Filtering a set of points in a "ppp" object by distance using marks - R-SIG-Geo

ASANTOS

Tue, Sep 15, 2020 1:52 PM #

Dear R-Sig-Geo Members,

I'd like to find any way to filtering a set of points in a "ppp" object by minimum distance just only between different marks. In my example:

#Package
library(spatstat)

#Point process example - ants
data(ants)
ants.ppp<-ppp(x=ants$x,y=ants$y,marks=rep("antNests",length(ants$x)),window=Window(ants))


# Create a artificial point pattern - termites
termites <- rpoispp(0.0005, win=Window(ants))
termites.ppp<-ppp(x=termites$x,y=termites$y,marks=rep("termiNests",length(termites$x)),window=Window(ants))


#Join ants.ppp and termites.ppp
insects.ppp<-superimpose(ants.ppp,termites.ppp)


#If I try to use subset function:

subset(insects.ppp, pairdist(insects.ppp) > 20 & marks=="termiNests")

#Marked planar point pattern: 223 points #marks are of storage type 
?character? #window: polygonal boundary #enclosing rectangle: [-25, 803] 
x [-49, 717] units (one unit = 0.5 feet) #Warning message: #In ppp(X[, 
1], X[, 2], window = win, marks = marx, check = check) : # 70751 out of 
70974 points had NA or NaN coordinate values, and were discarded

Not the desirable result yet, because I'd like to calculate just only the > 20 "termiNests" to "antNests" marks and not the "termiNests" with "termiNests" too.

Please any ideas?

Thanks in advanced,

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/0000-0001-8232-6722
ResearchGate: www.researchgate.net/profile/Alexandre_Santos10
Publons: https://publons.com/researcher/3085587/alexandre-dos-santos/
--


	[[alternative HTML version deleted]]

Marcelino de la Cruz Rot

Wed, Sep 16, 2020 12:18 AM #

Hi Alexandre,

may be this?


ddd <- nndist(insects.ppp, by=factor(insects.ppp$marks))
subset(insects.ppp,? marks=="termiNests" & ddd[,"termiNests"] >20)


Cheers,

Marcelino


El 15/09/2020 a las 22:52, ASANTOS via R-sig-Geo escribi?:

Marcelino de la Cruz Rot
Depto. de Biolog?a y Geolog?a
F?sica y Qu?mica Inorg?nica
Universidad Rey Juan Carlos
M?stoles Espa?a

Marcelino de la Cruz Rot

Wed, Sep 16, 2020 3:15 AM #

Sorry, I meant to say

subset(insects.ppp, marks=="termiNests" & ddd[,"antNests"] >20)

El 16/09/2020 a las 9:18, Marcelino de la Cruz Rot escribi?:

Marcelino de la Cruz Rot
Depto. de Biolog?a y Geolog?a
F?sica y Qu?mica Inorg?nica
Universidad Rey Juan Carlos
M?stoles Espa?a

ASANTOS

Wed, Sep 16, 2020 5:04 AM #

Hi Marcelino,

Thanks, I just make a little change in your code:

ddd <- nndist(insects.ppp, by=factor(insects.ppp$marks))
subset(insects.ppp,? marks=="termiNests" & ddd[,"antNests"] >20)

I put `ddd[,"antNests"] >20` despite `ddd[,"termiNests"] >20` because I 
need "termiNests" mark far 20 units to each "antNests"

Best wishes,

Alexandre

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/0000-0001-8232-6722
ResearchGate: www.researchgate.net/profile/Alexandre_Santos10
Publons: https://publons.com/researcher/3085587/alexandre-dos-santos/
--

Em 16/09/2020 03:18, Marcelino de la Cruz Rot escreveu:
> Hi Alexandre,
>
> may be this?
>
>
> ddd <- nndist(insects.ppp, by=factor(insects.ppp$marks))
> subset(insects.ppp,? marks=="termiNests" & ddd[,"termiNests"] >20)
>
>
> Cheers,
>
> Marcelino
>
>
> El 15/09/2020 a las 22:52, ASANTOS via R-sig-Geo escribi?:
>> Dear R-Sig-Geo Members,
>>
>> I'd like to find any way to filtering a set of points in a "ppp" 
>> object by minimum distance just only between different marks. In my 
>> example:
>>
>> #Package
>> library(spatstat)
>>
>> #Point process example - ants
>> data(ants)
>> ants.ppp<-ppp(x=ants$x,y=ants$y,marks=rep("antNests",length(ants$x)),window=Window(ants)) 
>>
>>
>>
>> # Create a artificial point pattern - termites
>> termites <- rpoispp(0.0005, win=Window(ants))
>> termites.ppp<-ppp(x=termites$x,y=termites$y,marks=rep("termiNests",length(termites$x)),window=Window(ants)) 
>>
>>
>>
>> #Join ants.ppp and termites.ppp
>> insects.ppp<-superimpose(ants.ppp,termites.ppp)
>>
>>
>> #If I try to use subset function:
>>
>> subset(insects.ppp, pairdist(insects.ppp) > 20 & marks=="termiNests")
>>
>> #Marked planar point pattern: 223 points #marks are of storage type
>> ?character? #window: polygonal boundary #enclosing rectangle: [-25, 803]
>> x [-49, 717] units (one unit = 0.5 feet) #Warning message: #In ppp(X[,
>> 1], X[, 2], window = win, marks = marx, check = check) : # 70751 out of
>> 70974 points had NA or NaN coordinate values, and were discarded
>>
>> Not the desirable result yet, because I'd like to calculate just only 
>> the > 20 "termiNests" to "antNests" marks and not the "termiNests" 
>> with "termiNests" too.
>>
>> Please any ideas?
>>
>> Thanks in advanced,
>>
>

ASANTOS

Wed, Sep 16, 2020 5:05 AM #

Hi Marcelino,

Thanks so much, I just make a little change in your code:

ddd <- nndist(insects.ppp, by=factor(insects.ppp$marks))
subset(insects.ppp,? marks=="termiNests" & ddd[,"antNests"] >20)

I put `ddd[,"antNests"] >20` despite `ddd[,"termiNests"] >20` because I 
need "termiNests" mark far 20 units to each "antNests".

Best wishes,

Alexandre

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/0000-0001-8232-6722
ResearchGate: www.researchgate.net/profile/Alexandre_Santos10
Publons: https://publons.com/researcher/3085587/alexandre-dos-santos/
--

Em 16/09/2020 03:18, Marcelino de la Cruz Rot escreveu:
> Hi Alexandre,
>
> may be this?
>
>
> ddd <- nndist(insects.ppp, by=factor(insects.ppp$marks))
> subset(insects.ppp,? marks=="termiNests" & ddd[,"termiNests"] >20)
>
>
> Cheers,
>
> Marcelino
>
>
> El 15/09/2020 a las 22:52, ASANTOS via R-sig-Geo escribi?:
>> Dear R-Sig-Geo Members,
>>
>> I'd like to find any way to filtering a set of points in a "ppp" 
>> object by minimum distance just only between different marks. In my 
>> example:
>>
>> #Package
>> library(spatstat)
>>
>> #Point process example - ants
>> data(ants)
>> ants.ppp<-ppp(x=ants$x,y=ants$y,marks=rep("antNests",length(ants$x)),window=Window(ants)) 
>>
>>
>>
>> # Create a artificial point pattern - termites
>> termites <- rpoispp(0.0005, win=Window(ants))
>> termites.ppp<-ppp(x=termites$x,y=termites$y,marks=rep("termiNests",length(termites$x)),window=Window(ants)) 
>>
>>
>>
>> #Join ants.ppp and termites.ppp
>> insects.ppp<-superimpose(ants.ppp,termites.ppp)
>>
>>
>> #If I try to use subset function:
>>
>> subset(insects.ppp, pairdist(insects.ppp) > 20 & marks=="termiNests")
>>
>> #Marked planar point pattern: 223 points #marks are of storage type
>> ?character? #window: polygonal boundary #enclosing rectangle: [-25, 803]
>> x [-49, 717] units (one unit = 0.5 feet) #Warning message: #In ppp(X[,
>> 1], X[, 2], window = win, marks = marx, check = check) : # 70751 out of
>> 70974 points had NA or NaN coordinate values, and were discarded
>>
>> Not the desirable result yet, because I'd like to calculate just only 
>> the > 20 "termiNests" to "antNests" marks and not the "termiNests" 
>> with "termiNests" too.
>>
>> Please any ideas?
>>
>> Thanks in advanced,
>>
>