[Vegan-commits] r1036 - pkg/vegan/inst/doc

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2009-10-07 09:06:36 +0200 (Wed, 07 Oct 2009)
New Revision: 1036

Modified:
   pkg/vegan/inst/doc/decision-vegan.Rnw
   pkg/vegan/inst/doc/diversity-vegan.Rnw
   pkg/vegan/inst/doc/intro-vegan.Rnw
Log:
typos

Modified: pkg/vegan/inst/doc/decision-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/decision-vegan.Rnw	2009-10-07 06:58:12 UTC (rev 1035)
+++ pkg/vegan/inst/doc/decision-vegan.Rnw	2009-10-07 07:06:36 UTC (rev 1036)
@@ -52,7 +52,7 @@
 
 The matrix temperature is intuitively simple
 (Fig. \ref{fig:nestedtemp}), but the the exact calculations were not
-explaind in the original publication \cite{AtmarPat93}.
+explained in the original publication \cite{AtmarPat93}.
 \begin{SCfigure}
 <<fig=true,echo=false,results=hide>>=
 data(sipoo)
@@ -108,8 +108,8 @@
     absence, $i$ and $j$ are row and column indices, and $n$ is the
     number of rows. The equations give the indices for columns, but
     the indices can be reversed for corresponding row indexing.
-    Ordering by $s$ packs presences to the topleft corner, and
-    ordering by $t$ pack zeros away from the topleft corner. The final
+    Ordering by $s$ packs presences to the top left corner, and
+    ordering by $t$ pack zeros away from the top left corner. The final
     sorting should be ``a compromise'' \cite{RodGir06} between these
     scores, and \texttt{vegan} uses $s+t$.  The result should be cool,
     but the packing does not try to minimize the temperature
@@ -151,7 +151,7 @@
 tour'' which is quite a different problem than the one we face with
 null models.  The chess piece ``knight''\footnote{``Knight'' is
   ``Springer'' in German which is very appropriate as Springer was the
-  publisher of the paper on ``knight't tour''} has a track of history:
+  publisher of the paper on ``knight's tour''} has a track of history:
 a piece in a certain position could only have entered from some
 candidate squares. The filling of incidence matrix no such a history:
 if we know that the item last added was in certain row and column, we
@@ -170,7 +170,7 @@
     patterns: the rows and columns with one or a couple of presences
     were filled first, and the process was cornered to columns and
     rows with many presences. As a consequence, the the process tried
-    harder to fill that corner, and the result was a more tighlty
+    harder to fill that corner, and the result was a more tightly
     packed quadratic fill pattern than with other methods.
   \item The filling stage stops when no new points can be added
     without exceeding row or column totals. ``Backtracking'' means

Modified: pkg/vegan/inst/doc/diversity-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/diversity-vegan.Rnw	2009-10-07 06:58:12 UTC (rev 1035)
+++ pkg/vegan/inst/doc/diversity-vegan.Rnw	2009-10-07 07:06:36 UTC (rev 1036)
@@ -83,7 +83,7 @@
 or the corresponding Hill numbers $N_a = \exp(H_a)$.  Many common
 diversity indices are special cases of Hill numbers: $N_0 = S$, $N_1 =
 \exp(H')$, $N_2 = D_2$, and $N_\infty = 1/(\max p_i)$. The
-correspoding R\'{e}nyi diversities are $H_0 = \log(S)$, $H_1 = H'$, $H_2 =
+corresponding R\'{e}nyi diversities are $H_0 = \log(S)$, $H_1 = H'$, $H_2 =
 - \log(\sum p_i^2)$, and $H_\infty = - \log(\max p_i)$.  We select a
 random subset of five sites for R\'{e}nyi diversities:
 <<>>=
@@ -189,7 +189,7 @@
 
 \subsection{Taxonomic diversity: average distance of properties}
 
-The two basic indecies are called taxonomic diversity ($\Delta$) and
+The two basic indices are called taxonomic diversity ($\Delta$) and
 taxonomic distinctness ($\Delta^*$):
 \begin{align}
   \Delta &= \frac{\sum \sum_{i<j} \omega_{ij} x_i x_j}{n (n-1) / 2}\\
@@ -227,7 +227,7 @@
 Function \texttt{taxondive} implements indices of taxonomic diversity,
 and \texttt{taxa2dist} can be used to convert classification tables to
 taxonomic distances either with constant or variable step lengths
-between succesive categories. There is no taxonomic table for the BCI
+between successive categories. There is no taxonomic table for the BCI
 data in \texttt{vegan}\footnote{Actually I made such a classification,
   but taxonomic differences proved to be of little use in the Barro
   Colorado data: they only singled out sites with Monocots (palm
@@ -462,7 +462,7 @@
   \label{eq:beta}
   \beta = S/\bar \alpha - 1
 \end{equation}
-Substraction of one means that $\beta = 0$ when there are no excess
+Subtraction of one means that $\beta = 0$ when there are no excess
 species or no heterogeneity between sites. For this index, no specific
 functions are needed, but this index can be easily found with the help
 of \texttt{vegan} function \texttt{specnumber}:

Modified: pkg/vegan/inst/doc/intro-vegan.Rnw
===================================================================
--- pkg/vegan/inst/doc/intro-vegan.Rnw	2009-10-07 06:58:12 UTC (rev 1035)
+++ pkg/vegan/inst/doc/intro-vegan.Rnw	2009-10-07 07:06:36 UTC (rev 1036)
@@ -359,7 +359,7 @@
 @
 This partials out the effect of \texttt{Moisture} before analysing the
 effects of \texttt{A1} and \texttt{Management}.  This also influences
-the signficances of the terms:
+the significances of the terms:
 <<>>=
 anova(ord, by="term", perm=500)
 @