R help - Nov 2011 - Error in matrix, not ordered vectors or numerical value, and SIAR.

Help!

model1 <- siarmcmcdirichletv4(data, source, tef, concdep=0, 500000, 50000)

Error in matrix(1, ncol = (numsources + numiso) * numgroups, nrow
(siardata$iterations -  :
  invalid 'ncol' value (too large or NA)
In addition: Warning message:
In Ops.ordered((numsources + numiso), numgroups) :
  '*' is not meaningful for ordered factors

Previous message, but more problems: 

> The data set has 101 values, what can I use instead of letters? 
Why do you need to use letters? AFAIK this was only illustration what 
could be root of the error message. If the function requires ordered 
factor you can use 

your.ordered.factor <- ordered(your.unordered.factor) 

I do not remember original mail but to get rid of error message, the 
function probably needs as an input ordered factor or numeric values. You 
shall consult help page for this function which option is valid. 

as.numeric comes back as NA for the pond dataset (A3, A5, A7, B3, B7, C2) 

Cannot use ordered factor as * function does not work for this. ? And is
needed to run the model (see below). 

ANYONE know max length for dataset in SIAR? 

NOW getting following error: 

model1 <- siarmcmcdirichletv4(data, source, tef, concdep=0, 500000, 50000) 
Error in matrix(1, ncol = (numsources + numiso) * numgroups, nrow
(siardata$iterations -  :
  invalid 'ncol' value (too large or NA) 
In addition: Warning message: 
In Ops.ordered((numsources + numiso), numgroups) : 
  '*' is not meaningful for ordered factors 

Matrix 1 has only 6 vectors in column 1. 


Thank-you. 

Alex.


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Hi
> Help!
> 
> model1 <- siarmcmcdirichletv4(data, source, tef, concdep=0, 500000, 
50000)
> 
> Error in matrix(1, ncol = (numsources + numiso) * numgroups, nrow >
(siardata$iterations -  :
>   invalid 'ncol' value (too large or NA)
> In addition: Warning message:
> In Ops.ordered((numsources + numiso), numgroups) :
>   '*' is not meaningful for ordered factors
> 
> Previous message, but more problems: 
Maybe it is time to consult manual and help page for the function you use. 
For your convenience I coppied it below. I do not use the package so only 
few comments


siarmcmcdirichletv4(data, sources, corrections = 0, concdep = 0, 
iterations=200000, burnin=50000, howmany=Arguments

data A matrix with each food source as a seperate row and each isotope as 
a seperate
column.

^^^^^^^^^^^^^^^^^ most probably a numeric matrix

sources A matrix containing the mean and standard deviations of the 
fractionated correction
values for each of the isotopes. Also allows corrections = 0 for 
pre-corrected
data.

^^^^^^^^^^^^^^^^^ again a matrix (numeric) 

corrections A matrix containing the mean and standard deviations of the 
fractional correction
values for each of the isotopes. Also allows corrections = 0 for 
pre-corrected
data.

^^^^^^^^^^^^^^^^^^ and for the third time a numeric matrix

Only you know what are your data, sources and tef objects which you feed 
to the function. Why not to follow posting guide and uncover it to us, 
poor helpers.

Regards
Petr

> 
> 
> > The data set has 101 values, what can I use instead of letters? 
> 
> Why do you need to use letters? AFAIK this was only illustration what 
> could be root of the error message. If the function requires ordered 
> factor you can use 
> 
> your.ordered.factor <- ordered(your.unordered.factor) 
> 
> I do not remember original mail but to get rid of error message, the 
> function probably needs as an input ordered factor or numeric values. 
You 
> shall consult help page for this function which option is valid. 
> 
> as.numeric comes back as NA for the pond dataset (A3, A5, A7, B3, B7, 
C2) 
> 
> Cannot use ordered factor as * function does not work for this. ? And is
> needed to run the model (see below). 
> 
> ANYONE know max length for dataset in SIAR? 
> 
> NOW getting following error: 
> 
> model1 <- siarmcmcdirichletv4(data, source, tef, concdep=0, 500000, 
50000) 
> Error in matrix(1, ncol = (numsources + numiso) * numgroups, nrow >
(siardata$iterations -  :
>   invalid 'ncol' value (too large or NA) 
> In addition: Warning message: 
> In Ops.ordered((numsources + numiso), numgroups) : 
>   '*' is not meaningful for ordered factors 
> 
> Matrix 1 has only 6 vectors in column 1. 
> 
> 
> Thank-you. 
> 
> Alex.
> 
> 
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> View this message in context: http://r.789695.n4.nabble.com/Error-in-
> 
matrix-not-ordered-vectors-or-numerical-value-and-SIAR-tp4024578p4024578.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.

Thank-you Petr. 

I have consulted as many manuals and help pages, and search engines, and
trying various things in SIAR, but continuous errors prevail.. 

I have tried changing all matrices to numeric, but the first column , of the
two latter matrices, returns as NA. Any other suggestions? 

I had put in one of these messages more detail about data, see below. 


pond <- c("A3", "A3", "A3", "B3",
"B3", "B3","C2", "A7", "A7")
d13C <- c(-22.07, -20.39, -21.11...) 
d15N <- c(16.06, 17.13, 16.7, ...)
FConsumerData <- data.frame(pond, d13C, d15N)
FTEFData <- data.frame(tefsources, tefMeand13C, tefSDd13C, tefMeand15N,
tefSDd15N)
sources <- c("Copepoda", "Algal Paste",
"Amphipoda",
Meand13C <- c(-26.57, -20.41, -21.65,...
SDd13C <- c(1.78, 4.01, 1.46,...
Meand15N <- c(15.55, 9.58, 14.07...
SDd15N <- c(1.77, 1.34, 1.66,...
FSourceData <- data.frame(sources, Meand13C, SDd13C, Meand15N, SDd15N)
tefsources <- c("Copepoda", "Algal Paste",
"Amphipoda",...
tefMeand13C <- c(0.4, 0.4, 0.4,...
tefSDd13C <- c(1.3, 1.3, 1.3,
tefMeand15N <- c(3.4, 3.4, 3.4, 
tefSDd15N <- c(1.0, 1.0, 1.0, 

Hope that helps explain? 

?? 

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> 
> Re: [R] Odp:  Error in matrix, not ordered vectors or numerical value, 
and SIAR.
> 
> Thank-you Petr. 
> 
> I have consulted as many manuals and help pages, and search engines, and
> trying various things in SIAR, but continuous errors prevail.. 
> 
> I have tried changing all matrices to numeric, but the first column , of 
the
> two latter matrices, returns as NA. Any other suggestions? 
> 
> I had put in one of these messages more detail about data, see below. 
> 
> 
> pond <- c("A3", "A3", "A3",
"B3", "B3", "B3","C2", "A7",
"A7")
> d13C <- c(-22.07, -20.39, -21.11...) 
> d15N <- c(16.06, 17.13, 16.7, ...)
> FConsumerData <- data.frame(pond, d13C, d15N)
> FTEFData <- data.frame(tefsources, tefMeand13C, tefSDd13C, tefMeand15N,
> tefSDd15N)
> sources <- c("Copepoda", "Algal Paste",
"Amphipoda",
> Meand13C <- c(-26.57, -20.41, -21.65,...
> SDd13C <- c(1.78, 4.01, 1.46,...
> Meand15N <- c(15.55, 9.58, 14.07...
> SDd15N <- c(1.77, 1.34, 1.66,...
> FSourceData <- data.frame(sources, Meand13C, SDd13C, Meand15N, SDd15N)
> tefsources <- c("Copepoda", "Algal Paste",
"Amphipoda",...
> tefMeand13C <- c(0.4, 0.4, 0.4,...
> tefSDd13C <- c(1.3, 1.3, 1.3,
> tefMeand15N <- c(3.4, 3.4, 3.4, 
> tefSDd15N <- c(1.0, 1.0, 1.0, 
> 
> Hope that helps explain? 
Not much. 

FConsumerData is data frame with nonnumeric first column, the same is with 
FTEFData and FSourceData. If you change it to matrix you will get 
character matrix. Trying to change character values to numeric obviously 
leads to NA. How the poor R shall know what number it shall make from A3, 
B3, C2 or A7?

I do not use siar package but in the help page it is clearly stated that 
input shall be ***numeric*** matrices. Not data frames, not character 
values not factors. If you do not know distinction among those objects you 
shall look into R intro document (at least first 6 chapters) which should 
came along with your installation.

BTW, in help page there is

out <- 
siarmcmcdirichletv4(geese1demo,sourcesdemo,correctionsdemo,concdepdemo)

It does not produce any error does it?

If it does not produce any error it is sign that something is wrong with 
your data. Look at structure of your objects you are trying to evaluate 
and compare it with those demo objects.

str(object)

is the first option when something does not seem to be OK.

Regards
Petr



> 
> ?? 
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/Error-in-
> 
matrix-not-ordered-vectors-or-numerical-value-and-SIAR-tp4024578p4030650.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.