Hi Roman and all
That certainly helped a lot thanks. Data is now in the correct format and
comparable to the example data set.
Next problem that cropped up - I ran the F.cjs.estim function and got the
following error
> brtb.cjs = F.cjs.estim(
> capture=~x2+x3+x4+x5+x6+x7+x8+x9+x10+x11+x12+x13+x14+x15+x16+x17+x18,
> survival=~x1+x2+x3+x4+x5+x6+x7+x8+x9+x10+x11+x12+x13+x14+x15+x16+x17, brtb.mx)
Error in model.frame.default(formula = ~x1 + x2 + x3 + x4 + x5 + x6 + :
variable lengths differ (found for 'x8')
This has certainly thrown me. Ran traceback() to try and determine the
problem which resulted with
> traceback()7: model.frame.default(formula = ~x1 + x2 + x3 + x4 + x5 + x6 +
x7 + x8 + x9 + x10 + x11 + x12 + x13 + x14 + x15 + x16 +
x17, drop.unused.levels = TRUE)
6: model.frame(formula = ~x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 +
x9 + x10 + x11 + x12 + x13 + x14 + x15 + x16 + x17,
drop.unused.levels = TRUE)
5: eval(expr, envir, enclos)
4: eval(mf)
3: F.3d.model.matrix(as.formula(survival), nan, ns)
2: F.cr.model.matrix(capture, survival, nan, ns)
1: F.cjs.estim(~x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 + x10 + x11 +
x12 + x13 + x14 + x15 + x16 + x17 + x18, ~x1 + x2 + x3 +
x4 + x5 + x6 + x7 + x8 + x9 + x10 + x11 + x12 + x13 + x14 +
x15 + x16 + x17, brtb.mx)
Suggestions and comments appreciated.
Many thanks
Adam...
On 26 August 2013 16:10, Roman Luštrik <roman.lust...@gmail.com> wrote:
> Try coercing your data to matrix. You currently have a data.frame, which
> might matter to the package functions (I'm not familiar enough with the
> functions to be able to tell from the top of my head).
>
> as.matrix(my.data)
>
> A side note, here's how you would write a model that includes all
> (remaining) variables in your data:
>
> F.cjs.estim(~ ., data = ...)
>
> Notice the ., which means "all available".
>
> Cheers,
> Roman
>
>
>
> On Mon, Aug 26, 2013 at 8:01 AM, Adam Fawcett <adam.fawc...@mq.edu.au>wrote:
>
>> Hi Sarah and all
>>
>> Thanks for those couple of tips. They did help to show that the data
>> imported alright but that there was a distinct difference between my data
>> set and the example data set for used to demonstrate the mra package.
>>
>> I have attached subset of my data as suggested. Its formatted as a
>> tab-delimited text file with row names included (bird band numbers). I
>> have
>> tried importing with and without row names but this doesn't appear to make
>> any difference.
>>
>> To import to R, I have been using the following process.
>>
>> brtb <- read.table (file="filepath\\brtb.txt", header = TRUE, row.names =
>> 1, sep = "", colClasses="numeric")
>>
>> Inspecting the data using str(brtb) provides the following
>>
>> 'data.frame': 65 obs. of 19 variables:
>> $ C1 : num 0 0 0 0 0 0 0 0 1 1 ...
>> $ C2 : num 1 1 0 0 0 0 0 0 0 0 ...
>> $ C3 : num 1 0 1 1 1 1 1 1 0 0 ...
>> $ C4 : num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C5 : num 0 0 0 0 1 0 0 0 0 0 ...
>> $ C6 : num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C7 : num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C8 : num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C9 : num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C10: num 0 0 0 0 0 0 0 0 1 0 ...
>> $ C11: num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C12: num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C13: num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C14: num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C15: num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C16: num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C17: num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C18: num 0 0 0 0 0 0 0 0 0 0 ...
>> $ C19: num 0 0 0 0 0 0 0 0 0 0 ...
>>
>> The comparative example I am looking at from the mra package is the
>> dipper.histories data. Inspecting this with str(dipper.histories) provides
>> the following
>>
>> num [1:294, 1:7] 1 1 1 1 1 1 1 1 1 1 ...
>> - attr(*, "dimnames")=List of 2
>> ..$ : chr [1:294] "1" "2" "3" "4" ...
>> ..$ : chr [1:7] "h1" "h2" "h3" "h4" ...
>>
>> There is an obvious difference in the returned output from the str()
>> function. Inspection of both data frames shows they are formatted in a
>> similar way, or at least appear to be.
>>
>> With respect to the function I am attempting to run in mra, I have run the
>> examples routines as described in the mra manual using the supplied data.
>> Results as described. In attempting this on any of my own data as attached
>> I get an error message. The function I am trying to run is as follows
>>
>> brtb.cjs = F.cjs.estim(
>> ~x2+x3+x4+x5+x6+x7+x8+x9+x10+x11+x12+x13+x14+x15+x16+x17+x18,
>> ~x1+x2+x3+x4+x5+x6+x7+x8+x9+x10+x11+x12+x13+x14+x15+x16+x17, brtb)
>>
>>
>> Each time I get the following error
>>
>> Error in F.cjs.estim(~x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 + x10 + x11 +
>> :
>> Capture histories must consist of 0's, 1's, and 2's only.
>>
>> I have checked thru the data-set to make sure the data matches these
>> requirements, that there are no additional characters in the data-set,
>> etc.
>> and keep getting the same error. Have tried a different subsets of the
>> data, different import options, etc. but still no success.
>>
>> Am assuming the error lies with the format of the data imported to R but
>> cannot work out where or how to adjust to match the example.
>>
>> Any suggestions or advice on this one would be greatly appreciated.
>>
>> Cheers
>>
>> Adam...
>>
>>
>> On 25 August 2013 23:33, Sarah Goslee <sarah.gos...@gmail.com> wrote:
>>
>> > Hi,
>> >
>> > The first thing to do is str(yourdata) to double-check that your data
>> > import worked as expected. Particularly check that your data column
>> isn't
>> > actually of mode factor.
>> >
>> > If that doesn't give you a lead on solving the problem, posting a
>> > reproducible example here with a subset of your data provided using
>> dput()
>> > and the actual code you used will get you concrete answers, rather than
>> > random guesses.
>> >
>> > Sarah
>> >
>> >
>> > On Sunday, August 25, 2013, Adam Fawcett wrote:
>> >
>> >> Have been trying to analyse life history data collected from a long
>> term
>> >> mark-recapture study of birds using the package mra. While the analysis
>> >> works fine on the supplied example dataset, I keep getting error
>> messages
>> >> when running my data thru the F.cjs.estim function. Error message
>> states
>> >> that the data for this analysis must be either 1, 2 or0's. Have triple
>> >> checked my data and its all 1 & 0's as required.
>> >>
>> >> Problems is likely to be an issue with either the read.table function
>> to
>> >> import my data (all correctly formatted and transformed ready for the
>> >> analysis, possibly adding a character I have been able to remove, or
>> with
>> >> the mra package itself.
>> >>
>> >> Does anyone have experience using mra that could lend some advice.
>> >> Alternatively, has anyone struck this sort of problem before that could
>> >> suggest how to correct the problem.
>> >>
>> >> -
>> >>
>> >
>> >
>> > --
>> > Sarah Goslee
>> > http://www.stringpage.com
>> > http://www.sarahgoslee.com
>> > http://www.functionaldiversity.org
>> >
>>
>>
>>
>> --
>>
>> *Adam Fawcett
>> **Lecturer (GSE854 and GSE856)
>> *Department of Environment and Geography
>>
>> Macquarie University
>> NSW 2109 Australia
>>
>> M: + 61 427 929 554
>> <http://mq.edu.au>mq.edu.au
>>
>>
>>
>> CRICOS Provider Number 00002J
>>
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>
>
> --
> In God we trust, all others bring data.
>
--
*Adam Fawcett
**Lecturer (GSE854 and GSE856)
*Department of Environment and Geography
Macquarie University
NSW 2109 Australia
M: + 61 427 929 554
<http://mq.edu.au>mq.edu.au
CRICOS Provider Number 00002J
Please consider the environment before printing this email.
This email (including all attachments) is confidential. It may be subject
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