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AMFTom

2012-Apr-16 16:24 UTC

[R] Creating a point pattern with spatstat

I have presence/absence data in the following format:

	1	2	3	4	5	6	7	8	9	10	11	12
1	1	1	1	1	1	1	1	1	1	1	1	0
2	1	1	1	1	0	1	1	1	1	1	1	0
3	1	1	1	1	1	1	1	1	1	1	0	1
4	1	1	1	1	1	0	1	1	1	1	0	1
5	1	1	1	1	1	1	1	0	0	1	1	1
6	1	1	1	0	0	1	0	0	1	1	1	1
7	1	1	1	1	0	1	1	0	0	0	1	1
8	1	1	1	1	1	1	1	0	0	0	1	0
9	1	1	1	1	0	0	1	0	0	0	1	1
10	1	1	1	1	1	1	1	0	0	0	0	1
11	1	1	1	1	1	1	1	1	1	0	0	1
12	1	1	1	1	1	0	0	0	1	1	1	1

Which I want to use to create a ppp object in spatstat. I tried:
> X <- as.ppp(Lv2.8, owin(c(0, 12), c(0,12)))
and got 
> plot(X)       0        1 
0.000000 1.187939 

http://r.789695.n4.nabble.com/file/n4562047/attempt1_ppp.jpg 

Which obviously isn't what I'm after. To obtain a simple graphic of
where
points are present on the plot, should I convert the raw data to
non-numerical values? 
 Thanks,
Tom

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David L Carlson

2012-Apr-16 19:32 UTC

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[R] Creating a point pattern with spatstat

First you should read the documentation carefully and look at the examples.
Your data are tabular. Spatstat expects a row for each point with the x and
y coordinates for that point.

# First use dput() to create a version of the data that you can copy into
your r-help requests so we
# can easily generate the data set:

Lv2.8 <- structure(list(X1 = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
  1L, 1L), X2 = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
  X3 = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), X4 = c(1L, 
  1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 1L), X5 = c(1L, 0L, 1L, 
  1L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L), X6 = c(1L, 1L, 1L, 0L, 1L, 
  1L, 1L, 1L, 0L, 1L, 1L, 0L), X7 = c(1L, 1L, 1L, 1L, 1L, 0L, 1L, 
  1L, 1L, 1L, 1L, 0L), X8 = c(1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 
  0L, 1L, 0L), X9 = c(1L, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 
  1L), X10 = c(1L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L), 
  X11 = c(1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L, 1L), 
  X12 = c(0L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L)), .Names =
c("X1",

  "X2", "X3", "X4", "X5",
"X6", "X7", "X8", "X9", "X10",
"X11",
  "X12"), class = "data.frame", row.names = c(NA, -12L))

# Now generate matrices of coordinates x=1:12 and y=1:12 and combine them

x <- matrix(col(Lv2.8), nrow=144, ncol=1)
y <- matrix(row(Lv2.8), nrow=144, ncol=1)
xy <- cbind(x, y)

#  Now a matrix of the 1/0 values
z <- matrix(as.matrix(Lv2.8), nrow=144, ncol=1)

# Finally eliminate the coordinates that are empty
points <- xy[as.logical(z),]

# Now your commands will work (with the window expanded slightly)
X <- as.ppp(points, owin(c(0, 13), c(0,13)))
plot(X)

----------------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352



> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of AMFTom
> Sent: Monday, April 16, 2012 11:25 AM
> To: r-help at r-project.org
> Subject: [R] Creating a point pattern with spatstat
> 
> I have presence/absence data in the following format:
> 
> 	1	2	3	4	5	6	7	8	9
10	11> 	12
> 1	1	1	1	1	1	1	1	1	1
1	1> 	0
> 2	1	1	1	1	0	1	1	1	1
1	1> 	0
> 3	1	1	1	1	1	1	1	1	1
1	0> 	1
> 4	1	1	1	1	1	0	1	1	1
1	0> 	1
> 5	1	1	1	1	1	1	1	0	0
1	1> 	1
> 6	1	1	1	0	0	1	0	0	1
1	1> 	1
> 7	1	1	1	1	0	1	1	0	0
0	1> 	1
> 8	1	1	1	1	1	1	1	0	0
0	1> 	0
> 9	1	1	1	1	0	0	1	0	0
0	1> 	1
> 10	1	1	1	1	1	1	1	0	0
0	0> 	1
> 11	1	1	1	1	1	1	1	1	1
0	0> 	1
> 12	1	1	1	1	1	0	0	0	1
1	1> 	1
> 
> Which I want to use to create a ppp object in spatstat. I tried:
> 
> > X <- as.ppp(Lv2.8, owin(c(0, 12), c(0,12)))
> 
> and got
> 
> > plot(X)
>        0        1
> 0.000000 1.187939
> 
> http://r.789695.n4.nabble.com/file/n4562047/attempt1_ppp.jpg
> 
> Which obviously isn't what I'm after. To obtain a simple graphic of
> where
> points are present on the plot, should I convert the raw data to
> non-numerical values?
>  Thanks,
> Tom
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/Creating-a-
> point-pattern-with-spatstat-tp4562047p4562047.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.

AMFTom

2012-Apr-20 11:01 UTC

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[R] Creating a point pattern with spatstat

The graphic produced was what I was after, except it was inverted. The
original tabular data represents a plot as oriented in the field i.e. with
North at the top, South at the bottom. The graphic from this had South at
the top and North at the bottom, so I input the data the other way around
i.e. instead of:

X12 = c(0L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L)), 

I changed it to 

X12 = c(1L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 0L)),

Is there a way that R can read these data as Cartesian co-ordinates to save
having to write out the whole table every time? 

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