<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Dries,<div class=""><br class=""></div><div class=""> Definitely, that will be correct, add the other parameters and take a fixed value for the covariates that you are not showing. I agree that taking the mean would make more sense and it would make it clearer to explain. Your updated mortality is correct. </div><div class=""><div class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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;" class=""><br class="Apple-interchange-newline">Best,</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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;" class=""> Fernando</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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;" class=""><br class=""></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; 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;" class=""><div class="" style="font-size: 12px; orphans: 2; widows: 2;"><b class="">Fernando Colchero</b></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Assistant Professor</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Department of Mathematics and Computer Science</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Max-Planck Odense Center on the Biodemography of Aging</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;"><b class=""><i class=""><br class=""></i></b></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Tlf. +45 65 50 23 24</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Email <a href="mailto:colchero@imada.sdu.dk" class="">colchero@imada.sdu.dk</a></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Web <a href="http://www.sdu.dk/staff/colchero" class="">www.sdu.dk/staff/colchero</a></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Pers. web <a href="http://www.sdu.dk/staff/colchero" class="">www.colchero.com</a></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;">Adr. Campusvej 55, 5230, Odense, Dk</div><div class="" style="font-size: 12px; orphans: 2; widows: 2;"><br class=""></div><div class="" style="font-size: 12px; orphans: 2; widows: 2;"><b class="">University of Southern Denmark</b></div></div>
</div>
<br class=""><div><blockquote type="cite" class=""><div class="">On 28 Mar 2016, at 15:22, Dries Van de Loock <<a href="mailto:dries.vandeloock@ugent.be" class="">dries.vandeloock@ugent.be</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class="">Dear Fernando, <div class=""><br class=""></div><div class="">many, many thanks for this. It was <i class="">exactly</i> what I was looking for and will greatly improve our manuscript. </div><div class=""><br class=""></div><div class="">I have one questions remaining. </div><div class=""><br class=""></div><div class="">How should I approach this method when wanting to visualise the effect of one continuous variable from a multivariate model both including continuous and one categorical variable with 5 levels ?<br class=""></div><div class=""><br class=""></div><div class="">- Could I use the weighted average (=average c, b1 and b0 based on cohorts sample sizes) of the mortality estimates ? When just averaging, I have found that the mort rates were far too high as one cohort with just one case had high estimates. </div><div class="">- Could I just add another term <b class="">* exp(g * z) </b>to the model for each continuous variable and use the averaged predictor (z) value for the variable I'm not interested in ?</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">For example, we have a model : mort ~ LOC + SMI + GS</div><div class=""><br class=""></div><div class="">GS = groupsize (continuous)</div><div class="">SMI = mass (continuous, like above example)</div><div class="">LOC = location (5 levels, sample sizes differ hugely between cohorts)</div><div class=""><br class=""></div><div class="">When I want to visualise the effect of SMI solely, would this approach be correct : </div><div class=""><br class=""></div><div class=""><font face="monospace, monospace" class="">#define function</font></div><div class=""><div class=""><font face="monospace, monospace" class="">mort <- function(x, z1, z2, b, g) {</font></div><div class=""><font face="monospace, monospace" class=""> exp(g[1] * z1) * exp(g[2] * z2) * (b[1] + b[2] * b[3]^(b[2]) * x^(b[2] - 1))</font></div><div class=""><font face="monospace, monospace" class="">}</font></div><div class=""><font face="monospace, monospace" class=""><br class=""></font></div><div class=""><font face="monospace, monospace" class=""># define values</font></div><div class=""><font face="monospace, monospace" class="">x <- seq(1, 55, 1)</font></div><div class=""><font face="monospace, monospace" class="">z1 <- c(min(covariates$SMI),max(covariates$SMI)) # min and max value of the continuous variable of interest</font></div><div class=""><font face="monospace, monospace" class="">z2 <- mean(covariates$GS) # mean of the continuous variable not interested in to visualise</font></div><div class=""><font face="monospace, monospace" class=""> c <- mean(out$coefficients[c(1:5),1]) # average of the c values of each LOC (c.LOC1, c.LOC2, etc.) (in this example not yet weighted)</font></div><div class=""><font face="monospace, monospace" class=""> b0 <- mean(out$coefficients[c(6:10),1]) # average of the b0 values of each LOC (b0.LOC1, b0.LOC2, etc.) (in this example not yet weighted)</font></div><div class=""><font face="monospace, monospace" class=""> b1 <- mean(out$coefficients[c(11:15),1])</font></div><div class=""><font face="monospace, monospace" class="">b <- c(c,b0,b1)</font></div><div class=""><font face="monospace, monospace" class="">g <- out.SMI$coefficients[c(16:17), 1] # g parameters</font></div><div class=""><font face="monospace, monospace" class=""><br class=""></font></div><div class=""><font face="monospace, monospace" class=""># calculate</font></div><div class=""><font face="monospace, monospace" class="">mumin <- mort(x, z1[1], z2, b, g)</font></div><div class=""><font face="monospace, monospace" class="">mumax <- mort(x, z1[2], z2, b, g)</font></div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">I hope the example and my question are clear. </div><div class=""><br class=""></div><div class="">Again, many thanks for your time invested in this and I'm looking forward to your reply !</div><div class=""><br class=""></div><div class="">Dries</div><div class=""><br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2016-03-26 8:25 GMT+01:00 Fernando Colchero <span dir="ltr" class=""><<a href="mailto:colchero@imada.sdu.dk" target="_blank" class="">colchero@imada.sdu.dk</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">
Dear Dries,
<div class=""><br class="">
</div>
<div class=""> Sorry for the late reply. This is certainly an issue we have not yet addressed with the package. Alternatively, you could produce a plot by extracting the information from the coefficients table in the BaSTA output. Here’s an option based on
your results:</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<span style="color:rgb(79,79,79)" class=""># Define the Weibull mortality with proportional hazards as:</span></div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<span style="" class="">mort </span><- <span style="color:rgb(195,136,9)" class="">
function</span>(<span style="" class="">x</span>, <span style="" class="">
z</span>,<span style="" class=""> b</span>,<span style="" class=""> g</span>) {</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<span style="white-space:pre-wrap" class=""></span>exp(<span style="" class="">g
</span>* <span style="" class="">z</span>) * (<span style="" class="">b</span>[<span style="color:rgb(4,82,24)" class="">1</span>] +
<span style="" class="">b</span>[<span style="color:rgb(4,82,24)" class="">2</span>] *
<span style="" class="">b</span>[<span style="color:rgb(4,82,24)" class="">3</span>]^(<span style="" class="">b</span>[<span style="color:rgb(4,82,24)" class="">2</span>]) *
<span style="" class="">x</span>^(<span style="" class="">b</span>[<span style="color:rgb(4,82,24)" class="">2</span>] -
<span style="color:rgb(4,82,24)" class="">1</span>))</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
}</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<br class="">
</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
where x is age, z is the SMI value, b is the vector of mortality parameters and g is the vector of proportional hazards parameters.</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153);min-height:20px" class="">
<br class="">
</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(79,79,79)" class="">
# Define x (I’m making up this range of ages…):</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<span style="" class="">x </span><- seq(<span style="color:rgb(4,82,24)" class="">0.1</span>,
<span style="color:rgb(4,82,24)" class="">5</span>,<span style="color:rgb(4,82,24)" class=""> 0.1</span>)</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153);min-height:20px" class="">
<br class="">
</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(79,79,79)" class="">
# Define the lower and upper bounds of z (these are also made up…):</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<span style="" class="">z </span><- c(<span style="color:rgb(4,82,24)" class="">3</span>,<span style="color:rgb(4,82,24)" class=""> 6</span>)</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153);min-height:20px" class="">
<br class="">
</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(79,79,79)" class="">
# Extract the b and g parameters:</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco" class="">
b <span style="color:rgb(6,26,153)" class=""><- </span>out<span style="color:rgb(6,26,153)" class="">$</span>coefficients<span style="color:rgb(6,26,153)" class="">[</span><span style="color:rgb(4,82,24)" class="">1</span><span style="color:rgb(6,26,153)" class="">:</span><span style="color:rgb(4,82,24)" class="">3</span><span style="color:rgb(6,26,153)" class="">,
</span><span style="color:rgb(4,82,24)" class="">1</span><span style="color:rgb(6,26,153)" class="">]</span></div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco" class="">
g<span style="color:rgb(6,26,153)" class=""> <- </span>out<span style="color:rgb(6,26,153)" class="">$</span>coefficients<span style="color:rgb(6,26,153)" class="">[</span><span style="color:rgb(4,82,24)" class="">4</span><span style="color:rgb(6,26,153)" class="">,
</span><span style="color:rgb(4,82,24)" class="">1</span><span style="color:rgb(6,26,153)" class="">]</span></div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153);min-height:20px" class="">
<br class="">
</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(79,79,79)" class="">
# Calculate the corresponding mortalities:</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<span style="" class="">mulow </span><- mort(<span style="" class="">x</span>,<span style="" class=""> z</span>[<span style="color:rgb(4,82,24)" class="">1</span>],
<span style="" class="">b</span>,<span style="" class=""> g</span>)</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<span style="" class="">muup </span><- mort(<span style="" class="">x</span>,<span style="" class=""> z</span>[<span style="color:rgb(4,82,24)" class="">2</span>],
<span style="" class="">b</span>, <span style="" class="">
g</span>)</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(79,79,79);min-height:20px" class="">
<br class="">
</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(79,79,79)" class="">
# Define the range for the y-axis:</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
<span style="" class="">ylim </span><- c(<span style="color:rgb(4,82,24)" class="">0</span>,<span style="color:rgb(4,82,24)" class="">
</span>max(c(<span style="" class="">mulow</span>,<span style="" class=""> muup</span>)))</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(79,79,79);min-height:20px" class="">
<br class="">
</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(79,79,79)" class="">
# Plot the results:</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco" class="">
<span style="color:rgb(6,26,153)" class="">plot(</span>x<span style="color:rgb(6,26,153)" class="">,</span> mulow<span style="color:rgb(6,26,153)" class="">,</span> col
<span style="color:rgb(6,26,153)" class="">=</span> <span style="color:rgb(4,82,24)" class="">
1</span><span style="color:rgb(6,26,153)" class="">,</span><span style="color:rgb(4,82,24)" class="">
</span>type <span style="color:rgb(6,26,153)" class="">= </span><span style="color:rgb(176,22,0)" class="">'l'</span><span style="color:rgb(6,26,153)" class="">,</span><span style="color:rgb(176,22,0)" class="">
</span>ylim <span style="color:rgb(6,26,153)" class="">=</span> ylim<span style="color:rgb(6,26,153)" class="">)</span></div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(6,26,153)" class="">
lines(<span style="" class="">x</span>,<span style="" class=""> muup</span>,
<span style="" class="">col </span>=<span style="" class="">
</span><span style="color:rgb(4,82,24)" class="">2</span>)</div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco;color:rgb(176,22,0)" class="">
<span style="color:rgb(6,26,153)" class="">legend(</span>'topright'<span style="color:rgb(6,26,153)" class="">,</span>
<span style="color:rgb(6,26,153)" class="">c(</span>"Low SMI"<span style="color:rgb(6,26,153)" class="">,
</span>"High SMI"<span style="color:rgb(6,26,153)" class="">), </span><span style="" class="">col
</span><span style="color:rgb(6,26,153)" class="">= c(</span><span style="color:rgb(4,82,24)" class="">1</span><span style="color:rgb(6,26,153)" class="">,</span><span style="color:rgb(4,82,24)" class=""> 2</span><span style="color:rgb(6,26,153)" class="">),</span></div>
<div style="margin:0px 0px 0px 4px;font-size:15.1px;font-family:Monaco" class="">
<span style="color:rgb(6,26,153)" class=""><span style="white-space:pre-wrap" class=""></span></span>lwd
<span style="color:rgb(6,26,153)" class="">=</span> <span style="color:rgb(4,82,24)" class="">
2</span><span style="color:rgb(6,26,153)" class="">)</span></div>
</div>
<div class=""><br class="">
</div>
<div class=""> Let me know if this is of any help.</div>
<div class="">
<div style="font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">
<br class="">
Best,</div>
<div style="font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">
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</div>
<div style="font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;" class="">
Fernando<br class="">
<br class="">
</div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
<b class="">Fernando Colchero</b></div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
Assistant Professor</div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
Department of Mathematics and Computer Science</div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
Max-Planck Odense Center on the Biodemography of Aging</div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
<b class=""><i class=""><br class="">
</i></b></div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
Tlf. <a href="tel:%2B45%2065%2050%2023%2024" value="+4565502324" target="_blank" class="">+45 65 50 23 24</a></div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
Email <a href="mailto:colchero@imada.sdu.dk" target="_blank" class="">colchero@imada.sdu.dk</a></div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
Web <a href="http://www.sdu.dk/staff/colchero" target="_blank" class="">www.sdu.dk/staff/colchero</a></div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
Pers. web <a href="http://www.sdu.dk/staff/colchero" target="_blank" class="">www.colchero.com</a></div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
Adr. Campusvej 55, 5230, Odense, Dk</div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
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</div>
<div style="font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: 12px;" class="">
<b class="">University of Southern Denmark</b></div>
</div>
<br class="">
<div class="">
<blockquote type="cite" class=""><div class=""><div class="">
<div class="">On 22 Mar 2016, at 11:32, Dries Van de Loock <<a href="mailto:dries.vandeloock@ugent.be" target="_blank" class="">dries.vandeloock@ugent.be</a>> wrote:</div>
<br class="">
</div></div><div class=""><div class=""><div class="">
<div dir="ltr" class=""><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">Dear BaSTA community,
</span></p>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">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" target="_blank" class="">
post-fledging survival in a afrotropical passerine</a>. </span></p>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">While
<i class="">plotfancybasta()</i> and <i class="">plot() </i>produce nice graphs for categorical variables, we are looking for a way to visualise the impact of
<b class="">continues covariates</b> on survival of the fledglings. </span></p>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">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>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div>
<pre style="line-height:10.25pt;background-image:initial;background-repeat:initial" class=""><span lang="EN-GB" style="font-size:8pt;font-family:Courier" class="">Coefficients:</span></pre>
<pre style="line-height:10.25pt;background-image:initial;background-repeat:initial" class=""><span lang="EN-GB" style="font-size:8pt;font-family:Courier" class=""> Estimate StdErr Lower95%CI Upper95%CI SerAutocor UpdateRate PotScaleReduc</span></pre>
<pre style="line-height:10.25pt;background-image:initial;background-repeat:initial" class=""><span lang="EN-GB" style="font-size:8pt;font-family:Courier" class="">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" class=""><span lang="EN-GB" style="font-size:8pt;font-family:Courier" class="">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" class=""><span lang="EN-GB" style="font-size:8pt;font-family:Courier" class="">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" class=""><span lang="EN-GB" style="font-size:8pt;font-family:Courier" class=""><span style="background-color:rgb(255,255,0)" class="">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" class=""><span lang="EN-GB" style="font-size:8pt;font-family:Courier" class="">pi.1 0.14211 0.01089 0.121642 0.163994 0.03578 1.0000 1.001</span></pre>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">We see two ways to visualise this</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class=""><br class="">
</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">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" class=""><br class="">
</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">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>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">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" class=""><br class="">
</span></p>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">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" class=""><br class="">
</span></p>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">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>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">Best wishes,
</span></p>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
</div><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">Dries Van de Loock</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">PhD student</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">Terrestrial Ecology Unit</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">Department of Biology</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">Ghent University</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">KL Ledeganckstraat 35</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">B-9000 Ghent, Belgium</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class="">Phone: <a href="tel:%2B32%20%280%299%20265%2050%2039" value="+3292655039" target="_blank" class="">+32 (0)9 265 50 39</a></span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span lang="EN-GB" class=""><a href="http://www.ecology.ugent.be/terec/" target="_blank" class="">http://www.ecology.ugent.be/terec/</a></span></p>
<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
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<div style="margin-bottom:0.0001pt" class=""><span lang="EN-GB" class=""> </span><br class="">
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