pages}{p.\space#1} 42 | 43 | %% Colon before pages normally 44 | \renewcommand*{\bibpagespunct}{\addcolon} 45 | 46 | %% Last name first (authors, editors, etc) 47 | \DeclareNameAlias{sortname}{last-first} 48 | \DeclareNameAlias{default}{last-first} 49 | 50 | %% Period after name and before year 51 | \DeclareDelimFormat[bib]{nameyeardelim}{\addperiod\space} 52 | \DeclareDelimFormat[biblist]{nameyeardelim}{\addperiod\space} 53 | 54 | 55 | %% Plain year without parentheses 56 | \renewbibmacro*{date+extrayear}{% 57 | \iffieldundef{labelyear} 58 | {} 59 | {% 60 | \iffieldsequal{year}{labelyear} 61 | {\printlabeldateextra}% 62 | {\printfield{labelyear}% 63 | \printfield{extrayear}}}} 64 | 65 | %% No issue or eid 66 | \renewbibmacro*{volume+number+eid}{% 67 | \printfield{volume}} 68 | 69 | %% Editor names before "editors" 70 | \renewbibmacro*{byeditor+others}{% 71 | \ifnameundef{editor} 72 | {} 73 | {\printnames[byeditor]{editor}% 74 | \setunit{\addcomma\space}% 75 | \usebibmacro{byeditor+othersstrg}% 76 | \clearname{editor}% 77 | \newunit}% 78 | \usebibmacro{byeditorx}% 79 | \usebibmacro{bytranslator+others}} 80 | 81 | %% no "by" for editors 82 | \DefineBibliographyStrings{english}{byeditor = {editor}, byeditor={editors}} 83 | 84 | %% modified from standard.bbx: remove language, "in" for journal 85 | \DeclareBibliographyDriver{article}{% 86 | \usebibmacro{bibindex}% 87 | \usebibmacro{begentry}% 88 | \usebibmacro{author/translator+others}% 89 | \setunit{\printdelim{nametitledelim}}\newblock 90 | \usebibmacro{title}% 91 | \newunit\newblock 92 | \usebibmacro{byauthor}% 93 | \newunit\newblock 94 | \usebibmacro{bytranslator+others}% 95 | \newunit\newblock 96 | \printfield{version}% 97 | \newunit\newblock 98 | \usebibmacro{journal+issuetitle}% 99 | \newunit 100 | \usebibmacro{byeditor+others}% 101 | \newunit 102 | \usebibmacro{note+pages}% 103 | \newunit\newblock 104 | \iftoggle{bbx:isbn} 105 | {\printfield{issn}} 106 | {}% 107 | \newunit\newblock 108 | \usebibmacro{doi+eprint+url}% 109 | \newunit\newblock 110 | \usebibmacro{addendum+pubstate}% 111 | \setunit{\bibpagerefpunct}\newblock 112 | \usebibmacro{pageref}% 113 | \newunit\newblock 114 | \iftoggle{bbx:related} 115 | {\usebibmacro{related:init}% 116 | \usebibmacro{related}} 117 | {}% 118 | \usebibmacro{finentry}} 119 | 120 | %% modified from standard.bbx: editor names first then booktitle 121 | \DeclareBibliographyDriver{incollection}{% 122 | \usebibmacro{bibindex}% 123 | \usebibmacro{begentry}% 124 | \usebibmacro{author/translator+others}% 125 | \setunit{\printdelim{nametitledelim}}\newblock 126 | \usebibmacro{title}% 127 | \newunit 128 | \printlist{language}% 129 | \newunit\newblock 130 | \usebibmacro{byauthor}% 131 | \newunit\newblock 132 | \usebibmacro{in:}% 133 | \usebibmacro{byeditor+others}% 134 | \newunit\newblock 135 | \usebibmacro{maintitle+booktitle}% 136 | \newunit\newblock 137 | \printfield{edition}% 138 | \newunit 139 | \iffieldundef{maintitle} 140 | {\printfield{volume}% 141 | \printfield{part}} 142 | {}% 143 | \newunit 144 | \printfield{volumes}% 145 | \newunit\newblock 146 | \usebibmacro{series+number}% 147 | \newunit\newblock 148 | \usebibmacro{publisher+location+date}% 149 | \newunit\newblock 150 | \addperiod\space\printfield{pages}% 151 | \newunit\newblock 152 | \iftoggle{bbx:isbn} 153 | {\printfield{isbn}} 154 | {}% 155 | \newunit\newblock 156 | \usebibmacro{doi+eprint+url}% 157 | \newunit\newblock 158 | \usebibmacro{addendum+pubstate}% 159 | \setunit{\bibpagerefpunct}\newblock 160 | \usebibmacro{pageref}% 161 | \newunit\newblock 162 | \iftoggle{bbx:related} 163 | {\usebibmacro{related:init}% 164 | \usebibmacro{related}} 165 | {}% 166 | \usebibmacro{finentry}} 167 | 168 | \endinput -------------------------------------------------------------------------------- /BES/bes.bbx: -------------------------------------------------------------------------------- 1 | \ProvidesFile{bes.bbx}[biblatex style for British Ecological Society journals] 2 | 3 | %% We build on the original author-year comp 4 | \RequireBibliographyStyle{standard} 5 | \RequireBibliographyStyle{authoryear-comp} 6 | 7 | %% General options to match the BES requirements 8 | \ExecuteBibliographyOptions 9 | { 10 | doi = false , 11 | eprint = false , 12 | giveninits = true , 13 | isbn = false , 14 | maxcitenames = 2 , 15 | mincitenames = 1 , 16 | url = true , 17 | dashed = false , 18 | sorting = nyt 19 | } 20 | 21 | \DefineBibliographyStrings{english}{% 22 | urlseen = {accessed}, 23 | } 24 | 25 | %% Only the year is important 26 | \AtEveryBibitem{% 27 | \clearfield{day}% 28 | \clearfield{month}% 29 | \clearfield{endday}% 30 | \clearfield{endmonth}% 31 | } 32 | 33 | %% Titles are in upright, no quotes 34 | \DeclareFieldFormat[article,inbook,incollection,inproceedings,patent,unpublished]{title}{#1\isdot} 35 | 36 | %% Articles have no page number indication 37 | \DeclareFieldFormat[article]{pages}{#1} 38 | \DeclareFieldFormat[article]{title}{\emph{#1}} 39 | \DeclareFieldFormat[article]{volume}{\textbf{#1}} 40 | \DeclareFieldFormat[article]{journaltitle}{\mdseries{#1}} 41 | 42 | %% Last author is separated by an ampersand 43 | \renewcommand*{\finalnamedelim}{\addspace\&\space} 44 | 45 | %% Authors are Name, F.S. 46 | \DeclareNameAlias{sortname}{family-given} 47 | 48 | %% The initials are separated by a thin space, as per Bringhurst 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\clearname{editor}% 157 | }% 158 | \newunit\newblock 159 | \printfield{volumes}% 160 | \newunit\newblock 161 | \usebibmacro{series+number}% 162 | \newunit\newblock 163 | \printfield{note}% 164 | \newunit\newblock 165 | \usebibmacro{chapter+pages}% 166 | .\newblock 167 | \usebibmacro{publisher+location+date}% 168 | \newunit\newblock 169 | \usebibmacro{addendum+pubstate}% 170 | \setunit{\bibpagerefpunct}\newblock 171 | \usebibmacro{pageref}% 172 | \usebibmacro{finentry}% 173 | } 174 | 175 | \endinput 176 | -------------------------------------------------------------------------------- /main.bbl: -------------------------------------------------------------------------------- 1 | % $ biblatex auxiliary file $ 2 | % $ biblatex version 1.7 $ 3 | % Do not modify the above lines! 4 | % 5 | % This is an auxiliary file used by the 'biblatex' package. 6 | % This file may safely be deleted. It will be recreated as 7 | % required. 8 | % 9 | \begingroup 10 | \makeatletter 11 | \@ifundefined{ver@biblatex.sty} 12 | {\@latex@error 13 | {Missing 'biblatex' package} 14 | {The bibliography requires the 'biblatex' package.} 15 | \aftergroup\endinput} 16 | {} 17 | \endgroup 18 | 19 | \entry{Anderson2011}{article}{} 20 | \name{author}{14}{}{% 21 | {{}% 22 | {Anderson}{A.}% 23 | {Marti~J}{M.~J.}% 24 | {}{}% 25 | {}{}}% 26 | {{}% 27 | {Crist}{C.}% 28 | {Thomas~O}{T.~O.}% 29 | {}{}% 30 | {}{}}% 31 | {{}% 32 | {Chase}{C.}% 33 | {Jonathan~M}{J.~M.}% 34 | {}{}% 35 | {}{}}% 36 | {{}% 37 | {Vellend}{V.}% 38 | {Mark}{M.}% 39 | {}{}% 40 | {}{}}% 41 | {{}% 42 | {Inouye}{I.}% 43 | {Brian~D}{B.~D.}% 44 | {}{}% 45 | {}{}}% 46 | {{}% 47 | {Freestone}{F.}% 48 | {Amy~L}{A.~L.}% 49 | {}{}% 50 | {}{}}% 51 | {{}% 52 | {Sanders}{S.}% 53 | {Nathan~J}{N.~J.}% 54 | {}{}% 55 | {}{}}% 56 | {{}% 57 | {Cornell}{C.}% 58 | {Howard~V}{H.~V.}% 59 | {}{}% 60 | {}{}}% 61 | {{}% 62 | {Comita}{C.}% 63 | {Liza~S}{L.~S.}% 64 | {}{}% 65 | {}{}}% 66 | {{}% 67 | {Davies}{D.}% 68 | {Kendi~F}{K.~F.}% 69 | {}{}% 70 | {}{}}% 71 | {{}% 72 | {Harrison}{H.}% 73 | {Susan~P}{S.~P.}% 74 | {}{}% 75 | {}{}}% 76 | {{}% 77 | {Kraft}{K.}% 78 | {Nathan J~B}{N.~J.~B.}% 79 | {}{}% 80 | {}{}}% 81 | {{}% 82 | {Stegen}{S.}% 83 | {James~C}{J.~C.}% 84 | {}{}% 85 | {}{}}% 86 | {{}% 87 | {Swenson}{S.}% 88 | {Nathan~G}{N.~G.}% 89 | {}{}% 90 | {}{}}% 91 | } 92 | \list{publisher}{1}{% 93 | {Wiley Online Library}% 94 | } 95 | \keyw{Biodiversity,Biological,Coral Reefs,Ecology,El Nino-Southern 96 | Oscillation,Indonesia,Models,Multivariate Analysis} 97 | \strng{namehash}{AMJ+1} 98 | \strng{fullhash}{AMJCTOCJMVMIBDFALSNJCHVCLSDKFHSPKNJBSJCSNG1} 99 | \field{labelyear}{2011} 100 | \field{sortinit}{A} 101 | \field{abstract}{% 102 | A recent increase in studies of $\beta$ diversity has yielded a confusing 103 | array of concepts, measures and methods. Here, we provide a roadmap of the 104 | most widely used and ecologically relevant approaches for analysis through a 105 | series of mission statements. We distinguish two types of $\beta$ diversity: 106 | directional turnover along a gradient vs. non-directional variation. 107 | Different measures emphasize different properties of ecological data. Such 108 | properties include the degree of emphasis on presence/absence vs. relative 109 | abundance information and the inclusion vs. exclusion of joint absences. 110 | Judicious use of multiple measures in concert can uncover the underlying 111 | nature of patterns in $\beta$ diversity for a given dataset. A case study of 112 | Indonesian coral assemblages shows the utility of a multi-faceted approach. 113 | We advocate careful consideration of relevant questions, matched by 114 | appropriate analyses. The rigorous application of null models will also help 115 | to reveal potential processes driving observed patterns in $\beta$ 116 | diversity.% 117 | } 118 | \verb{doi} 119 | \verb 10.1111/j.1461-0248.2010.01552.x 120 | \endverb 121 | \field{issn}{1461-0248} 122 | \field{number}{1} 123 | \field{pages}{19\bibrangedash 28} 124 | \field{title}{{Navigating the multiple meanings of beta diversity: a roadmap 125 | for the practicing ecologist.}} 126 | \verb{url} 127 | \verb http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2010.01552.x/ful 128 | \verb l http://www.ncbi.nlm.nih.gov/pubmed/21070562 129 | \endverb 130 | \field{volume}{14} 131 | \verb{file} 132 | \verb :home/tpoisot/Documents/Papers/Ecology Letters/Anderson et al. - 2011 - 133 | \verb Navigating the multiple meanings of beta diversity a roadmap for the p 134 | \verb racticing ecologist.pdf:pdf 135 | \endverb 136 | \field{journaltitle}{Ecology Letters} 137 | \field{month}{01} 138 | \field{year}{2011} 139 | \endentry 140 | 141 | \entry{Darwin1859}{book}{} 142 | \name{author}{1}{}{% 143 | {{}% 144 | {Darwin}{D.}% 145 | {Charles}{C.}% 146 | {}{}% 147 | {}{}}% 148 | } 149 | \list{publisher}{1}{% 150 | {D. Appleton}% 151 | } 152 | \strng{namehash}{DC1} 153 | \strng{fullhash}{DC1} 154 | \field{labelyear}{1859} 155 | \field{sortinit}{D} 156 | \field{title}{{On the origin of species by means of natural selection, or the 157 | preservation of favoured races in the struggle for life}} 158 | \list{location}{1}{% 159 | {New York}% 160 | } 161 | \field{year}{1859} 162 | \endentry 163 | 164 | \entry{Dunne2006}{incollection}{} 165 | \name{author}{1}{}{% 166 | {{}% 167 | {Dunne}{D.}% 168 | {Jennifer~A}{J.~A.}% 169 | {}{}% 170 | {}{}}% 171 | } 172 | \name{editor}{2}{}{% 173 | {{}% 174 | {Pascual}{P.}% 175 | {Mercedes}{M.}% 176 | {}{}% 177 | {}{}}% 178 | {{}% 179 | {Dunne}{D.}% 180 | {Jennifer~A}{J.~A.}% 181 | {}{}% 182 | {}{}}% 183 | } 184 | \list{publisher}{1}{% 185 | {Oxford University Press}% 186 | } 187 | \strng{namehash}{DJA1} 188 | \strng{fullhash}{DJA1} 189 | \field{labelyear}{2006} 190 | \field{sortinit}{D} 191 | \field{booktitle}{Ecological Networks: Linking Structure to Dynamics in Food 192 | Webs} 193 | \field{pages}{27\bibrangedash 86} 194 | \field{title}{{The network structure of food webs}} 195 | \list{location}{1}{% 196 | {Oxford}% 197 | } 198 | \verb{file} 199 | \verb :home/tpoisot/Documents/Papers/Ecological Networks Linking Structure to 200 | \verb Dynamics in Food Webs/Dunne - 2006 - The network structure of food web 201 | \verb s.pdf:pdf 202 | \endverb 203 | \field{year}{2006} 204 | \endentry 205 | 206 | \entry{Elton1927}{book}{} 207 | \name{author}{1}{}{% 208 | {{}% 209 | {Elton}{E.}% 210 | {Charles~S}{C.~S.}% 211 | {}{}% 212 | {}{}}% 213 | } 214 | \list{publisher}{1}{% 215 | {University of Chicago Press}% 216 | } 217 | \strng{namehash}{ECS1} 218 | \strng{fullhash}{ECS1} 219 | \field{labelyear}{1927} 220 | \field{sortinit}{E} 221 | \field{booktitle}{Animal ecology} 222 | \field{title}{{Animal ecology}} 223 | \field{year}{1927} 224 | \endentry 225 | 226 | \entry{Frank1993}{article}{} 227 | \name{author}{1}{}{% 228 | {{}% 229 | {Frank}{F.}% 230 | {Steven~A}{S.~A.}% 231 | {}{}% 232 | {}{}}% 233 | } 234 | \list{publisher}{1}{% 235 | {Springer}% 236 | } 237 | \strng{namehash}{FSA1} 238 | \strng{fullhash}{FSA1} 239 | \field{labelyear}{1993} 240 | \field{extrayear}{1} 241 | \field{sortinit}{F} 242 | \field{number}{1} 243 | \field{pages}{45\bibrangedash 75} 244 | \field{title}{{Coevolutionary genetics of plants and pathogens}} 245 | \field{volume}{7} 246 | \verb{file} 247 | \verb :home/tpoisot/Documents/Papers/Evolutionary Ecology/Frank - 1993 - Coev 248 | \verb olutionary genetics of plants and pathogens.pdf:pdf 249 | \endverb 250 | \field{journaltitle}{Evolutionary Ecology} 251 | \field{year}{1993} 252 | \endentry 253 | 254 | \entry{Frank1993b}{article}{} 255 | \name{author}{1}{}{% 256 | {{}% 257 | {Frank}{F.}% 258 | {Steven~A}{S.~A.}% 259 | {}{}% 260 | {}{}}% 261 | } 262 | \strng{namehash}{FSA1} 263 | \strng{fullhash}{FSA1} 264 | \field{labelyear}{1993} 265 | \field{extrayear}{2} 266 | \field{sortinit}{F} 267 | \field{number}{6} 268 | \field{pages}{1721\bibrangedash 1732} 269 | \field{title}{{Evolution of host-parasite diversity}} 270 | \verb{url} 271 | \verb http://www.csa.com/partners/viewrecord.php?requester=gs\&collection=ENV 272 | \verb \&recid=3713621 273 | \endverb 274 | \field{volume}{47} 275 | \verb{file} 276 | \verb :home/tpoisot/Documents/Papers/Evolution/Frank - 1993 - Evolution of ho 277 | \verb st-parasite diversity.pdf:pdf 278 | \endverb 279 | \field{journaltitle}{Evolution} 280 | \field{year}{1993} 281 | \endentry 282 | 283 | \entry{Frank1993a}{article}{} 284 | \name{author}{1}{}{% 285 | {{}% 286 | {Frank}{F.}% 287 | {Steven~A}{S.~A.}% 288 | {}{}% 289 | {}{}}% 290 | } 291 | \list{publisher}{1}{% 292 | {The Royal Society}% 293 | } 294 | \strng{namehash}{FSA1} 295 | \strng{fullhash}{FSA1} 296 | \field{labelyear}{1993} 297 | \field{extrayear}{3} 298 | \field{sortinit}{F} 299 | \field{number}{1341} 300 | \field{pages}{191\bibrangedash 197} 301 | \field{title}{{Specificity versus detectable polymorphism in host-parasite 302 | genetics}} 303 | \field{volume}{254} 304 | \verb{file} 305 | \verb :home/tpoisot/Documents/Papers/Proceedings of the Royal Society B Biolo 306 | \verb gical Sciences/Frank - 1993 - Specificity versus detectable polymorphis 307 | \verb m in host-parasite genetics.pdf:pdf 308 | \endverb 309 | \field{journaltitle}{Proceedings of the Royal Society B: Biological Sciences} 310 | \field{year}{1993} 311 | \endentry 312 | 313 | \entry{Holt1996}{article}{} 314 | \name{author}{1}{}{% 315 | {{}% 316 | {Holt}{H.}% 317 | {R~D}{R.~D.}% 318 | {}{}% 319 | {}{}}% 320 | } 321 | \list{publisher}{1}{% 322 | {Springer}% 323 | } 324 | \strng{namehash}{HRD1} 325 | \strng{fullhash}{HRD1} 326 | \field{labelyear}{1996} 327 | \field{sortinit}{H} 328 | \field{number}{1} 329 | \field{pages}{1\bibrangedash 11} 330 | \field{title}{{Demographic constraints in evolution: towards unifying the 331 | evolutionary theories of senescence and niche conservatism}} 332 | \field{volume}{10} 333 | \field{journaltitle}{Evolutionary Ecology} 334 | \field{year}{1996} 335 | \endentry 336 | 337 | \entry{PoisotBJLS2010}{article}{} 338 | \name{author}{2}{}{% 339 | {{}% 340 | {Poisot}{P.}% 341 | {Timoth\'{e}e}{T.}% 342 | {}{}% 343 | {}{}}% 344 | {{}% 345 | {Desdevises}{D.}% 346 | {Yves}{Y.}% 347 | {}{}% 348 | {}{}}% 349 | } 350 | \list{publisher}{1}{% 351 | {John Wiley \& Sons}% 352 | } 353 | \keyw{lamellodiscus,morphometry,speciation} 354 | \strng{namehash}{PTDY1} 355 | \strng{fullhash}{PTDY1} 356 | \field{labelyear}{2010} 357 | \field{sortinit}{P} 358 | \field{abstract}{% 359 | In the present study, we used morphometry as a proxy to study the 360 | microevolution of generalist Lamellodiscus (Monogenea, Diplectanidae) 361 | species, comprising gill parasites of sparid fish. We investigated 147 362 | individuals, belonging to nine described species, regrouped in four 363 | morphotypes. Morphometric measurements were taken on sclerotized parts of the 364 | attachment organ. The formation of groups on the basis of the global 365 | morphometry within a host species, or between several host species, was 366 | assessed using both exploratory analyses (principal component analysis and 367 | clustering analysis) and statistical tests. We showed that: (1) for three out 368 | of four morphotypes, the global morphometry was significantly different 369 | according to host species used, and (2) the coexistence of two populations of 370 | Lamellodiscus elegans on Diplodus sargus could reflect an ongoing intra-host 371 | speciation event. We suggest that generalist Lamellodiscus are undergoing 372 | specialization on their different hosts, which may lead to speciation.% 373 | } 374 | \verb{doi} 375 | \verb 10.1111/j.1095-8312.2009.01381.x 376 | \endverb 377 | \field{issn}{00244066} 378 | \field{number}{3} 379 | \field{pages}{559\bibrangedash 569} 380 | \field{title}{{Putative speciation events in Lamellodiscus (Monogenea: 381 | Diplectanidae) assessed by a morphometric approach}} 382 | \verb{url} 383 | \verb http://doi.wiley.com/10.1111/j.1095-8312.2009.01381.x 384 | \endverb 385 | \field{volume}{99} 386 | \verb{file} 387 | \verb :home/tpoisot/Documents/Papers/Biological Journal of the Linnean Societ 388 | \verb y/Poisot, Desdevises - 2010 - Putative speciation events in Lamellodisc 389 | \verb us (Monogenea Diplectanidae) assessed by a morphometric approach.pdf:pd 390 | \verb f 391 | \endverb 392 | \field{journaltitle}{Biological Journal of the Linnean Society} 393 | \field{month}{02} 394 | \field{year}{2010} 395 | \endentry 396 | 397 | \entry{R-Development-Core-Team2008}{manual}{} 398 | \name{author}{1}{}{% 399 | {{}% 400 | {{R Development Core Team}}{R.}% 401 | {}{}% 402 | {}{}% 403 | {}{}}% 404 | } 405 | \list{organization}{1}{% 406 | {R Foundation for Statistical Computing}% 407 | } 408 | \strng{namehash}{R1} 409 | \strng{fullhash}{R1} 410 | \field{labelyear}{2008} 411 | \field{sortinit}{R} 412 | \field{title}{{R: A Language and Environment for Statistical Computing}} 413 | \verb{url} 414 | \verb http://www.r-project.org 415 | \endverb 416 | \list{location}{1}{% 417 | {Vienna, Austria}% 418 | } 419 | \field{annotation}{% 420 | \{ISBN\} 3-900051-07-0% 421 | } 422 | \field{year}{2008} 423 | \endentry 424 | 425 | \entry{Tuomisto2010}{article}{} 426 | \name{author}{1}{}{% 427 | {{}% 428 | {Tuomisto}{T.}% 429 | {Hanna}{H.}% 430 | {}{}% 431 | {}{}}% 432 | } 433 | \strng{namehash}{TH1} 434 | \strng{fullhash}{TH1} 435 | \field{labelyear}{2010} 436 | \field{sortinit}{T} 437 | \verb{doi} 438 | \verb 10.1111/j.1600-0587.2009.05880.x 439 | \endverb 440 | \field{issn}{09067590} 441 | \field{number}{1} 442 | \field{pages}{2\bibrangedash 22} 443 | \field{title}{{A diversity of beta diversities: straightening up a concept 444 | gone awry. Part 1. Defining beta diversity as a function of alpha and gamma 445 | diversity}} 446 | \verb{url} 447 | \verb http://doi.wiley.com/10.1111/j.1600-0587.2009.05880.x 448 | \endverb 449 | \field{volume}{33} 450 | \verb{file} 451 | \verb :home/tpoisot/Documents/Papers/Ecography/Tuomisto - 2010 - A diversity 452 | \verb of beta diversities straightening up a concept gone awry. Part 1. Defin 453 | \verb ing beta diversity as a function of alpha and gamma diversity.pdf:pdf 454 | \endverb 455 | \field{journaltitle}{Ecography} 456 | \field{month}{02} 457 | \field{year}{2010} 458 | \endentry 459 | 460 | \entry{Tuomisto2011}{article}{} 461 | \name{author}{1}{}{% 462 | {{}% 463 | {Tuomisto}{T.}% 464 | {Hanna}{H.}% 465 | {}{}% 466 | {}{}}% 467 | } 468 | \keyw{alpha diversity \'{a} beta,diversity \'{a},gamma diversity \'{a} 469 | diversity,information on,partitioning \'{a} species turnover,quantifying 470 | taxonomic diversity requires,terminology,the need for consistent} 471 | \strng{namehash}{TH1} 472 | \strng{fullhash}{TH1} 473 | \field{labelyear}{2011} 474 | \field{sortinit}{T} 475 | \field{abstract}{% 476 | Meaningful quantification of species diversity requires that both 'species' 477 | and 'diversity' are unambiguously defined. Rigorous rules of nomenclature 478 | exist to ensure that each species has a single unique name, but the naming of 479 | concepts is much more variable. As a consequence, 'diversity' has been 480 | defined in so many different ways that its ability to transfer accurate 481 | information has been compromised. This problem can be solved by defining 482 | 'diversity' as the effective number of species (or other types of interest), 483 | and using the term 'true diversity' to specify that this narrow concept is 484 | being used (analogously to using the term 'true bugs' when adhering to a 485 | narrow circumscription of 'bugs'). Other measures related to diversity (such 486 | as entropies and probabilities) continue to be useful, but they represent 487 | different phenomena and should therefore be referred to by different names. 488 | Total species diversity in a dataset can be partitioned into two components 489 | in several different ways. The components of a specific multiplicative 490 | partitioning can be called true alpha diversity and true beta diversity. When 491 | the partitioning is done in some other way, the resulting components are 492 | different and should be called by other names. For example, the beta 493 | component of additive partitioning does not equal true beta diversity, but 494 | can logically be called species turnover. All the phenomena that have been 495 | called 'beta diversity' in the ecological literature have also been called by 496 | alternative unique names. Consequently, a consistent terminology is already 497 | available; only a general agreement to use it is lacking.% 498 | } 499 | \verb{doi} 500 | \verb 10.1007/s00442-011-2128-4 501 | \endverb 502 | \field{issn}{1432-1939} 503 | \field{pages}{903\bibrangedash 911} 504 | \field{title}{{Commentary: do we have a consistent terminology for species 505 | diversity? Yes, if we choose to use it.}} 506 | \verb{url} 507 | \verb http://www.ncbi.nlm.nih.gov/pubmed/21947563 508 | \endverb 509 | \field{volume}{167} 510 | \verb{file} 511 | \verb :home/tpoisot/Documents/Papers/Oecologia/Tuomisto - 2011 - Commentary d 512 | \verb o we have a consistent terminology for species diversity Yes, if we cho 513 | \verb ose to use it.pdf:pdf 514 | \endverb 515 | \field{journaltitle}{Oecologia} 516 | \field{month}{09} 517 | \field{year}{2011} 518 | \endentry 519 | 520 | \entry{Yang2012}{article}{} 521 | \name{author}{2}{}{% 522 | {{}% 523 | {Yang}{Y.}% 524 | {Ziheng}{Z.}% 525 | {}{}% 526 | {}{}}% 527 | {{}% 528 | {Rannala}{R.}% 529 | {Bruce}{B.}% 530 | {}{}% 531 | {}{}}% 532 | } 533 | \list{publisher}{1}{% 534 | {Nature Publishing Group}% 535 | } 536 | \strng{namehash}{YZRB1} 537 | \strng{fullhash}{YZRB1} 538 | \field{labelyear}{2012} 539 | \field{sortinit}{Y} 540 | \verb{doi} 541 | \verb 10.1038/nrg3186 542 | \endverb 543 | \field{issn}{1471-0056} 544 | \field{number}{May} 545 | \field{title}{{Molecular phylogenetics: principles and practice}} 546 | \verb{url} 547 | \verb http://www.nature.com/doifinder/10.1038/nrg3186 548 | \endverb 549 | \field{volume}{13} 550 | \verb{file} 551 | \verb :home/tpoisot/Documents/Papers/Nature Reviews Genetics/Yang, Rannala - 552 | \verb 2012 - Molecular phylogenetics principles and practice.pdf:pdf 553 | \endverb 554 | \field{journaltitle}{Nature Reviews Genetics} 555 | \field{month}{03} 556 | \field{year}{2012} 557 | \endentry 558 | 559 | \lossort 560 | \endlossort 561 | 562 | \endinput 563 | -------------------------------------------------------------------------------- /main.log: -------------------------------------------------------------------------------- 1 | This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) (format=pdflatex 2012.7.20) 18 SEP 2012 11:52 2 | entering extended mode 3 | %&-line parsing enabled. 4 | **main.tex 5 | (./main.tex 6 | LaTeX2e <2009/09/24> 7 | Babel and 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