[Vegan-commits] r2576 - pkg/vegan/inst/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jul 22 12:54:03 CEST 2013
Author: jarioksa
Date: 2013-07-22 12:54:03 +0200 (Mon, 22 Jul 2013)
New Revision: 2576
Modified:
pkg/vegan/inst/doc/decision-vegan.Rnw
pkg/vegan/inst/doc/diversity-vegan.Rnw
pkg/vegan/inst/doc/vegan.bib
pkg/vegan/inst/doc/vegan.sty
Log:
add references to diversity
Modified: pkg/vegan/inst/doc/decision-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/decision-vegan.Rnw 2013-07-22 10:51:42 UTC (rev 2575)
+++ pkg/vegan/inst/doc/decision-vegan.Rnw 2013-07-22 10:54:03 UTC (rev 2576)
@@ -3,8 +3,6 @@
\documentclass[a4paper,10pt,twocolumn]{article}
\usepackage{vegan} % package options and redefinitions
-\usepackage[round]{natbib}
-\renewcommand{\cite}{\citep}
\author{Jari Oksanen}
\title{Design decisions and implementation details in vegan}
@@ -16,6 +14,8 @@
%% need no \usepackage{Sweave}
\begin{document}
+\bibliographystyle{jss}
+
\SweaveOpts{strip.white=true}
<<echo=false,results=hide>>=
@@ -807,7 +807,6 @@
primarily WA scores in plotting. However, the user makes the ultimate
choice, since both scores are available.
-\bibliographystyle{plainnat}
\bibliography{vegan}
\end{document}
Modified: pkg/vegan/inst/doc/diversity-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/diversity-vegan.Rnw 2013-07-22 10:51:42 UTC (rev 2575)
+++ pkg/vegan/inst/doc/diversity-vegan.Rnw 2013-07-22 10:54:03 UTC (rev 2576)
@@ -3,6 +3,10 @@
\documentclass[a4paper,10pt,twocolumn]{article}
\usepackage{vegan} %% vegan setup
+%% TODO: SSarrhenius, adipart, beals update, betadisper
+%% expansion (+ permutest), contribdiv, eventstar, multipart, refer to
+%% FD, check Kindt reference to specaccum, check estimateR ref
+
\title{Vegan: ecological diversity} \author{Jari Oksanen}
\date{\footnotesize{$ $Id$ $
@@ -11,6 +15,7 @@
%% need no \usepackage{Sweave}
\begin{document}
+\bibliographystyle{jss}
\SweaveOpts{strip.white=true}
<<echo=false>>=
@@ -58,7 +63,7 @@
\section{Diversity indices}
Function \code{diversity} finds the most commonly used diversity
-indices:
+indices \citep{Hill73number}:
\begin{align}
H &= - \sum_{i=1}^S p_i \log_b p_i & \text{Shannon--Weaver}\\
D_1 &= 1 - \sum_{i=1}^S p_i^2 &\text{Simpson}\\
@@ -85,7 +90,7 @@
the numbers of species.
\pkg{vegan} also can estimate series of R\'{e}nyi and Tsallis
-diversities. R{\'e}nyi diversity of order $a$ is:
+diversities. R{\'e}nyi diversity of order $a$ is \citep{Hill73number}:
\begin{equation}
H_a = \frac{1}{1-a} \log \sum_{i=1}^S p_i^a
\end{equation}
@@ -94,7 +99,7 @@
\exp(H')$, $N_2 = D_2$, and $N_\infty = 1/(\max p_i)$. The
corresponding R\'{e}nyi diversities are $H_0 = \log(S)$, $H_1 = H'$, $H_2 =
- \log(\sum p_i^2)$, and $H_\infty = - \log(\max p_i)$.
-Tsallis diversity of order $q$ is:
+Tsallis diversity of order $q$ is \citep{Tothmeresz95}:
\begin{equation}
H_q = \frac{1}{q-1} \left(1 - \sum_{i=1}^S p^q \right) \, .
\end{equation}
@@ -128,7 +133,7 @@
\end{figure}
Finally, the $\alpha$ parameter of Fisher's log-series can be used as
-a diversity index:
+a diversity index \citep{FisherEtal43}:
<<>>=
alpha <- fisher.alpha(BCI)
@
@@ -139,7 +144,7 @@
richness actually may be caused by differences in sample size. To
solve this problem, we may try to rarefy species richness to the same
number of individuals. Expected number of species in a community
-rarefied from $N$ to $n$ individuals is:
+rarefied from $N$ to $n$ individuals is \citep{Hurlbert71}:
\begin{multline}
\label{eq:rare}
\hat S_n = \sum_{i=1}^S (1 - q_i),\\ \text{where} \quad q_i = {N-x_i
@@ -150,7 +155,7 @@
$N$, and $q_i$ give the probabilities that species $i$ does \emph{not} occur in a
sample of size $n$. This is defined only when $N-x_i > n$, but for
other cases $q_i = 0$ or the species is sure to occur in the sample.
-The variance of rarefied richness is:
+The variance of rarefied richness is \citep{HeckEtal75}:
\begin{multline}
\label{eq:rarevar}
s^2 = q_i (1-q_i) \\ + 2 \sum_{i=1}^S \sum_{j>i} \left[ {N- x_i - x_j
@@ -186,16 +191,17 @@
richness:
<<>>=
all(rank(Srar) == rank(S2))
-@
+@
Moreover, the rarefied richness for two individuals is a finite
-sample variant of Simpson's diversity index (or, more precisely of
-$D_1 + 1$), and these two are almost identical in BCI:
+sample variant of Simpson's diversity index \citep{Hurlbert71}\,--\,or
+more precisely of $D_1 + 1$, and these two are almost identical in
+BCI:
<<>>=
range(diversity(BCI, "simp") - (S2 -1))
-@
+@
Rarefaction is sometimes presented as an ecologically meaningful
-alternative to dubious diversity indices, but the differences really
-seem to be small.
+alternative to dubious diversity indices \citep{Hurlbert71}, but the
+differences really seem to be small.
\section{Taxonomic and functional diversity}
@@ -208,8 +214,8 @@
\subsection{Taxonomic diversity: average distance of traits}
-The two basic indices are called taxonomic diversity ($\Delta$) and
-taxonomic distinctness ($\Delta^*$):
+The two basic indices are called taxonomic diversity $\Delta$ and
+taxonomic distinctness $\Delta^*$ \citep{ClarkeWarwick98}:
\begin{align}
\Delta &= \frac{\sum \sum_{i<j} \omega_{ij} x_i x_j}{n (n-1) / 2}\\
\Delta^* &= \frac{\sum \sum_{i<j} \omega_{ij} x_i x_j}{\sum \sum_{i<j} x_i x_j}
@@ -225,23 +231,23 @@
species richness, but lower case $s$ is used here in accordance with
the original papers on taxonomic diversity}
to give $s \Delta^+$, or it can be used to estimate an index of
-variation in taxonomic distinctness $\Lambda^+$:
+variation in taxonomic distinctness $\Lambda^+$ \citep{ClarkeWarwick01}:
\begin{equation}
\Lambda^+ = \frac{\sum \sum_{i<j} \omega_{ij}^2}{n (n-1) / 2} - (\Delta^+)^2
\end{equation}
We still need the taxonomic differences among species ($\omega$) to
-calculate the indices. These can be any
-distance structure among species, but usually it is found from
-established hierarchic taxonomy. Typical coding is that differences
-among species in the same genus is $1$, among the same family it is
-$2$ etc. However, the taxonomic differences are scaled to maximum
-$100$ for easier comparison between different data sets and
-taxonomies. Alternatively, it is possible to scale steps between
-taxonomic level proportional to the reduction in the number of
-categories: if almost all genera have only one species, it does not
-make a great difference if two individuals belong to a different
-species or to a different genus.
+calculate the indices. These can be any distance structure among
+species, but usually it is found from established hierarchic
+taxonomy. Typical coding is that differences among species in the same
+genus is $1$, among the same family it is $2$ etc. However, the
+taxonomic differences are scaled to maximum $100$ for easier
+comparison between different data sets and taxonomies. Alternatively,
+it is possible to scale steps between taxonomic level proportional to
+the reduction in the number of categories \citep{ClarkeWarwick99}: if
+almost all genera have only one species, it does not make a great
+difference if two individuals belong to a different species or to a
+different genus.
Function \code{taxondive} implements indices of taxonomic diversity,
and \code{taxa2dist} can be used to convert classification tables to
@@ -277,14 +283,15 @@
species traits. The argument for using trees is that in this way a
single deviant species will have a small influence, since its
difference is evaluated only once instead of evaluating its distance
-to all other species.
+to all other species \citep{PetcheyGaston06}.
Function \code{treedive} implements functional diversity defined as
the total branch length in a trait dendrogram connecting all species,
-but excluding the unnecessary root segments of the tree. The example
-uses the taxonomic distances of the previous chapter. These are first
-converted to a hierarchic clustering (which actually were their
-original form before \code{taxa2dist} converted them into distances)
+but excluding the unnecessary root segments of the tree
+\citep{PetcheyGaston02, PetcheyGaston06}. The example uses the
+taxonomic distances of the previous chapter. These are first converted
+to a hierarchic clustering (which actually were their original form
+before \code{taxa2dist} converted them into distances)
<<>>=
tr <- hclust(taxdis, "aver")
mod <- treedive(dune, tr)
@@ -301,7 +308,7 @@
\subsection{Fisher and Preston}
In Fisher's log-series, the expected number of species $\hat f$ with $n$
-individuals is:
+individuals is \citep{FisherEtal43}:
\begin{equation}
\hat f_n = \frac{\alpha x^n}{n}
\end{equation}
@@ -336,26 +343,25 @@
@
Preston's log-normal model is the main challenger to Fisher's
-log-series. Instead of plotting species by frequencies, it bins
-species into frequency classes of increasing sizes. As a result,
-upper bins with high range of frequencies become more common, and
-sometimes the result looks similar to Gaussian distribution truncated
-at the left.
+log-series \citep{Preston48}. Instead of plotting species by
+frequencies, it bins species into frequency classes of increasing
+sizes. As a result, upper bins with high range of frequencies become
+more common, and sometimes the result looks similar to Gaussian
+distribution truncated at the left.
There are two alternative functions for the log-normal model:
-\code{prestonfit} and \code{prestondistr}. Function
-\code{prestonfit} uses traditionally binning approach, and is burdened
-with arbitrary choices of binning limits and treatment of ties. It
-seems that Preston split ties between adjacent octaves: only half of
-the species observed once were in the first octave, and half were
-transferred to the next octave, and the same for all species at the
-octave limits occurring 2, 4, 8, 16\ldots times. Function
+\code{prestonfit} and \code{prestondistr}. Function \code{prestonfit}
+uses traditionally binning approach, and is burdened with arbitrary
+choices of binning limits and treatment of ties. It seems that Preston
+split ties between adjacent octaves: only half of the species observed
+once were in the first octave, and half were transferred to the next
+octave, and the same for all species at the octave limits occurring 2,
+4, 8, 16\ldots times \citep{WilliamsonGaston05}. Function
\code{prestonfit} can either split the ties or keep all limit cases in
-the lower octave.
-Function \code{prestondistr} directly
-maximizes truncated log-normal likelihood without binning data, and it
-is the recommended alternative. Log-normal models usually fit poorly
-to the BCI data, but here our random plot (number \Sexpr{k}):
+the lower octave. Function \code{prestondistr} directly maximizes
+truncated log-normal likelihood without binning data, and it is the
+recommended alternative. Log-normal models usually fit poorly to the
+BCI data, but here our random plot (number \Sexpr{k}):
<<>>=
prestondistr(BCI[k,])
@
@@ -364,11 +370,11 @@
An alternative approach to species abundance distribution is to plot
logarithmic abundances in decreasing order, or against ranks of
-species. These are known as ranked abundance
+species \citep{Whittaker65}. These are known as ranked abundance
distribution curves, species abundance curves, dominance--diversity
-curves or Whittaker plots.
-Function \code{radfit} fits some of the most popular models using
-maximum likelihood estimation:
+curves or Whittaker plots. Function \code{radfit} fits some of the
+most popular models \citep{Bastow91} using maximum likelihood
+estimation:
\begin{align}
\hat a_r &= \frac{N}{S} \sum_{k=r}^S \frac{1}{k} &\text{brokenstick}\\
\hat a_r &= N \alpha (1-\alpha)^{r-1} & \text{preemption} \\
@@ -430,7 +436,8 @@
they happen to be, and repeated accumulation in random order. In
addition, there are three analytic models. Rarefaction pools
individuals together, and applies rarefaction equation (\ref{eq:rare})
-to these individuals. Kindt's exact accumulator resembles rarefaction:
+to these individuals. Kindt's exact accumulator resembles rarefaction
+\citep{UglandEtal03}:
\begin{multline}
\label{eq:kindt}
\hat S_n = \sum_{i=1}^S (1 - p_i), \, \\ \text{where} \quad p_i = {N- f_i
@@ -446,7 +453,7 @@
where $r_{ij}$ is the correlation coefficient between species $i$ and
$j$. Both of these are unpublished: eq. \ref{eq:kindt} was developed
by Roeland Kindt, and eq. \ref{eq:kindtvar} by Jari Oksanen. The third
-analytic method was suggested by Coleman:
+analytic method was suggested by \citet{Coleman82}:
\begin{equation}
\label{eq:cole}
S_n = \sum_{i=1}^S (1 - p_i), \, \text{where} \quad p_i = \left(1 - \frac{1}{n}\right)^{f_i}
@@ -471,18 +478,18 @@
\subsection{Beta diversity}
-Whittaker divided diversity into various components. The best known
-are diversity in one spot that he called alpha diversity, and the
-diversity along gradients that he called beta diversity. The basic
-diversity indices are indices of alpha diversity. Beta diversity
-should be studied with respect to gradients, but almost everybody
-understand that as a measure of general heterogeneity: how many more
-species do you have in a collection of sites compared to an average
-site.
+\citet{Whittaker60} divided diversity into various components. The
+best known are diversity in one spot that he called alpha diversity,
+and the diversity along gradients that he called beta diversity. The
+basic diversity indices are indices of alpha diversity. Beta diversity
+should be studied with respect to gradients \citep{Whittaker60}, but
+almost everybody understand that as a measure of general heterogeneity
+\citep{Tuomisto10a, Tuomisto10b}: how many more species do you have in
+a collection of sites compared to an average site.
The best known index of beta diversity is based on the ratio of total
-number of species in a collection of sites ($S$) and the average
-richness per one site ($\bar \alpha$):
+number of species in a collection of sites $S$ and the average
+richness per one site $\bar \alpha$ \citep{Tuomisto10a}:
\begin{equation}
\label{eq:beta}
\beta = S/\bar \alpha - 1
@@ -497,8 +504,8 @@
The index of eq. \ref{eq:beta} is problematic because $S$ increases
with the number of sites even when sites are all subsets of the same
-community. Whittaker noticed this, and suggested the index to be
-found from pairwise comparison of sites. If the number of shared
+community. \citet{Whittaker60} noticed this, and suggested the index
+to be found from pairwise comparison of sites. If the number of shared
species in two sites is $a$, and the numbers of species unique to each
site are $b$ and $c$, then $\bar \alpha = (2a + b + c)/2$ and $S =
a+b+c$, and index \ref{eq:beta} can be expressed as:
@@ -516,8 +523,8 @@
There are many other definitions of beta diversity in addition to
eq. \ref{eq:beta}. All commonly used indices can be found using
-\code{betadiver}. The indices in \code{betadiver} can be referred
-to by subscript name, or index number:
+\code{betadiver} \citep{KoleffEtal03}. The indices in \code{betadiver}
+can be referred to by subscript name, or index number:
<<>>=
betadiver(help=TRUE)
@
@@ -545,10 +552,10 @@
estimate $z$ for any pair of sites.
Function \code{betadisper} can be used to analyse beta diversities
-with respect to classes or factors. There is no such classification
-available for the Barro Colorado Island data, and the example studies
-beta diversities in the management classes of the dune meadows
-(Fig. \ref{fig:betadisper}):
+with respect to classes or factors \citep{Anderson06, AndersonEtal06}.
+There is no such classification available for the Barro Colorado
+Island data, and the example studies beta diversities in the
+management classes of the dune meadows (Fig. \ref{fig:betadisper}):
<<>>=
data(dune)
data(dune.env)
@@ -580,7 +587,7 @@
once or twice.
Function \code{specpool} implements the following models to estimate
-the pool size $S_p$:
+the pool size $S_p$ \citep{SmithVanBelle84, Chao87}:
\begin{align}
S_p &= S_o + \frac{f_1^2}{2 f_2} & \text{Chao}\\
S_p &= S_o + f_1 \frac{N-1}{N} & \text{1st order Jackknife}\\
@@ -595,21 +602,21 @@
idea in bootstrap that if we repeat sampling (with replacement) from
the same data, we miss as many species as we missed originally.
-The variance estimators of Chao is:
+The variance the estimator of \citet{Chao87} is:
\begin{equation}
s^2 = f_2 \left(\frac{G^4}{4} + G^3 + \frac{G^2}{2} \right), \,
\text{where}\quad G = \frac{f_1}{f_2}
\end{equation}
The variance of the first-order jackknife is based on the number of
``singletons'' $r$ (species occurring only once in the data) in sample
-plots:
+plots \citep{SmithVanBelle84}:
\begin{equation}
s^2 = \left(\sum_{i=1}^N r_i^2 - \frac{f_1}{N}\right) \frac{N-1}{N}
\end{equation}
Variance of the second-order jackknife is not evaluated in
\code{specpool} (but contributions are welcome).
For the variance of bootstrap estimator, it is practical to define a
-new variable $q_i = (1-p_i)^N$ for each species:
+new variable $q_i = (1-p_i)^N$ for each species \citep{SmithVanBelle84}:
\begin{multline}
s^2 = \sum_{i=1}^{S_o} q_i (1-q_i) + 2 \sum \sum Z_p ,\\ \text{where}\; Z_p = \dots
\end{multline}
@@ -685,7 +692,8 @@
a species. The probability for each species at each site is assessed
from other species occurring on the site.
-Function \code{beals} implement Beals smoothing:
+Function \code{beals} implement Beals smoothing \citep{McCune87,
+ DeCaceresLegendre08}:
<<>>=
smo <- beals(BCI)
@
@@ -707,4 +715,6 @@
\label{fig:beals}
\end{figure}
+\bibliography{vegan}
+
\end{document}
Modified: pkg/vegan/inst/doc/vegan.bib
===================================================================
--- pkg/vegan/inst/doc/vegan.bib 2013-07-22 10:51:42 UTC (rev 2575)
+++ pkg/vegan/inst/doc/vegan.bib 2013-07-22 10:54:03 UTC (rev 2576)
@@ -1,3 +1,260 @@
+
+
+ at Article{DeCaceresLegendre08,
+ author = {M. {D}e~{C}{\'a}ceres and P. Legendre},
+ title = {Beals smoothing revisited},
+ journal = {Oecologia},
+ year = 2008,
+ volume = 156,
+ pages = {657--669}
+}
+
+ at Article{McCune87,
+ author = {B. Mc{C}une},
+ title = {Improving community ordination with the {B}eals
+ smoothing function},
+ journal = {Ecoscience},
+ year = 1987,
+ volume = 1,
+ pages = {82--86}
+}
+
+ at Article{Chao87,
+ author = {A. Chao},
+ title = {Estimating the population size for capture-recapture
+ data with unequal catchability},
+ journal = {Biometrics},
+ year = 1987,
+ volume = 43,
+ pages = {783--791}
+}
+
+ at Article{SmithVanBelle84,
+ author = {E. P. Smith and G. {van Belle}},
+ title = {Nonparametric estimation of species richness},
+ journal = {Biometrics},
+ year = 1984,
+ volume = 40,
+ pages = {119--129}
+}
+
+ at Article{AndersonEtal06,
+ author = {M. J. Anderson and K. E. Ellingsen and
+ B. H. Mc{A}rdle},
+ title = {Multivariate dispersion as a measure of beta
+ diversity},
+ journal = {Ecology Letters},
+ year = 2006,
+ volume = 9,
+ pages = {683--693}
+}
+
+ at Article{Anderson06,
+ author = {M. J. Anderson},
+ title = {Distance-based tests for homogeneity of multivariate
+ dispersions},
+ journal = {Biometrics},
+ year = 2006,
+ volume = 62,
+ pages = {245--253}
+}
+
+ at Article{KoleffEtal03,
+ author = {P. Koleff and K. J. Gaston and J. J. Lennon},
+ title = {Measuring beta diversity for presence-absence data},
+ journal = {Journal of Animal Ecology},
+ year = 2003,
+ volume = 72,
+ pages = {367--382}
+}
+
+ at Article{Tuomisto10b,
+ author = {H. Tuomisto},
+ title = {A diversity of beta diversities: straightening up a
+ concept gone awry. 2. Quantifying beta diversity and
+ related phenomena},
+ journal = {Ecography},
+ year = 2010,
+ volume = 33,
+ pages = {23--45}
+}
+
+ at Article{Tuomisto10a,
+ author = {H. Tuomisto},
+ title = {A diversity of beta diversities: straightening up a
+ concept gone awry. 1. Defining beta diversity as a
+ function of alpha and gamma diversity},
+ journal = {Ecography},
+ year = 2010,
+ volume = 33,
+ pages = {2--22}
+}
+
+ at Article{Whittaker60,
+ author = {R. H. Whittaker},
+ title = {Vegetation of {S}iskiyou mountains, {O}regon and
+ {C}alifornia},
+ journal = {Ecological Monographs},
+ year = 1960,
+ volume = 30,
+ pages = {279--338}
+}
+
+ at Article{Coleman82,
+ author = {B. D. Coleman and M. A. Mares and M. R. Willis and Y. Hsieh},
+ title = {Randomness, area and species richness},
+ journal = {Ecology},
+ year = 1982,
+ volume = 63,
+ pages = {1121--1133}}
+
+ at Article{UglandEtal03,
+ author = {K. I. Ugland and J. S. Gray and K. E. Ellingsen},
+ title = {The species-accumulation curve and estimation of
+ species richness},
+ journal = {Journal of Animal Ecology},
+ year = 2003,
+ volume = 72,
+ pages = {888--897}
+}
+
+ at Article{Bastow91,
+ author = {J. Bastow Wilson},
+ title = {Methods of fitting dominance/diversity curves},
+ journal = {Journal of Vegetation Science},
+ year = 1991,
+ volume = 2,
+ pages = {35--46}
+}
+
+ at Article{Whittaker65,
+ author = {R. H. Whittaker},
+ title = {Dominance and diversity in plant communities},
+ journal = {Science},
+ year = 1965,
+ volume = 147,
+ pages = {250--260}}
+
+ at Article{WilliamsonGaston05,
+ author = {M. Williamson and K. J. Gaston},
+ title = {The lognormal distribution is not an appropriate
+ null hypothesis for the species-abundance
+ distribution},
+ journal = {Journal of Animal Ecology},
+ year = 2005,
+ volume = 74,
+ pages = {409--422}
+}
+
+ at Article{Preston48,
+ author = {F. W. Preston},
+ title = {The commonness and rarity of species},
+ journal = {Ecology},
+ year = 1948,
+ volume = 29,
+ pages = {254--283}
+}
+
+ at Article{PetcheyGaston06,
+ author = {O. L. Petchey and K. J. Gaston},
+ title = {Functional diversity: back to basics and looking forward},
+ journal = {Ecology Letters},
+ year = 2006,
+ volume = 9,
+ pages = {741--758}
+}
+
+ at Article{PetcheyGaston02,
+ author = {O. L. Petchey and K. J. Gaston},
+ title = {Functional diversity ({FD}), species richness and
+ community composition},
+ journal = {Ecology Letters},
+ year = 2002,
+ volume = 5,
+ pages = {402--411}
+}
+
+ at Article{ClarkeWarwick99,
+ author = {K. R. Clarke and R. M Warwick},
+ title = {The taxonomic distinctness measure of biodiversity:
+ weighting of step lengths between hierarchical
+ levels},
+ journal = {Marine Ecology Progress Series},
+ year = 1999,
+ volume = 184,
+ pages = {21--29}
+}
+
+ at Article{ClarkeWarwick01,
+ author = {K. R. Clarke and R. M Warwick},
+ title = {A further biodiversity index applicable to species
+ lists: variation in taxonomic distinctness},
+ journal = {Marine Ecology Progress Series},
+ year = 2001,
+ volume = 216,
+ pages = {265--278}
+}
+
+ at Article{ClarkeWarwick98,
+ author = {K. R. Clarke and R. M Warwick},
+ title = {A taxonomic distinctness index and its statistical
+ properties},
+ journal = {Journal of Applied Ecology},
+ year = 1998,
+ volume = 35,
+ pages = {523--531}
+}
+
+ at Article{HeckEtal75,
+ author = {K. L. Heck and G. {van~Belle} and D. Simberloff},
+ title = {Explicit calculation of the rarefaction diversity
+ measurement and the determination of sufficient
+ sample size},
+ journal = {Ecology},
+ year = 1975,
+ volume = 56,
+ pages = {1459--1461}
+}
+
+ at Article{Hurlbert71,
+ author = {S. H. Hurlbert},
+ title = {The nonconcept of species diversity: a critique and
+ alternative parameters},
+ journal = {Ecology},
+ year = 1971,
+ volume = 52,
+ pages = {577--586}
+}
+
+ at Article{FisherEtal43,
+ author = {R. A. Fisher and A. S. Corbet and C. B. Williams},
+ title = {The relation between the number of species and the
+ number of individuals in a random sample of animal
+ population},
+ journal = {Journal of Animal Ecology},
+ year = 1943,
+ volume = 12,
+ pages = {42--58}
+}
+
+ at Article{Tothmeresz95,
+ author = {B. Tothmeresz},
+ title = {Comparison of different methods for diversity ordering},
+ journal = {Journal of Vegetation Science},
+ year = 1995,
+ volume = 6,
+ pages = {283--290}}
+
+ at Article{Hill73number,
+ author = {M. O. Hill},
+ title = {Diversity and evenness: a unifying notation and its
+ consequences},
+ journal = {Ecology},
+ year = 1973,
+ volume = 54,
+ pages = {427--473}
+}
+
@Book{Sedgewick90,
author = {R. Sedgewick},
title = {Algorithms in {C}},
Modified: pkg/vegan/inst/doc/vegan.sty
===================================================================
--- pkg/vegan/inst/doc/vegan.sty 2013-07-22 10:51:42 UTC (rev 2575)
+++ pkg/vegan/inst/doc/vegan.sty 2013-07-22 10:54:03 UTC (rev 2576)
@@ -19,6 +19,8 @@
\usepackage{booktabs}
\usepackage{Sweave}
\usepackage{hyperref}
+\usepackage[round]{natbib}
+\renewcommand{\cite}{\citep}
%% layout depends on the number of columns
\if at twocolumn
\renewenvironment{Schunk}{\par\footnotesize}{} % smaller examples
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