Questions tagged [spatstat]
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14 questions
0 votes
0 answers
31 views
Assessing goodness-of-fit in a determinantal point process model
I am using determinantal point process models dppm from spatstat.model to do inference on biological data due to their property ...
- 1
1 vote
0 answers
36 views
How to model both clustering and inhibition between marks in multitype point patterns (spatial transcriptomics)?
I have a large dataset from spatial transcriptomics. This is essentially a dense (>c.75million) multitype (~500) marked point pattern dataset where each mark is a gene label, and each point is ...
- 11
3 votes
2 answers
74 views
Point pattern analysis: Large deviations in Hopkins-Skellam metric for the same data in spatstat
I am interested in using the Hopkins-Skellam metric to compare multiple spatial point patterns and test potential associations with some experimental variables. While repeating some of the analysis ...
- 33
1 vote
1 answer
101 views
Limit of Ripley's K function as r goes to infinity?
Considering the Ripley's K function as used in spatial point-process analysis, or the closely related L function, I am wondering what the limit of the function is as r approaches infinity. I am aware ...
1 vote
0 answers
102 views
Image Blur - Disc Kernel [closed]
I'm trying to use the blur() function from the spatstat package in R to blur an image. One ...
1 vote
0 answers
35 views
Why is my L-cross type function not showing me the correct results?
Hi I'm trying to spatially analyse two point patterns in relation to each other: macrophage cells and tumour cells. The images I have generated coordinates from shows that the macrophages group ...
- 11
0 votes
1 answer
103 views
Simulation envelopes for Foxall J not containing the line y=1 (fully reproducible example)
During some exploratory analysis of my data I noticed that when Jfox was calculated for a point pattern relative to some polygons, I frequently obtained that the pooled envelopes area did not include ...
- 349
2 votes
1 answer
148 views
pointwise envelopes not including Theoretical line Foxall J
I am computing pointwise envelopes for the Foxall's J function to investigate the whether some point patterns of interest are clustered, avoid or are independent from other point patterns or polygons. ...
- 349
1 vote
0 answers
77 views
Do I correctly apply hierarchical clustering and K-means on the resource-selection-function values?
I'm trying to find the best way to classify bivariate point patterns in spatstat according to the relationship between two point species: Point pattern ...
- 21
1 vote
0 answers
108 views
Point pattern classification with spatstat: how to choose the right bandwidth for the kernel density?
I'm trying to find the best way to classify bivariate point patterns in spatstat according to the relationship between two point species: Point pattern ...
- 21
0 votes
1 answer
159 views
Extracting the fitted expected number of points from mppm in spatstat (in R)
When fitting a Poisson process model on multiple point patters using the spatstat R package (mppm function), is there a computationally efficient way to extract the fitted expected number of points ...
- 1
0 votes
0 answers
14 views
spatstat::plot.envelope observed line longer than significance band [duplicate]
Using the R package spatstat I'm plotting pooled pointwise envelopes of the function Jfox calculated for different point pattern in an hyperframe. The workflow is ...
- 349
1 vote
2 answers
268 views
spatstat::plot.envelope observed line longer than shading
Using the R package spatstat I'm plotting pooled pointwise envelopes of the function Jfox calculated for different point pattern in an hyperframe. The workflow is ...
- 349
3 votes
1 answer
220 views
What is the "sensible default" for the Kest function of the spatstat package?
I'm reading the documentation on the Kest function (page 731) from the spatstat package. For the argument $r$, that is the "Vector of values for the argument $...
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