DSM- extract the CV as shapefile

[Lisa Marie Leclerc]

Hi, 

I was wondering what will be the R script to extract the CV of a DSM, as a shapefile to visualize the variance estimate in ARC GIS.  

Thanks 

Lisa

[Eric Rexstad]

Lisa

Here is a very simple answer to your question, based upon the use of dsm_var_gam​ for estimating uncertainty from your dsm​ model. The following code is based around the example provided at this case study website

Example `dsm` analysis: pantropical dolphins in the Gulf of Mexico Example spatial analysis of pantropical spotted dolphins. examples.distancesampling.org

I have omitted much of the code, leaving the fitting of a simple dsm​ model to data and using dsm_var_gam​ for variance estimation. I encourage you to look at the help​ for the function dsm_var_gam​ to learn the structure of the object produced by this function.

library(dsm)

load("mexdolphins-extra.rda")

data(mexdolphins)

library(rgdal)

library(maptools)

library(plyr)

proj4string(survey.area) <- CRS("+proj=longlat +datum=WGS84")

lcc_proj4 <- CRS("+proj=lcc +lat_1=20 +lat_2=60 +lat_0=40 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs ")

survey.area <- spTransform(survey.area, CRSobj=lcc_proj4)

survey.area <- data.frame(survey.area@polygons[[1]]@Polygons[[1]]@coords)

names(survey.area) <- c("x", "y")

library(Distance)

detfc.hr.null <- ds(distdata, max(distdata$distance), key="hr", adjustment=NULL)

dsm.xy.depth <- dsm(count~s(x,y,k=10) + s(depth,k=20), detfc.hr.null, segdata, obsdata, method="REML")

summary(dsm.xy.depth)

plot(dsm.xy.depth, select=2)

dsm.xy.depth.pred <- predict(dsm.xy.depth, preddata, preddata$area)

preddata.var <- split(preddata, 1:nrow(preddata))

dsm.xy.depth.var <- dsm_var_gam(dsm.xy.depth, pred.data=preddata.var,off.set=preddata$area)

summary(dsm.xy.depth.var)

cv.by.gridcell <- sqrt(dsm.xy.depth.var$pred.var)/dsm.xy.depth.pred

The final step produces CV values for all 1374 prediction grid cells in this project. I have not attached the spatial coordinates to these CV values. Those spatial coordinates are contained in the object pred.polys​ You can combine the two to create something I suspect you can export to ArcGIS.  I suspected the main part of your question was how to compute the CV from the elements contained within an object created by dsm_var_gam​. I hope this answers your question.

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From: distance...@googlegroups.com <distance...@googlegroups.com> on behalf of Lisa Marie Leclerc <lisalec...@gmail.com>
Sent: 29 April 2024 15:43
To: distance-sampling <distance...@googlegroups.com>
Subject: [distance-sampling] DSM- extract the CV as shapefile

 

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