[Vegan-commits] r563 - in devel/lmodel2: . R inst/doc man

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

Author: jarioksa
Date: 2008-11-13 10:17:04 +0100 (Thu, 13 Nov 2008)
New Revision: 563

Modified:
   devel/lmodel2/DESCRIPTION
   devel/lmodel2/R/lmodel2.R
   devel/lmodel2/inst/doc/mod2user.Rnw
   devel/lmodel2/man/lmodel2.Rd
Log:
lmodel2: documentation tweaks

Modified: devel/lmodel2/DESCRIPTION
===================================================================
--- devel/lmodel2/DESCRIPTION	2008-11-12 10:44:33 UTC (rev 562)
+++ devel/lmodel2/DESCRIPTION	2008-11-13 09:17:04 UTC (rev 563)
@@ -1,7 +1,7 @@
 Package: lmodel2
 Type: Package
 Title: Model II Regression
-Version: 1.5
+Version: 1.6
 Date: 2008-11-12
 Author: Pierre Legendre
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: devel/lmodel2/R/lmodel2.R
===================================================================
--- devel/lmodel2/R/lmodel2.R	2008-11-12 10:44:33 UTC (rev 562)
+++ devel/lmodel2/R/lmodel2.R	2008-11-13 09:17:04 UTC (rev 563)
@@ -302,9 +302,9 @@
     function(x, ...)
 {
 ## Print the regression results
-    cat("\nModel II regression\n")
-    cat("\nCall:\n")
-    cat(deparse(x$call), "\n\n")
+    cat("\nModel II regression\n\n")
+    writeLines(strwrap(pasteCall(x$call)))
+    cat("\n")
     cat("n =",x$n,"  r =",x$r,"  r-square =",x$rsquare,'\n')
     cat("Parametric P-values:   2-tailed =",x$P.param,
         "   1-tailed =",x$P.param/2,'\n')

Modified: devel/lmodel2/inst/doc/mod2user.Rnw
===================================================================
--- devel/lmodel2/inst/doc/mod2user.Rnw	2008-11-12 10:44:33 UTC (rev 562)
+++ devel/lmodel2/inst/doc/mod2user.Rnw	2008-11-13 09:17:04 UTC (rev 563)
@@ -33,9 +33,9 @@
 \SweaveOpts{strip.white=true}
 <<echo=false>>=
 require(lmodel2)
-par(mfrow=c(1,1))
-par(mar=c(3,3,1,0)+.1)
 options(width=72)
+figset <- function() par(mar=c(4,4,1,1)+.1)
+options(SweaveHooks = list(fig = figset))
 @
 
 
@@ -392,7 +392,7 @@
       = -5.67$};
     \draw (11,0) -- (11+3/2.75, 3) node[near end,sloped,above]{MA
       regression line} node[right]{$b_1 = 2.75$};
-    \draw (11,0) -- (11+2.5/0.84, 2.5) node[midway,sloped,above]{Lower
+    \draw (11,0) -- (11+2/0.84, 2) node[near end,sloped,above]{Lower
       bound of CI} node[right]{$b_{1 \inf} =0.84$};
     \draw[font=\large] (0,3) node{(a)};
     \draw[font=\large] (8,3) node{(b)};
@@ -431,7 +431,7 @@
 \subsection{Surgical unit data}
 \label{sec:exa1}
 
-\subsubsection{Input data}
+%\subsubsection{Input data}
 
 This example compares observations to the values forecasted by a
 model. A hospital surgical unit wanted to forecast survival of
@@ -448,8 +448,6 @@
 is the following:
 
 
-
-
 \begin{equation*}
 \hat Y = 1.388778 + 0.005653 X_3 + 0.139015 X_4
 \end{equation*}
@@ -502,7 +500,7 @@
 \subsection{Eagle rays and \emph{Macomona} bivalves}
 \label{sec:exa2}
 
-\subsubsection{Input data}
+%\subsubsection{Input data}
 
 The following table presents observations at 20 sites from a study on
 predator-prey relationships \citep{Hines.ea97}. $y$ is the number of
@@ -582,7 +580,7 @@
 
 \subsection{Cabezon spawning}%
 \label{sec:exa3}%
-\subsubsection{Input data}
+%\subsubsection{Input data}
 
 The following table presents data used by \citet[Box
 14.12]{SokalRohlf95} to illustrate model II regression analysis. They
@@ -645,7 +643,7 @@
 \subsection{Highly correlated random variables}
 \label{sec:exa4}
 
-\subsubsection{Input data}
+%\subsubsection{Input data}
 
 \citet{Mesple.ea96} generated a variable $X$ containing 100 values
 drawn at random from a uniform distribution in the interval $[0,
@@ -687,7 +685,7 @@
 \subsection{Uncorrelated random variables}
 \label{sec:exa5}
 
-\subsubsection{Input data}
+%\subsubsection{Input data}
 
 Two vectors of 100 random data drawn from a normal distribution
 $\mathcal{N}(0, 1)$ were generated. One expects to find a null

Modified: devel/lmodel2/man/lmodel2.Rd
===================================================================
--- devel/lmodel2/man/lmodel2.Rd	2008-11-12 10:44:33 UTC (rev 562)
+++ devel/lmodel2/man/lmodel2.Rd	2008-11-13 09:17:04 UTC (rev 563)
@@ -131,15 +131,17 @@
 op <- par(mfrow = c(1,2))
 plot(Ex2.res, "SMA")
 plot(Ex2.res, "RMA")
-
+par(op)
 ## Example 3 (cabezon spawning)
+op <- par(mfrow = c(1,2))
 data(mod2ex3)
 Ex3.res <- lmodel2(No_eggs ~ Mass, data=mod2ex3, "relative", "relative", 99)
 Ex3.res
 plot(Ex3.res, "SMA")
 plot(Ex3.res, "RMA")
-
+par(op)
 ## Example 4 (highly correlated random variables)
+op <- par(mfrow=c(1,2))
 data(mod2ex4)
 Ex4.res <- lmodel2(y ~ x, data=mod2ex4, "interval", "interval", 99)
 Ex4.res