[Basta-users] difficulty with CensusToCaptHist

[Shafkat Khan]

Hello Owen:

Thanks a bunch for the prompt response! Your suggestion worked great and I
was able to compile the matrices into a BaSTA object. I'm able to run the
basta function for the default values just fine, but am having trouble with
multiple chains.

I'm using this code:
out1<-basta(object = VC2, studyStart = 2009, studyEnd = 2017,
            nsim = 4, parallel = TRUE, ncpus = 4)

And getting this error message:
Error in basta.default(object = VC2, studyStart = 2009, studyEnd = 2017,  :
  could not find function "requireNamespace"

I'm not sure what I need to do to avoid this error and run multiple
chains/simulations. Any idea will be much appreciated. I can send on the
data files if that would help. Many thanks!

Shafkat

Shafkat Khan
Ph.D Candidate
Odum School of Ecology
University of Georgia


On Mon, Mar 21, 2016 at 5:18 PM, Owen Jones <jones at biology.sdu.dk> wrote:

> Hi Shafkat,
>
> That looks like a bug.
> I’ll investigate and get back to you ASAP.
>
> In the meantime you could simply replace the ID with the rowname.
> i.e.
>
> x$ID <- rownames(x)
>
>
> Best wishes,
> Owen
>
> On 21 Mar 2016, at 21:37, Shafkat Khan <shafkat.khan at gmail.com> wrote:
>
> Hello:
>
> I've been trying to use CensusToCaptHist function on a dataset. Upon
> converting the detection dataset that I have (with ID and Date (of
> detection) as column header, the resulting matrix attributes seemingly new
> IDs to the existing record. E.g.
>
>      ID 2009 2010 2011 2012 2013 2014 2015 2016 2017
> 1     1    0    0    1    1    1    0    1    0    1
> 10    2    0    0    0    0    1    0    1    0    1
> 100   3    0    0    1    0    0    0    0    0    0
> 101   4    0    0    1    0    0    0    0    0    0
> 102   5    0    0    1    0    0    0    0    0    0
> 103   6    0    0    1    0    0    0    0    0    0
> 104   7    0    0    1    0    0    0    0    0    0
> 105   8    0    0    1    0    0    0    0    0    0
>
> Here, the ID I had listed in the census file doesn't match up with the
> output matrix IDs. For example, the second record, the ID #10 from the
> input file gets relabelled as ID # 2 in the output, which doesn't match the
> birth/death file I have with the initial IDs. Subsequently, the Datacheck
> results in an error message, which basically says that a bunch of the IDs
> have measurements after death or before birth, which I imagine is from
> being mismatched with original IDs.
>
> Is there a bug in the program? Or am I missing something? I formatted the
> datasets pretty much after the BaSTA users guide/vignette. I'm using the
> version 1.9.4 that I downloaded from the website and I'm using Rstudio. I
> have checked my data several times so that birthdeath and the
> detection/census files agree on dates when a given individual is
> alive/detected. Any help is much appreciated!
>
> Shafkat
> Shafkat Khan
> Ph.D Candidate
> Odum School of Ecology
> University of Georgia
>
>
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