Questions tagged [spatstat]
spatstat is a package for the statistical software suite R to conduct spatial point pattern analysis and modeling
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Cluster/cox models and models including the lag of residuals return no confidence interval for coefficients
I am trying to explain the localisation of a series of points (urban commons) in Amsterdam using a series of indicators linked to urban form and land uses and prices. However, almost any model I try ...
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How to create a ppp spatstat object from a sf object
I am trying to create a ppp object from a sf object in R.
I am using the population-weighted centroids in Minnesota from 2020 census data. You can find the data here: https://www2.census.gov/geo/docs/...
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Rasterise a point pattern in R
I have a set of georeferenced points within an area for which I want to know the spatial distribution (sparse/clustered) according to a regular grid.
I thought to describe the pattern using the Clark-...
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ks.test in spatstat package
I'm trying to make ks.test on my data in spatstat package. I use ppp function to create my pattern named ppp then when i try this code:
ks.test(ppp,"x") as in the documentation it says ...
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Accounting for minimum distance between points when conducting point pattern analyses in spatstat
I've noticed an issue when performing exploratory analyses of my point pattern. When plotting a G function in spatstat, I've noticed G values remain near zero up to an r of around 5 micron [see below ...
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Tessellation will not display quadrat totals when plotted (spatstat, R)
I have tessellated an image, and am trying to plot the number of quadrats that appear in each tessellated region.
I have two problems here:
My tessellated image will not plot with my gw_ppp points, ...
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Creating a point pattern (ppp) error using SpatStat in R: "Only projected coordinates may be converted to spatstat class objects"
I have a point dataset, and I am taked with filtering out duplicate coordinates, removing all points that are outside of a specified county shapefile, and then creating a ppp points object. However, ...
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Extract a network from spatstat to graph object in igraph using R
I am looking for an efficient way to transfer a linear network (class linnet) from spatstat, e. g. library(spatstat); data('chicago'); net <- spatstat.linnet::domain.lpp(chicago) to a 'graph' ...
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Plot points in spastat ppp object
I am new to spatstat package and I am trying to make a point patten map with a shape file and some case points. I was able to plot the shape file plot but I just don't know how to make the points on ...
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Calculating the cross-nearest-neighbor distance in spatstat
I wish to calculate the cross-nearest-neighbor distance between two point patterns in spatstat.
According to Pr. Sadahiro, the cross-nearest-neighbor distance is defined as:
My inputs are sf datasets,...
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How do you convert SpatialPoints object to PPP object?
I have a shapefile layer of polygons (houses in a city) that I want to run a kernel density on using the density() function in spatstat in R. To get my polygons as points I turned them into ...
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R statspat package (or similar pkg) and convert back to spatial objects
I've been testing the waters and doing some basic overview on the statspat package. This is a complex package and would likely require some serious effort to jump in and then get familiar with the ...
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Shapefile vector point to ppp spatstat with polygon windows
I always get error to this when converting shapefile point to ppp spatstat that windowed by a polygon shapefile
# polygon that to be window
neighborhoods <- st_read("neighborhoods/...
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Estimating spatial autocorrelation from counts on linear network [closed]
I'm working with count data sampled along roadways. I would like to estimate the spatial autocorrelation of the counts, but I'm having trouble wrapping my head around how to incorporate the network ...
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Error in converting shapefiles into spatstat window
I wish to import shapefiles of the Seoul Capital Area to use as a window in spatstat. The SCA is the combination of the Seoul, Incheon, and Gyeonggi-do level-1 administrative areas of South Korea.
I ...
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How much W shape effects on the cross correlation of points in R
I am analyzing cross-correlation between these two-point data sets (all the analyses have been performed in R: by using Kcross, Lcross functions).
In the first trial, I was using an irregular ...
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The confidence level alfa value for spatial randomness with Ripley K and L function
I have a point set of the spatial distribution of twitter posts relevant to a certain event.
I would like to evaluate evidence for clustering or dispersion of points. This is usually performed by ...
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Replicated Point Pattern: Get Density Variance Between Replicated Patterns and Subtract from Composite
I have written a lengthy code that dissects differently shaped/sized windows into recognizable components (individual cells in the image), gets the point density within each cell, then builds a whole ...
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calculate distance of points from centroid
I have a spatialpoints object, and a spatialpolygonsdataframe, composed of rectangular cells, and which the spatialpoints fall into. What I would like is to determine which polygon in the ...
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DSpat::create.lines and spatstat::rlinegrid: Adding too many lines?
Does anybody know of an issue with either DSpat's create.lines or spatstat's rlinegrid? Whenever I use these functions on my Windows (owins), the output has far too many lines.
For example, if I run
...
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Connecting spatiallines or SpatialPoints based on minimum distance using R
Does anybody know of a way to create a single polygon (that will eventually be converted to an Owin) from either a spatialpoints object or a spatiallines object?
Here is an example of each:
Here's ...
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Aligning Multiple Polygons (Based on centroid possibly) [Spatstat, sf, sp]
I'm trying to create a composite/average of multiple similarly shaped polygons. I think the first step is most likely to align them via the centroid of each polygon.
Does anybody know of a tool to ...
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QGIS enabling R via plugin
System Ubuntu 19.10, QGIS 3.4
I am trying to utilise R in QGIS for Ripley's K function.
The sample R script 'Scatterplot' works with the Processing R Provider plugin, which indicates r-base is ...
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Generating pattern in each of set of polygons using sp (r)?
I have an object of class SpatialPolygonsDataFrame, and for each polygon in the dataframe I have a number of points I would like to generate in that polygon (e.g. I have 130 polygons, and I have a ...
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R (spatstat, sp, sf): Grid a single polygon, divide, alphanumeric labels based on column/row
I am trying to take a polygon and add grid lines over top, then divide the polygon into many polygons based on the grids. I've accomplished this through st_make_grid() and raster::intersect().
The ...
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Multiple Spatial Point Patterns, create "average" heatmap
I am using R's spatstat package to analyze spatial patterns of objects across plant leaves.
Let's say I have 10 leaves, each with corresponding X,Y coordinates of the objects and a window in the ...
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Point.in.polygon function in sf package miscalculate the distribution of points
I am using point.in.polygon function in sf package to determine whether a set of data fall within a polygon or not.
Here is a snippet of the data and polygon visualization
As the figure shows, there ...
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Convert ppp object to multitpe object
I am working on spatial point pattern analysis using R.
I have two sets of coordinates, both defined inside a 32*20 region.
I first convert two data sets to ppp objects:
Tumor_CD8 <- ppp(...
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Test the relationship between two point patterns
I have two point patterns obtained from medical images. Points are used to represent cell markers.
By visualization, the point pattern A is extremely possible to be a subset of point pattern B. So is ...
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Generating Pseudo-Absences in spatialEco?
I want to generate pseudo absences based on kernel density estimate from a linear feature spatial line layer, where pseudo absences have a higher probability of being sampled near a line.
I have ...
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Adjusting resolution of spatstat::pixellate.psp() output
I am trying to accomplish exactly what is being done in this question: Convert line shapefile to raster, value=total length of lines within cell using spatstat::pixellate.psp() technique (see third ...
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Kernel Density Map points rejected as outside window
I am trying to make a kernel density plot of a points shapefile like so:
library(rgdal)
library(spatstat)
library(maptools)
points <- readOGR(dsn = "C:\\Documents",
layer = "...
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One-dimensional data in spatstat
I have data of one-dimensional points (locations in a straight line). I want to check if the cluster poisson process models or Cox models are a good fit for the data.
Since my data only has x-...
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How to have a Raster output of a ppm model in spastat
I am trying to compare the outputs of species distribution models. My current code uses the following function to calculate TSS scores.
TSS_Score<-function(TrueBinary, Raster) {
Raster[]<-as....
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Error in pairdist calculation
I'm trying to calculate pair distances among the points of my dataset. I have point in EPSG:3857.
This is the code I ran:
I import the data, then:
coordinates(datPb) <- c("X","Y")
proj4string(...
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Removing frame/plot borders from plot.im output
I am plotting point density using the plot.im command in spatstat, and my output always has a frame around the plotted image that becomes thicker when I increase resolution for export. I tried frame=F,...
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Creating polygonal windows for spatial analysis in r
I am attempting to normalize a spatial point pattern using a population density raster in r. My problem is that the function I am trying to run is recognizing the "white space" around the raster I am ...
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Calculating road density in R using kernel density? [closed]
I have a large (~70MB) shapefile of roads and want to convert this to a raster with road density in each cell.
My initial approach was to directly calculate the lengths of line segments in each cell ...
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Adding 'marks' to point file in spatstat?
Using help on this site I have already got the following code from where I can perform certain analyses. However, I'd now like to perform analyses on a certain variable (column z) within the point ...
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Adding point shapefile layer to polygon shapefile window in R?
I'm new to Spatstat for R and I'm trying to add a point layer to a window I've created from a polygon. I see questions like this have been asked before but I still can't get what I need from the ...
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R package spatstat: How to use point process model covariate as factor when pixel image values are numeric
I am trying to model a point process with an image covariate using the ppm() function in the spatstat package in R. I convert my raster to an im object
for use with spatstat, and I run into a problem ...
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Converting raster to im object for point process model covariate in R?
I am trying to convert a raster object to an .im object for use with a point process model in the spatstat package in R.
I begin by creating the raster from a tiff file using the raster() package. No ...
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How to find highest kernel density point
I've been using spatstat to analyse point patterns in R. Here's an example to put this in context:
library(spatstat)
library(maptools) # to convert sp class to ppp
Some point data:
set.seed(1985)
x ...
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How can I connect my point pattern shapefile with my polygon window in R?
I would like to do some spatial statistics in R. I have a point layer called '1983' that represents the distribution of one species, and a polygon layer called 'SA-R' that represents the study area.
...
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Python equivalent of spatstat's spatial point process functions
Is there a free Python package (i.e. PySAL?) that implements the standard summary statistics for spatial point processes, e.g. the F, G, J, and K functions?
I'm happy to use R (i.e. spatstat) if that'...
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R - Crop a pixel image produced by spatstat with a boundary shape
i am using the very good spatial statistic package spatstat to produce probability maps of spatial point patterns.
Here is a simple working result from the examples to try out.
require(spatstat)
...
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How to get the second nearest neighbor between two point patterns in R?
Is there a way to get the distances for the second nearest neighbor between two point patterns in R? The spatstat package has a function called nncross but it only applies to the nearest neighbors ...
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Using R with ArcGIS Desktop?
I've used the integration of R with QGIS, and found it a very uesful tool. Having taken a look at the R toolbox extension for 9 and the extension for 10 it appears they both offer only point ...
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