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 > > Please consider the environment before printing this email. > This email (including all attachments) is confidential. It may be subject > to legal professional privilege and/or protected by copyright. If you > receive it in error do not use it or disclose it, notify the sender > immediately, delete it from your system and destroy any copies. The > University does not guarantee that any email or attachment is secure or > free from viruses or other defects. The University is not responsible for > emails that are personal or unrelated to the Universityâs functions. > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > -- In God we trust, all others bring data. [[alternative HTML version deleted]]
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