<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Note that the sim.CI object returned by stock.growth.rate() is not a confidence interval in the statistical sense; rather, it is a measure of convergence (it goes to zero as the length of your simulation goes to infinity).<div class=""><br class=""></div><div class="">A confidence interval that reflected uncertainty in your estimate of demography (e.g., the fact that you only have four annual IPMs) would involve resampling your data/models and then running the stochastic growth rate calculation to an adequate level of convergence for each sample. In your case, if you are resampling the annual IPMs, then there are only 4^4 = 256 equally likely possible combinations, so you could simply calculate them all (you could be more efficient by simulating only with the unique unordered sets and weighting by the appropriate binomial coefficient).</div><div class=""><br class=""></div><div class="">Bruce</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 27, 2016, at 10:23 AM, Eelke Jongejans <<a href="mailto:e.jongejans@science.ru.nl" class="">e.jongejans@science.ru.nl</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><p style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Dear Elena,</p><p style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">the function stochGrowthRateSampleList only returns the mean of the per-time-step population growth rates in a stochastic simulation. If you want to know the distribution of these per-time-step population growth rates you could write your own version of this function and make sure that that distribution is stored as well. On the other hand if you want a CI for the resulting mean stochastic population growth rate, you code write code in which stochGrowthRateSampleList is called multiple times, and analyse the resulting distribution of mean stochastic population growth rates. If other people have other solutions, please share them!<span class="Apple-converted-space"> </span><br class=""></p><p style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Please also note the description of the stochGrowthRateSampleList function, that reads "Note that the function stoch.growth.rate in the package popbio does this more efficiently and with more useful output; but may fail for large bin numbers.".<br class=""></p><p style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">I hope this helps,</p><p style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">Eelke<br class=""></p><p style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><br class=""></p><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><div class="moz-cite-prefix" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);">On 20-Jul-16 1:48 PM, Elena S. wrote:<br class=""></div><blockquote cite="mid:DUB127-W831364287C23FD15264FC3A0080@phx.gbl" type="cite" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><div dir="ltr" class=""><font face="Calibri,sans-serif" size="3" style="font-size: 12pt;" class=""><br id="FontBreak" class=""></font>Hi,<br class=""><br class="">I try to calculate CI (confidence intervals) for my stochastic population growth rate. I started with 4 IPM (four years of study), then I run the following function:<br class=""><br class="">exp(stochGrowthRateSampleList(list(IPM9,IPM10,IPM11,IPM12),nRunIn = 100, tMax = 5000))<br class=""><br class="">or the following ones, based on the IPMpack manual (Metcalf et al. 2014):<br class=""><br class="">exp(stochGrowthRateSampleList(nRunIn=100,tMax=5000,listIPMmatrix=list(IPM9,IPM10,IPM11,IPM12),<br class=""> <span class="Apple-converted-space"> </span>listPmatrix=list(Pmatrix9,Pmatrix10,Pmatrix11,Pmatrix12),<span class="Apple-converted-space"> </span><br class=""> <span class="Apple-converted-space"> </span>listFmatrix=list(Fmatrix9,Fmatrix10,Fmatrix11,Fmatrix12),<br class=""> <span class="Apple-converted-space"> </span>seedList=NULL,<br class=""> <span class="Apple-converted-space"> </span>densDep=FALSE))<br class=""><br class="">and I obtained a stochastic lambda of 1.25, but, at the moment, I don't know how to calculate the confidence intervals.<br class=""><br class="">Anyone can help me?<br class=""><br class="">Thanks in advance,<br class=""><br class="">best regards,<br class=""><br class="">Elena<br class=""><br class=""><br class=""><br class="">_________________________________________________________<br class="">Dott.ssa Elena Sulis, PhD<br class=""><font size="2" style="font-size: 10pt;" class="">Centro Conservazione Biodiversitΰ (CCB)</font><br class=""><font size="2" style="font-size: 10pt;" class="">Sezione Botanica - Dipartimento di Scienze della Vita e dell'Ambiente (DISVA)</font><font size="2" style="font-size: 10pt;" class=""><br class=""></font><font size="2" style="font-size: 10pt;" class="">Universitΰ degli Studi di Cagliari</font><font size="2" style="font-size: 10pt;" class=""><br class=""></font><font size="2" style="font-size: 10pt;" class="">V.le Sant'Ignazio da Laconi, 11-13</font><font size="2" style="font-size: 10pt;" class=""><br class=""></font><font size="2" style="font-size: 10pt;" class="">09123 Cagliari (ITALIA)</font><font size="2" style="font-size: 10pt;" class=""><br class=""></font><font size="2" style="font-size: 10pt;" class="">Tel: +39-0706753509</font><br class=""><i class="">E-mail:</i><span class="Apple-converted-space"> </span><a class="moz-txt-link-abbreviated" href="mailto:elenasulis@hotmail.it">elenasulis@hotmail.it</a><span class="Apple-converted-space"> </span><br class=""><i class="">Skype:</i><span class="Apple-converted-space"> </span>elena.sulis<br class=""></div><br class=""><fieldset class="mimeAttachmentHeader"></fieldset><br class=""><pre wrap="" class="">_______________________________________________
IPMpack-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:IPMpack-users@lists.r-forge.r-project.org">IPMpack-users@lists.r-forge.r-project.org</a>
<a class="moz-txt-link-freetext" href="http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/ipmpack-users">http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/ipmpack-users</a>
</pre></blockquote><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">IPMpack-users mailing list</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><a href="mailto:IPMpack-users@lists.r-forge.r-project.org" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">IPMpack-users@lists.r-forge.r-project.org</a><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""><a href="http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/ipmpack-users" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/ipmpack-users</a><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class=""></div></blockquote></div><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; text-align: start; text-indent: 0px; widows: auto; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">--</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Bruce Kendall</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:kendall@bren.ucsb.edu" class="">kendall@bren.ucsb.edu</a></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://kendall.bren.ucsb.edu" class="">http://kendall.bren.ucsb.edu</a> </div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Skype: brucekendall64</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> #########################################</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> #### I am on sabbatical through Sept 2016 ####</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class=""> #########################################</div><div class=""><br class=""></div><div style="border: 0px; margin: 0px; padding: 0px; line-height: 18px; font-family: Arial, Helvetica, sans-serif;" class=""><div style="font-family: Helvetica; line-height: normal;" class="">=============================</div></div></div><div style="border: 0px; margin: 0px; padding: 0px;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; line-height: normal;" class=""><div class="">Address through Aug. 2016:</div><div class=""></div><div class="">Department of Zoology<br class="">University of Oxford<br class="">The Tinbergen Building<br class="">South Parks Road<br class="">Oxford<br class="">OX1 3PS<br class="">United Kingdom</div><div class="">Tel: <span class="Apple-converted-space"> </span><span class="Apple-tab-span" style="white-space: pre;"> </span>+44 (0)1865 271139</div><div class="">Mob:<span class="Apple-converted-space"> </span><span class="Apple-tab-span" style="white-space: pre;"> </span>+44 (0)7534 514781</div><div class="">Home:<span class="Apple-tab-span" style="white-space: pre;"> </span>+44 (0)1865 515349</div></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; line-height: normal;" class=""><br class=""></div><div class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="border: 0px; margin: 0px; padding: 0px; line-height: 18px; font-family: Arial, Helvetica, sans-serif;" class=""><div style="font-family: Helvetica; line-height: normal;" class=""><br class=""></div></div></div></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div style="font-family: Helvetica; line-height: normal;" class="">===========================================</div></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><div class="">Permanent address:</div><div class=""></div></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="orphans: 2; widows: 2;" class="">Bren School of Environmental Science</span><span style="orphans: 2; widows: 2;" class=""> & Management</span></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="orphans: 2; widows: 2;" class="">University of California, Santa Barbara</span><br style="orphans: 2; widows: 2;" class=""><span style="orphans: 2; widows: 2;" class="">Santa Barbara, CA 93106-5131</span></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">USA<br style="orphans: 2; widows: 2;" class=""><span style="orphans: 2; widows: 2;" class="">Tel: +1 (805) 893-7539</span></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; orphans: 2; widows: 2;" class=""><div style="orphans: auto; widows: auto;" class="">===========================================</div><div style="orphans: auto; widows: auto;" class=""></div></div></div></div></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
</div>
<br class=""></div></body></html>