README.md

In mdsumner/scspatstat: Common Forms for `spatstat` Structures

scspatstat

The goal of scspatstat is to convert spatstat data structures to a generic common form that that can be used for conversion a wide variety of data structures.

This is work in progress and at a very early stage. More to come.

Example

This is a basic example showing the component decomposition of a spatstat point pattern.

library(scspatstat)
#> Loading required package: silicate
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
data("chorley", package = "spatstat.data")
sc_object(chorley) %>% slice(2L)
#> # A tibble: 1 x 2
#>   object_  mark  
#>   <chr>    <fct> 
#> 1 93b18381 larynx

data("nbfires", package= "spatstat.data")
sc_path(spatstat::as.owin(nbfires))
#> # A tibble: 6 x 4
#>   object_ type      ncoords_ path_   
#>   <chr>   <chr>        <int> <chr>   
#> 1 1       polygonal      500 e3fa5d01
#> 2 2       polygonal       54 750dce73
#> 3 3       polygonal       92 8473c6e7
#> 4 4       polygonal       79 d339ae80
#> 5 5       polygonal       66 619e2045
#> 6 6       polygonal       80 590ebdd7

print(sc_coord(spatstat::as.owin(nbfires)), n = 5)
#> # A tibble: 871 x 2
#>       x     y
#>   <dbl> <dbl>
#> 1   412   123
#> 2   415   124
#> 3   415   124
#> 4   416   123
#> 5   419   122
#> # ... with 866 more rows

With these three components working sc_coord, sc_object and sc_path, and using the framework in sc, the parent package can use these in generic form. We can already convert to PATH and then on to other models for these polygonal forms in spatstat.

library(scspatstat)
str(nbfires_path <- silicate::PATH(spatstat::as.owin(nbfires)))
#> List of 4
#>  $ object          :Classes 'tbl_df', 'tbl' and 'data.frame':    1 obs. of  5 variables:
#>   ..$ type      : chr "polygonal"
#>   ..$ singular  : chr "km"
#>   ..$ plural    : chr "km"
#>   ..$ multiplier: num 0.404
#>   ..$ object_   : chr "a03120f9"
#>  $ path            :Classes 'tbl_df', 'tbl' and 'data.frame':    6 obs. of  4 variables:
#>   ..$ object_ : chr [1:6] "1" "2" "3" "4" ...
#>   ..$ type    : chr [1:6] "polygonal" "polygonal" "polygonal" "polygonal" ...
#>   ..$ ncoords_: int [1:6] 500 54 92 79 66 80
#>   ..$ path_   : chr [1:6] "9029371a" "cc508bdf" "649fd705" "74cc44ea" ...
#>  $ path_link_vertex:Classes 'tbl_df', 'tbl' and 'data.frame':    871 obs. of  2 variables:
#>   ..$ path_  : chr [1:871] "9029371a" "9029371a" "9029371a" "9029371a" ...
#>   ..$ vertex_: chr [1:871] "803ce52e" "cbe70647" "e3e059ac" "dc1adfe2" ...
#>  $ vertex          :Classes 'tbl_df', 'tbl' and 'data.frame':    871 obs. of  3 variables:
#>   ..$ x      : num [1:871] 412 415 415 416 419 ...
#>   ..$ y      : num [1:871] 123 124 124 123 122 ...
#>   ..$ vertex_: chr [1:871] "803ce52e" "cbe70647" "e3e059ac" "dc1adfe2" ...
#>  - attr(*, "class")= chr [1:2] "PATH" "sc"
#>  - attr(*, "join_ramp")= chr [1:4] "object" "path" "path_link_vertex" "vertex"

SC(nbfires_path)
#> $object
#> # A tibble: 1 x 5
#>   type      singular plural multiplier object_ 
#>   <chr>     <chr>    <chr>       <dbl> <chr>   
#> 1 polygonal km       km          0.404 a03120f9
#> 
#> $object_link_edge
#> # A tibble: 865 x 2
#>    edge_    object_
#>    <chr>    <chr>  
#>  1 9af05d8c 1      
#>  2 a3aa5a4b 1      
#>  3 c717aff4 1      
#>  4 26827710 1      
#>  5 76f55d42 1      
#>  6 ce933960 1      
#>  7 74035c99 1      
#>  8 151cfa9f 1      
#>  9 5f23185d 1      
#> 10 dbafa8ae 1      
#> # ... with 855 more rows
#> 
#> $edge
#> # A tibble: 865 x 3
#>    .vertex0 .vertex1 edge_   
#>    <chr>    <chr>    <chr>   
#>  1 803ce52e cbe70647 9af05d8c
#>  2 cbe70647 e3e059ac a3aa5a4b
#>  3 e3e059ac dc1adfe2 c717aff4
#>  4 dc1adfe2 f0b92282 26827710
#>  5 f0b92282 916115bf 76f55d42
#>  6 916115bf 1e06a473 ce933960
#>  7 1e06a473 e3f8d802 74035c99
#>  8 e3f8d802 e7e9da37 151cfa9f
#>  9 e7e9da37 3dee1ea0 5f23185d
#> 10 3dee1ea0 c875483e dbafa8ae
#> # ... with 855 more rows
#> 
#> $vertex
#> # A tibble: 871 x 3
#>        x     y vertex_ 
#>    <dbl> <dbl> <chr>   
#>  1   412   123 803ce52e
#>  2   415   124 cbe70647
#>  3   415   124 e3e059ac
#>  4   416   123 dc1adfe2
#>  5   419   122 f0b92282
#>  6   424   123 916115bf
#>  7   430   125 1e06a473
#>  8   431   133 e3f8d802
#>  9   436   132 e7e9da37
#> 10   436   128 3dee1ea0
#> # ... with 861 more rows
#> 
#> attr(,"class")
#> [1] "SC" "sc"

(Note that owin is supported only on its own, and points ppp and line segments psp are supported separately. We need a way to intermingle structured "windows" and the underlying patterns, but for now I consider that a higher specialization than silicate itself.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

mdsumner/scspatstat documentation built on May 22, 2019, 5:06 p.m.