[R] Problems using hetcor (polycor)

[Birgitle]

Thanks Mark and I am sorry that I forgot to adapt the Classe-vector.

This should work now

library(methods)
setClass("of")
setAs("character", "of", function(from) as.ordered(from))

Classe72<-cclasses <- c(rep("factor", 55),  rep("numeric",6), rep ("factor",
12))

TestPart<-read.table("TestPart.txt", header=TRUE,row.names=1,
na.strings="NA" ,colClasses = Classe72)

library(polycor)

TestPart.hetcor<-hetcor(TestPart, use="complete.obs")

Mark Difford wrote:
> 
> Hi Birgitle,
> 
> You need to get this right if someone is going to spend their time helping
> you. Your code doesn't work: You have specified more columns in colClasses
> than you have in the provided data set.
> 
>> TestPart<-read.table("TestPart.txt", header=TRUE,row.names=1,
>> na.strings="NA" ,colClasses = Classe81)
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, 
> : 
>   line 1 did not have 82 elements
> 
>> TestPart<-read.table("TestPart.txt", header=TRUE,row.names=1,
>> na.strings="NA")
> Warning message:
> In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>   number of items read is not a multiple of the number of columns
> 
>> length(names(TestPart))
> [1] 72
> 
>> length(Classe81)
> [1] 82
> 
> That will never work.
> 
> HTH, Mark.
> 
> 
> Birgitle wrote:
>> 
>> Sorry if this post should be long but I tried to give you a piece of my
>> data to reproduce my error message using hetcor:
>> 
>> Fehler in result$rho : $ operator is invalid for atomic vectors
>> Zusätzlich: Warning messages:
>> 1: In polychor(x, y, ML = ML, std.err = std.err) :
>>   1 row with zero marginal removed
>> 2: In polychor(x, y, ML = ML, std.err = std.err) :
>>   the table has fewer than 2 rows
>> 
>> 
>> Error in result$rho : $ operator is invalid for atomic vectors
>> Additional: Warning message:
>> 1: In polychor(x, y, ML = ML, std.err = std.err) :
>>   1 row with zero marginal removed
>> 2: In polychor(x, y, ML = ML, std.err = std.err) :
>>   the table has fewer than 2 rows
>> 
>> Use tab delimited data at the end of the post.
>> Copy in Texteditor and save as TestPart.txt 
>> 
>> Then use the following code
>> 
>> library(methods)
>> setClass("of")
>> setAs("character", "of", function(from) as.ordered(from)) 
>> 
>> Classe81<-cclasses <- c(rep("factor", 64),  rep("numeric",6), rep ("of",
>> 12))
>> 
>> TestPart<-read.table("TestPart.txt", header=TRUE,row.names=1,
>> na.strings="NA" ,colClasses = Classe81)
>> 
>> str(TestPart)
>> 
>> library(polycor)
>> 
>> TestPart.hetcor<-hetcor(TestPart, use="complete.obs")
>> 
>> this will produce the above mentioned error message that I can not
>> interprete.
>> 
>> Would be great if somebody could help me to solve the problem.
>> 
>> Thanks
>> 
>> B.
>> 
>> 
>> 
>> 
>> 	1	2	3	4	7	8	9	10	12	13	14	15	16	17	18	19	21	22	23	25	27	28	29	30	31	33
>> 34	35	36	37	38	39	40	41	42	43	44	45	46	47	48	49	50	51	52	53	54	55	56	58
>> 59	60	61	62	63	64	65	66	67	68	69	70	71	72	73	74	75	76	77	78	79	80
>> AX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	1	0	0	0	0	0	1	0	0	0	1	0	0	0
>> 0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	1	25	5	9	1	8.5	2.5	3	5	2	2	3	3	1	1	1
>> 2	1	2
>> BX	1	1	0	0	1	0	0	1	NA	NA	NA	0	0	0	0	1	0	0	1	0	0	1	0	NA	NA	NA	NA	NA	NA	NA
>> NA	0	0	0	1	0	NA	NA	NA	NA	NA	NA	NA	0	0	0	0	1	1	0	0	0	1	1	NA	NA	6	1	3.25
>> 2.25	5	5	2	2	3	3	1	1	1	1	1	1
>> CX	1	1	0	0	1	0	0	1	1	0	0	0	1	0	1	0	0	1	0	1	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0
>> 0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	15	3.5	6	1	5.5	5.5	5	5	2	2	1	2	1	1
>> 1	1	2	2
>> DX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	1	0	0	1	0	1	0	0	0	1	0	0	0	0
>> 1	1	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	1	0	50	17.5	7.5	2.5	8.5	5	5	5	2	2	2	3	1
>> 1	1	1	3	3
>> EX	1	0	1	0	1	0	0	1	NA	NA	NA	0	0	0	1	1	0	1	1	0	1	0	0	0	0	0	0	1	0	0	0	0	1	0
>> 0	0	0	0	0	0	1	0	0	0	0	0	1	0	1	0	0	0	1	0	NA	NA	14.5	30	13	2.5	3	3	1	1	4	4
>> 1	1	1	1	1	1
>> FX	1	0	1	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	1	1	0	0	1	1	0	0	0	1
>> 1	1	0	0	0	1	0	0	0	0	0	1	0	1	0	1	1	0	0	165	25	11.5	15	12	6.5	5	5	1	1	3	3	1
>> 1	1	1	4	5
>> GX	1	0	1	0	1	0	0	1	0	0	1	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	1	0	0	1	1	0	1	0	0
>> 1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	0	1	0	40	20	14.5	9.5	11	10	3	3	1	1	1	3	1
>> 1	3	4	1	3
>> HX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	NA	NA	NA	NA	NA	NA	NA	NA
>> NA	NA	NA	NA	NA	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1	0	1	0	70	18.5	1	12.5	7.2	7.2
>> 5	5	2	2	3	3	3	3	1	1	2	4
>> JX	1	0	1	0	1	0	0	1	0	0	0	0	0	1	1	0	0	1	0	1	0	0	0	0	1	0	1	0	0	0	0	0	1	1	0
>> 0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	65	9	11	18	4.5	3.75	1	3	2	3	2	2	1	1
>> 1	1	2	2
>> KX	1	0	1	0	1	0	0	1	NA	NA	NA	0	0	1	0	0	0	0	1	0	1	0	0	0	0	0	1	1	0	0	1	0	0	1
>> 1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	NA	NA	4.25	4.5	2.1	1.6	3	3	2	2	2
>> 3	1	1	1	2	1	1
>> LX	1	0	0	1	1	0	0	1	0	1	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	0	1	1	0	0	1	1	0	0
>> 0	0	1	0	0	0	0	0	0	1	0	0	1	0	0	0	0	1	0	80	32.5	13	4	8.5	5.25	2	3	3	3	3	3	1
>> 1	1	1	3	4
>> MX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	1	1	0	1	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	1	1	0	0	0	0	0	0	0	0	0	1	45	7.5	14	1	11	5.5	3	4	2	2	3	3	1	1
>> 1	1	2	3
>> NX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	1	0	0	1	0	0	1	1	0	0	0	1	0	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	42.5	12.5	17.5	1	11	NA	5	5	2	2	3	3
>> 1	1	1	1	1	2
>> OX	1	1	0	0	1	0	0	1	NA	NA	NA	0	0	0	0	1	0	0	1	0	1	0	1	0	1	1	0	0	0	0	0	0	0	0
>> 1	0	0	0	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	1	NA	NA	25	1	25	NA	3	4	1	2	3	3	1	1
>> 3	3	1	1
>> PX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	1	0	0	1	0	0	1	1	0	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	0	1	1	0	0	0	0	0	0	0	0	1	42.5	11.5	21.5	2	25	NA	4	5	2	2	3	3
>> 1	1	1	2	1	2
>> QX	1	1	0	0	1	0	0	1	NA	NA	NA	0	0	0	1	1	0	0	1	1	0	0	0	0	1	1	1	0	0	0	0	0	0	0
>> 1	0	0	1	0	0	1	0	0	1	1	0	0	0	0	0	0	0	0	1	NA	NA	27.5	1.5	19	NA	3	3	2	2	3	3
>> 1	1	1	2	1	1
>> RX	1	1	0	0	1	0	0	1	NA	NA	NA	0	0	0	0	1	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0
>> 1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	0	0	0	0	1	NA	NA	30	1	24	NA	3	4	2	2	3	3	1	1
>> 3	3	1	1
>> SX	1	1	0	0	1	0	0	1	0	0	1	0	0	0	1	1	0	1	0	1	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	47.5	20	22.5	2	15	NA	5	5	2	2	3	3	1
>> 1	1	1	2	2
>> TX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	40	11	15	1.5	11.5	NA	5	5	2	3	3	3	1
>> 1	1	1	2	2
>> UX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	1	1	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1
>> 0	0	1	0	0	1	0	0	1	1	0	0	0	0	0	0	0	0	1	65	35	39	2.5	20	NA	3	4	2	2	3	3	1	1
>> 2	2	1	2
>> VX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	1	1	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	0	1	1	0	0	0	0	0	0	0	0	1	85	10.5	19.5	1.5	13.5	NA	5	5	2	3	3
>> 3	1	1	2	2	2	2
>> WX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	1	1	0	0	0	0	0	1	1	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	155	18	30	2	17.5	NA	5	5	2	3	3	3	1	1
>> 1	2	2	3
>> XX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	90	10.5	25	1	19	NA	5	5	2	2	3	3	1	1
>> 1	1	2	3
>> YX	1	1	0	0	1	0	0	1	NA	NA	NA	0	0	0	0	1	0	0	1	1	1	1	0	0	0	1	0	1	0	0	0	0	0	0
>> 1	0	0	1	0	0	1	0	0	1	1	0	0	0	0	0	0	0	0	1	NA	NA	30	2.5	20.25	NA	3	3	2	2	3	3
>> 1	1	2	2	1	1
>> ZX	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0
>> 0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	1	105	25	37.5	1	37.5	2.25	5	5	2	3	3	3
>> 1	1	1	1	2	2
>> AY	0	1	1	0	1	1	1	0	1	0	0	0	0	0	0	1	0	1	1	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1
>> 1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	85	6.5	11.5	3	11.5	3.25	5	5	2	2	3	4
>> 1	1	1	2	2	4
>> BY	0	0	1	0	1	0	1	0	0	1	0	0	0	0	0	1	0	1	0	1	0	1	0	0	1	0	1	0	0	0	0	0	1	1	0
>> 0	0	1	0	0	1	0	0	0	0	0	1	1	0	0	0	0	1	0	38	10	6.5	8	3	2.5	4	5	2	2	2	3	1	1	1
>> 2	2	3
>> CY	0	1	0	0	0	1	1	0	1	0	0	0	1	1	1	1	0	1	0	0	1	0	0	1	1	0	0	0	0	0	1	0	1	1	1
>> 1	1	1	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	15	3.5	5	1.5	3.25	3.5	5	5	2	3	2	2	1
>> 1	1	1	2	2
>> DY	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	1	0	0	1	0	NA	NA	NA	NA	NA	NA	NA	NA
>> NA	NA	NA	NA	NA	1	0	0	0	0	0	0	0	0	1	0	0	1	0	0	1	0	0	70	20	NA	NA	5.5	3.5	5
>> 5	3	3	3	3	3	3	1	1	9	9
>> EY	0	0	0	1	1	0	0	1	1	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0
>> 0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	0	20	7	8	25	5.5	3.25	3	3	3	3	3	3	1	1
>> 1	1	2	2
>> FY	0	0	0	1	1	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	1	1
>> 1	1	0	0	0	1	0	0	0	0	0	1	0	1	0	0	0	1	0	150	25	13	24	11.5	4.5	5	5	3	3	4	4	1
>> 1	1	1	5	6
>> GY	0	0	0	1	1	0	0	1	1	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	1	0	0
>> 0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	50	15	12.5	17.5	8.5	5.75	3	3	3	3	2
>> 3	1	1	1	1	2	3
>> HY	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0
>> 1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	110	15	9.5	7.5	11	3.35	5	5	3	3	4	4
>> 3	3	1	1	4	5
>> JY	0	0	0	1	1	0	0	1	1	1	0	0	1	1	0	0	0	1	0	1	0	0	0	0	0	1	0	1	0	0	0	0	1	0	0
>> 0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	1	0	60	11.5	10	30	3.25	3.75	3	3	2	2	1	1
>> 1	1	1	1	2	3
>> KY	0	0	0	1	1	0	0	1	NA	NA	NA	1	0	1	0	0	1	0	1	0	1	1	0	1	1	0	1	0	0	0	0	0	0	0
>> 1	0	0	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	1	NA	NA	6.5	23	2.25	1	1	2	2	2	3	3	1
>> 1	2	2	2	2
>> LY	0	0	1	0	1	0	0	1	0	1	0	0	0	0	1	0	0	1	0	1	1	0	0	0	1	0	1	0	0	0	0	0	1	0	0
>> 0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	52.5	20	11	5	6.25	4.25	2	2	2	2	3	3
>> 1	1	1	1	2	4
>> MY	0	1	1	0	0	1	0	1	0	1	0	0	1	1	0	0	0	0	1	0	1	0	0	0	0	0	1	1	0	0	0	0	1	0	0
>> 0	0	0	1	0	0	1	0	0	0	0	1	0	0	0	0	1	0	0	60	15	3	15	1.5	1.25	5	5	2	2	2	2	1	1
>> 1	1	6	6
>> NY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	1	1	0	1	1	0	1	1	0	0	0	1	1	0	0	1	0	0	1	0	0
>> 0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	1	0	0	50	14	3.75	25	2.85	2.4	5	5	2	2	1	2
>> 1	1	1	1	5	6
>> OY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	1	0	0	1	0	0	0	0	1	0	0	1	0	0	1	0	1
>> 0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	0	0	45	14	4	15	2.75	1.75	5	5	2	2	2	3	1
>> 1	2	3	5	5
>> PY	0	0	1	1	0	1	0	1	0	1	0	0	0	0	0	1	0	0	1	0	0	1	0	0	0	0	1	0	0	1	0	0	1	1	1
>> 0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	0	1	60	18.5	3.75	15	2.75	2.1	5	5	2	2	2
>> 3	1	1	1	2	4	6
>> QY	0	0	1	0	0	1	0	1	0	1	0	0	0	1	1	1	0	0	1	1	0	1	0	0	1	1	1	0	0	0	0	0	0	1	1
>> 0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	0	0	0	1	290	90	8.5	22.5	2.75	2.25	5	5	2	2	2
>> 3	1	1	1	2	7	7
>> RY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	1	0	0	1	0	0	0	0	1	0	0	1	0	0	1	1	1
>> 0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	1	0	55	15.5	7.5	14	7	2.25	5	5	2	2	3	3	1
>> 1	2	3	2	4
>> SY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0
>> 0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	0	0	1	0	55	20	5.5	30	4.5	2.5	5	5	2	2	3	3	1
>> 1	1	1	4	5
>> TY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	1	0	0	0	0	1	0	0	1	0	0	1	1	0
>> 0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	1	0	0	40	15	4.5	25	2.75	1.75	5	5	2	2	3	3
>> 1	1	1	1	4	6
>> UY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	1	1	0	0	1	1	0	0	0	0	0	1	1	0	0	1	0	0	1	0	1
>> 0	0	1	0	1	1	0	0	0	0	0	1	1	0	0	0	0	1	0	200	27.5	6.5	25	2.45	2.25	5	5	2	2	2
>> 3	1	1	1	2	7	7
>> VY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	1	1	0	0	1	1	0	1	0	0	1	0	1	0	0	1	0	0	1	1	1
>> 0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	0	1	0	135	17.5	5.5	17.5	2.75	2.25	5	5	2	2
>> 2	3	1	1	1	2	5	7
>> WY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	1	0	1	0	0	1	1	0	1	0	1
>> 1	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	0	1	240	35	5.5	14	3.25	2.75	5	5	2	2	2	3
>> 1	1	1	2	7	7
>> XY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	1	1	0	0	1	1	0	0	0	0	0	1	0	0	0	1	0	0	1	0	0
>> 0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	1	0	0	175	27.5	4	10.5	2.5	1.875	5	5	2	2	2
>> 2	1	1	1	1	6	7
>> YY	0	0	1	0	0	1	0	1	0	1	0	0	0	0	1	1	0	0	1	1	0	1	0	0	1	1	1	0	0	0	0	0	0	0	1
>> 0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	0	0	0	1	230	42.5	5.6	25	2.5	2.5	5	5	2	2	2	2
>> 1	1	1	2	5	7
>> ZY	0	1	0	0	0	1	0	1	0	1	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0
>> 1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	115	35	10.5	20	7.5	6.5	5	5	1	1	3	3
>> 1	1	1
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 	
>> 
> 
> 


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