[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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