R version 3.3.2 Patched (2017-01-11 r71965) -- "Sincere Pumpkin Patch"
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Platform: x86_64-pc-linux-gnu (64-bit)
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> library(cluster)
>
> data(animals)
> (mani <- mona(animals))
Revised data:
war fly ver end gro hai
ant 0 0 0 0 1 0
bee 0 1 0 0 1 1
cat 1 0 1 0 0 1
cpl 0 0 0 0 0 1
chi 1 0 1 1 1 1
cow 1 0 1 0 1 1
duc 1 1 1 0 1 0
eag 1 1 1 1 0 0
ele 1 0 1 1 1 0
fly 0 1 0 0 0 0
fro 0 0 1 1 0 0
her 0 0 1 0 1 0
lio 1 0 1 1 1 1
liz 0 0 1 0 0 0
lob 0 0 0 0 0 0
man 1 0 1 1 1 1
rab 1 0 1 0 1 1
sal 0 0 1 0 0 0
spi 0 0 0 0 0 1
wha 1 0 1 1 1 0
Order of objects:
[1] ant cpl spi lob bee fly fro her liz sal cat cow rab chi lio man ele wha duc
[20] eag
Variable used:
[1] gro NULL hai fly gro ver end gro NULL war gro NULL end NULL NULL
[16] hai NULL fly end
Separation step:
[1] 4 0 5 3 4 2 3 4 0 1 4 0 3 0 0 4 0 2 3
Available components:
[1] "data" "order" "variable" "step" "call" "order.lab"
>
> str(mani)
List of 6
$ data : int [1:20, 1:6] 0 0 1 0 1 1 1 1 1 0 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:20] "ant" "bee" "cat" "cpl" ...
.. ..$ : chr [1:6] "war" "fly" "ver" "end" ...
$ order : int [1:20] 1 4 19 15 2 10 11 12 14 18 ...
$ variable : chr [1:19] "gro" "NULL" "hai" "fly" ...
$ step : int [1:19] 4 0 5 3 4 2 3 4 0 1 ...
$ call : language mona(x = animals)
$ order.lab: chr [1:20] "ant" "cpl" "spi" "lob" ...
- attr(*, "class")= chr "mona"
>
> ## Check all "too many NA" and other illegal cases
> ani.NA <- animals; ani.NA[4,] <- NA
> aniNA <- within(animals, { end[2:9] <- NA })
> aniN2 <- animals; aniN2[cbind(1:6, c(3, 1, 4:6, 2))] <- NA
> ani.non2 <- within(animals, end[7] <- 3 )
> ani.idNA <- within(animals, end[!is.na(end)] <- 1 )
> ## use tools::assertError() {once you don't use *.Rout.save anymore}
> try( mona(ani.NA) )
Error in mona(ani.NA) :
No clustering performed, an object was found with all values missing.
> try( mona(aniNA) )
Error in mona(aniNA) :
No clustering performed, found variable with more than half values missing.
> try( mona(aniN2) )
Error in mona(aniN2) :
No clustering performed, all variables have at least one missing value.
> try( mona(ani.non2) )
Error in mona(ani.non2) :
All variables must be binary (e.g., factor with 2 levels).
> try( mona(ani.idNA) )
Error in mona(ani.idNA) :
All variables must be binary (e.g., factor with 2 levels).
>
> if(require(MASS)) {
+
+ if(R.version$major != "1" || as.numeric(R.version$minor) >= 7)
+ RNGversion("1.6")
+ set.seed(253)
+ n <- 512; p <- 3
+ Sig <- diag(p); Sig[] <- 0.8 ^ abs(col(Sig) - row(Sig))
+ x3 <- mvrnorm(n, rep(0,p), Sig) >= 0
+ x <- cbind(x3, rbinom(n, size=1, prob = 1/2))
+
+ print(sapply(as.data.frame(x), table))
+
+ mx <- mona(x)
+ str(mx)
+ print(lapply(mx[c(1,3,4)], table))
+ }
Loading required package: MASS
V1 V2 V3 V4
0 244 245 261 238
1 268 267 251 274
List of 5
$ data : int [1:512, 1:4] 0 0 0 0 1 1 1 0 1 0 ...
$ order : int [1:512] 1 137 154 204 353 398 30 52 69 85 ...
$ variable: int [1:511] 0 0 0 0 0 3 0 0 0 0 ...
$ step : int [1:511] 0 0 0 0 0 4 0 0 0 0 ...
$ call : language mona(x = x)
- attr(*, "class")= chr "mona"
$data
0 1
988 1060
$variable
0 1 2 3 4
496 4 1 5 5
$step
0 1 2 3 4
496 1 2 4 8
Warning message:
In RNGkind("Marsaglia-Multicarry", "Buggy Kinderman-Ramage") :
buggy version of Kinderman-Ramage generator used
>
> proc.time()
user system elapsed
0.168 0.035 0.279