If you don't receive a satisfactory answer here in a day or so, post
on the R-sig-geo list where the experts in this sort of thing hang
around.
Cheers,
Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Brea
Hello ,
I am trying the spatstat package installation
on R 3.3.0
the package is spatstat_1.63-3.tar.gz
,the OS is oracle enterprise linux 7
at the end I receive the error
Error : .onAttach failed in attachNamespace() for 'spatstat', details:
call: if (today - as.Date(rdate) > 365) {
error: mi
Try fasterize, converting to spatstat from raster is straightforward, happy
to help.
https://github.com/ecohealthalliance/fasterize
Cheers, Mije
On Fri, 2 Jun 2017, 07:45 Rolf Turner, wrote:
>
> On 02/06/17 01:17, lluis.hurt...@uv.es wrote:
>
> > Dear all,
> >
> > I am currently working with t
On 02/06/17 01:17, lluis.hurt...@uv.es wrote:
Dear all,
I am currently working with the spatstat package, using windows and pixel
images.
First:
My aim is to transform a shapefile (see attached) into a pixel image.
My idea is to start transforming the shapefile into a Spatial Polygon file:
This looks like to would be better to ask on R-sig-geo, instead of R-help.
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 6/1/17, 6:17 AM, "R-help on behalf of lluis.hurt...@uv.es"
wrote:
Dear all,
I am cur
Dear all,
I am currently working with the spatstat package, using windows and pixel
images.
First:
My aim is to transform a shapefile (see attached) into a pixel image.
My idea is to start transforming the shapefile into a Spatial Polygon file:
x <- readShapeSpatial("21441.shp")
y <- as(
Dear all,
I am currently working with the spatstat package, using windows and pixel
images.
First:
My aim is to transform a shapefile (see attached) into a pixel image.
My idea is to start transforming the shapefile into a Spatial Polygon file:
x <- readShapeSpatial("21441.shp")
y <- as(
You should use:
plot(density(rmh(mod,new.coef=c(1,200
Sorry, my bad, typo in the example code.
(2) However, even when the correct call is given you still wind up
with identical densities!!!
Hm. I think this may be a bug; I'll will check with the other
authors of spatstat and repor
There was indeed a bug in rmh() w.r.t. the "new.coeff" argument.
The bug has been fixed and will not be present in the next release of
spatstat.
cheers,
Rolf Turner
On 16/09/14 16:30, Sebastian Schutte wrote:
Thanks so much for your comments. Sorry for not having sent a running
example from
OK. Two things are going wrong.
(1) There is an error in your code. You are passing the new.coef
argument to density() and not to rmh(). The function density() has no
such argument, but has a "..." argument, so "new.coef" simply gets ignored.
You should use:
plot(density(rmh(mod,new.coef=
Thanks so much for your comments. Sorry for not having sent a running
example from the start. Here it is:
library (spatstat)
#Load example data
data(demopat)
#Generate a random point pattern within the polygon
set.seed(12345)
pdat <- rpoint(200,win=demopat$window)
#Generate a distmap, which wi
Your example is not reproducible. We don't have "cshape" or "im.pop"
(and are possibly lacking other bits and pieces; I didn't check the
details since the example fails to run from the get-go). Please provide
a *reproducible* example.
Also I am puzzled by the line
mod <- ppm (ppp, ~ pop
Dear R and spatstat developers,
Thanks so much for the time and effort that you invest into this awesome
software. I have a problem simulating from a Point Process Model in
spatstat. In summary, the option "new.coef" should allow me to use a
fitted model and change its beta coefficients before
Dear R and spatstat developers,
Thanks so much for the time and effort that you invest into this awesome
software. I have a problem simulating from a Point Process Model in
spatstat. In summary, the option "new.coef" should allow me to use a
fitted model and change its beta coefficients before
There appears to be a small bug in the code. What is happening is that
occasionally there are simulated points that lie inside your triangular
window but do not lie inside any pixel of the image created from your
"distorigin()" function.
This will be fixed in a future release of spatstat.
Dear R-help list,
I'm using the excellent spatstat package to fit an inhomogeneous Matern
cluster point process model, but unfortunately I'm unable to simulate new
data points from the fitted object.
Specifically, I get the following error message:
Error in rthin(result, P) :
some points of X
On 07/07/13 22:12, catalin roibu wrote:
Dear R users,
Is there a possibility to extract only the r, CI's envelope and L function
from the output of spatstat?
I use this code
E <- alltypes(df1, Kest, nsim = 100, envelope =
TRUE,savepatterns=TRUE,correction="isotropic")
And second question, is ther
Dear R users,
Is there a possibility to extract only the r, CI's envelope and L function
from the output of spatstat?
I use this code
E <- alltypes(df1, Kest, nsim = 100, envelope =
TRUE,savepatterns=TRUE,correction="isotropic")
And second question, is there a possibility to modify the margin of pl
Questions about spatstat should be directed to the R-Sig-Geo list, or
better still, to the package maintainers.
To add a bit to what Blaser Nello has already told you:
(1) Your syntax in respect of the use of the min() function is indeed
incomprehensibly bizarre.
(2) Blaser Nello has indicated
Questions about spatstat should be directed to the R-Sig-Geo list, or
better still, to the package maintainers.
To add a bit to what Blaser Nello has already told you:
(1) Your syntax in respect of the use of the min() function is indeed
incomprehensibly bizarre.
(2) Blaser Nello has indicated
)
danta=ppp(Datos$x,Datos$y,c(1177842,1180213),c(1013581,1015575))
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of papao
Sent: Freitag, 22. März 2013 00:20
To: R-help@r-project.org
Subject: [R] spatstat error
Good day
Im working
Good day
Im working with some coordinates, and want to create a PPP object, I found
that error:
> Datos=read.table("puntos_texto.txt",dec=".",sep="\t",header=T)
> summary(Datos)
id y x
Min. : 1.0 Min. :1013581 Min. :1177842
Thanks.
On Thu, 07 Feb 2013 11:46:36 +
Rui Barradas wrote:
> Hello,
>
> Try the following.
>
> > maintainer("spatstat")
> [1] "Adrian Baddeley "
>
>
> Hope this helps,
>
> Rui Barradas
>
> Em 07-02-2013 02:05, Hiroshi Saito escreveu:
> > Dear sir,
> >
> > Which mailing list is approp
It is also acceptable (and often useful) to ask on the R-Sig-Geo list.
Bug reports should of course be sent to Prof. Baddeley.
cheers,
Rolf Turner
On 02/08/2013 12:46 AM, Rui Barradas wrote:
Hello,
Try the following.
> maintainer("spatstat")
[1] "Adrian Baddeley "
Hope this h
P. S. I just noticed that you referred to the envelopes produced as
"confidence" envelopes.
They are ***NOT*** confidence envelopes!!! They are "critical" envelopes.
This is a very different concept. Repeat after me, 50 times:
critical envelopes, critical envelopes, critical envelopes, .
You can solve this problem by actually *reading* the error
message. Evidently the object "point" is a marked point pattern
whose marks are in the form of a data frame.
So either:
(1) Do not create "point" as a marked point pattern --- i.e.
don't add a "marks" component when you create
Hello,
I am writing cause I have a problem when try to create confidence envelopes
in spatstat.
I have a point data representing firms in my study area.
When I try to create confidence envelopes the error message turns up:
[> p <- envelope(point, fun=Kest, nsim=99)
Error in marks.ppp(Y, dfok = FA
Hello,
Try the following.
> maintainer("spatstat")
[1] "Adrian Baddeley "
Hope this helps,
Rui Barradas
Em 07-02-2013 02:05, Hiroshi Saito escreveu:
Dear sir,
Which mailing list is appropriate to ask for kstest in spatstat?
Regards,
Hiroshi Saito
*
Hiroshi Saito:
E
Dear sir,
Which mailing list is appropriate to ask for kstest in spatstat?
Regards,
Hiroshi Saito
*
Hiroshi Saito:
E-MAIL: saito.hiro...@lab.ntt.co.jp
http://www9.plala.or.jp/hslab/
PHONE: +81 422 59 4300
FAX: +81 422 59 6364
__
On 24/11/12 06:36, AMFTom wrote:
I normally use the following code to create a figure displaying the mark
correlation function for the point pattern process "A":
M<-markcorr(A)
plot(M)
I have now started to use the following code to perform 1000 Monte Carlo
simulations of Complete Spatial Rand
I normally use the following code to create a figure displaying the mark
correlation function for the point pattern process "A":
M<-markcorr(A)
plot(M)
I have now started to use the following code to perform 1000 Monte Carlo
simulations of Complete Spatial Randomness (CSR). It is a Monte Carlo t
Sebastian Pucilowski writes:
> What are the minimum number of points in a point pattern before a
> clustering analysis using a Ripley K function loses any meaning?
It depends what are your definition of `meaningful'.
The K-function doesn't become meaningless (undefined) until there are fewer
Hello,
What are the minimum number of points in a point pattern before a
clustering analysis using a Ripley K function loses any meaning?
I haven't been able to find much comment in the literature about this
--- instead case examples typically use 100-200 points as a minimum.
Regards,
Sebastian
Yes I am an active spatstat use
On Wednesday, 28 March 2012, Rolf Turner wrote:
>
> This is a cry for help. My apologies for taking up bandwidth
> with an issue that is not really on topic. But I really do want
> to acquire the requested information.
>
> In the course of preparing my PBRF (perf
Further to my cri de coeur of yesterday, asking people to indicate
whether they are "active spatstat users". I've had quite a few replies
but I'd like a lot more. Please answer; it'll only take you a few seconds.
Just reply to this email with a "Yes" (yes I am an active spatstat user)
or "No" (
"No I am not an active spatstat user".
David Winsemius, MD
West Hartford, CT
__
R-help@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 c
This is a cry for help. My apologies for taking up bandwidth
with an issue that is not really on topic. But I really do want
to acquire the requested information.
In the course of preparing my PBRF (performance based research
funds) portfolio for the upcoming PBRF exercise here in New Zealand,
On 16/03/12 23:02, Lucie V wrote:
Dear R users,
I wish to run spatial point pattern analysis (e.g. pair correlation function,
mark correlation function) for which I need to create an observation window
(window=owin) from which the spatial analysis is generated. The command I used
to create th
Dear R users,
I wish to run spatial point pattern analysis (e.g. pair correlation function,
mark correlation function) for which I need to create an observation window
(window=owin) from which the spatial analysis is generated. The command I used
to create this observation window as
Basically the problem is that you have a *VERY* old version of spatstat.
Upgrade!
Comments interpolated below.
On 05/12/11 21:52, karajamu wrote:
I forgot to change the header, so I guess no one read my mail. That's why I'm
trying it again...
Hello everbody,
I am new to this mailing list
I forgot to change the header, so I guess no one read my mail. That's why I'm
trying it again...
>
>
> Hello everbody,
>
> I am new to this mailing list and hope to find some help.
> I'm trying to get into the spatstat package and encountered two problems.
> First a graphical one:
> There i
Hej,
Thanks for the idea. I will try and see if I can make progress.
+ I appologise for the shortcut explanations. I'll dedicate myself to
greater accuracy in future.
tkd
--
View this message in context:
http://r.789695.n4.nabble.com/spatstat-owin-image-tp3837023p3843284.html
Sent from the R he
On 24/09/11 02:32, tkdweber wrote:
Dear Community
I am at my wits end and seek advice.
My wish is to plot coordinates (x,y in WGS84_UMTS for the ones interested)
of sampling points.
This I can do by the standard spatstat prodcedure via owin.
You appear to be rather confused from the very
Dear Community
I am at my wits end and seek advice.
My wish is to plot coordinates (x,y in WGS84_UMTS for the ones interested)
of sampling points.
This I can do by the standard spatstat prodcedure via owin. I then try to
add an image, which is
a map/satellite photo in the background.
Firstly
Prob
On 17/04/11 02:17, Gregory Ryslik wrote:
Hi Mr. Turner,
You are correct that I am confused a bit by the RCode. Basically, I have 3772
observations of data and only about 500
500? You said 944 previously. Doesn't really matter, but.
of them correspond to where "people" exist. For the ot
On 17/04/11 02:17, Gregory Ryslik wrote:
Hi Mr. Turner,
You are correct that I am confused a bit by the RCode. Basically, I have 3772
observations of data and only about 500
500? You said 944 previously. Doesn't really matter, but.
of them correspond to where "people" exist. For the ot
Hi Mr. Turner,
You are correct that I am confused a bit by the RCode. Basically, I have 3772
observations of data and only about 500 of them correspond to where "people"
exist. For the other observations, I just have the covariate values so I
thought that this was appropriate. Thus, where "pe
On 16/04/11 15:50, Gregory Ryslik wrote:
Hi Everyone,
I am trying to figure out the spatstat package for the first time and am having
some trouble. Unfortunately, I can't post my data set but I'll hopefully post
enough details for some help.
I want to model the intensity of a spatial point pr
Hi Everyone,
I am trying to figure out the spatstat package for the first time and am having
some trouble. Unfortunately, I can't post my data set but I'll hopefully post
enough details for some help.
I want to model the intensity of a spatial point process using 2 covariates
from my data. Aft
Hello R users,
I am fitting spatial point process models in spatstat using ppm and my models
actually contain spatial covariates. The results of the models are returned
with some levels of the covariates absent. eg when I fit a model with "aspect"
using:
ppm(points, ~aspect, covariates=list(
Hi all,
I am using "spatstat" to investigate the spatial structure of some plant
populations, and I want to detect these patters with IPP and a Thomas
process based on pair-correlation function. I know the function "pcfinhom"
is available to characterize the IPP, but I have no idea about how to us
Hello,
I
am using the Kinhom function to plot envelopes from my fitted
inhomogeneous models in spatstat. But the results I obtain do not have a
theoretical value (theo). They only give me the "hi", "lo", "r" and
"mmean" values but no "theo". Please can anyone help?
Mike.
[[al
Hello,
I am facing an error when I try to plot envelopes of a fitted model in
spatstat. My model is fitted using the Geyer Saturation process as follows:
*> geyer.fit<-ppm(points, ~el+asp, Geyer(r=1, sat=2), covariates=list(el=el,
asp=asp))*
It fits well, but when I try to plot the envelopes to t
Hello,
I have fitted a Poisson Process model in spatstat using
>fit1<-ppm(points, ~elevation, covariates=list(elevation=elevation.im))
This far, everything went well, but I try to simulate the fitted model using
the function:
>sim1<-rmh(fit1)
But I get the error message:
"Extracting model infor
Hello R Users,
I am trying to do a quadrat count defined by covariate properties in
spatstat. I have read my elevation raster into R (from ascii) and converted
to class "im" for use in spatstat.
Now I have point data of class "ppp" which window is the same extent as the
elevation image. I can conve
Hello R Users,
I am trying to do a quadrat count defined by covariate properties in
spatstat. I have read my elevation raster into R (from ascii) and converted
to class "im" for use in spatstat.
Now I have point data of class "ppp" which window is the same extent as the
elevation image. I can conve
You can't specify it in rthin, which I can understand for the simple
reason that this violates the independence of the sampling. If you put
a fixed limit on your resampling, the chance of being selected depends
on when some point is selected.
You could do it by hacking the object :
rthin.exact <-
Fellow Users,
In Spatstat, if you have a ppp object with, say 100 points, how do you
create another ppp containing a random selection, N, of the original?
You can tell the function 'rthin' to make a sub-selection of points, i.e.
"every point is removed with probability 0.5" but you CAN'T set N e
On 21/11/2009, at 12:01 AM, rudi1...@gmx.de wrote:
Hello,
could please somebody help me. I want to apply the mark correlation
function but for radii up to 75 meters (in 75 individual 1m steps).
Unfortunately, "There is a sensible default for the values of the
argument r at which the mark
Hello,
could please somebody help me. I want to apply the mark correlation function
but for radii up to 75 meters (in 75 individual 1m steps). Unfortunately,
"There is a sensible default for the values of the argument r at which the mark
correlation function kf (r) should be evaluated", so that
If 'X' is a data frame containing columns 'x', 'y' and 'value, try
m <- with(X, tapply(value, list(y,x), all))
z <- im(m, xcol=sort(unique(X$x)), yrow=sort(unique(X$y)))
w <- as.owin(z)
This will only work if the x, y values form a rectangular grid in some
order.
Adri
In the first instance, questions about contributed packages should be
addressed to the package maintainers rather than to the R-help list.
On 20/10/2009, at 2:06 AM, Javier PB wrote:
Dear users,
I am trying to export polygons from Arcmap into Spatstat to run some
simulations using functions a
Dear users,
I am trying to export polygons from Arcmap into Spatstat to run some
simulations using functions available in Spatstat package.
One particular area to be exported is formed by a number of polygons
defining the external boundaries of the area (as a groups of islands) and a
number of p
Hi,
I am new to spatial statistics and have a few basic queries. I am
analysing the spatial pattern of trees on a large plot. I wanted to
know if there is there some way of obtaining estimates of the number
of clusters and cluster-radius (in an iterative fashion) after fitting
a spatial point proc
Dear all,
I need to change the default of "r" when plotting the
output of the envelope function of spatstat package.
I can do this manually for the Lest output:
## Example from spatstat Kest help
data(cells)
L <- Lest(cells, correction="isotropic", r=seq(from=0,to=0.5, by=0.05))
x11(1000,400)
Peter Dalgaard wrote:
> Richard Chirgwin wrote:
>> Hi all,
>>
>> I am trying to install Spatstat on OpenSUSE 11.1.
>> install.packages("spatstat", dependencies = TRUE)
>> fails on the basis of various compiler packages (full message below).
>>
>> I have gcc version 4.3.2, which shou
Richard Chirgwin wrote:
Hi all,
I am trying to install Spatstat on OpenSUSE 11.1.
install.packages("spatstat", dependencies = TRUE)
fails on the basis of various compiler packages (full message below).
I have gcc version 4.3.2, which should include gfortran and g++ - so I'm not
Hi all,
I am trying to install Spatstat on OpenSUSE 11.1.
install.packages("spatstat", dependencies = TRUE)
fails on the basis of various compiler packages (full message below).
I have gcc version 4.3.2, which should include gfortran and g++ - so I'm not
sure what to do!
Gough Lauren wrote:
I'm using spatstat to investigate the spatial structure of an arid shrub
population. The first-order intensity of my data does not appear to be
homogenous, so I would like to use inhomogeneous techniques. I realise
there is a inhomogeneous K-function available in spatstat, b
On 2/12/2008, at 4:30 AM, Gough Lauren wrote:
Hi all,
I'm using spatstat to investigate the spatial structure of an arid
shrub
population. The first-order intensity of my data does not appear
to be
homogenous, so I would like to use inhomogeneous techniques. I
realise
there is a inhom
Hi all,
I'm using spatstat to investigate the spatial structure of an arid shrub
population. The first-order intensity of my data does not appear to be
homogenous, so I would like to use inhomogeneous techniques. I realise
there is a inhomogeneous K-function available in spatstat, but there
does
Hello,
I would like to use the spatstat package to generate realizations from a
spatial birth death process. The death rate is dependent on the pairwise
interaction function.
1 - I'd like to know how to define my own interaction potential function
2 - I'm not sure which model to use for a birth d
tober 2008 05:34
To: R-help Forum
Cc: Gough Lauren; Rolf Turner
Subject: Re: [R] Spatstat help - quadratcount query
Gough, Lauren wrote:
>
>> I am using quadratcount in spatstat to divide a window containing a
>> point pattern into a grid of quadrats containing the intensity of
>&
Gough, Lauren wrote:
I am using quadratcount in spatstat to divide a window containing a
point pattern into a grid of quadrats containing the intensity of
points in each quadrat.
However, when I look at the data for quadrat counts it seems the
function is not keeping the size of the quad
Hi all,
I am using quadratcount in spatstat to divide a window containing a
point pattern into a grid of quadrats containing the intensity of points
in each quadrat. My data is in UTM co-ordinates. My window is defined
as follows:
>p15<-ppp(x,y,window=owin(c(341710,342100),c(3126465,3126780)),m
Arthur Weiss wrote:
Hi everyone,
I am using the package "spatstat" for ploting kernel maps of my data.
It is a marked point pattern, the result of mosquito surveillance in a
area in a week.
For each trap, the number of individuals captured is the mark of the
point.
plot(density(X, weights=
On 10/10/2008, at 4:48 AM, Arthur Weiss wrote:
Hi everyone,
I am using the package "spatstat" for ploting kernel maps of my data.
It is a marked point pattern, the result of mosquito surveillance in a
area in a week.
For each trap, the number of individuals captured is the mark of
the point.
Hi everyone,
I am using the package "spatstat" for ploting kernel maps of my data.
It is a marked point pattern, the result of mosquito surveillance in a
area in a week.
For each trap, the number of individuals captured is the mark of the point.
> plot(density(X, weights=X$marks))
makes a nice k
Hi,
Is it possible to tabulate (count) points generated by spatstat ppp() using
any regular Grid created with owin()?
The idea is to count No of points in each grid cell.
Any other method available?
Paulo
__
R-help@r-project.org mailing list
https://st
Hi all,
Is there a mailing list for spatstat R package?
Another question: Can I find some ebooks on Spatial Pattern Analysis to be
downloaded?
Finally, how can I use a shapefile as "mask" on spatstat? I read the polygon
using maptools::read.shape function and now I would like to use this shape
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