Package to analyse population time series (trend analysis)

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Package to analyse population time series (trend analysis)

Manuel Spínola-2
Dear list members,

What is the appropriate package to analyze population time series (trend
analysis) when you have one count per year.

Best,

Manuel

--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
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COSTA RICA
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Re: Package to analyse population time series (trend analysis)

Peter Solymos-2
Manuel,

There are few ecology focused packages besides ARIMA() and the forecast
package, for example:

- popbio (based mostly on the Matrix Population Models by Caswell (2001)
and Quantitative Conservation Biology by Morris and Doak (2002).

- PVAClone, that uses JAGS and is based on Nadeem, K., Lele S. R., 2012.
Likelihood based population viability analysis in the presence of
observation error. Oikos 121, 1656–1664.

I am sure there are other packages as well that I am not aware of...

Cheers,

Peter

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Alberta Biodiversity Monitoring Institute http://www.abmi.ca
Boreal Avian Modelling Project http://www.borealbirds.ca

On Wed, Oct 19, 2016 at 6:47 AM, Manuel Spínola <[hidden email]>
wrote:

> Dear list members,
>
> What is the appropriate package to analyze population time series (trend
> analysis) when you have one count per year.
>
> Best,
>
> Manuel
>
> --
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> [hidden email] <[hidden email]>
> [hidden email]
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río <https://sites.google.com/
> site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

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Re: Package to analyse population time series (trend analysis)

Philippi, Tom
In reply to this post by Manuel Spínola-2
Manuel--
The proper package depends entirely on what your data are: how many sites
you collect counts for, whether those sites are a probability sample over
an area or the only locations you are making inferences about (e.g., census
counts), whether those counts have Poisson error, overdispersion (e.g.,
aggregation) or zero-inflation (e.g., extra 0s from bad weather or bad
sites), imperfect detection, marked individuals, whether you expect a
linear or only monotonic trend, whether you have covariates that vary by
year (e.g., annual precipitation or winter NINO3.4), or or other aspects I
haven't yet dealt with.

A bit more information about what you have in terms of data, and about the
questions you are interested within the broad definition of "trend" might
get you informed answers.

Tom 2



On Wed, Oct 19, 2016 at 5:47 AM, Manuel Spínola <[hidden email]>
wrote:

> Dear list members,
>
> What is the appropriate package to analyze population time series (trend
> analysis) when you have one count per year.
>
> Best,
>
> Manuel
>
> --
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> [hidden email] <[hidden email]>
> [hidden email]
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río <https://sites.google.com/
> site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

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Re: Package to analyse population time series (trend analysis)

Manuel Spínola-2
Thank you very much to both.

I analyzing counts of flying Ara macaw over a bridge.  I could have the
data for 2 more sites, but essentially is one site.  There are monthly
counts, but I am planning to use the maximum count for each year.  These
are not census data, only counts with imperfect detection.  My goal is to
do a trend analysis for those counts, of course I know the limitation of
the data and I know that  the biological interpretation of the results will
be challenging.

Best,

Manuel



2016-10-19 12:05 GMT-06:00 Philippi, Tom <[hidden email]>:

> Manuel--
> The proper package depends entirely on what your data are: how many sites
> you collect counts for, whether those sites are a probability sample over
> an area or the only locations you are making inferences about (e.g., census
> counts), whether those counts have Poisson error, overdispersion (e.g.,
> aggregation) or zero-inflation (e.g., extra 0s from bad weather or bad
> sites), imperfect detection, marked individuals, whether you expect a
> linear or only monotonic trend, whether you have covariates that vary by
> year (e.g., annual precipitation or winter NINO3.4), or or other aspects I
> haven't yet dealt with.
>
> A bit more information about what you have in terms of data, and about the
> questions you are interested within the broad definition of "trend" might
> get you informed answers.
>
> Tom 2
>
>
>
> On Wed, Oct 19, 2016 at 5:47 AM, Manuel Spínola <[hidden email]>
> wrote:
>
>> Dear list members,
>>
>> What is the appropriate package to analyze population time series (trend
>> analysis) when you have one count per year.
>>
>> Best,
>>
>> Manuel
>>
>> --
>> *Manuel Spínola, Ph.D.*
>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>> Universidad Nacional
>> Apartado 1350-3000
>> Heredia
>> COSTA RICA
>> [hidden email] <[hidden email]>
>> [hidden email]
>> Teléfono: (506) 8706 - 4662
>> Personal website: Lobito de río <https://sites.google.com/site
>> /lobitoderio/>
>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>
>


--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
[hidden email] <[hidden email]>
[hidden email]
Teléfono: (506) 8706 - 4662
Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

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