[R-sig-Geo] Calculate shortest distance between points belonging to different polygons
Thierry Onkelinx
thierry.onkelinx at inbo.be
Tue Feb 17 13:41:27 CET 2015
Can you provide a reproducible example?
The output of as.data.frame(nndist(randp.ppp, by = randp.ppp$Polygon_ID))
should be a data.frame with one row per point and one column per polygon.
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
2015-02-17 13:31 GMT+01:00 Ivan Palmegiani <pan.sapiens.it at gmail.com>:
> Dear Thierry,
>
> Thanks for your prompt reply!
> I must admit I'm not familiar with ddply(), I'd need further advice from
> you.
>
> > randp.ppp<-as.ppp(randp.df)
> > randp.hs.ppp
> marked planar point pattern: 100 points
> Mark variables: Point_ID, Polygon_ ID
> window: rectangle = [650602.2, 766311.2] x [7503238, 7607430] units
>
> > distance<-as.data.frame(nndist(randp.ppp, by = randp.ppp$Polygon_ID))
> > distance
> nndist(randp.ppp, by = randp.hs.ppp$Polygon_ID)
> 1 2579.42199
> 2 1391.88915
> 3 59.85628
> ...
> ...
> 98 955.26483
> 99 3166.00894
> 100 705.25663
>
> > distance$Origin<-as.factor(randp.df$Polygon_ID)
> > distance$Origin
> [1] 13 6 12 5 5 12 12 10 8 3 5 13 3 3 10 3 5 3 13 3 2 3 12
> 6 5 13 3 2 3 3 9 1 3 4 12 6 12 12 10 2 13 3 6 3 3 6 3 9
> 1
> ...
> [99] 12 12
> Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13
>
> > ddply(distance, "Origin", function(x){
> + ignore.vars<-c(levels(x$Origin)[x$Origin[1]], "Origin")
> + x<-x[,!colnames(x) %in% ignore.vars]
> + data.frame(
> + Distance = apply(x, 1, min),
> + Target = colnames(x)[apply(x, 1, which.min)]
> + )
> + })
> Error: dim(X) must have a positive length
>
> Sorry but I can't spot the problem.
>
> Sincerely,
>
> Ivan
>
>
> On 17-Feb-15 13:21, Thierry Onkelinx wrote:
>
> Here is an example using ddply() to do the aggregation
>
> library(spatstat)
> library(plyr)
> n <- 100
> set.seed(123)
> point <- matrix(runif(2 * n), ncol = 2)
> colnames(point) <- c("X", "Y")
> point <- data.frame(point, Polygon = factor(LETTERS[kmeans(point,
> 13)$cluster]))
> pattern <- as.ppp(point, W = owin(0:1, 0:1))
>
> distance <- as.data.frame(nndist(pattern, by = pattern$marks))
> distance$Origin <- point$Polygon
> ddply(distance, "Origin", function(x){
> ignore.vars <- c(levels(x$Origin)[x$Origin[1]], "Origin")
> x <- x[, !colnames(x) %in% ignore.vars]
> data.frame(
> Distance = apply(x, 1, min),
> Target = colnames(x)[apply(x, 1, which.min)]
> )
> })
>
> Best regards,
>
> Thierry
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination 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
>
> 2015-02-17 11:35 GMT+01:00 Ivan Palmegiani <pan.sapiens.it at gmail.com>:
>
>> Dear members of the list,
>>
>> I'm handling a SpatialPointsDataFrame with 100 ramdom points distributed
>> within 13 different polygons.
>>
>> > randp
>> coordinates Point_ID Polygon_ ID
>> 0 (690926.8, 7522595) 1_hs 13
>> 1 (696727.1, 7576122) 2_hs 6
>> ...
>> ...
>> 98 (728199.9, 7549810) 99_hs 12
>> 99 (723428.1, 7545891) 100 <7545891%29%20%20%20100>_hs
>> 12
>>
>> I need to calculate the shortest distance between points belonging to
>> different polygons. Basically I'd like to do what nndist {spatstat} does.
>> The difference is that the distance should be calculated between groups of
>> points instead of within a group of points.
>>
>> I tried to use "aggregate" as suggested below but it didn't work out for
>> me.
>> http://www.inside-r.org/packages/cran/spatstat/docs/nndist
>>
>> Please find my try below:
>>
>> > randp.df<-data.frame(randp)
>> > randp.hs.df
>> Point_ID coords.x1 coords.x2 Polygon_ ID
>> 0 1_hs 690926.8 7522595 13
>> 1 2_hs 696727.1 7576122 6
>> 2 3_hs 723480.7 7546594 12
>>
>> library(spatstat)
>>
>> # Calculate nearest neighbors within a polygon
>> > nn.within.pol<-nndist(randp.df[,c(2,3)],by=marks(randp.df$Polygon_ID))
>> > nn.within.pol
>> [1] 2579.42199 1391.88915 59.85628 734.95108 734.95108
>> 840.65125 957.47838 741.58160 955.26483 3307.59444 1361.64626
>> 2682.70690
>> ...
>> ...
>> [97] 1349.88694 955.26483 3166.00894 705.25663
>> # Ok but these are not the distances I need
>>
>> # Calculate nearest neighbors between polygons
>> nn.between.pol<-aggregate(nn.within.pol,
>> by=list(from=marks(randp.df$Polygon_ID)), min)
>> # Error in aggregate.data.frame(as.data.frame(x), ...) : arguments must
>> have same length
>>
>> > nn.between.hs<-aggregate(randp.hs.df[,c(2,3)],
>> by=list(randp.df$Polygon_ID), nndist)
>> > nn.between.hs
>>
>> The outcome is an asymmetric data frame (dim 13, 6) with a lot of empty
>> cells and values that look unlikely to be distances.
>>
>> The result I'd like to get is a matrix (dim 100, 1) with the distances
>> between each random point and its nearest neighbor belonging to a different
>> polygon (i.e. its nearest neighbor having a different Polygon_ID).
>>
>> Can someone kindly correct my script or suggest a function able to do the
>> job?
>>
>> Cheers,
>>
>> Ivan
>>
>> _______________________________________________
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>> R-sig-Geo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
>
>
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