[R] melt function chooses wrong id variable with large datasets

[Joachim Audenaert]

Hello,

This is a part of my dataset:

structure(list(januari = c(38.1, 32.4, 34.5, 20.7, 21.5, 23.1, 
29.7, 36.6, 36.1, 20.6, 20.4, 30.1, 38.7, 41.4, 37, 36, 37, 38, 
23, 26.7), februari = c(31.5, 36.2, 38.2, 26.4, 20.9, 21.5, 30.2, 
33.4, 32.6, 22.2, 21.7, 30, 35.7, 32.8, 39.3, 25.5, 23, 19.9, 
21.3, 20.8), maart = c(34.2, 27, 24.2, 19.9, 19.7, 21.5, 30.6, 
30, 19, 19.6, 20.6, 23.6, 17.9, 17.3, 21.4, 24.1, 20.9, 30.1, 
32.6, 21.3), april = c(26.3, 29.6, 30.3, 23.6, 28.4, 20.7, 24.1, 
27.3, 23.2, 18.3, 24.6, 27.4, 20.4, 18.1, 25.2, 19.8, 21, 23.7, 
19.6, 18.1), mei = c(23.7, 24, 17.2, 23.2, 25.2, 17.2, 16, 15.6, 
13.4, 16, 16.8, 14.6, 19.4, 21, 19.5, 18.5, 13.3, 13.7, 14.3, 
14.1), juni = c(17.7, 14.2, 16.6, 15.7, 13.7, 14.7, 13.1, 12.9, 
15.4, 11.9, 15.2, 15.3, 16.5, 16.1, 11.7, 11.2, 11.5, 10.8, 16.1, 
14.8), juli = c(15.7, 14.5, 10.8, 10.5, 13.4, 12.2, 13.2, 13, 
12.4, 13.1, 9.8, 10.5, 13.4, 11, 13.1, 15, 16.7, 16.1, 18.2, 
15.7), augustus = c(12.9, 12.8, 15.2, 14.5, 17.2, 14.5, 14.4, 
11, 13.1, 13.6, 14.6, 12.7, 13.6, 12.7, 15.5, 17.4, 15.2, 14.2, 
17.7, 19.2), september = c(15.6, 15.5, 15.9, 15.1, 16, 19.4, 
21.5, 23.7, 18.7, 23.8, 18, 16.2, 18.5, 20.6, 18.3, 22.5, 26.9, 
19.4, 15.9, 20.5), oktober = c(21.4, 20.8, 14, 17, 23, 26.4, 
19.6, 22.7, 26.9, 14.7, 15.2, 19.8, 26.9, 20.2, 14.3, 14.8, 18.5, 
21.7, 21.4, 21.8), november = c(24.7, 26.2, 29, 21.6, 17.1, 16.9, 
19.1, 24.7, 25.4, 19.8, 18.2, 16.3, 17, 17.7, 15.5, 14.7, 15.8, 
19.9, 20.4, 23.3), december = c(19.8, 27, 21, 33, 22.6, 28.3, 
21.1, 19, 17.3, 27, 30.2, 24.8, 17.9, 17.9, 20.7, 30.9, 36.2, 
21, 20.2, 21.3), norm = c("45.8713463281901", "24.047250681782984", 
"3.7533684144746324", "38.594241119279324", "26.391897460120358", 
"61.746470001194638", "6.8321020448487992", "11.933109250115226", 
"51.951891096493924", "37.424611852237945", "5.1587836676942374", 
"36.552835044409434", "31.781209673851027", "29.09146215582853", 
"4.856812959269508", "5.3982910143166514", "46.553976273304215", 
"17.566272518985429", "20.552451905814117", "61.894775704479279"
)), .Names = c("januari", "februari", "maart", "april", "mei", 
"juni", "juli", "augustus", "september", "oktober", "november", 
"december", "norm"), row.names = c(NA, 20L), class = "data.frame")

I transform my dataset with the following script:

y <- melt(dataset,na.rm=TRUE)
variable <- y[,1] 
value <- y[,2]

and can then perform a levene test as follows:

LEVENE <- leveneTest(value~variable,y)

When the dataset is small, lets say less than 100 values per column 
everything works great. I get the message: 

No id variables; using all as measure variables

When the dataset is much bigger I get the following message

Using norm as id variables, why does this function pick norm as id 
variable? and how can I tell R that each column title is my variable

 
Met vriendelijke groeten - With kind regards,

Joachim Audenaert 
onderzoeker gewasbescherming - crop protection researcher

PCS | proefcentrum voor sierteelt - ornamental plant research

Schaessestraat 18, 9070 Destelbergen, België
T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95
E: joachim.audenaert at pcsierteelt.be | W: www.pcsierteelt.be 



From:   PIKAL Petr <petr.pikal at precheza.cz>
To:     Joachim Audenaert <Joachim.Audenaert at pcsierteelt.be>, 
"r-help at r-project.org" <r-help at r-project.org>
Date:   16/04/2015 12:13
Subject:        RE: [R]  melt function chooses wrong id variable with 
large datasets



Hi

There is something weird with your data and melt function.

AFAIK melt does not use first row as id.variables.

What is result of

str(dataset)

Instead of

melt(dataset,id.vars=dataset[1,], na.rm=TRUE)

melt expects something like

melt(dataset, id.vars=c("norm, "jaar"), na.rm=TRUE)

If you want more specific answer you shall show us part of your data, 
preferably copy output of

dput(dataset[1:20,])

into your mail.

Cheers
Petr

> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Joachim
> Audenaert
> Sent: Thursday, April 16, 2015 11:37 AM
> To: r-help at r-project.org
> Subject: [R] melt function chooses wrong id variable with large
> datasets
>
> Hello all,
>
> I'm using a large dataset consisting of 2 groups of data, 2 columns in
> excel with a header (group name) and 15 000 rows of data. I would like
> like to compare this data, so I transform my dataset with the melt
> function to get 1 column of data and 1 column of ID variables, then I
> can apply different statistical tests. With small datasets this works
> great, the melt function automatically chooses the name in row 1 as ID
> variable and melts the data, thus giving me a matrix with all ID
> variables in column one and the data accordingly in column 2.
> With this big dataset however it chooses the whole first column as ID
> variables in stead of the first row. Is there a reason why this happens
> and how can I make sure the first row is chosen as ID variabele and the
> lower rows as data?
>
> If I specify that I want the first row to be the id variable I also get
> error.
>
> melt(dataset,id.vars=dataset[1,], na.rm=TRUE)
>
> Error: id variables not found in data: norm, jaar
>
> Are there alternative ways to create a good reshaped dataset?
>
> Met vriendelijke groeten - With kind regards,
>
> Joachim Audenaert
> onderzoeker gewasbescherming - crop protection researcher
>
> PCS | proefcentrum voor sierteelt - ornamental plant research
>
> Schaessestraat 18, 9070 Destelbergen, Belgi
> T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95
> E: joachim.audenaert at pcsierteelt.be | W: www.pcsierteelt.be
>
> Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd? |
> Het PCS op LinkedIn Disclaimer | Please consider the environment before
> printing. Think green, keep it on the screen!
>       [[alternative HTML version deleted]]


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Disclaimer | Please consider the environment before printing. Think green,
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