Revise index correcting bad entries

Correct various wrong, missing and misplaced index entries.

R.as.calculator.Rnw

@@ -196,7 +196,7 @@ a + b
 a - a
 @
 
-As it can be seen in the first line above, another peculiarity of \Rpgrm, is what is frequently called ``recycling'' of arguments:\index{recycling@recycling of arguments} as vector \code{a} is of length 6, but the constant 1 is a vector of length 1, this 1 is extended by recycling into a vector of ones of the same length as the longest vector in the statement, in this case, \code{a}.\label{par:recycling:numeric}
+As it can be seen in the first line above, another peculiarity of \Rpgrm, is what is frequently called ``recycling'' of arguments:\index{recycling of arguments} as vector \code{a} is of length 6, but the constant 1 is a vector of length 1, this 1 is extended by recycling into a vector of ones of the same length as the longest vector in the statement, in this case, \code{a}.\label{par:recycling:numeric}
 
 Make sure you understand what calculations are taking place in the chunk above, and also the one below.
 
@@ -503,7 +503,8 @@ any(c > 20, na.rm=TRUE)
 @
 
 \begin{explainbox}
-\label{box:floats} \label{par:float}\index{floating point numbers!arithmetic|(}\index{machine arithmetic!precision|(}
+\label{box:floats} \label{par:float}
+\index{floating point numbers!arithmetic|(}\index{machine arithmetic!precision|(}
 \index{floats|see{floating point numbers}}\index{machine arithmetic!rounding errors}\index{Real numbers and computers}
 \index{EPS ($\epsilon$)|see{machine arithmetic precision}}%
 You may skip this box on first reading. See also page \pageref{par:float}. Here I give some examples for which the finite resolution of computer machine floats, as compared to Real numbers as defined in mathematics makes an important difference.
@@ -548,7 +549,7 @@ As \Rclass{integer} values are stored in machine memory without loss of precisio
 2147483699L
 @
 
-In those statements in the chunk below where at least one operand is \Rclass{double} the \Rclass{integer} operands are \emph{promoted} to \Rclass{double} before computation. A similar promotion does not take place when operations are among \Rclass{integer} values, resulting in \emph{overflow}\index{arithmetic overflow}\index{overflow!see{arithmetic overflow}}, meaning numbers that are too big to be represented as \Rclass{integer} values.
+In those statements in the chunk below where at least one operand is \Rclass{double} the \Rclass{integer} operands are \emph{promoted} to \Rclass{double} before computation. A similar promotion does not take place when operations are among \Rclass{integer} values, resulting in \emph{overflow}\index{arithmetic overflow}\index{overflow|see{arithmetic overflow}}, meaning numbers that are too big to be represented as \Rclass{integer} values.
 
 <<machine-eps-04>>=
 2147483600L + 99L
@@ -1965,7 +1966,7 @@ Obtain the summary of \code{airquality} with function \Rfunction{summary()}, but
 
 \section{Plotting}
 \index{plots!base R graphics}
-Base \Rlang generic method \Rfunction{plot()} can be used to plot different data. It is a generic method that has specializations suitable for different kinds of objects (see section \ref{sec:script:objects:classes:methods} on page \pageref{sec:script:objects:classes:methods} for a brief introduction to objects, classes and methods). In this section we only very briefly demonstrate the use of the most common base \langname{R}'s graphics functions. They are well described in the book \citebooktitle{Murrell2011} \autocite{Murrell2011}. We will not describe the Lattice (based on S's Trellis) approach to plotting \autocite{Sarkar2008}. Instead we describe in detail the use of the \emph{grammar of graphics} and plotting with package \ggplot in chapter \ref{chap:R:plotting} starting on page \pageref{chap:R:plotting}.
+Base \Rlang generic method \Rfunction{plot()} can be used to plot different data. It is a generic method that has specializations suitable for different kinds of objects (see section \ref{sec:script:objects:classes:methods} on page \pageref{sec:script:objects:classes:methods} for a brief introduction to objects, classes and methods). In this section we only very briefly demonstrate the use of the most common base \Rlang's graphics functions. They are well described in the book \citebooktitle{Murrell2011} \autocite{Murrell2011}. We will not describe the Lattice (based on S's Trellis) approach to plotting \autocite{Sarkar2008}. Instead we describe in detail the use of the \emph{grammar of graphics} and plotting with package \ggplot in chapter \ref{chap:R:plotting} starting on page \pageref{chap:R:plotting}.
 
 It is possible to pass two variables (here columns from a data frame) directly as arguments to the \code{x} and \code{y} parameters of \Rfunction{plot()}.
 

R.data.io.Rnw

@@ -378,7 +378,7 @@ cat(readLines('my-file2.txt'), sep = '\n')
 \subsection[readr]{\pkgname{readr}}\label{sec:files:readr}
 \index{importing data!text files|(}
 
-<<>>=
+<<eval=FALSE, include=FALSE>>=
 citation(package = "readr")
 @
 
@@ -468,7 +468,7 @@ XML files contain text with special markup. Several modern data exchange formats
 
 \subsection['xml2']{\pkgname{xml2}}
 
-<<xml2-00>>=
+<<xml2-00, eval=FALSE, include=FALSE>>=
 citation(package = "xml2")
 @
 
@@ -502,7 +502,7 @@ If we have access to the original software used for creating a worksheet or work
 \subsection['readxl']{\pkgname{readxl}}\label{sec:files:excel}
 \index{importing data!.xlsx files|(}
 
-<<readxl-00>>=
+<<readxl-00, eval=FALSE, include=FALSE>>=
 citation(package = "readxl")
 @
 
@@ -537,7 +537,7 @@ Of the remaining arguments, the most useful ones have the same names and play si
 
 \subsection['xlsx']{\pkgname{xlsx}}
 
-<<xlsx-00>>=
+<<xlsx-00, eval=FALSE, include=FALSE>>=
 citation(package = "xlsx")
 @
 
@@ -590,7 +590,7 @@ There are two different comprehensive packages for importing data saved from oth
 
 \subsection[foreign]{\pkgname{foreign}}
 
-<<foreign-00>>=
+<<foreign-00, eval=FALSE, include=FALSE>>=
 citation(package = "foreign")
 @
 
@@ -619,7 +619,7 @@ The functions in \pkgname{foreign} can return data frames, but not always this i
 
 \subsection[haven]{\pkgname{haven}}
 
-<<haven-00>>=
+<<haven-00, eval=FALSE, include=FALSE>>=
 citation(package = "haven")
 @
 
@@ -666,7 +666,7 @@ As sometimes \pgrmname{NetCDF} files are large, it is good that it is possible t
 
 \subsection[ncdf4]{\pkgname{ncdf4}}
 
-<<ncdf4-00>>=
+<<ncdf4-00, eval=FALSE, include=FALSE>>=
 citation(package = "ncdf4")
 @
 
@@ -715,7 +715,7 @@ If we want to read in several grid points, we can use several different approach
 
 \subsection[tidync]{\pkgname{tidync}}
 
-<<tidync-00>>=
+<<tidync-00, eval=FALSE, include=FALSE>>=
 citation(package = "tidync")
 @
 
@@ -836,7 +836,7 @@ Numerous\index{internet-of-things} modern data acquisition devices based on micr
 
 \subsection[jsonlite]{\pkgname{jsonlite}}
 
-<<iot-00>>=
+<<iot-00, eval=FALSE, include=FALSE>>=
 citation(package = "jsonlite")
 @
 
@@ -876,13 +876,13 @@ The minimum, mean and maximum values for each logging interval, need to be split
 
 \section{Databases}\label{sec:data:db}
 \index{importing data!databases|(}
-<<dbplyr-00a>>=
+<<dbplyr-00a, eval=FALSE, include=FALSE>>=
 citation(package = "dbplyr")
 @
-<<dbplyr-00b>>=
+<<dbplyr-00b, eval=FALSE, include=FALSE>>=
 citation(package = "DBI")
 @
-<<dbplyr-00c>>=
+<<dbplyr-00c, eval=FALSE, include=FALSE>>=
 citation(package = "RSQLite")
 @
 
@@ -897,7 +897,7 @@ copy_to(con, weather_wk_25_2019.tb, "weather",
         temporary = FALSE,
         indexes = list(
           c("month_name", "calendar_year", "solar_time"),
-          "time", 
+          "time",
           "sun_elevation",
           "was_sunny",
           "day_of_year",
@@ -906,7 +906,7 @@ copy_to(con, weather_wk_25_2019.tb, "weather",
 )
 weather.db <- tbl(con, "weather")
 colnames(weather.db)
-weather.db %.>% 
+weather.db %.>%
   filter(., sun_elevation > 5) %.>%
   group_by(., day_of_year) %.>%
   summarise(., energy_Wh = sum(global_watt, na.rm = TRUE) * 60 / 3600)