character in
the vector (pch= c(1, 3)) to the first level in the grouping variable
(year).
Thank you very much in advance.
Best,
Manuel Spínola
--
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
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Apartado 1350-3000
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of analysis?
I am trying to get the confidence interval of the difference (I am not
interested in the t and P values).
Thank you very much in advance.
Best,
Manuel Spínola
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Apartado 1350-3000
be meaningless in
method bray
2: In vegdist(avesp.esp, dist = jaccard) : missing values in results
I have sites (point counts) without species, is it a problem?
Thank you very much in advance.
Best,
Manuel Spínola
--
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Instituto Internacional en Conservación y Manejo de Vida
to
interpret the resulting plot in the same way that a constrained
ordination, for example CCA?
Thank you very much in advance.
Best,
Manuel
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Universidad Nacional
Apartado 1350-3000
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Dear Jacob,
May be you can use cluster sampling or adaptive cluster sampling
(Design-based estimation) to get a density estimate.
Best,
Manuel Spínola
Capelle, Jacob wrote:
Dear all,
I have a kind of a theoretical question from which I hope it might interest you and hopefully can help me
value when analyzing frequencies in R?
Is it possible to obtain standardized Pearson residuals in this situation?
Thank you very much in advance.
Best,
Manuel Spínola
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Message-
From: Manuel Spínola
Sent: 02.07.2009, 23:17
To: r-sig-ecology@r-project.org
Subject: [R-sig-eco] Statistics applied to Geography using R
Dear list members,
Do you know any references for statistics applied to geography that are
in some way related to R?
I think it will be ok also
be the subject)
Year: from 2002 to 2007
My data set is unbalanced (the counties do not have information for all
the years).
Thank you very much in advance.
Best,
Manuel Spínola
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
/software.html
Best,
Manuel Spínola
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax: (506) 2237-7036
Peter Solymos wrote:
Dear
, is this the way to analyze a repeated measure design in R?
The counties (localidad) are all the county that I am interested, is
that still random?
Thank you very much in advance.
Best,
Manuel Spínola
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida
Dear list members,
Is there any function to do zero-truncated poisson or zero-truncated
negative binomail in R?
Thank you very much in advance.
Best,
Manuel Spínola
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350
, Adjusted R-squared: 0.4525
F-statistic: 5.545 on 2 and 9 DF, p-value: 0.02696
Any idea why?
Best,
Manuel Spínola
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
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mspin...@una.ac.cr
mspinol
with a saturated model?
How is the way to model this type of data (1 categorical response
variable and 6 explanatory factors)?
I also used classification trees for the data but the error is bigger
after the first split.
Best,
Manuel
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax: (506) 2237-7036
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'.' 0.1 ' ' 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 433.04 on 319 degrees of freedom
Residual deviance: 424.30 on 314 degrees of freedom
(25 observations deleted due to missingness)
AIC: 436.3
Number of Fisher Scoring iterations: 4
--
Manuel Spínola
for each variable in the model.
Thank you very much in advance.
Best,
Manuel
--
Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax
the se (and
the confidence limits) for different predictors in the model to obtain
a plot for each predictor like the effect package does.
Thank you very much in advance.
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad
at each site
(i.e., the number of visits to the sites varies)?
I am trying to get also an estimate of the detection probability, but it
seems that this parameter is not included in those functions.
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida
message:
In distfun(comm, method = distance, ...) :
data have empty species which influence the results im method raup
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin
your data. That is
only informational, and not an error.
Cheers, Jari Oksanen
--
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277
) will influence your data.
That is
only informational, and not an error.
Cheers, Jari Oksanen
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Instituto
Dear list members,
I would like to include sites names with blank spaces in an ordiplot for
an nmds (in vegan).
How I do that?
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA
Gavin and Jari, thank you very much.
Actually, I am interested in both, sites and species. I have 3000
species (tropical forest trees) and I am trying to read the txt file
with read.table. I tried also read.delim, but I don't know how to bring
the sites names in the plot. I guess now I have
Thank you very much Gavin.
I understand now.
Best,
Manuel
On 01/04/2011 05:29 a.m., Gavin Simpson wrote:
On Fri, 2011-04-01 at 05:14 -0600, Manuel SpÃnola wrote:
Gavin and Jari, thank you very much.
Actually, I am interested in both, sites and species. I have 3000
species (tropical
for influencia.
How can I make a complete new object with only the observations for
AID and that the only level for influencia is indeed AID?
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
was creating a new data frame with only AID as a
level for influencia.
How can I make a complete new object with only the observations for
AID and that the only level for influencia is indeed AID?
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida
Thank you Christian.
Following your suggestion I got the following result,
pa2 = subset(pa, influencia==AP)
pa2$influencia-as.factor(pa2$influencia)
levels(pa$influencia)
[1] AID AII AP
On 24/04/2011 07:42 a.m., Christian Parker wrote:
You are creating a new object, but the columns that
Thank you very much Gustavo.
That works.
Manuel
On 24/04/2011 08:30 a.m., Gustavo Carvalho wrote:
pa2- subset(pa, influencia==AP)
pa2$influencia- factor(pa2$influencia)
levels(pa2$influencia)
On Sun, Apr 24, 2011 at 11:24 AM, Manuel SpÃnolamspinol...@gmail.com
wrote:
Thank you very
Thank you for all the responses.
Is there a way to do a complete data set from an object in R?
I have a data set with more than 3000 columns.
The subsetting is ok but it could be dangerous if you are using other
factors to do some analysis as you need to specify the levels for all
your factors
AM, Manuel Spínola wrote:
Thank you for all the responses.
Is there a way to do a complete data set from an object in R?
I have a data set with more than 3000 columns.
The subsetting is ok but it could be dangerous if you are using other
factors to do some analysis as you need to specify
)
How can I change the names of the levels of the 2 conditioning variables in
the strip?
I want to use: Enfriado and No enfriado instead of chilled and
nonchilled for Treatmente, and A and B instead of Quebec and
Mississippi for Type.
Thank you very much in advance.
Manuel
--
*Manuel Spínola
* Treatment,
groups = Plant, type = b, lty = rep(1:3, 4), strip = strip.custom(
var.name = c(Type,
Treatment ), strip.names = c(T,T), style = 3), data = CO2)
Johannes
On Fri, Jun 24, 2011 at 8:18 AM, Manuel Spínola mspinol...@gmail.com
wrote:
Dear list members,
I am trying the following
)
1 2
1.0460148 0.9468983
Thank you very much in advance.
Best,
Manuel
--
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506
-- Forwarded message --
From: Manuel Spínola mspinol...@gmail.com
Date: 2012/3/11
Subject: Re: [R-sig-eco] Landscape ecology in R
To: Sarah Goslee sarah.gos...@gmail.com
Thank you Sarah and Stephen,
I am in contact with Paul Galpern who developed some tutorials on landscape
Sefick sas0...@auburn.edu
Third hit in a google search for: landscape ecology R
http://nricaribou.cc.umanitoba.ca/R/
On 03/09/2012 04:53 PM, Manuel Spínola wrote:
Dear list members,
I am looking for any reference or material on landscape ecology analysis in
R.
Thank you very much
is that the practitioner that will be presented the results
won't be very happy with
regression-cofficients, model-comparisons, AIC and friends. contrary,
ctree would yield an intuitive and simple result which i would fancy for
this purpose!
yours,
kay
2012/3/21 Manuel Spínola mspinol...@gmail.com
? Is R not capable of doing the same type of
analysis?
Any input will be appreciated.
Best,
Manuel
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Thank you very much Jari,
Using weakties = FALSE it works very well. The results are similar to the
book.
Best,
Manuel
e.mds = metaMDS(especies, distance = bray, weakties = FALSE)
Run 0 stress 0.1088505
Run 1 stress 0.113103
Run 2 stress 0.1356066
Run 3 stress 0.1088552
... procrustes: rmse
Dear list members,
Is there any package (and function) to assess carrying capacity for
biological population?
Best,
Manuel
--
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
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mspin
2012/6/28 Manuel Spínola mspinol...@gmail.com:
Dear list members,
Is there any package (and function) to assess carrying capacity for
biological population?
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
item2 5 4
item3 3 5
item3 4 3
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax
I guess I am not setting the condition in a proper way.
Best,
Manuel
--
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax
(2, 10), y=c(2, 0))
xx[xx!=0]=1
xx
x y
1 1 1
2 1 0
Bret
On 7/3/2012 8:12 PM, Manuel Spínola wrote:
Dear list members,
I want to recode a data frame but do it for several variables at the same
time. I want to give all the values or equal than 1 a value of 1 and
all
the remaining
], yy)
bret
On 7/3/2012 9:18 PM, Manuel Spínola wrote:
Thank you Bret.
What if I need to leave out some variables from my data frame. I have 22
variables and I need to leave the 2 first variables out of the condition.
Best,
Manuel
2012/7/3 Bret Collier b...@tamu.edu
Manuel
Dear list members,
Is there any simple example for teaching purposes on how to use R to
analyze a time series in a biological monitoring context?
Best,
Manuel
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
:05 AM, Manuel Spínola wrote:
Dear list members,
Is there any simple example for teaching purposes on how to use R to
analyze a time series in a biological monitoring context?
Best,
Manuel
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,] 0 0 0 0 0 0
[2,] 0 1 0 0 1 0
[3,] 0 0 0 0 0 0
[4,] 0 1 1 1 1 1
[5,] 1 1 1 0 1 0
[6,] 1 0 0 0 0 1
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto
Adrian,
You can take a look at the R package wild1.
Best,
Manuel Spínola
2012/9/6 AdRiAnA HuMaNeS adrihuma...@yahoo.com
Hi Rlisters:
I'm doing survival analysis comparing 8 populations. I've used the
survdiff function for comparing survival curves and the result I obtained
says
Alberta, T6G 2E9, Canada AB
soly...@ualberta.ca, Ph 780.492.8534, http://psolymos.github.com
Alberta Biodiversity Monitoring Institute, http://www.abmi.ca
Boreal Avian Modelling Project, http://www.borealbirds.ca
2012/10/25 Manuel Spínola mspinol...@gmail.com:
Dear list members,
I want
)
val
[1] NA
Thank you very much in advance,
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono: (506) 2277-3598
Fax: (506) 2237
.: 1428117
Warning while fitting theta: iteration limit reached
2 x log-likelihood: -59.058
Best,
Manuel
--
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol
Postdoctoral Researcher, Ponciano Lab
Biology Department, University of Florida
http://people.biology.ufl.edu/mbrooks
On 3 Feb 2013, at 10:16 AM, Manuel Spínola wrote:
Dear list members,
I am fitting a negative binomial model but I get a very large dispersion
parameter. Why is that?
quine.nb2
Thank you very much to all that answered my question, some one of you asked
me to be more specific, here is my question again:
I hava a data frame:
col1 col2 col3 col4 col5 col6
01 1 0 ac
10 0 0 ad
01 1 1 bd
I want to
/Rcmdr/doc/Commander-ru.pdf':
Permission denied
Any idea how to solve this issue?
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.ac.cr
mspinol...@gmail.com
Teléfono
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Universidad Nacional
Apartado 1350-3000
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COSTA
Dear Bruce,
Besides any other problems I can see that you consider FA as a factor and
that could be a problem with your data set.
Manuel
2014-07-30 7:10 GMT-06:00 Bruce Miller batsnc...@gmail.com:
Hi all,
Sorry this is a bit long, but the explanation of what I want to do needs
to be clear
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 1
ble ~ occasion * treatment + (occasion |
plot/subplot)
Is the model parameterization correct?
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.cr <mspin...@una
relationships?
Thank you very much in advance,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.cr <mspin...@una.ac.cr>
mspinol...@gmail.com
Teléfono: (506) 8706 - 4662
Pe
hics grDevices utils datasets methods base
>> >
>> > other attached packages:
>> > [1] mvpart_1.6-2
>> >
>> > loaded via a namespace (and not attached):
>> > [1] compiler_3.4.0
>>
>>
>> However, there are
8
>> >
>> > attached base packages:
>> > [1] stats graphics grDevices utils datasets methods base
>> >
>> > other attached packages:
>> > [1] mvpart_1.6-2
>> >
>> > loaded via a namespace (and not attached):
>
Thank you Ralf,
But I guess is not going to be newer versions and could be incompatible
with newer version of R, so at some moment there will be no accessibility
to the package.
Manuel
2017-06-24 5:25 GMT-06:00 Ralf Schäfer :
> Dear Manuel
>
> despite it has been
the effect size (the difference between estimates) with
the 95% confidence limits.
Is there any package that allow me to do that?
Best,
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.cr <mspin...@una.ac.cr>
mspinol...@gmail.com
Teléfono: (506) 8706 - 4662
Personal website: Lobito de río <https://sites.google
0.6, 0.9)
table <- data.frame(columna1, columna2, columna3)
kable(table)
How can I include the math symbol in the table?
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.cr
paste("<= ", c(0.3, 0.5, 0.8))
> column3 <- paste("<= ", c(0.5, 0.6, 0.9))
>
> table <- data.frame(column1, column2, column3)
>
> table
>
>
> "
>
>
>
> Watch out not to mix English with Spanish while scripting fast.
>
>
> Pura Vida!
ANALYSIS OF SPATIAL ECOLOGICAL DATA USING
> R #MVSP
> Prof. Pierre Legendre, Dr. Olivier Gauthier - Date and location to be
> confirmed
>
>
> --
> Oliver Hooker PhD.
> PR statistics
>
> 2017 publications -
>
> Ecosystem size predicts eco-morphological variab
d location to be
> confirmed
>
>
> --
> Oliver Hooker PhD.
> PR statistics
>
> 2017 publications -
>
> Ecosystem size predicts eco-morphological variability in post-glacial
> diversification. Ecology and Evolution. In press.
>
> The physiological costs of prey switching reinforce foraging
.
Is the following model parameterization appropriate in the lme4 package:
mod_adi_01 <- lmer(ADI ~ Season*CoverType + (1 | Point) + (1 | Month) + (1
| Day) + (1 | Hour), data = df_01, REML = FALSE)
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silves
demy of Science
> http://www.bugsmapsandmath.com
>
> ---*/
>
> ________
> From: R-sig-ecology on behalf of
> Manuel Spínola
> Sent: Thursday, June 18, 2020 1:20 PM
> To: r-sig-ecology@r-proj
0 a las 11:41, Rich Shepard ()
escribió:
> On Thu, 18 Jun 2020, Manuel Spínola wrote:
>
> > I teach statistics to students in ecology and environmental sciences
> > fields and I would like to know if you could point me in the right
> > direction of sources of ecolog
Thank you very much Rich.
Manuel
El jue., 18 jun. 2020 a las 12:11, Rich Shepard ()
escribió:
> On Thu, 18 Jun 2020, Manuel Spínola wrote:
>
> > I teach mainly to wildlife ecology students.
>
> Manuel,
>
> I'm a stream ecologist/fluvial geomorphologist but have run
nation of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> ///////////
>
> <https://www.inbo.be>
Thank you very much Mollie.
Manuel
El jue., 18 jun. 2020 a las 14:12, Mollie Brooks ()
escribió:
>
>
> On 18Jun 2020, at 19:58, Manuel Spínola wrote:
>
> Thank you very much Rich.
>
> Yes, you are right, is a very broad spectrum.
>
> I teach mainly to wildlife ecolog
and multivariate
statistics.
Manuel Spínola
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.cr
mspinol...@gmail.com
Teléfono: (506) 8706 - 4662
Personal website: Lobito de río
842 | mike.mahoney@gmail.com
>
>
> On Thu, Jun 18, 2020 at 2:14 PM Manuel Spínola
> wrote:
>
>> Thank you very much Rich.
>>
>> Manuel
>>
>> El jue., 18 jun. 2020 a las 12:11, Rich Shepard (<
>> rshep...@appl-ecosys.com>)
>>
(1 | location) + (1 | day/hour/min), data =
my_data)
Thank you very much in advance.
Manuel
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspin...@una.cr
mspinol...@gmail.com
Teléfono: (
HTML version deleted]]
>
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>
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U
than empirical estimation form a "continuous"
> datastream of limited duration. That approach also helps me think about
> the spatial concordance of the correlated errors: which are site-specific,
> which are concordant across all of the sites.
>
> Tom
>
> -Original Messa
to take into account the temporal
autocorrelation of the data, but I am asking to optimize the data
collection, before modeling.
Thank you very much in advance.
Manuel
--
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Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado
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