Update for deprecations in 'readxl' and 'ggplot2'

These edits avoid triggering inconsequential warnings.

R.data.io.Rnw

@@ -467,7 +467,7 @@ options(tibble.print_max = 3, tibble.print_min = 3)
 The \code{write\_} functions from \pkgname{readr} are the counterpart to \code{write.} functions from \pkgname{utils}. In addition to the expected \Rfunction{write\_csv()}, \Rfunction{write\_csv2()}, \Rfunction{write\_tsv()} and \Rfunction{write\_delim()}, \pkgname{readr} provides functions that write \pgrmname{MS-Excel}-friendly CSV files. We demonstrate here the use of \Rfunction{write\_excel\_csv()} to produce a text file with comma-separated fields suitable for import into \pgrmname{MS-Excel}.
 
 <<readr-10>>=
-write_excel_csv(my.df, path = "my-file6.csv")
+write_excel_csv(my.df, file = "my-file6.csv")
 file.show("my-file6.csv", pager = "console")
 @
 
@@ -511,7 +511,7 @@ Package \pkgname{xml2} provides functions for reading and parsing \langname{XTML
 We first read a web page with function \Rfunction{read\_html()}, and explore its structure.
 
 <<xml2-01>>=
-web_page <- read_html("http://r4photobiology.info/R/index.html")
+web_page <- read_html("https://r.r4photobiology.info/index.html")
 html_structure(web_page)
 @
 

R.plotting.Rnw

@@ -463,7 +463,7 @@ It is also possible to use characters as shapes. The character is centered on th
 <<scatter-12>>=
 ggplot(data = mtcars, aes(x = disp, y = mpg, shape = factor(cyl))) +
   geom_point(size = 2.5) +
-  scale_shape_manual(values = c("4", "6", "8"), guide = FALSE)
+  scale_shape_manual(values = c("4", "6", "8"), guide = "none")
 @
 
 \begin{infobox}
@@ -923,7 +923,7 @@ mtcars %.>%
   summarize(., mean.mpg = mean(mpg)) %.>%
   ggplot(data = .,
          aes(factor(cyl), mean.mpg, fill = factor(cyl))) +
-  scale_fill_discrete(guide = FALSE) +
+  scale_fill_discrete(guide = "none") +
   scale_y_continuous(name = NULL) +
     geom_col() +
     theme_bw(8) -> my.plot
@@ -948,7 +948,7 @@ p.main <- ggplot(data = mtcars, aes(x = disp, y = mpg, color = factor(cyl))) +
 p.inset <- p.main +
   coord_cartesian(xlim = c(270, 330), ylim = c(14, 19)) +
   labs(x = NULL, y = NULL) +
-  scale_color_discrete(guide = FALSE) +
+  scale_color_discrete(guide = "none") +
   theme_bw(8) + theme(aspect.ratio = 1)
 p.main +
   geom_plot(x = 480, y = 34, label = list(p.inset), vp.height = 1/2,
@@ -1919,7 +1919,7 @@ opts_chunk$set(opts_fig_wide)
 \index{grammar of graphics!size scales|(}
 For the \code{size} \emph{aesthetic}, several scales are available, both discrete and continuous. They do not differ much from those already described above. \emph{Geometries} \gggeom{geom\_point()}, \gggeom{geom\_line()}, \gggeom{geom\_hline()}, \gggeom{geom\_vline()}, \gggeom{geom\_text()}, \gggeom{geom\_label()} obey \code{size} as expected. In the case of \gggeom{geom\_bar()}, \gggeom{geom\_col()}, \gggeom{geom\_area()} and all other geometric elements bordered by lines, \code{size} is obeyed by these border lines. In fact, other aesthetics natural for lines such as \code{linetype} also apply to these borders.
 
-When using \code{size} scales, \code{breaks} and \code{labels} affect the key or \code{guide}. In scales that produce a key passing \code{guide = FALSE} removes the key corresponding to the scale.
+When using \code{size} scales, \code{breaks} and \code{labels} affect the key or \code{guide}. In scales that produce a key passing \code{guide = "none"} removes the key corresponding to the scale.
 \index{grammar of graphics!size scales|)}
 
 \subsection{Color and fill}

appendixes.prj

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appendixes.prj.bak

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cloudindex.idx

@@ -973,8 +973,8 @@
 \indexentry{read\_table()}{307}
 \indexentry{read\_delim()}{307}
 \indexentry{read\_tsv()}{307}
-\indexentry{read\_fwf()}{307}
-\indexentry{read.fortran()}{307}
+\indexentry{read\_fwf()}{308}
+\indexentry{read.fortran()}{308}
 \indexentry{write\_csv()}{309}
 \indexentry{write\_csv2()}{309}
 \indexentry{write\_tsv()}{309}