[R-sig-Geo] Simple Ripley's CRS test for market point patters

[ASANTOS]

Thanks for your help Marcelino e for the careful explanation Rolf Turner 
and so sorry about my post script configuration, I expected that I 
solved that in my new post.

First my variable area is a marked point (attribute or auxiliary 
information about my point process - page 7 and not a spatial covariate, 
effect in the outcome of my experimental area - page 50). Based in this 
information, my hypophyses is that the *size of ant nests* a cause of 
ecological intraspecific competition for resources (such as food and 
territory) *have different patterns of spatial distribution*, for this:

#Packages
require(spatstat)
require(sp)

# Create some points that represents ant nests

xp<-c(371278.588,371250.722,371272.618,371328.421,371349.974,
371311.95,371296.265,371406.46,371411.551,371329.041,371338.081,
371334.182,371333.756,371299.818,371254.374,371193.673,371172.836,
371173.803,371153.73,371165.051,371140.417,371168.279,371166.367,
371180.575,371132.664,371129.791,371232.919,371208.502,371289.462,
371207.595,371219.008,371139.921,371133.215,371061.467,371053.69,
371099.897,371108.782,371112.52,371114.241,371176.236,371159.185,
371159.291,371158.552,370978.252,371120.03,371116.993)

yp<-c(8246507.94,8246493.176,8246465.974,8246464.413,8246403.465,
8246386.098,8246432.144,8246394.827,8246366.201,8246337.626,
8246311.125,8246300.039,8246299.594,8246298.072,8246379.351,
8246431.998,8246423.913,8246423.476,8246431.658,8246418.226,
8246400.161,8246396.891,8246394.225,8246400.391,8246370.244,
8246367.019,8246311.075,8246255.174,8246255.085,8246226.514,
8246215.847,8246337.316,8246330.197,8246311.197,8246304.183,
8246239.282,8246239.887,8246241.678,8246240.361,8246167.364,
8246171.581,8246171.803,8246169.807,8246293.57,8246183.194,8246189.926)

#Now I have the size of each nest (marked process)

area<-c(117,30,4,341,15,160,35,280,108,168,63,143,2,48,182,42,
88,56,27,156,288,45,49,234,72,270,91,40,304,56,35,4,56.7,9,4.6,
105,133,135,23.92,190,12.9,15.2,192.78,104,255,24)

# Make a countour for the window creation
W <- convexhull.xy(xp,yp)


# Class of nests size - large, medium and small
acat <- cut(area,breaks=c(-Inf,25,55,Inf),right=FALSE, 
labels=c("s","m","l"))

#Create a ppp object

syn.ppp <- ppp(x=xp,y=yp,window=W, marks=acat)

# Test intensity hypothesis

f1 <- ppm(syn.ppp) # Same (constant) intensity for each area category.
f2 <- ppm(syn.ppp ~ marks) # Allows different (constant) intensity for 
each area category.
anova(f1,f2,test="Chi")

#0.002015 ** OK, the hypothesis that the intensities are the same was 
reject, but intensities is not the question.

Based in my initial hypothesis, I've like to show envelopes and observed 
values of the use of some function for the three point patters (large, 
medium and small ant nest size)under CSR. And for this I try to:

kS<-envelope(syn.ppp[syn.ppp$acat=="s"], nsim=99,fun=Kest)

plot(kS,lwd=list(3,1,1,1), main="")

kM<-envelope(syn.ppp[syn.ppp$acat=="m"], nsim=99,fun=Kest)

plot(kM,lwd=list(3,1,1,1), main="")

kL<-envelope(syn.ppp[syn.ppp$acat=="l"], nsim=99,fun=Kest)

plot(kL,lwd=list(3,1,1,1), main="")

But doesn't work yet. My approach now sounds correct?

Thanks in advanced,

Alexandre


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Alexandre dos Santos
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Em 23/07/2019 22:00, Rolf Turner escreveu:
>
> Thanks to Marcelino for chiming in on this.?? I should have responded 
> earlier, but was "busy on a personal matter".
>
> To add to what Marcelino said:
>
> (1) Your post in HTML was horribly garbled and a struggle to read. 
> *PLEASE* set your email client so that it does *NOT* post in HTML when 
> posting to this list.
>
> (2) A very minor point:?? Your construction of "syn.ppp" was 
> unnecessarily complicated and convoluted.?? You could simply do:
>
> ?????? syn.ppp?? <- ppp(x=xp,y=yp,window=W,marks=area)
>
> (3) You appear to be confused as to the distinction between "marks" 
> and "covariates".???? These are superficially similar but conceptually 
> completely different.?? What you are dealing with is *marks*.?? There are
> no covariates involved.?? See [1], p. 147.
>
> (4) Your calls to envelope() are mal-formed; the expression "area >= 
> 0" and "area < 25" will be taken as the values of "nrank" and ... who 
> knows what??? Did you not notice the warning messages you got about 
> there being something wrong with "nrank"?
>
> You are being hopelessly na??ve in expecting envelope() to interpret 
> "area >= 0" and "area < 25" in the way you want it to interpret them.
> The spatstat package does not read minds.
>
> Marcelino has shown you how to make a proper call.
>
> (5) Since you are interested in categorising "area" into groups, 
> rather than being interested in the *numerical* value of area, you 
> should do the categorisation explicitly:
>
> acat <- cut(area,breaks=c(-Inf,25,55,Inf),right=FALSE,
> ?????????????????????? labels=c("s","m","l")
> # right=FALSE since you want "area < 25" rather than
> # "area <= 25" --- although this makes no difference for the
> # area values actually used.
>
> syn.ppp <- ppp(x=xp,y=yp,marks=acat)
>
> (6) It is not clear to me what your "research question" is.?? Do you 
> want to test whether the intensities differ between the area 
> categories? Unless my thinking is hopelessly confused, this has 
> nothing to do with (or at least does not require the use of) the 
> envelope() function:
>
> f1 <- ppm(syn.ppp) # Same (constant) intensity for each area category.
> f2 <- ppm(syn.ppp ~ marks) # Allows different (constant) intensity
> ???????????????????????????????????????????????????? # for each area category.
> anova(f1,f2,test="Chi")
>
> This test (not surprisingly) rejects the hypothesis that the 
> intensities are the same; p-value = 0.0020.
>
> If this is not the hypothesis that you are interested in, please 
> clarify your thinking and your question, and get back to us.
>
> cheers,
>
> Rolf Turner
>

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