<div dir="ltr"><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Dear BaSTA community, </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Thanks to your help and BaSTA, we could
statistically confirm some of our expectations on <a href="http://lists.r-forge.r-project.org/pipermail/basta-users/2015-October/000131.html">post-fledging survival in a afrotropical passerine</a>. </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">While <i>plotfancybasta()</i> and <i>plot() </i>produce
nice graphs for categorical variables, we are looking for a way to visualise the
impact of <b>continues covariates</b> on survival of the fledglings. </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">More specifically, we fitted a
weibull survival curve with makeham shape + mass at fledging (SMI) as a
covariate (base model + 1 covariate) and find a negative relation with
mortality (CI does not include zero). </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><pre style="line-height:10.25pt;background-image:initial;background-repeat:initial"><span lang="EN-GB" style="font-size:8pt;font-family:Courier;color:black">Coefficients:</span></pre><pre style="line-height:10.25pt;background-image:initial;background-repeat:initial"><span lang="EN-GB" style="font-size:8pt;font-family:Courier;color:black">          Estimate  StdErr Lower95%CI Upper95%CI SerAutocor UpdateRate PotScaleReduc</span></pre><pre style="line-height:10.25pt;background-image:initial;background-repeat:initial"><span lang="EN-GB" style="font-size:8pt;font-family:Courier;color:black">c          0.02704 0.01595   0.009527   0.066033    0.56051     0.2223         1.017</span></pre><pre style="line-height:10.25pt;background-image:initial;background-repeat:initial"><span lang="EN-GB" style="font-size:8pt;font-family:Courier;color:black">b0         0.06541 0.06751   0.001576   0.252938    0.38508     0.2605         1.002</span></pre><pre style="line-height:10.25pt;background-image:initial;background-repeat:initial"><span lang="EN-GB" style="font-size:8pt;font-family:Courier;color:black">b1         0.90422 0.63824   0.043231   2.358846    0.06547     0.2501         1.001</span></pre><pre style="line-height:10.25pt;background-image:initial;background-repeat:initial"><span lang="EN-GB" style="font-size:8pt;font-family:Courier;color:black"><span style="background-color:rgb(255,255,0)">gamma.SMI -0.03971 0.01978  -0.083632  -0.006801</span>    0.55284     0.2526         1.003</span></pre><pre style="line-height:10.25pt;background-image:initial;background-repeat:initial"><span lang="EN-GB" style="font-size:8pt;font-family:Courier;color:black">pi.1       0.14211 0.01089   0.121642   0.163994    0.03578     1.0000         1.001</span></pre><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">We see two ways to visualise this</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"><br></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">1. Daily mortality rates over a two
month period (y-axis) plotted against time (x-axis) for a discrete number of
SMI values. As such, you visualise the mortality shape for a number of SMI
values over a two month period. </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"><br></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">2. The cumulative mortality probabilities
(y-axis) after a two month period plotted against SMI (x-axis). We then expect
that cumulative mortality probabilities will decrease with increasing SMI.</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">To do this, we could use the
estimates to calculate (i) the daily mortality rates over a two month period
and use these to calculate (ii) the cumulative mortality probabilities after a
two month period for a discrete number of SMI values within the measured range (for
example : 20, 25,30,35). </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"><br></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">While we successfully calculate
daily mortality rates fitting the estimates in the function (b0 * b1 * ((b1 *
k)^(b0 - 1))) + c) when no covariates were added to the model, we failed to
find a method on how to include the gamma estimate in the function. </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"><br></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Any help on how we can calculate
daily mortality rates for a specific value of the covariate and be able to
produce these graphs is highly appreciated. </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Best wishes, </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Dries Van de Loock</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">PhD student</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Terrestrial Ecology Unit</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Department of Biology</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Ghent University</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">KL Ledeganckstraat 35</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">B-9000 Ghent, Belgium</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB">Phone: +32 (0)9 265 50 39</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"><a href="http://www.ecology.ugent.be/terec/">http://www.ecology.ugent.be/terec/</a></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB"> </span></p><p class="MsoNormal" style="margin-bottom:0.0001pt">































































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