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use correct template raster and run 1 disturbance at a time #6

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use correct template raster and run 1 disturbance at a time #6

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33 changes: 21 additions & 12 deletions tests/spatial_integration_test/run_spatial_test.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,10 @@

## It is important to set the virtual environment when calling Python scripts
## from R. This does it:

library(reproducible) #install from CRAN if missing
#you will need googledrive
library(googledrive)
library(reticulate)
virtualenv_list()
#[1] "r-reticulate"
Expand All @@ -16,15 +20,15 @@ reticulate::import("sys")$executable

## This imports the libcbm Python scripts maintained by Scott Morken for the
## CAT and checks the version.
libcbm <- reticulate::import("libcbm")
print(reticulate::py_get_attr(libcbm, "__version__"))
# libcbm <- reticulate::import("libcbm")
# print(reticulate::py_get_attr(libcbm, "__version__"))
#'2.6.0'

## Scott modified a version of libcbmr that also needs to be loaded. This does
## it.
install.packages("remotes")
remotes::install_github("smorken/libcbmr")
library(libcbmr)
# install.packages("remotes")
# remotes::install_github("smorken/libcbmr")
devtools::load_all(".")

## Modifications to find inputs to the stand alone version CBM_core provided to
## Scott from CBoisvenue
Expand All @@ -42,7 +46,11 @@ disturbance_rasters <- {
rasts
}

ldsp_test_area <- terra::rast(file.path(inputsScott,"ldSp_TestArea.tif"))
ldsp_test_area <- reproducible::prepInputs(url = "https://drive.google.com/file/d/1eqRaj3txJBQHnMJ_WWLnUY-Gx5XAW69S/view?usp=drive_link",
destinationPath = "tests/spatial_integration_test/")
#this object is actually 30 x 30 metres and has the correct number of pixels to match spatialDT
disturbance_rasters <- reproducible::postProcess(disturbance_rasters, rasterToMatch = ldsp_test_area,
method = "near")

#extract the growth increments from the nested environments
gc_df <- NULL
Expand Down Expand Up @@ -153,7 +161,7 @@ colnames(spinup_parameter_redup) <- c("spinup_record_idx", "pixelGroup")
growth_increment_pre_merge <- data.frame(
pixelGroup = spatial_inv_gc_merge$pixelGroup,
gcid = spatial_inv_gc_merge$growth_curve_id,
sw_hw = as.integer(spatial_inv_gc_merge$is_sw)
sw_hw = as.integer(spatial_inv_gc_merge$is_sw) #this is already in spinup paramters
)
growth_increment_pre_merge <- growth_increment_pre_merge[
!duplicated(growth_increment_pre_merge$pixelGroup),
Expand Down Expand Up @@ -238,12 +246,13 @@ cbm_simulation_records$cbm_record_id <- as.integer(
rownames(cbm_simulation_records)
)

#TODO: figure out which pixelGroups are disturbed on the annual basis.
cbm_simulation_records <- cbm_simulation_records[
c(
"ldSp_TestArea",
"1998",
"1999",
"2000",
# "1999",
# "2000",
"cbm_record_id",
"spinup_record_idx"
)
Expand All @@ -259,9 +268,9 @@ cbm_simulation_records_expand <- merge(
spatial_data_merge,
by = c(
"ldSp_TestArea",
"1998",
"1999",
"2000"
"1998"#,
# "1999",
# "2000"
),
all.y = TRUE
)
Expand Down