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

> require(hamlet)
Loading required package: hamlet

> data(vcapwide)

> vcapwide[1:2, ]
      CastrationDate CageAtAllocation   Group TreatmentInitiationWeek
ID003         100413            13489 Vehicle                  Week10
ID007         170413            13810     MDV                  Week10
         Submatch    ID PSAWeek2 PSAWeek3 PSAWeek4 PSAWeek5 PSAWeek6 PSAWeek7
ID003  Submatch_1 ID003     7.67    14.76    24.78     2.03     5.97     8.16
ID007 Submatch_10 ID007     2.01     5.17     8.59    14.62     1.99     2.81
      PSAWeek8 PSAWeek9 PSAWeek10 PSAWeek11 PSAWeek12 PSAWeek13 PSAWeek14
ID003    13.72    16.57     21.30     45.69     54.50     53.55     27.64
ID007     4.23     5.38      7.55      9.70     17.45     22.79     21.88
      BWWeek0 BWWeek1 BWWeek2 BWWeek3 BWWeek4 BWWeek5 BWWeek6 BWWeek7 BWWeek8
ID003    30.5    31.7    32.6    33.8    33.9    32.2    32.6    32.6    33.2
ID007    28.8    30.0    30.6    31.6    32.9    32.4    32.0    31.1    30.3
      BWWeek9 BWWeek10 BWWeek11 BWWeek12 BWWeek13 BWWeek14
ID003    34.2     35.0     36.1     37.9     37.5     39.7
ID007    30.5     31.6     31.7     32.4     33.5     33.3

> data(vcaplong)

> vcaplong[1:3, ]
     PSA  log2PSA   BW   Submatch    ID Week DrugWeek   Group Vehicle ARN MDV
11 21.30 4.412782 35.0 Submatch_1 ID003   10        0 Vehicle       1   0   0
12 45.69 5.513807 36.1 Submatch_1 ID003   11        1 Vehicle       1   0   0
13 54.50 5.768184 37.9 Submatch_1 ID003   12        2 Vehicle       1   0   0

> ex <- read.table(file = "example.csv", sep = ";", 
+     dec = ",", stringsAsFactors = F, header = T)

> ex
   Animal PSA.week.10..ug.l. PSA.week.9..ug.l. Body.weight.week.10..g.
1   ID003              21.30             16.57                    35.0
2   ID007               7.55              5.38                    31.6
3   ID008              23.58             17.40                    33.6
4   ID009              13.17             11.14                    31.7
5   ID010               9.90              9.33                    34.1
6   ID016              15.05             15.29                    39.6
7   ID018              13.53             12.14                    34.0
8   ID025              13.13             10.91                    33.3
9   ID027               9.59              8.79                    32.0
10  ID031               7.04              6.95                    36.6
11  ID032               8.49              8.02                    34.9
12  ID037              13.74             13.38                    32.4
13  ID040              23.62             19.15                    35.9
14  ID045              14.27              9.80                    34.8
15  ID047               6.57              6.28                    31.9
16  ID054              34.72             27.14                    32.1
17  ID056              28.15             22.05                    32.2
18  ID058               9.74              7.68                    34.0

> d <- dist(ex[, 2:4])

> d <- as.matrix(d)

> d <- round(d, 2)

> require(xtable)
Loading required package: xtable
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'xtable'

> print(xtable(d, caption = "Euclidean distance matrix D for 18 animals", 
+     label = "tab:eucld"), scalebox = 0.7)

  When sourcing 'introduction.R':
Error: could not find function "xtable"
Execution halted

  'introduction.Rnw'... failed