Treshold suitabillity map
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Ana Tišljar
May 8, 2024, 10:05:52 AMMay 8
to Wallace Ecological Modeling App
Hello Wallace Team!
What do I need to do to hide or remove occurrence points when mapping threshold suitability for the training region (example attached)?
I used Wallace a while back and was able to map threshold suitability without the occurrence points being visible, and it is what I need to do now as well, but can’t seem to figure it out. I tried restarting R and Wallace a few times, but it didn’t change the result.
Any advice on how to approach this?
Kind regards,
Ana
Wallace Ecological Modeling App
May 17, 2024, 1:23:16 PMMay 17
to Wallace Ecological Modeling App
Hi Ana,
I can see how having the occ points visible can be frustrating. You have two options:
1. You can download your raster prediction (from the Save tab) and open it in a GIS program (such as ArcMap or QGIS).
2. You can download your session code (from the Reproduce tab, download an Rmd) and run your analyses inside RStudio. The section on visualizing your prediction can be edited to remove the code for adding the occ points. I can't give exact line numbers, because it will be specific to your work, but will look something like this:
In the ###Visualize chunk:
# Generate map
m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap)
m %>%
leaflet::addLegend("bottomright", colors = c('gray', 'blue'),
title = "Thresholded Suitability<br>(Training)",
labels = c("predicted absence", "predicted presence"),
opacity = 1, layerId = "train") %>%
#add occurrence data
addCircleMarkers(data = occs_Ba, lat = ~latitude, lng = ~longitude,
radius = 5, color = 'red', fill = TRUE, fillColor = "red",
fillOpacity = 0.2, weight = 2, popup = ~pop) %>%
##Add model prediction
addRasterImage(predSel_Ba, colors = rasPal, opacity = 0.7,
group = 'vis', layerId = 'mapPred', method = "ngb") %>%
##add background polygons
addPolygons(data = bgExt_Ba, fill = FALSE,
weight = 4, color = "blue", group = 'proj')
The part in red can be removed to remove the occ pts.
Bethany Johnson
The Wallace Team
I can see how having the occ points visible can be frustrating. You have two options:
1. You can download your raster prediction (from the Save tab) and open it in a GIS program (such as ArcMap or QGIS).
2. You can download your session code (from the Reproduce tab, download an Rmd) and run your analyses inside RStudio. The section on visualizing your prediction can be edited to remove the code for adding the occ points. I can't give exact line numbers, because it will be specific to your work, but will look something like this:
In the ###Visualize chunk:
# Generate map
m <- leaflet() %>% addProviderTiles(providers$Esri.WorldTopoMap)
m %>%
leaflet::addLegend("bottomright", colors = c('gray', 'blue'),
title = "Thresholded Suitability<br>(Training)",
labels = c("predicted absence", "predicted presence"),
opacity = 1, layerId = "train") %>%
#add occurrence data
addCircleMarkers(data = occs_Ba, lat = ~latitude, lng = ~longitude,
radius = 5, color = 'red', fill = TRUE, fillColor = "red",
fillOpacity = 0.2, weight = 2, popup = ~pop) %>%
##Add model prediction
addRasterImage(predSel_Ba, colors = rasPal, opacity = 0.7,
group = 'vis', layerId = 'mapPred', method = "ngb") %>%
##add background polygons
addPolygons(data = bgExt_Ba, fill = FALSE,
weight = 4, color = "blue", group = 'proj')
The part in red can be removed to remove the occ pts.
Bethany Johnson
The Wallace Team
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