[R-sig-Geo] No neighbours in sample using spatcounts package in R

[chris english]

Nick,

Perhaps a pitch it to the maintainer and report back here? I was just
fooling around and it was the
structure of n.temp that was driving my approach, but each input finds its
way in thru the formula. Still
haven't had time to run this thru debugonce() as i am trying to flee a
non-country, god help me, with dogs.
And, where I know this actually does't help much, I'll try to look at it
later. Have to get off the turkish keyboard and
back to my own machine/

Chris



On Fri, Oct 21, 2016 at 1:46 AM, Nick van Doormaal <
nick.vandoormaal at gmail.com> wrote:

> Hi Chris,
>
> Thank you very much for your time and effort to help me out. Much
> appreciated!
> When I checked the structure of the example dataset, it seems that all the
> variables are numerical. That's why I thought that replacing all the NAs
> with 0s would be an okay way.
>
> library(spatcounts)
> data(sim.nmat)
> str(sim.nmat)
> 'data.frame':   100 obs. of  6 variables:
>  $ V1: num  1 2 3 4 5 6 7 8 9 10 ...
>  $ V2: num  11 12 13 14 15 16 17 18 19 20 ...
>  $ V3: num  2 1 2 3 4 5 6 7 8 9 ...
>  $ V4: num  0 3 4 5 6 7 8 9 10 0 ...
>  $ V5: num  0 0 0 0 0 0 0 0 0 0 ...
>  $ V6: num  2 3 3 3 3 3 3 3 3 2 ...
>
> str(n.temp)
> 'data.frame':   63 obs. of  6 variables:
>  $ V1: num  1 2 7 13 14 16 19 20 21 22 ...
>  $ V2: num  1 1 1 1 1 1 1 1 1 1 ...
>  $ V3: num  2 1 1 23 1 26 1 30 31 32 ...
>  $ V4: num  1 1 1 1 13 1 1 19 22 21 ...
>  $ V5: num  1 1 1 14 1 1 20 1 1 23 ...
>  $ V6: num  1 1 0 2 1 1 1 2 2 3 ...
>
> I think it has something to do with the combination of nmat (ntemp) and
> gmat (gtemp)...but I can't really figure out how or why.
>
> On 20 October 2016 at 12:20, chris english <englishchristophera at gmail.com>
> wrote:
>
>> Nick,
>>
>> I get the same error running your code.
>>
>> set.seed(987654321)
>>
>> library(spatcounts)
>> data("sim.Yin")
>> data("sim.fm.X")
>> data("sim.gmat")
>> data("sim.nmat")
>> data("sim.region")
>> AllData <- cbind(sim.Yin, sim.region, sim.fm.X)
>> colnames(AllData)[1:2] <- c("Yin", "Region")
>>
>> idx <- sample(1:nrow(AllData), 100, replace=TRUE)
>> newdata.df <- AllData[idx,]
>> newdata.df <- newdata.df[order(newdata.df$Region),]
>> X <- as.data.frame(newdata.df[,3:4])
>> region <- as.data.frame(newdata.df$Region)
>> colnames(region) <- "V1"
>> Yin <- as.data.frame(newdata.df$Yin)
>>
>> temp.idx <- sort(unique(newdata.df$Region))
>> g.temp <- sim.gmat[temp.idx,temp.idx]
>>
>> TotalN <- rowSums(g.temp) ##CHECK IF THERE ARE ZEROS PRESENT
>> > is.element(0, n.temp$V6)
>> [1] TRUE # after a few run thru's of idx to is.element
>>
>> n.temp <- sim.nmat[temp.idx,]
>> n.temp$V2 <- temp.idx[match(n.temp$V2, temp.idx)]
>> n.temp$V3 <- temp.idx[match(n.temp$V3, temp.idx)]
>> n.temp$V4 <- temp.idx[match(n.temp$V4, temp.idx)]
>> n.temp$V5 <- temp.idx[match(n.temp$V5, temp.idx)]
>> n.temp$V6 <- TotalN
>>
>> > class(n.temp$V1)
>> [1] "numeric"
>> > class(n.temp$V2)
>> [1] "integer"
>> > class(n.temp$V3)
>> [1] "integer"
>> > class(n.temp$V4)
>> [1] "integer"
>> > class(n.temp$V5)
>> [1] "integer"
>> > class(n.temp$V6)
>> [1] "numeric"
>>
>> # here, essentially checking what NA might be replaced with by class
>> # and wondering if a small numeric is desirable (0.001), $V1 & $v6
>> # and your 0 for integers ($V2-V5)
>>
>> Well, a bunch of different tries and the error persists.
>>
>> > n.temp[is.na(n.temp)] <- 1
>> > n.temp$V6[7] <- 10
>> > n.temp$V6[24] <- 10
>> > n.temp$V6[28] <- 0.001
>> >
>> > n.temp$V6[28] <- 10
>>
>> > which(n.temp$V6 == 0)
>> integer(0)
>>
>>
>> > Yin.NB <- est.sc(Yin, ~ X[,1] + X[,2] -1,
>> + region, model="NB", g.temp, n.temp, totalit=10) ##ERROR
>> Error: NA/NaN/Inf in foreign function call (arg 1)
>>
>> So, i guess i'd do a debugonce(est.sc) and find out which foreign
>> function is disappointing or
>> disappointed by the inputs, but the culprit does not appear to be TotalN.
>>
>> HTH,
>>
>> Chris
>>
>>
>>
>> On Wed, Oct 19, 2016 at 4:01 PM, Nick van Doormaal <
>> nick.vandoormaal at gmail.com> wrote:
>>
>>> Dear list members,
>>>
>>> I'm trying to do a bootstrap of a spatial count model using the
>>> *spatcounts-package* in R. However, resampling with replacement may lead
>>> to
>>> "islands", because sometimes no neighbors will be selected. I believe
>>> this
>>> is causing the error message: Error: NA/NaN/Inf in foreign function call
>>> (arg 1). Can somebody confirm this if this indeed the case? If so, is
>>> there
>>> a way to get around it, so that I would still be able to carry out a
>>> bootstrap?
>>>
>>> Please find below the code to recreate the problem using the example
>>> dataset of the spatcounts package.
>>>
>>> Thank you for your time and I hope somebody can help me out a bit.
>>>
>>> ####START CODE#####
>>> set.seed(987654321)
>>>
>>> library(spatcounts)
>>>
>>> AllData <- cbind(sim.Yin, sim.region, sim.fm.X)
>>> colnames(AllData)[1:2] <- c("Yin", "Region")
>>>
>>> idx <- sample(1:nrow(AllData), 100, replace=TRUE)
>>> newdata.df <- AllData[idx,]
>>> newdata.df <- newdata.df[order(newdata.df$Region),]
>>> X <- as.data.frame(newdata.df[,3:4])
>>> region <- as.data.frame(newdata.df$Region)
>>> colnames(region) <- "V1"
>>> Yin <- as.data.frame(newdata.df$Yin)
>>>
>>> temp.idx <- sort(unique(newdata.df$Region))
>>> g.temp <- sim.gmat[temp.idx,temp.idx]
>>>
>>> TotalN <- rowSums(g.temp) ##CHECK IF THERE ARE ZEROS PRESENT IN THIS
>>> VECTOR.##OTHERWISE RUN AGAIN UNTIL AT LEAST ONE ZERO
>>>
>>> n.temp <- sim.nmat[temp.idx,]
>>> n.temp$V2 <- temp.idx[match(n.temp$V2, temp.idx)]
>>> n.temp$V3 <- temp.idx[match(n.temp$V3, temp.idx)]
>>> n.temp$V4 <- temp.idx[match(n.temp$V4, temp.idx)]
>>> n.temp$V5 <- temp.idx[match(n.temp$V5, temp.idx)]
>>> n.temp$V6 <- TotalN
>>>
>>> n.temp[is.na(n.temp)] <- 0
>>>
>>> Yin.NB <- est.sc(Yin, ~ X[,1] + X[,2] -1,
>>> region, model="NB", g.temp, n.temp, totalit=10) ##ERROR
>>>
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>>>
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>>
>>
>

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