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Dear Sergey,<br>
<br>
These consecutive steps in the reproduction pathway should go into a
single fecundity object. You have to specify the 'Family' and
'Transform' arguments in the order of the reproduction steps which
you specify in a list that is given to 'Formula'. Transform concerns
the response variable, and should be 'none', unless you want the
relate e.g. the log of the number of offspring to size (in which
case Transform=c("none","log"). Your code could look like the lines
below. Please note that I have given arbitrary values to
meanOffspringSize and sdOffspringSize because your data snippet does
not contain offspring size information. If your full dataset does
include seedlings (stage=size=NA), you do not need to specify
meanOffspringSize and sdOffspringSize.<br>
<br>
fv1<-makeFecObj(dataf=dat, Formula=list(fec1~size,fec2~size),
Family=c("binomial","gaussian"), Transform=c("none","none"),
meanOffspringSize=1, sdOffspringSize=1)<br>
<br>
par(mfrow=c(2,1))<br>
plot(dat$size,dat$fec1)<br>
x<-seq(2000)<br>
lines(x,predict(fv1@fitFec[[1]],data.frame(size=x),type="response"),col="red")<br>
plot(dat$size,dat$fec2)<br>
lines(x,predict(fv1@fitFec[[2]],data.frame(size=x),type="response"),col="blue")<br>
<br>
I hope this gets you on your way,<br>
Eelke<br>
<br>
<br>
<div class="moz-cite-prefix">On 4/8/2013 7:16 PM, Sergey Berg wrote:<br>
</div>
<blockquote
cite="mid:CALb9Bd=35O-XMtqVNgzV6ADtDffDrqHGqf_05YQnGUO5yC6Ydw@mail.gmail.com"
type="cite">Good afternoon,<br>
<br>
I am hoping to get some help in using IPMpack for evaluating the
population growth rate of a monocarpic plant species. I've read
the documentation provided for the IPMpack R package, but I'm
having a bit of trouble with defining the fecundity objects.<br>
<br>
I have five main parameters - size, sizeNext, surv, fec1, and
fec2. fec1 is a binary variable that measures if a plant
successfully produced offspring (and subsequently died, fec1=1) or
not (fec1=0). fec2 is the number of offspring produced by the
plant given fec1=1. I'm trying to understand whether these two
variables need to create separate fecundity objects or if they
should be combined into a single object, and how to do so.<br>
<br>
I was successfully able to define the growth and survival objects
via these commands<br>
gr1<-makeGrowthObj(dataf=dat,Formula=sizeNext~size)<br>
sv1<-makeSurvObj(dataf=dat,Formula=surv~size+size2)<br>
but the fecundity objects<br>
fv1<-makeFecObj(dataf=dat,Formula=fec1~size,Family="gaussian",Transform="log")<br>
are giving "Error in split.default(X, group) : first argument must
be a vector"<br>
<br>
I've included a portion of the data below if that helps.<br>
size sizeNext surv fec1 fec2 stage stageNext<br>
2704 150 NA 0 0 NA continuous continuous<br>
2705 225 NA 0 0 NA continuous continuous<br>
2706 800 NA 0 1 699 continuous continuous<br>
2707 1260 NA 0 1 1279 continuous continuous<br>
2708 1380 NA 0 1 1926 continuous continuous<br>
2709 1859 NA 0 1 1587 continuous continuous<br>
2710 156 165 1 0 NA continuous continuous<br>
2711 72 200 1 0 NA continuous continuous<br>
2712 108 210 1 0 NA continuous continuous<br>
<br>
Thank you very much in advance for any advice,<br>
<br>
Sergey<br clear="all">
<br>
-- <br>
Sergey S. Berg<br>
National Science Foundation Research Fellow<br>
Conservation Biology Graduate Program<br>
FWCB Collegiate Fee Committee<br>
CB Seminar Planning Committee<br>
<br>
University of Minnesota<br>
174 McNeal Hall<br>
1985 Buford Ave<br>
St. Paul, MN 55108
<br>
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<br>
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