Revise preface, edit R.plotting.Rnw to make sure it works with ggplot…

…2 and write a few sections in new file R.more.plotting.Rnw.

R.more.plotting.Rnw

@@ -41,14 +41,14 @@ Package \ggpmisc provides new stats: \code{stat\_peaks()}, \code{stat\_valleys()
 <<>>=
 lynx.df <- data.frame(year = as.numeric(time(lynx)), lynx = as.matrix(lynx))
 @
- 
+
 <<>>=
 ggplot(lynx.df, aes(year, lynx)) + geom_line() +
   stat_peaks(colour = "red") +
-  stat_peaks(geom = "text", colour = "red", 
+  stat_peaks(geom = "text", colour = "red",
              vjust = -0.5, x.label.fmt = "%4.0f") +
   stat_valleys(colour = "blue") +
-  stat_valleys(geom = "text", colour = "blue", 
+  stat_valleys(geom = "text", colour = "blue",
                vjust = 1.5, x.label.fmt = "%4.0f") +
   ylim(-100, 7300)
 @
@@ -57,7 +57,7 @@ ggplot(lynx.df, aes(year, lynx)) + geom_line() +
 ggplot(lynx.df, aes(year, lynx)) + geom_line() +
   stat_peaks(colour = "red") +
   stat_peaks(geom = "rug", colour = "red") +
-  stat_peaks(geom = "text", colour = "red", 
+  stat_peaks(geom = "text", colour = "red",
              vjust = -0.5, x.label.fmt = "%4.0f") +
   ylim(NA, 7300)
 
@@ -76,38 +76,39 @@ ggplot(lynx.df, aes(year, lynx)) + geom_line() +
   stat_peaks(colour = "red") +
   stat_peaks(geom = "rug", colour = "red") +
   stat_peaks(geom = "text", colour = "red",
-             hjust = -0.1, label.fmt = "%4.0f", 
+             hjust = -0.1, label.fmt = "%4.0f",
              angle = 90, size = rel(2),
-             aes(label = paste(..y.label.., 
+             aes(label = paste(..y.label..,
                                "skins in year", ..x.label..))) +
   stat_valleys(colour = "blue") +
   stat_valleys(geom = "rug", colour = "blue") +
   stat_valleys(geom = "text", colour = "blue",
-             hjust = -0.1, vjust = 1, label.fmt = "%4.0f", 
+             hjust = -0.1, vjust = 1, label.fmt = "%4.0f",
              angle = 90, size = rel(2),
-             aes(label = paste(..y.label.., 
+             aes(label = paste(..y.label..,
                                "skins in year", ..x.label..))) +
   ylim(NA, 10000)
 @
 
-Of course, if one finds use for it, the peaks and/or valleys can be plotted on their own.
+Of course, if one finds use for it, the peaks and/or valleys can be plotted on their own. Here we plot an "envelope" using \code{geom\_line()}.
 
 <<>>=
-ggplot(lynx.df, aes(year, lynx)) + 
+ggplot(lynx.df, aes(year, lynx)) +
   stat_peaks(geom = "line") + stat_valleys(geom = "line")
 @
+
 \subsection{Learning and/or debugging}
 
-A very simple stat named \code{stat\_debug()} can save the work of adding print statements to the code of stats to get information about what data is being passed to the \code{compute\_group()} function. Because the code of this function is stored in a \code{ggproto} object, at the moment it is impossible to directly set breakpoints in it. This stat may also help users diagnose problems with the mapping of aesthetics in their code or just get a better idea of how the internals of \ggplot work.
+A very simple stat named \code{stat\_debug()} can save the work of adding print statements to the code of stats to get information about what data is being passed to the \code{compute\_group()} function. Because the code of this function is stored in a \code{ggproto} object, at the moment it is impossible to directly set breakpoints in it. This \code{stat\_debug()} may also help users diagnose problems with the mapping of aesthetics in their code or just get a better idea of how the internals of \ggplot work.
 
 <<>>=
 ggplot(lynx.df, aes(year, lynx)) + geom_line() +
   stat_debug(alpha = 0.8)
 @
 
 <<>>=
-lynx.df$century <- ifelse(lynx.df$year >= 1900, "XX", "XIX") 
-ggplot(lynx.df, aes(year, lynx, color = century)) + 
+lynx.df$century <- ifelse(lynx.df$year >= 1900, "XX", "XIX")
+ggplot(lynx.df, aes(year, lynx, color = century)) +
   geom_line() +
   stat_debug(alpha = 0.8, size = rel(2.5))
 @
@@ -116,7 +117,7 @@ ggplot(lynx.df, aes(year, lynx, color = century)) +
 
 \subsection{New geoms}
 
-Package \ggrepel provides two new geoms: \code{geom\_text\_repel} and \code{geom\_label\_repel}. They are used similarly to \code{geom\_text} and \code{geom\_label} but the text or labels ``repel'' each other so that they rarely overlap unless the plot is very crowded. 
+Package \ggrepel provides two new geoms: \code{geom\_text\_repel} and \code{geom\_label\_repel}. They are used similarly to \code{geom\_text} and \code{geom\_label} but the text or labels ``repel'' each other so that they rarely overlap unless the plot is very crowded.
 
 
 <<>>=

appendixes.prj

@@ -13,7 +13,7 @@ TeX:RNW:UTF-8
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 abbrev.sty
 TeX:STY
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+1060850 0 20 1 18 50 200 200 1593 649 0 0 417 306 -1 -1 0 0 2 0 0 2 1 0 50 18  0 0 0
 usingr.sty
 TeX:STY
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@@ -25,13 +25,13 @@ TeX:RNW
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 R.more.plotting.Rnw
 TeX:RNW
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 :\aphalo\Documents\R bits and pieces\polynomials\polynomials.Rmd
 DATA
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+5243122 0 0 1 0 1 0 0 1418 354 1 0 78 0 -1 -1 0 0 4 0 0 4 1 0 1 0  0 0 0
 :\aphalo\Documents\RPackages\ggpmisc\vignettes\examples.Rmd
 DATA
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+5243122 1 176 1 181 1 25 25 1443 379 1 0 78 496 -1 -1 0 0 4 0 0 4 1 0 1 181  0 0 0
 R.plotting.Rnw
 TeX:RNW
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@@ -40,7 +40,7 @@ BibTeX
 1049586 1 0 10 0 22 150 150 1543 599 0 1 230 0 -1 -1 0 0 23 0 0 23 1 0 22 0  0 -1 0
 R.plot-manip.Rnw
 TeX:RNW
-17838075 0 -1 0 -1 1346 175 175 1568 624 0 1 50 497 -1 -1 0 0 40 -1 -1 40 1 0 1346 -1  0 -1 0
+17838075 0 -1 0 -1 1346 175 175 1568 624 0 1 50 496 -1 -1 0 0 40 -1 -1 40 1 0 1346 -1  0 -1 0
 R.maps.Rnw
 TeX:RNW
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@@ -49,7 +49,7 @@ TeX:RNW
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 using-r.main.tex
 TeX:UTF-8
-286273531 8 -1 10808 -1 10794 0 0 1393 449 0 1 41 256 -1 -1 0 0 104 -1 -1 104 1 0 10794 -1  0 -1 0
+286273531 8 -1 10808 -1 10794 0 0 1393 449 0 1 230 256 -1 -1 0 0 104 -1 -1 104 1 0 10794 -1  0 -1 0
 r4photobiology.sty
 TeX:STY
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@@ -329,5 +329,6 @@ TeX:AUX
 *R.scripts.Rnw
 *R.data.Rnw
 *R.plotting.Rnw
+*R.more.plotting.Rnw
 *R.maps.Rnw
 <

using-r.main.Rnw

@@ -108,9 +108,11 @@ getwd()
 \chapter*{Preface}
 
 This series of Notes cover different aspects of the use of R. They are meant to be use as a complement to a course or book, as explanations
-are short and terse. We do not discuss here statistics, just R as a tool and language for data manipulation and display.
+are short and terse. We do not discuss here statistics, just R as a tool and language for data manipulation and display. The idea is a bit like how children learn a language: they work-out what the rules are simply by listening to people speak. I do give some explanations and comments, but the idea of this notes is mainly for you to use the numerous examples to find-out by yourself the overall patterns and coding philosophy behind the R language.
 
-<<child-r-calc, child='R.as.calculator.Rnw', eval=FALSE>>=
+This is work-in-progress. I will appreciate suggestions for further examples, notification of errors and unclear things and any bigger contributions. Many of the examples here have been collected from diverse sources over many years and because of this not all sources are acknowledged. If you recognize any example as yours or someone else's please let me know so that I can add a proper acknowledgement.
+
+<<child-r-calc, child='R.as.calculator.Rnw', eval=TRUE>>=
 @
 
 <<child-r-scripts, child='R.scripts.Rnw', eval=FALSE>>=
@@ -122,10 +124,10 @@ are short and terse. We do not discuss here statistics, just R as a tool and lan
 <<child-r-plotting, child='R.plotting.Rnw', eval=FALSE>>=
 @
 
-<<child-r-plotting, child='R.more.plotting.Rnw', eval=TRUE>>=
+<<child-r-more-plotting, child='R.more.plotting.Rnw', eval=FALSE>>=
 @
 
-<<child-r-plotting, child='R.maps.Rnw', eval=FALSE>>=
+<<child-r-maps, child='R.maps.Rnw', eval=FALSE>>=
 @