[Vegan-commits] r2308 - in branches/2.0: inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Sep 29 09:02:21 CEST 2012
Author: jarioksa
Date: 2012-09-29 09:02:20 +0200 (Sat, 29 Sep 2012)
New Revision: 2308
Modified:
branches/2.0/inst/ChangeLog
branches/2.0/man/RsquareAdj.Rd
branches/2.0/man/add1.cca.Rd
branches/2.0/man/adonis.Rd
branches/2.0/man/anova.cca.Rd
branches/2.0/man/decostand.Rd
branches/2.0/man/designdist.Rd
branches/2.0/man/fisherfit.Rd
branches/2.0/man/goodness.metaMDS.Rd
branches/2.0/man/humpfit.Rd
branches/2.0/man/isomap.Rd
branches/2.0/man/kendall.global.Rd
branches/2.0/man/make.cepnames.Rd
branches/2.0/man/metaMDS.Rd
branches/2.0/man/ordiplot3d.Rd
branches/2.0/man/ordisurf.Rd
branches/2.0/man/predict.cca.Rd
branches/2.0/man/raupcrick.Rd
branches/2.0/man/specaccum.Rd
branches/2.0/man/stepacross.Rd
branches/2.0/man/treedive.Rd
Log:
merge -r2307: no linebreaks within \code{}
Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/inst/ChangeLog 2012-09-29 07:02:20 UTC (rev 2308)
@@ -4,6 +4,7 @@
Version 2.0-5 (opened June 18, 2012)
+ * merge r2307: no line breaks within \code{} in Rd.
* merge r2305: proofread Rd files a..b.
* merge r2299: fix broken \link{}s in docs.
* merge r2297: upgrade docs for L&L 2012 (3r ed.)
Modified: branches/2.0/man/RsquareAdj.Rd
===================================================================
--- branches/2.0/man/RsquareAdj.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/RsquareAdj.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -48,8 +48,9 @@
\eqn{R^2}{R-squared}. The adjusted \eqn{R^2}{R-squared} is found as
the difference of adjusted \eqn{R^2}{R-squared} values of joint effect
of partial and constraining terms and partial term alone, and it is
- the same as the adjusted \eqn{R^2}{R-squared} of component \code{[a] =
- X1|X2} in two-component variation partition in \code{\link{varpart}}.
+ the same as the adjusted \eqn{R^2}{R-squared} of component
+ \code{[a] = X1|X2} in two-component variation partition in
+ \code{\link{varpart}}.
}
\value{ The functions return a list of items \code{r.squared} and
Modified: branches/2.0/man/add1.cca.Rd
===================================================================
--- branches/2.0/man/add1.cca.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/add1.cca.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -42,8 +42,8 @@
\code{\link{step}} have no firm basis, and setting argument \code{test
= "permutation"} may help in getting useful insight into validity of
model building. Function \code{\link{ordistep}} calls alternately
- \code{drop1.cca} and \code{add1.cca} with argument \code{test =
- "permutation"} and selects variables by their permutation
+ \code{drop1.cca} and \code{add1.cca} with argument
+ \code{test = "permutation"} and selects variables by their permutation
\eqn{P}-values. Meticulous use of \code{add1.cca} and
\code{drop1.cca} will allow more judicious model building.
Modified: branches/2.0/man/adonis.Rd
===================================================================
--- branches/2.0/man/adonis.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/adonis.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -90,8 +90,8 @@
characteristics. Further, the precise meaning of hypothesis tests will
depend upon precisely what is permuted. The strata argument keeps groups
intact for a particular hypothesis test where one does not want to
-permute the data among particular groups. For instance, \code{strata =
-B} causes permutations among levels of \code{A} but retains data within
+permute the data among particular groups. For instance, \code{strata = B}
+causes permutations among levels of \code{A} but retains data within
levels of \code{B} (no permutation among levels of \code{B}). See
\code{\link{permutations}} for additional details on permutation tests
in Vegan.
Modified: branches/2.0/man/anova.cca.Rd
===================================================================
--- branches/2.0/man/anova.cca.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/anova.cca.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -107,8 +107,8 @@
argument \code{permutations}, or if this is missing, by \code{step}.
Community data are permuted with choice \code{model = "direct"},
- residuals after partial CCA/RDA/CAP with choice \code{model =
- "reduced"} (default), and residuals after CCA/RDA/CAP under choice
+ residuals after partial CCA/RDA/CAP with choice \code{model = "reduced"}
+ (default), and residuals after CCA/RDA/CAP under choice
\code{model = "full"}. If there is no partial CCA/RDA/CAP stage,
\code{model = "reduced"} simply permutes the data and is equivalent to
\code{model = "direct"}. The test statistic is ``pseudo-\eqn{F}'',
Modified: branches/2.0/man/decostand.Rd
===================================================================
--- branches/2.0/man/decostand.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/decostand.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -50,8 +50,7 @@
distance, the distances should be similar to the
Chi-square distance used in correspondence analysis. However, the
results from \code{\link{cmdscale}} would still differ, since
- CA is a weighted ordination method (default \code{MARGIN =
- 1}).
+ CA is a weighted ordination method (default \code{MARGIN = 1}).
\item \code{hellinger}: square root of \code{method = "total"}
(Legendre & Gallagher 2001).
\item \code{log}: logarithmic transformation as suggested by
Modified: branches/2.0/man/designdist.Rd
===================================================================
--- branches/2.0/man/designdist.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/designdist.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -29,8 +29,8 @@
\item{terms}{How shared and total components are found. For vectors
\code{x} and \code{y} the \code{"quadratic"} terms are \code{J = sum(x*y)},
\code{A = sum(x^2)}, \code{B = sum(y^2)}, and \code{"minimum"} terms
- are \code{J = sum(pmin(x,y))}, \code{A = sum(x)} and \code{B =
- sum(y)}, and \code{"binary"} terms are either of these after transforming
+ are \code{J = sum(pmin(x,y))}, \code{A = sum(x)} and \code{B = sum(y)},
+ and \code{"binary"} terms are either of these after transforming
data into binary form (shared number of species, and number of
species for each row). }
\item{abcd}{Use 2x2 contingency table notation for binary data:
@@ -72,8 +72,8 @@
If you want to implement binary dissimilarities based on the 2x2
contingency table notation, you can set \code{abcd = TRUE}. In this
- notation \code{a = J}, \code{b = A-J}, \code{c = B-J}, \code{d =
- P-A-B+J}. This notation is often used instead of the more more
+ notation \code{a = J}, \code{b = A-J}, \code{c = B-J}, \code{d = P-A-B+J}.
+ This notation is often used instead of the more more
tangible default notation for reasons that are opaque to me.
}
Modified: branches/2.0/man/fisherfit.Rd
===================================================================
--- branches/2.0/man/fisherfit.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/fisherfit.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -111,8 +111,8 @@
second octave are transferred to the higher one as well, but this is
usually not as large a number of species. This practise makes data
look more lognormal by reducing the usually high lowest
- octaves. This can be achieved by setting argument \code{tiesplit =
- TRUE}. With \code{tiesplit = FALSE} the frequencies are not split,
+ octaves. This can be achieved by setting argument \code{tiesplit = TRUE}.
+ With \code{tiesplit = FALSE} the frequencies are not split,
but all ones are in the lowest octave, all twos in the second, etc.
Williamson & Gaston (2005) discuss alternative definitions in
detail, and they should be consulted for a critical review of
@@ -128,8 +128,8 @@
on the left so that some rare species are not observed. Function
\code{prestonfit} fits the truncated lognormal model as a second
degree log-polynomial to the octave pooled data using Poisson (when
- \eqn{tiesplit = FALSE}) or quasi-Poisson (when \eqn{tiesplit =
- TRUE}). error. Function \code{prestondistr} fits left-truncated
+ \code{tiesplit = FALSE}) or quasi-Poisson (when \code{tiesplit = TRUE})
+ error. Function \code{prestondistr} fits left-truncated
Normal distribution to \eqn{\log_2}{log2} transformed non-pooled
observations with direct maximization of log-likelihood. Function
\code{prestondistr} is modelled after function
Modified: branches/2.0/man/goodness.metaMDS.Rd
===================================================================
--- branches/2.0/man/goodness.metaMDS.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/goodness.metaMDS.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -27,8 +27,8 @@
number of points. }
\item{p.col, l.col}{Point and line colours.}
\item{lwd}{Line width. For \code{\link{monoMDS}} the default is
- \code{lwd = 1} if more than two lines are drawn, and \code{lwd =
- 2} otherwise.}
+ \code{lwd = 1} if more than two lines are drawn, and \code{lwd = 2}
+ otherwise.}
\item{\dots}{Other parameters to functions, e.g. graphical parameters.}
}
\details{
Modified: branches/2.0/man/humpfit.Rd
===================================================================
--- branches/2.0/man/humpfit.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/humpfit.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -93,9 +93,9 @@
methods. In addition, it can be accessed by the following methods
for \code{\link{glm}} objects: \code{\link{AIC}},
\code{\link{extractAIC}}, \code{\link{deviance}},
- \code{\link{coef}}, \code{\link{residuals.glm}} (except \code{type =
- "partial"}), \code{\link{fitted}}, and perhaps some others. In
- addition, function \code{\link[ellipse]{ellipse.glm}} (package
+ \code{\link{coef}}, \code{\link{residuals.glm}} (except
+ \code{type = "partial"}), \code{\link{fitted}}, and perhaps some others.
+ In addition, function \code{\link[ellipse]{ellipse.glm}} (package
\pkg{ellipse}) can be used to draw approximate confidence ellipses
for pairs of parameters, if the normal assumptions look appropriate.
}
Modified: branches/2.0/man/isomap.Rd
===================================================================
--- branches/2.0/man/isomap.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/isomap.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -40,8 +40,8 @@
\item{type}{Plot observations either as \code{"points"},
\code{"text"} or use \code{"none"} to plot no observations. The
- \code{"text"} will use \code{\link{ordilabel}} if \code{net =
- TRUE} and \code{\link{ordiplot}} if \code{net = FALSE}, and pass
+ \code{"text"} will use \code{\link{ordilabel}} if \code{net = TRUE}
+ and \code{\link{ordiplot}} if \code{net = FALSE}, and pass
extra arguments to these functions.}
\item{web}{Colour of the web in \pkg{rgl} graphics.}
Modified: branches/2.0/man/kendall.global.Rd
===================================================================
--- branches/2.0/man/kendall.global.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/kendall.global.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -53,15 +53,16 @@
compute Ward's agglomerative clustering of a matrix of correlations
among the species. In detail: (1.1) compute a Pearson or Spearman
correlation matrix (\code{correl.matrix}) among the species; (1.2)
- turn it into a distance matrix: \code{mat.D =
- as.dist(1-correl.matrix)}; (1.3) carry out Ward's hierarchical
- clustering of that matrix using \code{hclust}: \code{clust.ward =
- hclust(mat.D, "ward")}; (1.4) plot the dendrogram:
+ turn it into a distance matrix: \code{mat.D = as.dist(1-correl.matrix)};
+ (1.3) carry out Ward's hierarchical
+ clustering of that matrix using \code{hclust}:
+ \code{clust.ward = hclust(mat.D, "ward")}; (1.4) plot the dendrogram:
\code{plot(clust.ward, hang=-1)}; (1.5) cut the dendrogram in two
- groups, retrieve the vector of species membership: \code{group.2 =
- cutree(clust.ward, k=2)}. (1.6) After steps 2 and 3 below, you may
- have to come back and try divisions of the species into k = 3, 4, 5,
- \dots groups.
+ groups, retrieve the vector of species membership:
+ \code{group.2 = cutree(clust.ward, k=2)}. (1.6) After steps 2 and 3 below,
+ you may
+ have to come back and try divisions of the species into k = \eqn{3, 4, 5, \dots}
+ groups.
(2) Compute global tests of significance of the 2 (or more) groups
using the function \code{kendall.global} and the vector defining the
Modified: branches/2.0/man/make.cepnames.Rd
===================================================================
--- branches/2.0/man/make.cepnames.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/make.cepnames.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -28,8 +28,8 @@
function first makes valid \R names using \code{\link{make.names}},
and then splits these into elemets. The CEP name is made by taking
the four first letters of the first element, and four first letters
- of the last (default) or the second element (with \code{seconditem =
- TRUE}). If there was only one name element, it is
+ of the last (default) or the second element (with
+ \code{seconditem = TRUE}). If there was only one name element, it is
\code{\link{abbreviate}}d to eight letters. Finally, the names are
made unique which may add numbers to duplicated names.
Modified: branches/2.0/man/metaMDS.Rd
===================================================================
--- branches/2.0/man/metaMDS.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/metaMDS.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -114,8 +114,7 @@
\code{"fail"} or \code{"add"} a small positive value, or
\code{"ignore"}. \code{\link{monoMDS}} accepts zero dissimilarities
and the default is \code{zerodist = "ignore"}, but with
- \code{\link[MASS]{isoMDS}} you may need to set \code{zerodist =
- "add"}.}
+ \code{\link[MASS]{isoMDS}} you may need to set \code{zerodist = "add"}.}
\item{distfun}{Dissimilarity function. Any function returning a
\code{dist} object and accepting argument \code{method} can be used
Modified: branches/2.0/man/ordiplot3d.Rd
===================================================================
--- branches/2.0/man/ordiplot3d.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/ordiplot3d.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -41,8 +41,7 @@
text labels.}
\item{ax.col}{Axis colour (concerns only the crossed axes through the
origin).}
- \item{text}{Text to override the default with \code{type =
- "t"}.}
+ \item{text}{Text to override the default with \code{type = "t"}.}
\item{envfit}{Fitted environmental variables from \code{\link{envfit}}
displayed in the graph.}
\item{xlab, ylab, zlab}{Axis labels passed to
Modified: branches/2.0/man/ordisurf.Rd
===================================================================
--- branches/2.0/man/ordisurf.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/ordisurf.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -113,9 +113,9 @@
Wood, 2011). The addition of this extra penalty is invoked by
setting argument \code{select} to \code{TRUE}. The function plots
the fitted contours with convex hull of data points either over an
- existing ordination diagram or draws a new plot. If \code{select ==
- TRUE} and the smooth is effectively penalised out of the model, no
- contours will be plotted.
+ existing ordination diagram or draws a new plot. If
+ \code{select = TRUE} and the smooth is effectively penalised out of
+ the model, no contours will be plotted.
\code{\link[mgcv]{gam}} determines the degree of smoothness for the
fitted response surface during model fitting. Argument \code{method}
Modified: branches/2.0/man/predict.cca.Rd
===================================================================
--- branches/2.0/man/predict.cca.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/predict.cca.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -44,8 +44,8 @@
\item{newdata}{New data frame to be used in prediction or in
calibration. Usually this a new community data frame, but with
- \code{type = "lc"} and for constrained component with \code{type =
- "response"} and \code{type = "working"} it must be an environment
+ \code{type = "lc"} and for constrained component with
+ \code{type = "response"} and \code{type = "working"} it must be a
data frame. The \code{newdata} must have the same number of rows as
the original community data for a \code{\link{cca}} result with
\code{type = "response"} or \code{type = "working"}. If the
@@ -112,9 +112,9 @@
\code{type = "lc"} the function finds the linear combination scores
for sites from environmental data. In that case the new data frame
must contain all constraining and conditioning environmental variables
- of the model formula. With \code{type = "response"} or \code{type =
- "working"} the new data must contain envinronmental variables if
- constrained component is desired, and community data matrix if
+ of the model formula. With \code{type = "response"} or
+ \code{type = "working"} the new data must contain envinronmental variables
+ if constrained component is desired, and community data matrix if
residual or unconstrained component is desired. With these types, the
function uses \code{newdata} to find new \code{"lc"} (constrained) or
\code{"wa"} scores (unconstrained) and then finding the response or
Modified: branches/2.0/man/raupcrick.Rd
===================================================================
--- branches/2.0/man/raupcrick.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/raupcrick.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -85,8 +85,8 @@
\pkg{vegan}. Chase et al. (2011) script with \code{split = TRUE}
uses half of tied simulation values to calculate a distance measure,
and that choice cannot be directly reproduced in vegan (it is the
- average of \pkg{vegan} \code{raupcrick} results with \code{chase =
- TRUE} and \code{chase = FALSE}).}
+ average of \pkg{vegan} \code{raupcrick} results with
+ \code{chase = TRUE} and \code{chase = FALSE}).}
\seealso{The function is based on \code{\link{oecosimu}}. Function
\code{\link{vegdist}} with {method = "raup"} implements a related
Modified: branches/2.0/man/specaccum.Rd
===================================================================
--- branches/2.0/man/specaccum.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/specaccum.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -39,8 +39,7 @@
expected richness following
Coleman et al. 1982, and \code{"rarefaction"} finds the mean when
accumulating individuals instead of sites. }
- \item{permutations}{Number of permutations with \code{method =
- "random"}.}
+ \item{permutations}{Number of permutations with \code{method = "random"}.}
\item{conditioned}{ Estimation of standard deviation is conditional on
the empirical dataset for the exact SAC}
\item{gamma}{Method for estimating the total extrapolated number of species in the
@@ -101,8 +100,8 @@
achieves this by applying function \code{\link{rarefy}} with number of individuals
corresponding to average number of individuals per site.
- The function has a \code{plot} method. In addition, \code{method =
- "random"} has \code{summary} and \code{boxplot} methods.
+ The function has a \code{plot} method. In addition, \code{method = "random"}
+ has \code{summary} and \code{boxplot} methods.
Function \code{predict} can return the values corresponding to
\code{newdata} using linear (\code{\link{approx}}) or spline
Modified: branches/2.0/man/stepacross.Rd
===================================================================
--- branches/2.0/man/stepacross.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/stepacross.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -46,8 +46,8 @@
\code{toolong}.
De'ath (1999) suggested a simplified method known as extended
- dissimilarities, which are calculated with \code{path =
- "extended"}. In this method, dissimilarities that are
+ dissimilarities, which are calculated with \code{path = "extended"}.
+ In this method, dissimilarities that are
\code{toolong} or longer are first made \code{NA}, and then the function
tries to replace these \code{NA} dissimilarities with a path through
single stepping stone points. If not all \code{NA} could be
@@ -68,8 +68,8 @@
\code{toolong} is zero or negative, the function does not make any
dissimilarities into \code{NA}. If there are no \code{NA}s in the
input and \code{toolong = 0}, \code{path = "shortest"}
- will find shorter paths for semi-metric indices, and \code{path =
- "extended"} will do nothing. Function \code{\link{no.shared}} can be
+ will find shorter paths for semi-metric indices, and \code{path = "extended"}
+ will do nothing. Function \code{\link{no.shared}} can be
used to set dissimilarities to \code{NA}.
If the data are disconnected or there is no path between all points,
@@ -82,8 +82,8 @@
Alternative \code{path = "shortest"} uses Dijkstra's method for
finding flexible shortest paths, implemented as priority-first search
- for dense graphs (Sedgewick 1990). Alternative \code{path =
- "extended"} follows De'ath (1999), but implementation is simpler
+ for dense graphs (Sedgewick 1990). Alternative \code{path = "extended"}
+ follows De'ath (1999), but implementation is simpler
than in his code.
}
Modified: branches/2.0/man/treedive.Rd
===================================================================
--- branches/2.0/man/treedive.Rd 2012-09-29 06:58:32 UTC (rev 2307)
+++ branches/2.0/man/treedive.Rd 2012-09-29 07:02:20 UTC (rev 2308)
@@ -66,9 +66,9 @@
species traits contain \code{\link{factor}} or \code{\link{ordered}}
factor variables, it is recommended to use Gower distances for mixed
data (function \code{\link[cluster]{daisy}} in package \pkg{cluster}),
- and usually the recommended clustering method is UPGMA (\code{method =
- "average"} in function \code{\link{hclust}}) (Podani and Schmera
- 2006).
+ and usually the recommended clustering method is UPGMA
+ (\code{method = "average"} in function \code{\link{hclust}})
+ (Podani and Schmera 2006).
It is possible to analyse the non-randomness of functional diversity
using \code{\link{oecosimu}}. This needs specifying an adequate Null
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