Re: [R-sig-Geo] rgdal travis error: configure: error: gdal-config not found or not executable.

2020-03-19 Thread Edzer Pebesma 
Maybe this:
https://github.com/edzer/sf_dep/blob/master/.travis.yml

On 3/19/20 8:26 PM, Joe Lewis wrote:
> Hi,
> 
> Thanks for the help.
> 
> I've incorporated some from sf's travis file, but it's still failing
> unfortunately.
> 
> # R for travis: see documentation at 
> https://docs.travis-ci.com/user/languages/r
> 
> language: R
> sudo: false
> cache: packages
> 
> r:
>   - oldrel
>   - release
>   - devel
> 
> repos:
>   CRAN: https://cran.rstudio.com
>   rforge: http://R-Forge.R-project.org
> 
> before_install:
>   - R -e 'install.packages("rgdal", repos="http://R-Forge.R-project.org";)'
> 
> apt_packages:
> - gdal-bin
> - libgdal-dev
> - libxml2-dev
> - libproj-dev
> - libprotobuf-dev
> - protobuf-compiler
> - libv8-3.14-dev
> - libjq-dev
> - libudunits2-dev
> - libproj-dev
> - libgeos-dev
> - libspatialite-dev
> - libgdal-dev
> 
> - libjson-c-dev
> 
> 
> https://travis-ci.org/github/josephlewis/leastcostpath/builds/664541703
> 
> Any ideas?
> 
> Thanks.
> 
> Kind regards,
> Joseph Lewis
> 
> On Wed, Mar 18, 2020 at 4:04 PM Edzer Pebesma 
> wrote:
> 
>> At least libgdal-dev and libproj-dev are missing. You can have a look at
>> https://github.com/r-spatial/sf/blob/master/.travis.yml (but that tries
>> to do quite a bit more).
>>
>> On 3/18/20 3:21 PM, Joe Lewis wrote:
>>> Hi,
>>>
>>> I'm testing a package using travis and I keep getting an error message
>>> about rgdal not being found or executable. I've been trying to piece
>>> together things I've found online but to no avail.
>>>
>>> https://travis-ci.org/github/josephlewis/leastcostpath/builds/663944787
>>>
>>> travis.yml
>>>
>>> # R for travis: see documentation at
>>> https://docs.travis-ci.com/user/languages/r
>>>
>>> language: R
>>> sudo: false
>>> cache: packages
>>>
>>> repos:
>>>   CRAN: https://cran.rstudio.com
>>>   rforge: http://R-Forge.R-project.org
>>>
>>> apt_packages:
>>> - gdal-bin
>>>
>>> before_install:
>>> install.packages("rgdal", repos="http://R-Forge.R-project.org";)
>>>
>>>
>>> Any help would be appreciated.
>>>
>>> Thanks.
>>>
>>> Kind regards,
>>> Joseph Lewis
>>>
>>>   [[alternative HTML version deleted]]
>>>
>>> ___
>>> R-sig-Geo mailing list
>>> R-sig-Geo@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>> --
>> Edzer Pebesma
>> Institute for Geoinformatics
>> Heisenbergstrasse 2, 48149 Muenster, Germany
>> Phone: +49 251 8333081
>> ___
>> R-sig-Geo mailing list
>> R-sig-Geo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
> 
>   [[alternative HTML version deleted]]
> 
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> 

-- 
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48149 Muenster, Germany
Phone: +49 251 8333081


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Re: [R-sig-Geo] rgdal travis error: configure: error: gdal-config not found or not executable.

2020-03-19 Thread Joe Lewis 
Hi,

Thanks for the help.

I've incorporated some from sf's travis file, but it's still failing
unfortunately.

# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r

language: R
sudo: false
cache: packages

r:
  - oldrel
  - release
  - devel

repos:
  CRAN: https://cran.rstudio.com
  rforge: http://R-Forge.R-project.org

before_install:
  - R -e 'install.packages("rgdal", repos="http://R-Forge.R-project.org";)'

apt_packages:
- gdal-bin
- libgdal-dev
- libxml2-dev
- libproj-dev
- libprotobuf-dev
- protobuf-compiler
- libv8-3.14-dev
- libjq-dev
- libudunits2-dev
- libproj-dev
- libgeos-dev
- libspatialite-dev
- libgdal-dev

- libjson-c-dev


https://travis-ci.org/github/josephlewis/leastcostpath/builds/664541703

Any ideas?

Thanks.

Kind regards,
Joseph Lewis

On Wed, Mar 18, 2020 at 4:04 PM Edzer Pebesma 
wrote:

> At least libgdal-dev and libproj-dev are missing. You can have a look at
> https://github.com/r-spatial/sf/blob/master/.travis.yml (but that tries
> to do quite a bit more).
>
> On 3/18/20 3:21 PM, Joe Lewis wrote:
> > Hi,
> >
> > I'm testing a package using travis and I keep getting an error message
> > about rgdal not being found or executable. I've been trying to piece
> > together things I've found online but to no avail.
> >
> > https://travis-ci.org/github/josephlewis/leastcostpath/builds/663944787
> >
> > travis.yml
> >
> > # R for travis: see documentation at
> > https://docs.travis-ci.com/user/languages/r
> >
> > language: R
> > sudo: false
> > cache: packages
> >
> > repos:
> >   CRAN: https://cran.rstudio.com
> >   rforge: http://R-Forge.R-project.org
> >
> > apt_packages:
> > - gdal-bin
> >
> > before_install:
> > install.packages("rgdal", repos="http://R-Forge.R-project.org";)
> >
> >
> > Any help would be appreciated.
> >
> > Thanks.
> >
> > Kind regards,
> > Joseph Lewis
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > R-sig-Geo mailing list
> > R-sig-Geo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
>
> --
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48149 Muenster, Germany
> Phone: +49 251 8333081
> ___
> R-sig-Geo mailing list
> R-sig-Geo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

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[R-sig-Geo] Fitting an Inhomogeneous Poisson model

2020-03-19 Thread ASANTOS via R-sig-Geo 
Dear R-Sig-Geo members,

I've like to fitting an Inhomogeneous Poisson model and I have one 
question about better approaches and/or steps order for this.

### Simulating Inhomogeneous Poisson process
library(spatstat)
cI <- rpoispp(function(x, y) {200 * x^2}, lmax = 1000)
cII <- rpoispp(function(x, y) {50 * y^2}, lmax = 1000)
cIII <- rpoispp(function(x,y) {100 * exp(-3*x)}, lmax = 1000)
ant<-superimpose(cI=cI,cII=cII,cIII=cIII)

#Fitting a Poisson model with an intensity that is log-linear in the 
cartesian coordinates with marks
m1<-ppm(ant, ~x + y + marks) # Allows different (constant) intensity for 
each category

#Now I fitting a Inhomogeneous Poisson model with an intensity that is 
log-quadratic in the cartesian coordinates
#with marks

m2<-ppm(ant, ~polynom(x,y,2) + marks)

#Comparing the models
anova(m1,m2,test="Chi")
#Pr(>Chi) = 0.8497 No difference and I choose the more parsimonious 
model m1.

#But if I make the models coefficients inspection:
m1#First model
#� Estimate� S.E.� CI95.lo��� CI95.hi Ztest� Zval
#(Intercept)� 3.0370358 0.3075106� 2.434326133� 3.6397455�� *** 9.876199
#x��� 1.3466820 0.3453355� 0.669836907� 2.0235272�� *** 3.899634
#y��� 0.6497591 0.3338675 -0.004609147� 1.3041274 1.946159
#markscII��� -1.4190842 0.2877424 -1.983048959 -0.8551194�� *** -4.931787
#markscIII�� -0.6306268 0.2154810 -1.052961828 -0.2082918��� ** -2.926601
m2 #Second model
#�� Estimate� S.E.�� CI95.lo��� CI95.hi Ztest��� Zval
#(Intercept)� 3.31439533 0.6095378� 2.119723� 4.5090674�� *** 5.43755529
#x��� 0.05883185 1.5736189 -3.025405� 3.1430683 0.03738634
#y��� 0.53037435 1.5536416 -2.514707� 3.5754559 0.34137497
#I(x^2)�� 1.16253158 1.2939978 -1.373658� 3.6987207 0.89840303
#I(x * y) 0.04678026 1.1589111 -2.224644� 2.3182043 0.04036570
#I(y^2)�� 0.08747001 1.2903205 -2.441512� 2.6164518 0.06778937
#markscII��� -1.41908418 0.2877424 -1.983049 -0.8551194�� *** -4.93178655
#markscIII�� -0.63062682 0.2154810 -1.052962 -0.2082918��� ** -2.92660056

I was so astonished with the no significance of I(x^2) by Ztest and my 
question is
whats is the better workflow for improve models of this nature:

1) Try the new models with several cartesian coordinates combinations 
and degrees (first),
2) Try the new models with pair-wise comparison between levels (marks) 
(second),
3) Comparing with null model.

or another approach and/or step order?

-- 
Alexandre dos Santos
Geotechnologies and Spatial Statistics applied to Forest Entomology
Instituto Federal de Mato Grosso (IFMT) - Campus Caceres
Caixa Postal 244 (PO Box)
Avenida dos Ramires, s/n - Vila Real
Caceres - MT - CEP 78201-380 (ZIP code)
Phone: (+55) 65 99686-6970 / (+55) 65 3221-2674
Lattes CV: http://lattes.cnpq.br/1360403201088680
OrcID: orcid.org/-0001-8232-6722
ResearchGate: www.researchgate.net/profile/Alexandre_Santos10
Publons: https://publons.com/researcher/3085587/alexandre-dos-santos/
--


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