R help - Feb 2012 - Dataframes in PLS package

I have been working with the pls procedure and have problems getting the
procedure to work with matrix or frame data.  I suspect the problem lies in
my understanding of frames, but can't find anything in the documentation
that will help. 

Here is what I have done:

I read in an 10000 x 8 table of data, and assign the first four columns to
matrix A and the second four to matrix B

pls <-    read.table("C:/Users/Chris/Desktop/SEM Book/SEM Stat
Example/Simple Header Data for SEM.csv",    header=TRUE, sep=",",
na.strings="NA", dec=".", strip.white=TRUE)
A <- c(pls[1],pls[2],pls[3],pls[4])
B <- c(pls[5],pls[6],pls[7],pls[8])

I then put these into the data.fram C, retaining the matrix structure per
guidelines in the JSS article on the pls package

C <- data.frame(h = I(as.matrix(A)), c = I(as.matrix(B)))
showData(C, placement='-20+200', font=getRcmdr('logFont'),
maxwidth=80,
maxheight=30)

63  55 1 0  44  37200 4 0
145  52 1 1  33  69300 4 1
104  32 0 1  68  56900 3 1
109  69 1 1  94  44300 6 1
221  61 0 1  72  79800 6 0
110  40 1 1  48  17600 5 1
194  41 0 0  85  58100 4 0
120  76 1 1  19  76700 3 0
210  61 0 0  41  37600 1 0
243 101 1 1  57  40800 5 1
163  62 0 1  64    400 3 0


So the h. and the c. columns should be matrices that I can regress in plsr
function:

apls <- plsr(h ~ c, data = C)
summary(apls)

But this gives me:   [34] ERROR:    invalid type (list) for variable 'h'

I can get the plsr function to work with scalars for both predictor and
response.   Can anyone tell me where I have gone wrong on the pls input?

apls <- plsr(w ~ h, data = pls)
summary(apls)

Data: 	X dimension: 10000 1 
	Y dimension: 10000 1
Fit method: kernelpls
Number of components considered: 1
TRAINING: % variance explained
   1 comps
X  100.000
w    2.293


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westland <westland at uic.edu> writes:
> Here is what I have done:
>
> I read in an 10000 x 8 table of data, and assign the first four columns to
> matrix A and the second four to matrix B
>
> pls <-    read.table("C:/Users/Chris/Desktop/SEM Book/SEM Stat
> Example/Simple Header Data for SEM.csv",    header=TRUE,
sep=",",
> na.strings="NA", dec=".", strip.white=TRUE)
The problem is here:
> A <- c(pls[1],pls[2],pls[3],pls[4])
> B <- c(pls[5],pls[6],pls[7],pls[8])
This creates lists A and B, not data frames.

Either use cbind() instead of c(), or simply say

A <- pls[,1:4]
B <- pls[,5:8]

The the rest should work.

Btw. it is probably a good idea to avoid single-character names for
variables.  Especially c and C, because they are names of functions in R.

-- 
Regards,
Bj?rn-Helge Mevik

It's nice to cc the list for archival reasons -- it also usually gets
you a faster response as more folks can see how the thread develops.

The problem is that the colnames aren't ctually depy and indx: they
are depy.w, depy.h, etc. If you want to model, you need to use those
as is: e.g., with your code

eqn <- structure(list(depy.w = c(63L, 145L, 104L, 109L, 221L, 110L,
194L, 120L, 210L, 243L, 163L, 93L, 167L, 232L, 112L, 185L, 103L,
202L, 203L, 207L, 239L, 109L, 112L, 176L, 126L, 145L, 125L, 191L,
110L, 92L), depy.h = c(55L, 52L, 32L, 69L, 61L, 40L, 41L, 76L,
61L, 101L, 62L, 55L, 61L, 65L, 52L, 52L, 43L, 87L, 57L, 37L,
74L, 44L, 45L, 52L, 54L, 51L, 66L, 53L, 43L, 36L), depy.d = c(1L,
1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L,
0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 0L), depy.s = c(0L,
1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 1L,
1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), indx.a = c(44L,
33L, 68L, 94L, 72L, 48L, 85L, 19L, 41L, 57L, 64L, 27L, 64L, 32L,
31L, 88L, 80L, 70L, 68L, 58L, 42L, 87L, 69L, 52L, 45L, 25L, 66L,
80L, 17L, 70L), indx.i = c(37200L, 69300L, 56900L, 44300L, 79800L,
17600L, 58100L, 76700L, 37600L, 40800L, 400L, 33400L, 6000L,
7400L, 94000L, 84200L, 0L, 0L, 43300L, 0L, 68600L, 47300L, 16100L,
95900L, 69200L, 12200L, 7500L, 70600L, 11400L, 0L), indx.r = c(4L,
4L, 3L, 6L, 6L, 5L, 4L, 3L, 1L, 5L, 3L, 3L, 5L, 1L, 6L, 4L, 2L,
1L, 4L, 1L, 4L, 6L, 1L, 6L, 4L, 2L, 2L, 5L, 3L, 4L), indx.x = c(0L,
1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 2L, 0L, 0L, 1L, 0L,
0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L)), .Names =
c("depy.w",
"depy.h", "depy.d", "depy.s", "indx.a",
"indx.i", "indx.r", "indx.x"
), row.names = c(NA, 30L), class = "data.frame")

library(pls)

apls <- plsr(depy.w + depy.h + depy.d + depy.s ~ ., data=eqn) # Works
like a charm

I don't believe there's a way to do wildcard names in general
(something like depy.*, but I'd welcome correction) but you can save
some key strokes by using the "." term to mean "everything else I
haven't already used"

Hope this helps,

Michael



On Sun, Mar 4, 2012 at 1:30 PM, Chris Westland <westland at uic.edu>
wrote:
> Thanks Michael. ?I had tried to drop the I(as.matrix(...)) conversions, and
> fiddled with a number of other permutations of code ... I still can't
seem
> to get it right.
>
> The col names appear to be depy and indx ... here is the output (and the
> rows are just line numbers)
>
>
>
>> colnames(eqn)
>
> [1] "depy.w" "depy.h" "depy.d"
"depy.s" "indx.a" "indx.i" "indx.r"
> "indx.x"row>
>
>
>
>> rownames(eqn)
>
> ????[1]
>
"1"?????"2"?????"3"?????"4"?????"5"?????"6"?????"7"?????"8"?????"9"?????"10"????"11"????"12"????"13"????"14"????"15"????"16"????"17"????"18"????"19"????"20"????"21"????"22"????"23"????"24"????"25"????"26"????"27"????"28"
>
> ???[29] "29"????"30"????"31"?.etc.
>
>
>
>
>
>
> Here is the dput(eqn) ?and showData for the file 'eqn':
>
>
>
>> dput(head(eqn, 30))
>
> structure(list(depy.w = c(63L, 145L, 104L, 109L, 221L, 110L,
>
> 194L, 120L, 210L, 243L, 163L, 93L, 167L, 232L, 112L, 185L, 103L,
>
> 202L, 203L, 207L, 239L, 109L, 112L, 176L, 126L, 145L, 125L, 191L,
>
> 110L, 92L), depy.h = c(55L, 52L, 32L, 69L, 61L, 40L, 41L, 76L,
>
> 61L, 101L, 62L, 55L, 61L, 65L, 52L, 52L, 43L, 87L, 57L, 37L,
>
> 74L, 44L, 45L, 52L, 54L, 51L, 66L, 53L, 43L, 36L), depy.d = c(1L,
>
> 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L,
>
> 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 0L), depy.s = c(0L,
>
> 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 1L, 0L, 1L,
>
> 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), indx.a = c(44L,
>
> 33L, 68L, 94L, 72L, 48L, 85L, 19L, 41L, 57L, 64L, 27L, 64L, 32L,
>
> 31L, 88L, 80L, 70L, 68L, 58L, 42L, 87L, 69L, 52L, 45L, 25L, 66L,
>
> 80L, 17L, 70L), indx.i = c(37200L, 69300L, 56900L, 44300L, 79800L,
>
> 17600L, 58100L, 76700L, 37600L, 40800L, 400L, 33400L, 6000L,
>
> 7400L, 94000L, 84200L, 0L, 0L, 43300L, 0L, 68600L, 47300L, 16100L,
>
> 95900L, 69200L, 12200L, 7500L, 70600L, 11400L, 0L), indx.r = c(4L,
>
> 4L, 3L, 6L, 6L, 5L, 4L, 3L, 1L, 5L, 3L, 3L, 5L, 1L, 6L, 4L, 2L,
>
> 1L, 4L, 1L, 4L, 6L, 1L, 6L, 4L, 2L, 2L, 5L, 3L, 4L), indx.x = c(0L,
>
> 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 2L, 0L, 0L, 1L, 0L,
>
> 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L)), .Names =
c("depy.w",
>
> "depy.h", "depy.d", "depy.s",
"indx.a", "indx.i", "indx.r", "indx.x"
>
> ), row.names = c(NA, 30L), class = "data.frame")
>
>
>
>
>
>
>
>> showData(eqn)
>
>
>
> depy.w depy.h depy.d depy.s indx.a indx.i indx.r indx.x
>
> ? 63???? 55????? 1????? 0???? 44? 37200????? 4????? 0
>
> ?? 145???? 52????? 1????? 1???? 33? 69300????? 4????? 1
>
> ?? 104???? 32????? 0????? 1???? 68? 56900????? 3????? 1
>
> ?? 109???? 69????? 1????? 1???? 94? 44300??? ??6????? 1
>
> ?? 221???? 61????? 0????? 1???? 72? 79800????? 6????? 0
>
> ?? 110???? 40????? 1????? 1???? 48? 17600????? 5????? 1
>
> ?? 194???? 41????? 0????? 0???? 85? 58100????? 4????? 0
>
> ?? 120???? 76????? 1????? 1???? 19? 76700????? 3????? 0
>
> ?? 210???? 61????? 0????? 0???? 41? 37600????? 1????? 0 ... etc.
>
>
>
>
> Initially, I had input a file 'pls' with the script:
>
>
> dep <- pls[,1:4]
>
> ind <- pls[,5:8]
>
> eqn <- data.frame(depy = dep, indx = ind)
>
> apls <- plsr(depy ~ indx, data=eqn)
>
>
> .... and this gives me ? [7] ERROR: ?object 'depy' not found
>
>
> Note that the original input comes from a matrix 'pls' and my
intent is to
> convert this to data.frames that the plsr package can parse ... ?a
dput(pls)
> gives me ...
>
>
>
> ? .... lots and lots of leading line information ... ?0L, 0L, 1L, 2L, 0L,
> 0L, 1L, 1L, 0L, 0L, 0L, 2L, 1L, 0L, 1L,
>
> ? ? 2L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L,
>
> ? ? 0L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L,
>
> ? ? 1L, 0L, 1L, 1L, 1L, 1L)), .Names = c("w", "h",
"d", "s",
>
> "a", "i", "r", "x"), class =
"data.frame", row.names = c(NA,
>
> -10000L))
>
>
>
> If you have any other suggestions concerning how I might fiddle the files
to
> get them into a format that PLSR package would like, that would be great
>
>
> Chris Westland
>
>
>
> On Sat, Mar 3, 2012 at 8:17 PM, R. Michael Weylandt
> <michael.weylandt at gmail.com> wrote:
>>
>> Can you post dput(head(eqn, 30)) so we can take a look at your data?
>> It's something of a cryptic error and that would go a long way in
>> helping us help you.
>>
>> Without that though, I'm not sure you need the I(as.matrix.(dep))
and
>> I(as.matrix(ind)), I would imagine (untested) that eqn <-
>> data.frame(depy = dep, indx = ind) would work (probably better as I()
>> changes things just a little).
>>
>> I have a hunch that the colnames of eqn are not actually depy and indx
>> and that's what ultimately leads to the error. Can you look at
>> colnames(eqn) and use those exactly in the formula to plsr? That might
>> fix it.
>>
>> Michael
>>
>>
>>
>> On Sat, Mar 3, 2012 at 5:01 PM, westland <westland at uic.edu>
wrote:
>> > I am still/again having trouble getting PLSR to recognize the
input data
>> > frames. ? Here is what I have done:
>> >
>> > ?I read in an 10000 x 8 table of data to 'pls'
>> >
>> > assign the first four columns to ?matrix 'dep' and the
second four to
>> > matrix
>> > 'ind' with the following commands:
>> >
>> > dep <- pls[,1:4]
>> > ind <- pls[,5:8]
>> >
>> > I create the data.frame 'eqn' :
>> >
>> > eqn <- data.frame(depy = I(as.matrix(dep)), indx =
I(as.matrix(ind)))
>> >
>> > And run the PLSR package
>> >
>> > apls <- plsr(depy ~ indx, data=eqn)
>> >
>> > I seem to be getting either one of two error messages:
>> >
>> > [12] ERROR:
>> > ?invalid type (list) for variable 'dep'
>> > [13] ERROR:
>> > ?object of type 'closure' is not subsettable
>> >
>> > I'm sure now that this is a problem in my creation of
data.frames, but
>> > can't
>> > seem to find anything that describes the problem
>> >
>> >
>> > -----
>> > J. Christopher Westland
>> > Professor, Information & Decision Sciences, University of
Illinois -
>> > Chicago
>> > 601 S. Morgan Street (UH2400) Chicago, IL ? ?60607-7124
>> > Telephone ? ? ? +1.312.860.0587
>> > Google Voice ?+1.209.757.8849
>> > westland at uic.edu
>> > http://uic.edu/~westland
>> > --
>> > View this message in context:
>> >
http://r.789695.n4.nabble.com/Dataframes-in-PLS-package-tp4405798p4442436.html
>> > Sent from the R help mailing list archive at Nabble.com.
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
>
> --
> J. Christopher Westland
> Professor, Information & Decision Sciences, University of Illinois -
Chicago
> 601 S. Morgan Street (UH2400) Chicago, IL? ? 60607-7124
> Telephone? ? ?? +1.312.860.0587
> Google Voice? +1.209.757.8849
> westland at uic.edu
> http://uic.edu/~westland
>
>