Merge branch 'volatile-urls'

man/BCI.Rd

@@ -14,13 +14,14 @@ data(BCI.env)
 }
 \format{
 
-  A data frame with 50 plots (rows) of 1 hectare with counts of trees on
-  each plot with total of 225 species (columns). Full Latin names are
-  used for tree species. The names were updated against
-  \url{http://www.theplantlist.org} and Kress et al. (2009) which allows
-  matching 207 of species against \doi{10.5061/dryad.63q27} (Zanne et
-  al., 2014). The original species names are available as attribute
-  \code{original.names} of \code{BCI}. See Examples for changed names.
+  A data frame with 50 plots (rows) of 1 hectare with counts of trees
+  on each plot with total of 225 species (columns). Full Latin names
+  are used for tree species. The names were updated with The Plant
+  List web service (now phased out) and Kress et al. (2009) which
+  allows matching 207 of species against \doi{10.5061/dryad.63q27}
+  (Zanne et al., 2014). The original species names are available as
+  attribute \code{original.names} of \code{BCI}. See Examples for
+  changed names.
 
   For \code{BCI.env}, a data frame with 50 plots (rows) and nine site
   variables derived from Pyke et al. (2001) and Harms et al. (2001):

man/avgdist.Rd

@@ -50,7 +50,7 @@ avgdist(x, sample, distfun = vegdist, meanfun = mean,
   subsampled datasets by presenting the average of multiple random
   iterations. This function runs using the \code{\link{vegdist}}. This
   functionality has been utilized in the Mothur standalone microbial
-  ecology toolkit \href{https://mothur.org/wiki/Dist.shared}{here}.
+  ecology toolkit, see https://mothur.org/wiki/Dist.shared.
 
 }
 

man/dispindmorisita.Rd

@@ -93,12 +93,12 @@ Cummings Publishers.  }
 
 \author{\enc{Péter Sólymos}{Peter Solymos}, \email{solymos@ualberta.ca}}
 
-\note{ A common error found in several papers is that when standardizing
-as in the case (b), the denominator is given as \code{Muni - 1}. This
-results in a hiatus in the [0, 0.5] interval of the standardized
-index. The root of this typo is the book of Krebs (1999), see the Errata
-for the book (Page 217,
-\url{https://www.zoology.ubc.ca/~krebs/downloads/errors_2nd_printing.pdf}).
+\note{ A common error found in several papers is that when
+standardizing as in the case (b), the denominator is given as
+\code{Muni - 1}. This results in a hiatus in the [0, 0.5] interval of
+the standardized index. The root of this typo is the book of Krebs
+(1999), see the Errata for the book (Page 217, currently
+https://www.zoology.ubc.ca/~krebs/downloads/errors_2nd_printing.pdf).
 }
 
 \examples{

man/vegan-package.Rd

@@ -30,9 +30,6 @@ Most important changes in \pkg{vegan} documents can be read with
 \code{browseVignettes("vegan")}. The vignettes include a \pkg{vegan}
 FAQ, discussion on design decisions, short introduction to ordination
 and discussion on diversity methods.
-%A tutorial of the package at
-%\url{http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf} provides
-%a more thorough introduction to the package.
 
 To see the preferable citation of the package, type
 \code{citation("vegan")}.