<div dir="ltr">Hello Owen:<div><br></div><div>Thanks for the quick response and the update! Yes, the model/code runs fine with parallel=FALSE. I'll send on the data object to the email address you provided.</div><div><br></div><div>Secondly, I have a coding question. In my data, I have survivorship of individuals observed in plots located within high, mid, and low elevations. I would like to model the plots as nested within elevations and examine the effects of elevation on survivorship. I'm not sure what the syntax in this case would be. I imagine </div><div>newcovar2<-MakeCovMat(~Elev+Plot,data=covar) isn't correct, or atleast plot(x, plot.trace=FALSE) prints out effects of all possible combination of elevations and sites. </div><div><br></div><div>Would newcovar3<-MakeCovMat(~Elev+(Plot/Elev),data=covar) be the correct syntax to show that uniquely labeled plots are nested within elevations? </div><div><br></div><div>Your help is much appreciated!</div><div><br></div><div>Shafkat</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Shafkat Khan<div>Ph.D Candidate</div><div>Odum School of Ecology</div><div>University of Georgia</div><div><br></div><div>I sometimes write in a blog: <span style="font-family:Arial,Helvetica,sans-serif;font-size:13px;line-height:20px"><a href="http://catching-dreams-in-green-leaves.blogspot.com" target="_blank">catching-dreams-in-green-leaves.blogspot.com</a></span></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Mar 22, 2016 at 5:47 AM, Owen Jones <span dir="ltr"><<a href="mailto:jones@biology.sdu.dk" target="_blank">jones@biology.sdu.dk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi Shafkat,<br>
<br>
1) I have fixed the bug with CensusToCaptHist(). It will appear in the next version.
<div><br>
At the moment it is in the development version of BaSTA on GitHub.<br>
<br>
You can source that particular function like this:<br>
<br>
<font face="Menlo">install.packages("devtools")</font>
<div><font face="Menlo">library(devtools)</font></div>
<div><font face="Menlo"><br>
</font></div>
<div><font face="Menlo">source_url("<a href="https://raw.githubusercontent.com/fercol/BaSTA/master/pkg/R/CensusToCaptHist.R" target="_blank">https://raw.githubusercontent.com/fercol/BaSTA/master/pkg/R/CensusToCaptHist.R</a>”)</font></div>
<div><br>
The whole development version of the package can be installed like this:</div>
<div><font face="Menlo">library(devtools)</font></div>
<div><font face="Menlo">install_github("fercol/BaSTA/pkg")</font></div>
<br>
2) I have never seen the error message "could not find function “requireNamespace”” before.
<div><br>
</div>
<div>Does your model run with <font face="Menlo">parallel = FALSE</font>? </div>
<div>If you send your data file (off list to <a href="mailto:jones@biology.sdu.dk" target="_blank">
jones@biology.sdu.dk</a>) I will see if I get the same error and try to debug it.</div>
<div>It’d be best if you send your data as an Rdata object.</div>
<div>i.e. run: <font face="Menlo">save(VC2,file="VC2.RData”)</font></div>
<div><br>
</div>
<div>Best wishes,</div>
<div>Owen</div>
<div>
<div><br>
<br>
<blockquote type="cite"><div><div class="h5">On 22 Mar 2016, at 04:50, Shafkat Khan <<a href="mailto:shafkat.khan@gmail.com" target="_blank">shafkat.khan@gmail.com</a>> wrote:<br>
<br>
Hello Owen:<br>
<br>
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>
<br>
I'm using this code: <br>
out1<-basta(object = VC2, studyStart = 2009, studyEnd = 2017,<br>
nsim = 4, parallel = TRUE, ncpus = 4)<br>
<br>
And getting this error message: <br>
Error in basta.default(object = VC2, studyStart = 2009, studyEnd = 2017, : <br>
could not find function "requireNamespace"<br>
<br>
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>
<br>
Shafkat<br>
<br>
Shafkat Khan<br>
Ph.D Candidate<br>
Odum School of Ecology<br>
University of Georgia<br>
<br>
<br>
On Mon, Mar 21, 2016 at 5:18 PM, Owen Jones <<a href="mailto:jones@biology.sdu.dk" target="_blank">jones@biology.sdu.dk</a>> wrote:<br>
Hi Shafkat,<br>
<br>
That looks like a bug. <br>
I’ll investigate and get back to you ASAP.<br>
<br>
In the meantime you could simply replace the ID with the rowname.<br>
i.e.<br>
<br>
x$ID <- rownames(x)<br>
<br>
<br>
Best wishes,<br>
Owen<br>
<br>
</div></div><blockquote type="cite"><div><div class="h5">On 21 Mar 2016, at 21:37, Shafkat Khan <<a href="mailto:shafkat.khan@gmail.com" target="_blank">shafkat.khan@gmail.com</a>> wrote:<br>
<br>
Hello:<br>
<br>
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>
<br>
ID 2009 2010 2011 2012 2013 2014 2015 2016 2017<br>
1 1 0 0 1 1 1 0 1 0 1<br>
10 2 0 0 0 0 1 0 1 0 1<br>
100 3 0 0 1 0 0 0 0 0 0<br>
101 4 0 0 1 0 0 0 0 0 0<br>
102 5 0 0 1 0 0 0 0 0 0<br>
103 6 0 0 1 0 0 0 0 0 0<br>
104 7 0 0 1 0 0 0 0 0 0<br>
105 8 0 0 1 0 0 0 0 0 0<br>
<br>
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>
<br>
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>
<br>
Shafkat<br>
<br></div></div><span class="">
Shafkat Khan<br>
Ph.D Candidate<br>
Odum School of Ecology<br>
University of Georgia<br>
<br>
<br>
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