Sure! Although I'm not sure how to use dput()
Here is more detail and some data.... what I want is that  the repetitions
in Y (at the end) only have 1 or 0...

> library(reshape)
> library(car)
>
> ###Read in the occurence data
> occ.data <- read.table("Occ_short.csv",
header=TRUE,sep=",",na.strings=TRUE) #occ data from 2007-2008
> occ.data[1:30,]
    Año Punto Especie Pres Ruta_com Point Site Rep
1  2012    30    TYSA    1      108    30 1086   5
2  2012    26    VACH    1      108    26 1086   1
3  2012    27    VACH    1      108    27 1086   2
4  2012    26    ZEAU    1      108    26 1086   1
5  2012    27    ZEAU    1      108    27 1086   2
6  2012    28    ZEAU    1      108    28 1086   3
7  2012    30    ZEAU    1      108    30 1086   5
8  2012     7    TYSA    1      111     7 1112   2
9  2012     6    ZEAU    1      111     6 1112   1
10 2012    10    ZEAU    1      111    10 1112   5
11 2012    24    TYSA    1      111    24 1115   4
12 2012    23    VACH    1      111    23 1115   3
13 2012    21    ZEAU    1      111    21 1115   1
14 2012    23    ZEAU    1      111    23 1115   3
15 2012    24    ZEAU    1      111    24 1115   4
16 2012    25    ZEAU    1      111    25 1115   5
17 2012    28    AMHU    1      111    28 1116   3
18 2012    29    AMHU    1      111    29 1116   4
19 2012    30    AMHU    1      111    30 1116   5
20 2012    27    TYSA    1      111    27 1116   2
21 2012    26    VACH    1      111    26 1116   1
22 2012    27    VACH    1      111    27 1116   2
23 2012    26    ZEAU    1      111    26 1116   1
24 2012    27    ZEAU    1      111    27 1116   2
25 2012    29    ZEAU    1      111    29 1116   4
26 2012    28    ZOCA    1      111    28 1116   3
27 2012    29    ZOCA    1      111    29 1116   4
28 2012    30    ZOCA    1      111    30 1116   5
29 2012     5    AMHU    1      205     5 2051   5
30 2012     3    SILU    1      205     3 2051   3
>
> ########################################
> ###### RECODE SPECIES INTO GUILDS
> #########################################
>
> occ.data$guild<- recode(occ.data$Especie,
"c('AMHU','SILU','ZOCA')='gui4b';else='OTHER'")
> occ.data[1:30,]
    Año Punto Especie Pres Ruta_com Point Site Rep guild
1  2012    30    TYSA    1      108    30 1086   5 OTHER
2  2012    26    VACH    1      108    26 1086   1 OTHER
3  2012    27    VACH    1      108    27 1086   2 OTHER
4  2012    26    ZEAU    1      108    26 1086   1 OTHER
5  2012    27    ZEAU    1      108    27 1086   2 OTHER
6  2012    28    ZEAU    1      108    28 1086   3 OTHER
7  2012    30    ZEAU    1      108    30 1086   5 OTHER
8  2012     7    TYSA    1      111     7 1112   2 OTHER
9  2012     6    ZEAU    1      111     6 1112   1 OTHER
10 2012    10    ZEAU    1      111    10 1112   5 OTHER
11 2012    24    TYSA    1      111    24 1115   4 OTHER
12 2012    23    VACH    1      111    23 1115   3 OTHER
13 2012    21    ZEAU    1      111    21 1115   1 OTHER
14 2012    23    ZEAU    1      111    23 1115   3 OTHER
15 2012    24    ZEAU    1      111    24 1115   4 OTHER
16 2012    25    ZEAU    1      111    25 1115   5 OTHER
17 2012    28    AMHU    1      111    28 1116   3 gui4b
18 2012    29    AMHU    1      111    29 1116   4 gui4b
19 2012    30    AMHU    1      111    30 1116   5 gui4b
20 2012    27    TYSA    1      111    27 1116   2 OTHER
21 2012    26    VACH    1      111    26 1116   1 OTHER
22 2012    27    VACH    1      111    27 1116   2 OTHER
23 2012    26    ZEAU    1      111    26 1116   1 OTHER
24 2012    27    ZEAU    1      111    27 1116   2 OTHER
25 2012    29    ZEAU    1      111    29 1116   4 OTHER
26 2012    28    ZOCA    1      111    28 1116   3 gui4b
27 2012    29    ZOCA    1      111    29 1116   4 gui4b
28 2012    30    ZOCA    1      111    30 1116   5 gui4b
29 2012     5    AMHU    1      205     5 2051   5 gui4b
30 2012     3    SILU    1      205     3 2051   3 gui4b
>
> #############################################
> ####The detection/non-detection data is reshaped into a four dimensional
> #array "y" where the first dimension, j, is the point; the second
> #dimension, k, is the rep; the third dimension, i, is the guild; and the
last
> #dimension t, is the year
>
> junk.melt=melt(occ.data,id.var=c("guild", "Site", "Rep", "Año"),
measure.var="Pres")
> y=cast(junk.melt, Site ~ Rep ~ guild ~ Año)
Aggregation requires fun.aggregate: length used as default
> y
, , guild = gui4b, Año = 2012

      Rep
Site   1 2 3 4 5
  1086 0 0 0 0 0
  1112 0 0 0 0 0
  1115 0 0 0 0 0
  1116 0 0 2 2 2
  2051 1 0 1 1 3
  2055 1 0 0 3 2
  2056 0 1 1 0 0

, , guild = OTHER, Año = 2012

      Rep
Site   1 2 3 4 5
  1086 2 2 1 0 2
  1112 1 1 0 0 1
  1115 1 0 2 2 1
  1116 2 3 0 1 0
  2051 2 3 1 1 3
  2055 1 2 2 1 0
  2056 1 2 1 1 0

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