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Hi Shafkat,<br class="">
<br class="">
1) I have fixed the bug with CensusToCaptHist(). It will appear in the next version.
<div class=""><br class="">
At the moment it is in the development version of BaSTA on GitHub.<br class="">
<br class="">
You can source that particular function like this:<br class="">
<br class="">
<font face="Menlo" class="">install.packages("devtools")</font>
<div class=""><font face="Menlo" class="">library(devtools)</font></div>
<div class=""><font face="Menlo" class=""><br class="">
</font></div>
<div class=""><font face="Menlo" class="">source_url("<a href="https://raw.githubusercontent.com/fercol/BaSTA/master/pkg/R/CensusToCaptHist.R" class="">https://raw.githubusercontent.com/fercol/BaSTA/master/pkg/R/CensusToCaptHist.R</a>”)</font></div>
<div class=""><br class="">
The whole development version of the package can be installed like this:</div>
<div class=""><font face="Menlo" class="">library(devtools)</font></div>
<div class=""><font face="Menlo" class="">install_github("fercol/BaSTA/pkg")</font></div>
<br class="">
2) I have never seen the error message "could not find function “requireNamespace”” before.
<div class=""><br class="">
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<div class="">Does your model run with <font face="Menlo" class="">parallel = FALSE</font>? </div>
<div class="">If you send your data file (off list to <a href="mailto:jones@biology.sdu.dk" class="">
jones@biology.sdu.dk</a>) I will see if I get the same error and try to debug it.</div>
<div class="">It’d be best if you send your data as an Rdata object.</div>
<div class="">i.e. run: <font face="Menlo" class="">save(VC2,file="VC2.RData”)</font></div>
<div class=""><br class="">
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<div class="">Best wishes,</div>
<div class="">Owen</div>
<div class="">
<div class=""><br class="">
<br class="">
<blockquote type="cite" class="">On 22 Mar 2016, at 04:50, Shafkat Khan <<a href="mailto:shafkat.khan@gmail.com" class="">shafkat.khan@gmail.com</a>> wrote:<br class="">
<br class="">
Hello Owen:<br class="">
<br class="">
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. <br class="">
<br class="">
I'm using this code: <br class="">
out1<-basta(object = VC2, studyStart = 2009, studyEnd = 2017,<br class="">
nsim = 4, parallel = TRUE, ncpus = 4)<br class="">
<br class="">
And getting this error message: <br class="">
Error in basta.default(object = VC2, studyStart = 2009, studyEnd = 2017, : <br class="">
could not find function "requireNamespace"<br class="">
<br class="">
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!<br class="">
<br class="">
Shafkat<br class="">
<br class="">
Shafkat Khan<br class="">
Ph.D Candidate<br class="">
Odum School of Ecology<br class="">
University of Georgia<br class="">
<br class="">
<br class="">
On Mon, Mar 21, 2016 at 5:18 PM, Owen Jones <<a href="mailto:jones@biology.sdu.dk" class="">jones@biology.sdu.dk</a>> wrote:<br class="">
Hi Shafkat,<br class="">
<br class="">
That looks like a bug. <br class="">
I’ll investigate and get back to you ASAP.<br class="">
<br class="">
In the meantime you could simply replace the ID with the rowname.<br class="">
i.e.<br class="">
<br class="">
x$ID <- rownames(x)<br class="">
<br class="">
<br class="">
Best wishes,<br class="">
Owen<br class="">
<br class="">
<blockquote type="cite" class="">On 21 Mar 2016, at 21:37, Shafkat Khan <shafkat.khan@gmail.com> wrote:<br class="">
<br class="">
Hello:<br class="">
<br class="">
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.<br class="">
<br class="">
ID 2009 2010 2011 2012 2013 2014 2015 2016 2017<br class="">
1 1 0 0 1 1 1 0 1 0 1<br class="">
10 2 0 0 0 0 1 0 1 0 1<br class="">
100 3 0 0 1 0 0 0 0 0 0<br class="">
101 4 0 0 1 0 0 0 0 0 0<br class="">
102 5 0 0 1 0 0 0 0 0 0<br class="">
103 6 0 0 1 0 0 0 0 0 0<br class="">
104 7 0 0 1 0 0 0 0 0 0<br class="">
105 8 0 0 1 0 0 0 0 0 0<br class="">
<br class="">
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. <br class="">
<br class="">
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!<br class="">
<br class="">
Shafkat<br class="">
<br class="">
Shafkat Khan<br class="">
Ph.D Candidate<br class="">
Odum School of Ecology<br class="">
University of Georgia<br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
Basta-users mailing list<br class="">
Basta-users@lists.r-forge.r-project.org<br class="">
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/basta-users<br class="">
</blockquote>
<br class="">
<br class="">
</blockquote>
<br class="">
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