Errors in running code in vignettes:
when running code in 'Ch_analysing_longitudinal_dataI.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> library("Matrix")

> library("lme4")

  When sourcing 'Ch_analysing_longitudinal_dataI.R':
Error: there is no package called 'lme4'
Execution halted
when running code in 'Ch_analysing_longitudinal_dataII.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> options(digits = 3)

> if (!interactive()) {
+     print.summary.gee <- function(x, digits = NULL, quote = FALSE, 
+         prefix = "", ...) {
+         if (is.null(digi .... [TRUNCATED] 

> library("gee")

  When sourcing 'Ch_analysing_longitudinal_dataII.R':
Error: there is no package called 'gee'
Execution halted
when running code in 'Ch_analysis_of_variance.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> library("wordcloud")

  When sourcing 'Ch_analysis_of_variance.R':
Error: there is no package called 'wordcloud'
Execution halted
when running code in 'Ch_cluster_analysis.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> library("mclust")

  When sourcing 'Ch_cluster_analysis.R':
Error: there is no package called 'mclust'
Execution halted
when running code in 'Ch_conditional_inference.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> data("roomwidth", package = "HSAUR2")

> nobs <- table(roomwidth$unit)

> ties <- tapply(roomwidth$width, roomwidth$unit, function(x) length(x) - 
+     length(unique(x)))

> library("coin")

  When sourcing 'Ch_conditional_inference.R':
Error: there is no package called 'coin'
Execution halted
when running code in 'Ch_density_estimation.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> x <- library("KernSmooth")
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

> x <- library("flexmix")

  When sourcing 'Ch_density_estimation.R':
Error: there is no package called 'flexmix'
Execution halted
when running code in 'Ch_gam.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> library("mgcv")
Loading required package: nlme
This is mgcv 1.8-39. For overview type 'help("mgcv-package")'.

> library("mboost")

  When sourcing 'Ch_gam.R':
Error: there is no package called 'mboost'
Execution halted
when running code in 'Ch_graphical_display.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> xr <- range(USmelanoma$mortality) * c(0.9, 1.1)

> xr
[1]  77.4 251.9

> layout(matrix(1:2, nrow = 2))

> par(mar = par("mar") * c(0.8, 1, 1, 1))

> boxplot(USmelanoma$mortality, ylim = xr, horizontal = TRUE, 
+     xlab = "Mortality")

> hist(USmelanoma$mortality, xlim = xr, xlab = "", main = "", 
+     axes = FALSE, ylab = "")

> axis(1)

> plot(mortality ~ ocean, data = USmelanoma, xlab = "Contiguity to an ocean", 
+     ylab = "Mortality")

> dyes <- with(USmelanoma, density(mortality[ocean == 
+     "yes"]))

> dno <- with(USmelanoma, density(mortality[ocean == 
+     "no"]))

> plot(dyes, lty = 1, xlim = xr, main = "", ylim = c(0, 
+     0.018))

> lines(dno, lty = 2)

> legend("topleft", lty = 1:2, legend = c("Coastal State", 
+     "Land State"), bty = "n")

> layout(matrix(1:2, ncol = 2))

> plot(mortality ~ longitude, data = USmelanoma)

> plot(mortality ~ latitude, data = USmelanoma)

> plot(mortality ~ latitude, data = USmelanoma, pch = as.integer(USmelanoma$ocean))

> legend("topright", legend = c("Land state", "Coast state"), 
+     pch = 1:2, bty = "n")

> subset(USmelanoma, latitude < 32)
          mortality latitude longitude ocean
Florida         197     28.0      82.0   yes
Louisiana       190     31.2      91.8   yes
Texas           229     31.5      98.0   yes

> barplot(xtabs(~R_happy, data = CHFLS))

> xtabs(~R_happy + R_health, data = CHFLS)
                R_health
R_happy          Poor Not good Fair Good Excellent
  Very unhappy      2        7    4    1         0
  Not too happy     4       46   67   42        26
  Somewhat happy    3       77  350  459       166
  Very happy        1        9   40   80       150

> hh <- xtabs(~R_health + R_happy, data = CHFLS)

> plot(R_happy ~ R_health, data = CHFLS)

> layout(matrix(1:2, ncol = 2))

> plot(R_happy ~ log(R_income + 1), data = CHFLS)

> cdplot(R_happy ~ log(R_income + 1), data = CHFLS)

> library("lattice")

> lattice.options(default.theme = function() standard.theme("pdf", 
+     color = FALSE))

> print(xyplot(jitter(log(A_income + 0.5)) ~ jitter(log(R_income + 
+     0.5)) | R_edu, data = CHFLS))

> data("household", package = "HSAUR2")

> toLatex(HSAURtable(household), caption = paste("Household expenditure for single men and women."), 
+     label = "DAGD-household-tab")
\index{household data@\Robject{household} data}
\begin{center}
\begin{longtable}{ rrrrr }
\caption{\Robject{household} data. Household expenditure for single men and women. \label{DAGD-household-tab}}
\\
\hline
\Robject{housing} & \Robject{food} & \Robject{goods} & \Robject{service} & \Robject{gender} \\ \hline
\endfirsthead
\caption[]{\Robject{household} data (continued).} \\
\hline
\Robject{housing} & \Robject{food} & \Robject{goods} & \Robject{service} & \Robject{gender} \\ \hline
\endhead
820 & 114 & 183 & 154 & female \\
184 & 74 & 6 & 20 & female \\
921 & 66 & 1686 & 455 & female \\
488 & 80 & 103 & 115 & female \\
721 & 83 & 176 & 104 & female \\
614 & 55 & 441 & 193 & female \\
801 & 56 & 357 & 214 & female \\
396 & 59 & 61 & 80 & female \\
864 & 65 & 1618 & 352 & female \\
845 & 64 & 1935 & 414 & female \\
404 & 97 & 33 & 47 & female \\
781 & 47 & 1906 & 452 & female \\
457 & 103 & 136 & 108 & female \\
1029 & 71 & 244 & 189 & female \\
1047 & 90 & 653 & 298 & female \\
552 & 91 & 185 & 158 & female \\
718 & 104 & 583 & 304 & female \\
495 & 114 & 65 & 74 & female \\
382 & 77 & 230 & 147 & female \\
1090 & 59 & 313 & 177 & female \\
497 & 591 & 153 & 291 & male \\
839 & 942 & 302 & 365 & male \\
798 & 1308 & 668 & 584 & male \\
892 & 842 & 287 & 395 & male \\
1585 & 781 & 2476 & 1740 & male \\
755 & 764 & 428 & 438 & male \\
388 & 655 & 153 & 233 & male \\
617 & 879 & 757 & 719 & male \\
248 & 438 & 22 & 65 & male \\
1641 & 440 & 6471 & 2063 & male \\
1180 & 1243 & 768 & 813 & male \\
619 & 684 & 99 & 204 & male \\
253 & 422 & 15 & 48 & male \\
661 & 739 & 71 & 188 & male \\
1981 & 869 & 1489 & 1032 & male \\
1746 & 746 & 2662 & 1594 & male \\
1865 & 915 & 5184 & 1767 & male \\
238 & 522 & 29 & 75 & male \\
1199 & 1095 & 261 & 344 & male \\
1524 & 964 & 1739 & 1410 & male \\
\hline
\end{longtable}
\end{center}

> data("USstates", package = "HSAUR2")

> toLatex(HSAURtable(USstates), caption = paste("Socio-demographic variables for ten US states."), 
+     label = "DAGD-USstates-tab")
\index{USstates data@\Robject{USstates} data}
\begin{center}
\begin{longtable}{ rrrrrrr }
\caption{\Robject{USstates} data. Socio-demographic variables for ten US states. \label{DAGD-USstates-tab}}
\\
\hline
\Robject{Population} & \Robject{Income} & \Robject{Illiteracy} & \Robject{Life.Expectancy} & \Robject{Homicide} & \Robject{Graduates} & \Robject{Freezing} \\ \hline
\endfirsthead
\caption[]{\Robject{USstates} data (continued).} \\
\hline
\Robject{Population} & \Robject{Income} & \Robject{Illiteracy} & \Robject{Life.Expectancy} & \Robject{Homicide} & \Robject{Graduates} & \Robject{Freezing} \\ \hline
\endhead
3615 & 3624 & 2.1 & 69.05 & 15.1 & 41.3 & 20 \\
21198 & 5114 & 1.1 & 71.71 & 10.3 & 62.6 & 20 \\
2861 & 4628 & 0.5 & 72.56 & 2.3 & 59.0 & 140 \\
2341 & 3098 & 2.4 & 68.09 & 12.5 & 41.0 & 50 \\
812 & 4281 & 0.7 & 71.23 & 3.3 & 57.6 & 174 \\
10735 & 4561 & 0.8 & 70.82 & 7.4 & 53.2 & 124 \\
2284 & 4660 & 0.6 & 72.13 & 4.2 & 60.0 & 44 \\
11860 & 4449 & 1.0 & 70.43 & 6.1 & 50.2 & 126 \\
681 & 4167 & 0.5 & 72.08 & 1.7 & 52.3 & 172 \\
472 & 3907 & 0.6 & 71.64 & 5.5 & 57.1 & 168 \\
\hline
\end{longtable}
\end{center}

> data("suicides2", package = "HSAUR2")

> toLatex(HSAURtable(suicides2), caption = paste("Mortality rates per $100,000$ from male suicides."), 
+     label = "DAGD-suicides2-tab", rownames = .... [TRUNCATED] 
\index{suicides2 data@\Robject{suicides2} data}
\begin{center}
\begin{longtable}{l rrrrr }
\caption{\Robject{suicides2} data. Mortality rates per $100,000$ from male suicides. \label{DAGD-suicides2-tab}}
\\
\hline
  &  \Robject{A25.34} & \Robject{A35.44} & \Robject{A45.54} & \Robject{A55.64} & \Robject{A65.74} \\ \hline
\endfirsthead
\caption[]{\Robject{suicides2} data (continued).} \\
\hline
  &  \Robject{A25.34} & \Robject{A35.44} & \Robject{A45.54} & \Robject{A55.64} & \Robject{A65.74} \\ \hline
\endhead
Canada   &  22 & 27 & 31 & 34 & 24 \\
Israel   &  9 & 19 & 10 & 14 & 27 \\
Japan   &  22 & 19 & 21 & 31 & 49 \\
Austria   &  29 & 40 & 52 & 53 & 69 \\
France   &  16 & 25 & 36 & 47 & 56 \\
Germany   &  28 & 35 & 41 & 49 & 52 \\
Hungary   &  48 & 65 & 84 & 81 & 107 \\
Italy   &  7 & 8 & 11 & 18 & 27 \\
Netherlands   &  8 & 11 & 18 & 20 & 28 \\
Poland   &  26 & 29 & 36 & 32 & 28 \\
Spain   &  4 & 7 & 10 & 16 & 22 \\
Sweden   &  28 & 41 & 46 & 51 & 35 \\
Switzerland   &  22 & 34 & 41 & 50 & 51 \\
UK   &  10 & 13 & 15 & 17 & 22 \\
USA   &  20 & 22 & 28 & 33 & 37 \\
\hline
\end{longtable}
\end{center}

> data("banknote", package = "mclust")

  When sourcing 'Ch_graphical_display.R':
Error: there is no package called 'mclust'
Execution halted
when running code in 'Ch_meta_analysis.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> data("smoking", package = "HSAUR2")

> odds <- function(x) (x[1] * (x[4] - x[3]))/((x[2] - 
+     x[1]) * x[3])

> weight <- function(x) ((x[2] - x[1]) * x[3])/sum(x)

> W <- apply(smoking, 1, weight)

> Y <- apply(smoking, 1, odds)

> sum(W * Y)/sum(W)
[1] 1.664159

> library("rmeta")

  When sourcing 'Ch_meta_analysis.R':
Error: there is no package called 'rmeta'
Execution halted
when running code in 'Ch_multidimensional_scaling.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> x <- library("ape")

  When sourcing 'Ch_multidimensional_scaling.R':
Error: there is no package called 'ape'
Execution halted
when running code in 'Ch_multiple_linear_regression.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> library("wordcloud")

  When sourcing 'Ch_multiple_linear_regression.R':
Error: there is no package called 'wordcloud'
Execution halted
when running code in 'Ch_recursive_partitioning.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> library("vcd")

  When sourcing 'Ch_recursive_partitioning.R':
Error: there is no package called 'vcd'
Execution halted
when running code in 'Ch_simple_inference.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> library("vcd")

  When sourcing 'Ch_simple_inference.R':
Error: there is no package called 'vcd'
Execution halted
when running code in 'Ch_simultaneous_inference.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> library("multcomp")

  When sourcing 'Ch_simultaneous_inference.R':
Error: there is no package called 'multcomp'
Execution halted
when running code in 'Ch_survival_analysis.Rnw'

> rm(list = ls())

> s <- search()[-1]

> s <- s[-match(c("package:base", "package:stats", "package:graphics", 
+     "package:grDevices", "package:utils", "package:datasets", 
+     "packag ..." ... [TRUNCATED] 

> if (length(s) > 0) sapply(s, detach, character.only = TRUE)

> if (!file.exists("tables")) dir.create("tables")

> if (!file.exists("figures")) dir.create("figures")

> set.seed(290875)

> options(prompt = "R> ", continue = "+  ", width = 63, 
+     show.signif.stars = FALSE, SweaveHooks = list(leftpar = function() par(mai = par("mai") .... [TRUNCATED] 

> HSAURpkg <- require("HSAUR2")
Loading required package: HSAUR2
Loading required package: tools

> if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))

> rm(HSAURpkg)

> a <- Sys.setlocale("LC_ALL", "C")

> book <- TRUE

> refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", 
+     "MLR", "GLM", "DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", 
+     "MA", "PCA", "MDS ..." ... [TRUNCATED] 

> ch <- function(x) {
+     ch <- refs[which(refs[, 1] == x), ]
+     if (book) {
+         return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
+  .... [TRUNCATED] 

> if (file.exists("deparse.R")) source("deparse.R")

> setHook(packageEvent("lattice", "attach"), function(...) {
+     lattice.options(default.theme = function() standard.theme("pdf", 
+         color = .... [TRUNCATED] 

> book <- FALSE

> x <- library("survival")

> x <- library("coin")

  When sourcing 'Ch_survival_analysis.R':
Error: there is no package called 'coin'
Execution halted

  'Ch_analysing_longitudinal_dataI.Rnw' using 'UTF-8'... failed
  'Ch_analysing_longitudinal_dataII.Rnw' using 'UTF-8'... failed
  'Ch_analysis_of_variance.Rnw' using 'UTF-8'... failed
  'Ch_cluster_analysis.Rnw' using 'UTF-8'... failed
  'Ch_conditional_inference.Rnw' using 'UTF-8'... failed
  'Ch_density_estimation.Rnw' using 'UTF-8'... failed
  'Ch_errata.Rnw' using 'UTF-8'... OK
  'Ch_gam.Rnw' using 'UTF-8'... failed
  'Ch_graphical_display.Rnw' using 'UTF-8'... failed
  'Ch_introduction_to_R.Rnw' using 'UTF-8'... OK
  'Ch_logistic_regression_glm.Rnw' using 'UTF-8'... OK
  'Ch_meta_analysis.Rnw' using 'UTF-8'... failed
  'Ch_multidimensional_scaling.Rnw' using 'UTF-8'... failed
  'Ch_multiple_linear_regression.Rnw' using 'UTF-8'... failed
  'Ch_principal_components_analysis.Rnw' using 'UTF-8'... OK
  'Ch_recursive_partitioning.Rnw' using 'UTF-8'... failed
  'Ch_simple_inference.Rnw' using 'UTF-8'... failed
  'Ch_simultaneous_inference.Rnw' using 'UTF-8'... failed
  'Ch_survival_analysis.Rnw' using 'UTF-8'... failed