Bug in lastrees on CRAN for windows oldrel

[Jean-Romain]

See lidR results. Not able to reproduce the bug.

running examples for arch 'x64' ... ERROR
Running examples in 'lidR-Ex.R' failed
The error most likely occurred in:

> ### Name: lastrees
> ### Title: Individual tree segmentation
> ### Aliases: lastrees
>
> ### ** Examples
>
> LASfile <- system.file("extdata", "Tree.laz", package="lidR")
> las = readLAS(LASfile, XYZonly = TRUE, filter = "-drop_z_below 0")

[...]

> # segmentation (default parameters but th = 4 + extra output)
> extra = lastrees(las, "dalponte2016", chm, th = 4, extra = TRUE)
Error in as.vector(data) :
  no method for coercing this S4 class to a vector
Calls: lastrees -> dalponte2012 -> matrix -> as.vector
Execution halted

[shafrina]

Hi,

Could you please add function how to write individual tree boundary to shapefile after the lastrees segmentation?

[Jean-Romain]

Hi, could you please open a specific issue with more details about what you're expected. There are many way to achieve that.

[shafrina]

Hi,

I need to convert the crown segmented to shapefiles format (ESRI shapefiles). I know this could be achieved in a few ways, like using writeogr function from rgdal package or using maptools, but i don't know how to start after get the crown (after run the lastrees). My R skills is kinda basic. The result is pretty convincing, but i need to get it analyse in arcgis to compare it with my field crown.

[Jean-Romain]

(using the example given in the doc)

At the end, if you chose a method that enable for an output of the crown in raster format (i.e. dalponte or wartershed using extra = T). Then the raster package have all the tools you need to process and analyse your rasters. You should look at rasterToPolygon

extra = lastrees(las, "dalponte2016", chm, th = 4, extra = TRUE)

library(raster)

crown.shp <- rasterToPolygons(extra$Crown, dissolve = TRUE)

plot(chm)
plot(crown.shp, add = T)

You can also convert that into convex hulls with rgeos

crown.hull <- rgeos::gConvexHull(crown.shp, byid = T)

Then, writreOGR enable for writing a shapefile.

I'm not a specialist. You should look for better information from people who know more than me about these subjects. I can't teach you raster sp rgeos or maptools but I know that all you need already exists.

[shafrina]

Hi,

Yes it works to transfer the raster to spatial polygon dataframe. Thanks so much. i just simply run it as crown.shp <- rasterToPolygons(extra, dissolve = TRUE) and to save it as shapefiles: library(maptools) writePolyShape(crown.shp, "extdata.shp")

It doesn't delineate correctly when i compare it with field data. But anyhow, if adding morphological gradient it will improve the delineation especially my forest is tropical forest. I'm trying to find the coding in R to add the morphological formula to aid with the watershed method.