Re: [R-sig-Geo] Error in anyDuplicated.default(coords) message with trinb

2011-07-07 Thread Edzer Pebesma 
Jeff, ?tri2nb suggests you to try

tri2nb(coordinates(data.sp))

On 07/07/2011 03:52 PM, Stratford, Jeffrey wrote:
> Hi everyone,
> 
>  
> 
> I'm attempting to do some spatial analyses with a relatively simple data
> set and I'm running into some issues.  Here's my code:
> 
>  
> 
> sosp09 <- read.csv("f:\\sosp\\2009\\sosp09.means.csv", header=T)
> 
> sp.point <- cbind(sosp09$x, sosp09$y)
> 
> colnames(sp.point) <- c("LONG","LAT") 
> 
> # Projection: UTM Zone 17
> 
> proj <- CRS("+proj=utm +zone=18 +datum=WGS84")
> 
> # Create spatial object
> 
> data.sp <- SpatialPointsDataFrame(coords=sp.point, data=sosp09,
> proj4string=proj)
> 
> ## Bounding box of data points
> 
> bbox(data.sp)
> 
> #build neighborhood
> 
> sosp.neigh <- tri2nb(data.sp)
> 
>  
> 
> And, with the last step, I get 
> 
>  
> 
> Error in anyDuplicated.default(coords) : 
> 
>   anyDuplicated() applies only to vectors
> 
>  
> 
> I went through and removed duplicated rows by averaging the responses
> and I still get this message.  I also removed via rm() all the objected
> from the original analysis and I still get this message.  Any ideas
> what's going on?
> 
>  
> 
> Thanks,
> 
>  
> 
> Jeff
> 
>  
> 
> The data:
> 
>  
> 
>  
> 
> new("SpatialPointsDataFrame"
> 
> , data = structure(list(band = c(6467L, 6483L, 6466L, 6465L, 6463L,
> 6462L, 
> 
> 6498L, 6443L, 6496L, 6495L, 6459L, NA, 6458L, 6491L, 6446L, 6464L, 
> 
> NA, 6473L, 6444L, 6457L, 6468L, NA, 6485L, 6474L, 6445L, 6486L, 
> 
> 6488L, 6472L, 6493L, 6492L, 6471L, 6449L, 6453L, 6460L, 6482L
> 
> ), site = structure(c(19L, 26L, 18L, 17L, 15L, 14L, 35L, 1L, 
> 
> 34L, 33L, 12L, 8L, 11L, 30L, 4L, 16L, 5L, 23L, 2L, 10L, 20L, 
> 
> 9L, 27L, 24L, 3L, 28L, 29L, 22L, 32L, 31L, 21L, 6L, 7L, 13L, 
> 
> 25L), .Label = c("SOSP0901", "SOSP0902", "SOSP0903", "SOSP0904", 
> 
> "SOSP0905", "SOSP0906", "SOSP0908", "SOSP0909", "SOSP0910", "sosp0911", 
> 
> "sosp0912", "sosp0913", "sosp0914", "SOSP0915", "SOSP0916", "SOSP0917", 
> 
> "SOSP0918", "SOSP0919", "SOSP0920", "SOSP0921", "SOSP0925", "SOSP0926", 
> 
> "SOSP0927", "SOSP0928", "Sosp0934", "Sosp0935", "Sosp0936", "Sosp0937", 
> 
> "Sosp0938", "Sosp0940", "Sosp0941", "Sosp0942", "Sosp0943", "Sosp0944", 
> 
> "Sosp0946"), class = "factor"), sex = structure(c(1L, 1L, 1L, 
> 
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
> 
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
> 
> ), .Label = "M", class = "factor"), age = structure(c(1L, 1L, 
> 
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
> 
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
> 
> 1L), .Label = "AHY", class = "factor"), wing = c(66, 62, 66, 
> 
> 65, 65, 64.5, 66, 69, 64.5, 67.5, 66, 66.5, 68, 67, 66, 67, 64.5, 
> 
> 68, 65, 65, 66, 65.5, 65, 66, 64, 65, 65, 66, 66, 63, 67, 66, 
> 
> 66, 65, 64), tail = c(69, 67, 69, 66, 67, 65, 66, 68, 64, 67.5, 
> 
> 66, 66, 67, 67, 67, 70, 69, 64, 67, 69, 68, 65.5, 66, 67, 65, 
> 
> 66, 66, 68, 71, 55, 72, 62, 70, 70, 66), bill = c(9, 9.7, 9.6, 
> 
> 9.5, 9.6, 8.5, 9.2, 9.5, 8.4, 9.2, 9.9, 8.8, 8.8, 9.2, 8.6, 9.6, 
> 
> 9.15, 9.7, 9.7, 8.7, 8.9, 9.45, 8.8, 9.1, 9.2, 9.2, 9.1, 8.9, 
> 
> 9.6, 8.7, 9.2, 8.8, 9.2, 9, 9.3), tarsus = c(21.6, 20.6, 20.9, 
> 
> 21.8, 20.9, 19.6, 22, 21.5, 21.7, 21.3, 22.1, 21.15, 19.9, 22.4, 
> 
> 22, 20.1, 21.85, 21.6, 20.9, 21.5, 22.4, 21.5, 21.3, 21.2, 21.5, 
> 
> 20.6, 21.4, 21.4, 21.4, 21.7, 21.4, 21.1, 20.6, 20.1, 22.2), 
> 
> mass = c(20.8, 20.6, 21.1, 22.3, NA, 16.7, 23, 23.2, 20.7, 
> 
> 20.9, 27.3, 21.1, 21.4, 24.3, 23.2, 21.7, 22, 21, NA, 20.1, 
> 
> 20.5, 21.4, 20.5, 23.3, 21.5, 20.5, 20.8, 21, 21.3, 20.3, 
> 
> 20.4, 21, 22.9, 19.7, 21.5), x = c(1647222L, 1648242L, 1648272L, 
> 
> 1648422L, 1651242L, 1652472L, 1652472L, 1653042L, 1653282L, 
> 
> 1653372L, 1654092L, 1654212L, 1654362L, 1655082L, 1657032L, 
> 
> 1657212L, 1657272L, 1657932L, 1658292L, 1658412L, 1658772L, 
> 
> 1659072L, 1659192L, 1659342L, 1659702L, 1659762L, 1659912L, 
> 
> 1660692L, 1660872L, 1661022L, 1661082L, 1662042L, 1662192L, 
> 
> 1663362L, 1663512L), y = c(2207359L, 2206909L, 2207479L, 
> 
> 2202859L, 2203219L, 2204599L, 2198299L, 2194849L, 2202889L, 
> 
> 2208229L, 2199469L, 2199649L, 2199769L, 2202589L, 2198089L, 
> 
> 2201449L, 2198029L, 2201209L, 2202529L, 2201989L, 2203549L, 
> 
> 2202529L, 2203519L, 2201209L, 2202499L, 2204179L, 2203459L, 
> 
> 2200939L, 2208469L, 2208709L, 2201419L, 2204299L, 2204989L, 
> 
> 2206339L, 2202619L), urban1 = c(0.1724138, 0.2068966, 0.06896552, 
> 
> 0.2413793, 0.5172413, 0.34482762, 0.55172422, 0.138, 0.06896552, 
> 
> 0.03448276, 0.06896552, 1, 0.9655172, 0.4827586, 0.966, 0.8965516, 
> 
> 0.31, 1, 1, 0.9996, 0.79310346, 1, 1.0012, 0.9992, 
> 
> 1, 0.9998, 1, 0.999, 0.48275866, 1, 1.001, 1, 
> 
> 1, 1, 0.7241379), urban2 = c(0.2214765, 0.12751683, 0.18791945, 
> 
> 0.09395973, 0.24832219, 0.1946309, 0.32885906

[R-sig-Geo] Error in anyDuplicated.default(coords) message with trinb

2011-07-07 Thread Stratford, Jeffrey 
Hi everyone,

 

I'm attempting to do some spatial analyses with a relatively simple data
set and I'm running into some issues.  Here's my code:

 

sosp09 <- read.csv("f:\\sosp\\2009\\sosp09.means.csv", header=T)

sp.point <- cbind(sosp09$x, sosp09$y)

colnames(sp.point) <- c("LONG","LAT") 

# Projection: UTM Zone 17

proj <- CRS("+proj=utm +zone=18 +datum=WGS84")

# Create spatial object

data.sp <- SpatialPointsDataFrame(coords=sp.point, data=sosp09,
proj4string=proj)

## Bounding box of data points

bbox(data.sp)

#build neighborhood

sosp.neigh <- tri2nb(data.sp)

 

And, with the last step, I get 

 

Error in anyDuplicated.default(coords) : 

  anyDuplicated() applies only to vectors

 

I went through and removed duplicated rows by averaging the responses
and I still get this message.  I also removed via rm() all the objected
from the original analysis and I still get this message.  Any ideas
what's going on?

 

Thanks,

 

Jeff

 

The data:

 

 

new("SpatialPointsDataFrame"

, data = structure(list(band = c(6467L, 6483L, 6466L, 6465L, 6463L,
6462L, 

6498L, 6443L, 6496L, 6495L, 6459L, NA, 6458L, 6491L, 6446L, 6464L, 

NA, 6473L, 6444L, 6457L, 6468L, NA, 6485L, 6474L, 6445L, 6486L, 

6488L, 6472L, 6493L, 6492L, 6471L, 6449L, 6453L, 6460L, 6482L

), site = structure(c(19L, 26L, 18L, 17L, 15L, 14L, 35L, 1L, 

34L, 33L, 12L, 8L, 11L, 30L, 4L, 16L, 5L, 23L, 2L, 10L, 20L, 

9L, 27L, 24L, 3L, 28L, 29L, 22L, 32L, 31L, 21L, 6L, 7L, 13L, 

25L), .Label = c("SOSP0901", "SOSP0902", "SOSP0903", "SOSP0904", 

"SOSP0905", "SOSP0906", "SOSP0908", "SOSP0909", "SOSP0910", "sosp0911", 

"sosp0912", "sosp0913", "sosp0914", "SOSP0915", "SOSP0916", "SOSP0917", 

"SOSP0918", "SOSP0919", "SOSP0920", "SOSP0921", "SOSP0925", "SOSP0926", 

"SOSP0927", "SOSP0928", "Sosp0934", "Sosp0935", "Sosp0936", "Sosp0937", 

"Sosp0938", "Sosp0940", "Sosp0941", "Sosp0942", "Sosp0943", "Sosp0944", 

"Sosp0946"), class = "factor"), sex = structure(c(1L, 1L, 1L, 

1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 

1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L

), .Label = "M", class = "factor"), age = structure(c(1L, 1L, 

1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 

1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 

1L), .Label = "AHY", class = "factor"), wing = c(66, 62, 66, 

65, 65, 64.5, 66, 69, 64.5, 67.5, 66, 66.5, 68, 67, 66, 67, 64.5, 

68, 65, 65, 66, 65.5, 65, 66, 64, 65, 65, 66, 66, 63, 67, 66, 

66, 65, 64), tail = c(69, 67, 69, 66, 67, 65, 66, 68, 64, 67.5, 

66, 66, 67, 67, 67, 70, 69, 64, 67, 69, 68, 65.5, 66, 67, 65, 

66, 66, 68, 71, 55, 72, 62, 70, 70, 66), bill = c(9, 9.7, 9.6, 

9.5, 9.6, 8.5, 9.2, 9.5, 8.4, 9.2, 9.9, 8.8, 8.8, 9.2, 8.6, 9.6, 

9.15, 9.7, 9.7, 8.7, 8.9, 9.45, 8.8, 9.1, 9.2, 9.2, 9.1, 8.9, 

9.6, 8.7, 9.2, 8.8, 9.2, 9, 9.3), tarsus = c(21.6, 20.6, 20.9, 

21.8, 20.9, 19.6, 22, 21.5, 21.7, 21.3, 22.1, 21.15, 19.9, 22.4, 

22, 20.1, 21.85, 21.6, 20.9, 21.5, 22.4, 21.5, 21.3, 21.2, 21.5, 

20.6, 21.4, 21.4, 21.4, 21.7, 21.4, 21.1, 20.6, 20.1, 22.2), 

mass = c(20.8, 20.6, 21.1, 22.3, NA, 16.7, 23, 23.2, 20.7, 

20.9, 27.3, 21.1, 21.4, 24.3, 23.2, 21.7, 22, 21, NA, 20.1, 

20.5, 21.4, 20.5, 23.3, 21.5, 20.5, 20.8, 21, 21.3, 20.3, 

20.4, 21, 22.9, 19.7, 21.5), x = c(1647222L, 1648242L, 1648272L, 

1648422L, 1651242L, 1652472L, 1652472L, 1653042L, 1653282L, 

1653372L, 1654092L, 1654212L, 1654362L, 1655082L, 1657032L, 

1657212L, 1657272L, 1657932L, 1658292L, 1658412L, 1658772L, 

1659072L, 1659192L, 1659342L, 1659702L, 1659762L, 1659912L, 

1660692L, 1660872L, 1661022L, 1661082L, 1662042L, 1662192L, 

1663362L, 1663512L), y = c(2207359L, 2206909L, 2207479L, 

2202859L, 2203219L, 2204599L, 2198299L, 2194849L, 2202889L, 

2208229L, 2199469L, 2199649L, 2199769L, 2202589L, 2198089L, 

2201449L, 2198029L, 2201209L, 2202529L, 2201989L, 2203549L, 

2202529L, 2203519L, 2201209L, 2202499L, 2204179L, 2203459L, 

2200939L, 2208469L, 2208709L, 2201419L, 2204299L, 2204989L, 

2206339L, 2202619L), urban1 = c(0.1724138, 0.2068966, 0.06896552, 

0.2413793, 0.5172413, 0.34482762, 0.55172422, 0.138, 0.06896552, 

0.03448276, 0.06896552, 1, 0.9655172, 0.4827586, 0.966, 0.8965516, 

0.31, 1, 1, 0.9996, 0.79310346, 1, 1.0012, 0.9992, 

1, 0.9998, 1, 0.999, 0.48275866, 1, 1.001, 1, 

1, 1, 0.7241379), urban2 = c(0.2214765, 0.12751683, 0.18791945, 

0.09395973, 0.24832219, 0.1946309, 0.32885906, 0.315, 0.08724833, 

0.05369128, 0.3959732, 0.583892609, 0.77181212, 0.42281877, 

0.758, 0.6577181, 0.564, 1.0014, 0.993, 0.9997, 0.63758395, 

0.7919463, 1.0003, 1, 1, 1.001, 0.73154363, 1.0004, 

0.59731537, 0.8993289, 0.97315443, 1, 0.913, 1.0001, 

0.75838925), urbank = c(0.0976826, 0.210325588, 0.360516315, 

0.063361691, 0.060721623, 0.23995307, 0.18979175, 0.275, 

0.065708423, 0.1589909, 0.33294