Individual covariate plotting

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Individual covariate plotting

Postby Mardagosa » Wed Sep 22, 2021 8:51 pm

I am trying to plot the survival estimates for my model, which is affected by body size. I am using covariate.predictions but what I get is a straight line, indicating that larger body sizes have lower estimates of survival. Given the normal distribution of the data I was expecting a normal distribution of survival. Am I missing something from the analysis?
Mardagosa
 
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Re: Individual covariate plotting

Postby sbonner » Thu Sep 23, 2021 7:10 am

Hi Mardagosa,

What you are plotting is the survival probability as a function of the covariate, not the distribution of the survival values. Even then, the fact that the covariate is (approximately) normal does not mean that the survival probabilities will be normally distributed because the survival probability is (probably) a non-linear transformation of the covariate. This in part ensures that the survival probability remains between 0 and 1.

The fact that you are seeing a straight line in your plot either means that you are plotting the linear predictor or that the function is close to a straight line over the range of your covariate. The exact details depend on which link function you have selected when fitting the model (sin, logit, etc). Do the values on the y-axis make sense as probabilities (i.e., are they between 0 and 1)? If not, then you are plotting the linear predictor.

Cheers,

Simon
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Re: Individual covariate plotting

Postby Mardagosa » Thu Sep 23, 2021 10:06 am

Hi Simon,
This makes sense and I appreciate the clarity of your explanation. Thank you so much!
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Re: Individual covariate plotting

Postby Mnat » Mon Nov 01, 2021 5:48 am

Hi,
I'm sorry to ask this again, but I have the same issue, however, unfortunately didn't manage to solve it yet. I followed the code and instructions in the Appendix C and also in the Workshop notes with the weight example.
I also tried a more complex exampe with time varying covariates (temperatures) following the example "plotting environmental covariate relationships" in this forum http://www.phidot.org/forum/viewtopic.php?f=21&t=3044&p=9773&hilit=time+varying+covariates#p9773

But I always end up with a staight line and CIs and estimates that are all the same for each covariate value, no matter what I do.
Here is my very short and easy example. I would be glad if someone could tell me what's wrong.

Code: Select all
Mnat.size.processed=process.data(Mnat.size,model="CJS",begin.time=2003,groups=c("colony"))
Mnat.size.ddl=make.design.data(Mnat.size.processed)

Phi.size=list(formula=~size)
mod.size=mark(Mnat.size.processed, Mnat.size.ddl, model.parameters = list(Phi=Phi.size))

size.seq <- seq(37,44, by=0.5)

phibysize=covariate.predictions(mod.size,data=data.frame(size.seq), indices = c(1))




All values are the same. So its no surprise that I have a straight line

Code: Select all
> phibysize$estimates
   vcv.index model.index par.index covdata  estimate         se       lcl       ucl fixed
1          1           1         1    37.0 0.8523615 0.01082037 0.8298717 0.8723357     
2          2           1         1    37.5 0.8523615 0.01082037 0.8298717 0.8723357     
3          3           1         1    38.0 0.8523615 0.01082037 0.8298717 0.8723357     
4          4           1         1    38.5 0.8523615 0.01082037 0.8298717 0.8723357     
5          5           1         1    39.0 0.8523615 0.01082037 0.8298717 0.8723357     
6          6           1         1    39.5 0.8523615 0.01082037 0.8298717 0.8723357     
7          7           1         1    40.0 0.8523615 0.01082037 0.8298717 0.8723357     
8          8           1         1    40.5 0.8523615 0.01082037 0.8298717 0.8723357     
9          9           1         1    41.0 0.8523615 0.01082037 0.8298717 0.8723357     
10        10           1         1    41.5 0.8523615 0.01082037 0.8298717 0.8723357     
11        11           1         1    42.0 0.8523615 0.01082037 0.8298717 0.8723357     
12        12           1         1    42.5 0.8523615 0.01082037 0.8298717 0.8723357     
13        13           1         1    43.0 0.8523615 0.01082037 0.8298717 0.8723357     
14        14           1         1    43.5 0.8523615 0.01082037 0.8298717 0.8723357     
15        15           1         1    44.0 0.8523615 0.01082037 0.8298717 0.8723357


Code: Select all
plot(phibysize$estimates$covdata, phibysize$estimates$estimate, type = "l", lwd=2, ylim = c(0,1))
lines(phibysize$estimates$covdata, phibysize$estimates$lcl,lty=2)
lines(phibysize$estimates$covdata, phibysize$estimates$ucl,lty=2)




or if I follow the dipper rain example:

Code: Select all
Mnat_NSH_ch_easy$temp2002=rep(10.1,453)
Mnat_NSH_ch_easy$temp2003=rep(11.1,453)
Mnat_NSH_ch_easy$temp2004=rep(12.1,453)
Mnat_NSH_ch_easy$temp2005=rep(14.1,453)
Mnat_NSH_ch_easy$temp2006=rep(15.1,453)
Mnat_NSH_ch_easy$temp2007=rep(12.1,453)
Mnat_NSH_ch_easy$temp2008=rep(10.1,453)
Mnat_NSH_ch_easy$temp2009=rep(15.1,453)
Mnat_NSH_ch_easy$temp2010=rep(12.1,453)
Mnat_NSH_ch_easy$temp2011=rep(19.1,453)
Mnat_NSH_ch_easy$temp2012=rep(10.1,453)
Mnat_NSH_ch_easy$temp2013=rep(13.1,453)
Mnat_NSH_ch_easy$temp2014=rep(10.1,453)
Mnat_NSH_ch_easy$temp2015=rep(15.1,453)
Mnat_NSH_ch_easy$temp2016=rep(10.1,453)
Mnat_NSH_ch_easy$temp2017=rep(18.1,453)
Mnat_NSH_ch_easy$temp2018=rep(10.1,453)
Mnat_NSH_ch_easy$temp2019=rep(12.1,453)
Mnat_NSH_ch_easy$temp2020=rep(10.1,453)
Mnat_NSH_ch_easy$temp2021=rep(11.1,453)

Mnat.NSH.ch.easy.processed=process.data(Mnat_NSH_ch_easy,model="CJS",begin.time=2002,groups=c("MA","colony"))
Mnat.NSH.ch.easy.ddl=make.design.data(Mnat.NSH.ch.easy.processed)


Phi.temp=list(formula=~temp)

Phi.t<-mark(Mnat.NSH.ch.easy.processed, Mnat.NSH.ch.easy.ddl, model.parameters = list(Phi=Phi.temp, p=p.dot), adjust=TRUE)

predictions=covariate.predictions(Phi.t,data=data.frame(Temp2002=10:20),indices=1)$estimates
with(predictions,
     {
       plot(10:20,estimate,xlab="Rain",ylab="Survival",ylim=c(0,1))
       lines(10:20,lcl,lty=2)
       lines(10:20,ucl,lty=2)
     })



all estimates are the same.

Code: Select all
predictions$estimate
 [1] 0.8452862 0.8452862 0.8452862 0.8452862 0.8452862 0.8452862 0.8452862 0.8452862 0.8452862 0.8452862 0.8452862


I have no idea why :( even it there's no effect, the estimates shouldn't be all the same for each value?!

Tank you
best
Bianca
Mnat
 
Posts: 18
Joined: Wed Apr 10, 2019 4:28 am

Re: Individual covariate plotting

Postby jlaake » Mon Nov 01, 2021 2:04 pm

Below is from the help on covariate.predictions

The argument data is a dataframe containing values for the covariates used in the models. The names for the fields should match the names of the covariates used in the model.


size.seq is not the same as size

Now maybe I should have a message that fields in data do not match covariates, but it helps if you read the documentation especially when you are having a problem.
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Re: Individual covariate plotting

Postby Mnat » Tue Nov 02, 2021 2:55 am

ok, problem solved!
Thank you!
Mnat
 
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