NetLogo freezes with {sf} and {circular} functions #4
Description
Dear devs,
Here are some functions that freezes NetLogo 6.3.0:
sf::st_intersect()
circular::circular.mean()
I have come up with a minimum model where you can reproduce both freezing instances with the procedure calc-homerange and calc-movement-metrics, respectively. However, the model requires ESRI files to run. They are available in this link and also attached as .zip.
How to reproduce the freezing errors:
- setupSR > load-shape > move > calc-homerange (st_interesect)
- setupSR > load-shape > move > calc-movement-metrics (circular.mean)
I was able to reproduce the same freezing error in two machines. You can find the .txt model below (and also on the Drive link and on the .zip file).
Let me know if you need any other information.
Thank you.
PS: I was able to circumvent the use of these functions with other ones (namely amt::hr_overlap_feature() and base::mean()), but I thought it would be good to register the problem here.
Edit: when any function of the spatstat package throws a warning, NetLogo freezes. Example funcitons: as.owin(), ppp(), inside.owin(), dilation().
Machine 1 -----
DESKTOP-R12V3D6
Processor Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz 1.99 GHz
Installed RAM 16,0 GB (15,9 GB usable)
System type 64-bit operating system, x64-based processor
NetLogo 6.3
Windows 10 Home
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8
[3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.utf8
time zone: America/Sao_Paulo
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1
Machine 2 -----
pc9
Processor Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz 3.40 GHz
RAM 32,0 GB (31.8 USABLE)
System 64 bits (x64)
NetLogo 6.3
Windows 8 Pro
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
time zone: America/Sao_Paulo
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.1 tools_4.3.1 yaml_2.3.7
Model code -----
extensions [ sr gis ]
globals [ bb-gis bb-gis-shp ]
breed [ monkeys monkey ]
monkeys-own [
x_UTM y_UTM
X_coords
Y_coords
day_list
Name
]
to test
ca
setupSR
load-shape
move
calc-homerange
stop
end
to setupSR
ca
sr:setup
sr:run "library('tidyverse')"
sr:run "library(amt)"
sr:run "library('circular')"
end
to load-shape
ca
set-current-directory path
; load projection
gis:load-coordinate-system "Guarei_polyg_sept2022.prj" ; WGS_1984_UTM_Zone_22S
; load the poligon (.shp) to determine forest and matrix patches
set bb-gis-shp gis:load-dataset "Guarei_polyg_sept2022.shp" ; fragment/study area polygon
; define envelope
gis:set-world-envelope gis:envelope-of bb-gis-shp
; draw forest fragment
gis:set-drawing-color green
gis:draw bb-gis-shp 2
; shape for cropping home range
sr:run "shp <- 'Guarei_polyg_sept2022.shp' %>% sf::read_sf()"
; sr:run "shp <- sf::st_cast(shp, 'MULTIPOLYGON')"
print sr:runresult "shp"
print "===== read_sf debug ====="
end
to move
if count monkeys > 1 [
ask monkeys [ die ]
create-monkeys 1
]
if count monkeys = 0 [ create-monkeys 1 ]
if count monkeys = 1 [
ask monkeys [
pen-down
set X_coords []
set Y_coords []
set day_list []
set Name [who] of self
]
ask monkeys [
repeat n_steps [
move-to one-of patches
ask patch-here [ set pcolor white ]
set x_UTM (item 0 gis:envelope-of self)
set y_UTM (item 2 gis:envelope-of self)
set X_coords lput x_UTM X_coords
set Y_coords lput y_UTM Y_coords
set day_list lput 1 day_list
]
]
]
ask one-of monkeys [
(sr:set-agent-data-frame "tamarins" monkeys "who" "x_coords" "y_coords" "day_list")
; sr:run "print(typeof(tamarins))"
print "==== SR debugging 2 ==== "
; stop
sr:run "names(tamarins) <- c('Name', 'X', 'Y', 'day')"
print "==== SR debugging 3 ==== "
; stop
;;; split the data.frame into coordinates and factor variable
sr:run "xy <- tamarins[,c('X','Y', 'day')]"
sr:run "id <- tamarins$Name"
sr:run "db <- cbind(xy, id)"
sr:run "db_ <- db %>% make_track(.x=X, .y=Y, id = id, crs = 32722)"
; show r:get "colnames(db_)"
; show r:get "db_"
print "==== SR debugging 4 ==== "
; stop
]
end
to calc-homerange
print " ------------- Home range size ------------------ "
;MCP ===================================================
sr:run "db_MCP <- db_ %>% hr_mcp(., levels = c(0.50, 1.0))"
sr:run "db_MCP_area <- db_MCP %>% hr_area(.)"
print sr:runresult "db_MCP_area"
print "==== SR debugging 5 ==== "
; stop
; KDE ===================================================
sr:run "KDE <- db_ %>% hr_kde(., levels = c(0.50, 0.95))"
; print sr:runresult "db_KDE"
; stop
sr:run "KDE_area <- KDE %>% hr_area(.)"
print "==== SR debugging 6 ==== "
; stop
sr:run "KDE_area <- KDE_area %>% dplyr::select(-what)"
sr:run "KDE95 <- KDE_area %>% dplyr::filter(level == 0.95) %>% dplyr::select(area) %>% unlist() %>% as.vector()" ; %>% round(2) "
sr:run "KDE50 <- KDE_area %>% dplyr::filter(level == 0.50) %>% dplyr::select(area) %>% unlist() %>% as.vector()" ; %>% round(2) "
print "==== SR debugging 7 ==== "
; stop
;; NOT WORKING ;; =========================================================================
; (with st_intersection()) -> NetLogo freezes
; Transform KDE to sf
sr:run "KDE_sf <- amt::hr_isopleths(KDE) %>% sf::st_as_sf(., crs = 32722)"
print sr:runresult "KDE_sf"
print sr:runresult "str(KDE_sf)"
print "==== SR debugging 9 ==== "
; stop
; Transform KDE to sf and crop
sr:run "KDE_sf <- amt::hr_isopleths(KDE) %>% sf::st_as_sf(., crs = 32722)"
sr:run "cropped <- sf::st_intersection(KDE_sf, shp)"
print "==== SR debugging 10 ==== "
stop
end
to calc-movement-metrics
sr:run "mov1 <- db_ %>% mutate( step_length = step_lengths(., append_last = TRUE), turn_ang = direction_rel(., append_last = TRUE) )"
sr:run "mov1 <- mov1 %>% summarise( step_length_mean = mean(step_length, na.rm = TRUE), step_length_sd = sd(step_length, na.rm = TRUE), turn_ang_mean = circular::mean.circular(turn_ang, na.rm = TRUE), turn_ang_sd = circular::sd.circular(turn_ang, na.rm = TRUE) )"
end
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