diff --git a/src/model_fitting/abundance_model.R b/src/model_fitting/abundance_model.R
index 0e53fd2ec8ee60c2cbd4330cae1b37fe2705b3b8..bc661a0bde80b4b15e987d79e8bfcc08a4bb85da 100644
--- a/src/model_fitting/abundance_model.R
+++ b/src/model_fitting/abundance_model.R
@@ -141,7 +141,9 @@ print(paste("this is ESW aerial:", ESW_aerial))
NCS <- 1.12 #nest construction rate from Spehar et al. 2010
#NCS <- 1.18 # from Husson 2009
PNB <- 0.88 # proportion of nest builders from Spehar et al. 2010
-#PNB <- 0.89
+ #PNB <- 0.89 # from husson 2009
+# there is also a NCS for lower Kinabatangan, but not sure, where this is exactly
+
options("scipen" = 100, "digits" = 4)
diff --git a/src/resource_use/preparing_grid_resource_use.py b/src/resource_use/preparing_grid_resource_use.py
new file mode 100644
index 0000000000000000000000000000000000000000..78de0bd09d93ea1f18f00b18eaee85806b559275
--- /dev/null
+++ b/src/resource_use/preparing_grid_resource_use.py
@@ -0,0 +1,289 @@
+# -*- coding: utf-8 -*-
+"""
+Spyder Editor
+
+# script to prepare the grid with the resource use information
+# in the output file we will have a
+# a 1 at the first position if pixel has to be discarded
+# a 2 at the first position if the pixel is considered
+# a 1 at the second position for IDN
+# a 2 at the second position for MYS
+# a 0 - 5 at the 3rd position depending on the resource use category
+# the grid_id from the 4rth to the 10th position (6 positions)
+#
+# we will now clip with populations and then also do this in the
+# other resource use table, let's see how this looks like
+"""
+
+
+import numpy as np
+import MacPyver as mp
+import os
+
+
+"""
+# absence
+os.system("gdal_rasterize \
+-l absence_diss_exp \
+-burn 1 \
+-ot Float32 \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep_expanded_22_08_17.shp \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep_expanded_22_08_17.tif")
+
+os.system("gdal_rasterize \
+-l absence_shape_rep_expanded_22_08_17 \
+-burn 1 \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep_expanded_22_08_17.shp \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep_expanded_22_08_17.tif")
+
+os.system("gdalwarp \
+-t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-ot Float64 -r bilinear \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 \
+-ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep_expanded_22_08_17.tif \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_expanded_22_08_17_repro_res.tif"
+)
+
+os.system("gdalwarp \
+-t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-ot Float64 -r near \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 \
+-ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/future/grid.tif \
+/homes/mv39zilo/work/Borneo/data/future/grid_repro_res.tif"
+)
+
+
+os.system("gdalwarp \
+-t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-ot Float64 -r near \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 \
+-ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/predictors/cleaned_data/cleaned_predictors/dem.tif \
+/homes/mv39zilo/work/Borneo/data/predictors/cleaned_data/cleaned_predictors/dem_repro_res.tif"
+)
+
+"""
+
+
+
+
+
+absence_path = "/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_expanded_22_08_17_repro_res.tif"
+absence = mp.tiff.read_tif(absence_path, 1)
+
+grid_layer_path = "/homes/mv39zilo/work/Borneo/data/future/grid_repro_res.tif"
+grid = mp.tiff.read_tif(grid_layer_path, 1)
+
+
+grid = np.where(absence == 0, grid, 0)
+np.unique(grid)
+
+
+# now assigning number for each resource use
+# 0 - absence
+# 1 - plantation
+# 2 - deforestation
+# 3 - logging
+# 4 - primary forest < 750m
+# 5 - primary forest > 750
+# 6 - regrowth
+# 7 - plantations before 2000
+# 8 - other
+
+
+gaveau_defor_path = "/homes/mv39zilo/work/Borneo/data/predictors/raw_data/Remaining_forest_in_2015_and_deforestation_1973-2015/REGIONBorneo_FCDefDeg_1973to2015_CIFOR_repro_res.tif"
+gaveau_defor_raw = mp.tiff.read_tif(gaveau_defor_path, 1)
+gaveau_deforested = np.where((gaveau_defor_raw > 6 ) &
+ (gaveau_defor_raw < 10), 1, 0)
+gaveau_logged = np.where(gaveau_defor_raw == 2, 1, 0)
+gaveau_primary_forest = np.where(gaveau_defor_raw == 1, 1, 0)
+gaveau_regrowth = np.where(gaveau_defor_raw == 4, 1, 0)
+
+#plantation
+plantation_path = "/homes/mv39zilo/work/Borneo/data/predictors/raw_data/Land_cover_trajectory_before_oil-palm_and_pulpwood_establishment/raster_plantation.tif"
+plantations = mp.tiff.read_tif(plantation_path, 1)
+
+# old plantations
+old_plantations_path = "/homes/mv39zilo/work/Borneo/data/predictors/raw_data/Land_cover_trajectory_before_oil-palm_and_pulpwood_establishment/raster_plantation_old_repro_res.tif"
+old_plantations = mp.tiff.read_tif(old_plantations_path, 1)
+
+
+
+dem_path = "/homes/mv39zilo/work/Borneo/data/predictors/cleaned_data/cleaned_predictors/dem_repro_res.tif"
+dem = mp.tiff.read_tif(dem_path, 1)
+
+
+
+# elevation
+# --> how much of primary forest in high elevation
+
+# we can save some computing time by only considering
+# the grid and not everything, because abundance will only be
+# in rid
+grid = np.where((plantations == 1) &
+ (grid == 1), 1 , grid)
+grid = np.where((plantations == 0) &
+ (gaveau_deforested == 1)&
+ (grid == 1), 2 , grid)
+
+# 3 logged
+grid = np.where((plantations == 0) &
+ (gaveau_deforested == 0)&
+ (gaveau_logged == 1) &
+ (grid == 1), 3 , grid)
+# 4 primary forest
+grid = np.where((plantations == 0) &
+ (gaveau_deforested == 0)&
+ (gaveau_logged == 0) &
+ (gaveau_primary_forest == 1) &
+ (grid == 1), 4 , grid)
+
+# add here primary forest at high altitudes
+# because everywhere where we have primary forest
+# we no longer have a 1 in grid but a six we do it differently
+# 5 primary montane
+grid = np.where((grid == 4) &
+ (dem > 750), 5, grid)
+
+
+# 6 regrowth
+grid = np.where((plantations == 0) &
+ (gaveau_deforested == 0)&
+ (gaveau_logged == 0) &
+ (gaveau_primary_forest == 0) &
+ (gaveau_regrowth ==1) &
+ (grid == 1), 6 , grid)
+
+# 7 is old plantations
+
+grid = np.where((plantations == 0) &
+ (gaveau_deforested == 0)&
+ (gaveau_logged == 0) &
+ (gaveau_primary_forest == 0) &
+ (gaveau_regrowth == 0) &
+ (old_plantations == 1) &
+ (grid == 1), 7 , grid)
+
+
+
+# 8 is other
+grid = np.where((plantations == 0) &
+ (gaveau_deforested == 0)&
+ (gaveau_logged == 0) &
+ (gaveau_primary_forest == 0) &
+ (gaveau_regrowth ==0) &
+ (grid == 1), 8, grid)
+
+
+np.unique(grid)
+
+mp.tiff.write_tif(file_with_srid = grid_layer_path,
+ full_output_name = "/homes/mv39zilo/work/Borneo/data/resource_use/resource_use_grid.tif",
+ data = grid,
+ dtype = 0)
+
+
+# grid map with four categories
+# 0 - absence - 0
+# 1 - plantation - 1
+# 2 - deforestation - 1
+# 3 - logging - 1
+# 4 - primary forest < 750m - 2
+# 5 - primary forest > 750 - 2
+# 6 - regrowth - 2
+# 7 - plantations before 2000 - 3
+# 8 - other - 3
+
+grid_map = np.where((grid <= 3) &
+ (grid > 0), 1, 0)
+grid_map = np.where((grid <= 6) &
+ (grid > 3), 2, grid_map)
+grid_map = np.where((grid > 6), 3, grid_map)
+
+
+# need to clip this with the area in which we have orangutans in 1999
+year = 1999
+abundance_path = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/abundMod/testing_ae_and_absence/pipeline_results/ppln_ae75m_50-2017-02-28T18-00-52/prediction_map_" + str(year) + "_2017-02-28_repro_res.tif"
+abundance = mp.tiff.read_tif(abundance_path, 1)
+
+
+grid_map = np.where(abundance > 0.1, grid_map, 0)
+np.unique(grid_map)
+
+mp.tiff.write_tif(file_with_srid = grid_layer_path,
+ full_output_name = "/homes/mv39zilo/work/Borneo/data/resource_use/resource_use_grid_map.tif",
+ data = grid_map,
+ dtype = 0)
+"""
+# test
+indir = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use"
+abundance_layer_path = indir + "/abundance_pred_2015_no_absence.tif"
+# read the data
+abundance_data = mp.tiff.read_tif(abundance_layer_path, 1)
+
+test = np.where((grid == 0) &
+ (abundance_data > 0), abundance_data, 0)
+np.sum(test)
+mp.tiff.write_tif(file_with_srid = grid_layer_path,
+ full_output_name = "/homes/mv39zilo/work/Borneo/data/bootstrap/test.tif",
+ data = test,
+ dtype = 4)
+"""
+# rasterize borneo with info on country or province
+
+"""
+os.system("gdal_rasterize \
+-a ID_1 \
+-l Borneo \
+-ot Float32 \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif")
+
+os.system("gdal_rasterize \
+-a ID_1 \
+-l Borneo \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif")
+
+os.system("gdalwarp \
+-r near -t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo__province_repro_res.tif")
+
+os.system("gdal_rasterize \
+-a ID_0 \
+-l Borneo \
+-ot Float32 \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif")
+
+os.system("gdal_rasterize \
+-a ID_0 \
+-l Borneo \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif")
+
+os.system("gdalwarp \
+-r near -t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country_repro_res.tif")
+
+"""
diff --git a/src/validation/grid_mapping_for_resource_use.py b/src/validation/grid_mapping_for_resource_use.py
new file mode 100644
index 0000000000000000000000000000000000000000..092f97584b51bb6854d266b0ff68053b9ca7bb8b
--- /dev/null
+++ b/src/validation/grid_mapping_for_resource_use.py
@@ -0,0 +1,192 @@
+# -*- coding: utf-8 -*-
+"""
+Spyder Editor
+
+# script to prepare the grid with the resource use information
+# in the output file we will have a
+# a 1 at the first position if pixel has to be discarded
+# a 2 at the first position if the pixel is considered
+# a 1 at the second position for IDN
+# a 2 at the second position for MYS
+# a 0 - 5 at the 3rd position depending on the resource use category
+# the grid_id from the 4rth to the 10th position (6 positions)
+#
+# now assigning number for each resource use
+# now assigning number for each resource use
+# 0 - absence
+# 1 - plantation
+# 2 - deforestation
+# 3 - landcover change
+# 4 - logging
+# 5 - primary forest < 750m
+# 6 - primary forest > 750
+# 7 - regrowth
+# 8 - plantations before 2000
+# 9 - other
+"""
+
+
+import numpy as np
+import MacPyver as mp
+import os
+
+
+"""
+# absence
+os.system("gdal_rasterize \
+-l absence_shape_rep \
+-burn 1 \
+-ot Float32 \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.shp \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.tif")
+
+os.system("gdal_rasterize \
+-l absence_shape_rep \
+-burn 1 \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.shp \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.tif")
+
+os.system("gdalwarp \
+-t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-ot Float64 -r near \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 \
+-ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_rep.tif \
+/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_repro_res.tif"
+)
+
+os.system("gdalwarp \
+-t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-ot Float64 -r near \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 \
+-ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/future/grid.tif \
+/homes/mv39zilo/work/Borneo/data/future/grid_repro_res.tif"
+)
+
+
+
+"""
+
+absence_path = "/homes/mv39zilo/work/Borneo/data/response/cleaned_data/absence_shape/absence_shape_expanded_22_08_17_repro_res.tif"
+absence = mp.tiff.read_tif(absence_path, 1)
+
+# input grid with grid_ids as values
+
+grid = mp.tiff.read_tif("/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/future/grid_with_id_repro_res.tif", 1)
+np.unique(grid)
+
+resource_use = mp.tiff.read_tif("/homes/mv39zilo/work/Borneo/data/resource_use/resource_use_grid.tif", 1)
+np.unique(resource_use)
+
+country_layer_path = "/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country_repro_res.tif"
+borneo = mp.tiff.read_tif(country_layer_path, 1)
+"""
+# format
+1 0 0 0 0 0 000 000
+(1 / 2) 0 (3 / 6) 0 (1-9) 0 700 000
+out/in, MYS/IDN, category,grid_id
+"""
+
+# pixel is out / out
+resource_grid_1 = np.where(absence == 1, 100000000000, 200000000000)
+
+# country
+resource_grid_2 = np.where(borneo == 136, (resource_grid_1 + 3 * 1000000000),
+ resource_grid_1)
+resource_grid_3 = np.where(borneo == 106, (resource_grid_2 + 6 * 1000000000),
+ resource_grid_2)
+
+
+resource_grid_4 = np.where(resource_use > 0, (resource_grid_3 + resource_use * 10000000),
+ resource_grid_3)
+np.unique(resource_grid_4 )
+
+
+
+
+ # now assigning number for each resource use
+
+resource_grid_5 = np.where(grid > 0, (resource_grid_4 + grid),
+ resource_grid_4 )
+np.unique(resource_grid_5)
+
+
+mp.tiff.write_tif(file_with_srid = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/future/grid_with_id_repro_res.tif",
+ full_output_name = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use/resource_grid_absence_country_category_id.tif",
+ data = resource_grid_5,
+ dtype = 5)
+
+# use this in R script "prepare_boot_grid.R"
+
+
+"""
+# test
+indir = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use"
+abundance_layer_path = indir + "/abundance_pred_2015_no_absence.tif"
+# read the data
+abundance_data = mp.tiff.read_tif(abundance_layer_path, 1)
+
+test = np.where((grid == 0) &
+ (abundance_data > 0), abundance_data, 0)
+np.sum(test)
+mp.tiff.write_tif(file_with_srid = grid_layer_path,
+ full_output_name = "/homes/mv39zilo/work/Borneo/data/bootstrap/test.tif",
+ data = test,
+ dtype = 4)
+"""
+# rasterize borneo with info on country or province
+
+"""
+os.system("gdal_rasterize \
+-a ID_1 \
+-l Borneo \
+-ot Float32 \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif")
+
+os.system("gdal_rasterize \
+-a ID_1 \
+-l Borneo \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif")
+
+os.system("gdalwarp \
+-r near -t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province.tif \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo__province_repro_res.tif")
+
+os.system("gdal_rasterize \
+-a ID_0 \
+-l Borneo \
+-ot Float32 \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif")
+
+os.system("gdal_rasterize \
+-a ID_0 \
+-l Borneo \
+-ot Float32 \
+ -ts 1122 1293 \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo.shp \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif")
+
+os.system("gdalwarp \
+-r near -t_srs '+proj=aea +lat_1=7 +lat_2=-32 +lat_0=-15 +lon_0=125 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs' \
+-te -1751798.359 1267454.241 -629798.359 2560454.241 -ts 1122 1293 \
+-overwrite \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country.tif \
+/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_country_repro_res.tif")
+
+"""
diff --git a/src/validation/marias_boot_correct.R b/src/validation/marias_boot_correct.R
index d817ac9fa7860fca1eb189f01e3d91191b9d6c00..a65ae005d000c154aa3cccdceb328f7d0ebce5b2 100644
--- a/src/validation/marias_boot_correct.R
+++ b/src/validation/marias_boot_correct.R
@@ -89,7 +89,7 @@ options("scipen" = 100, "digits" = 4)
# load("/homes/mv39zilo/work/Borneo/outreach/Correspondance/November_2016/Roger/images/abundance_model_fitting_2016-12-02.RData")
-#indir <- "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/abundMod/testing_ae_and_absence/pipeline_results/ppln_ae75m_50-2017-02-28T18-00-52"
+#indir <- "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/abundMod/testing_ae_and_absence/pipeline_results/absence_density/ppln_ae75m_50-2017-02-28T18-00-52"
# include abundMod_results
#oreductirs_obs und m_terms
abundMod_results_path <- path.to.current(indir, "abundMod_results", "rds")
@@ -104,14 +104,13 @@ m_terms_path <- path.to.current(indir, "m_terms", "rds")
if(is_verbose){print(paste("m_terms_path", m_terms_path))}
m_terms <- readRDS(m_terms_path)
-
ests=apply(abundMod_results [, grepl(x=colnames(abundMod_results ), pattern="coeff")], 2, function(x){
x[is.na(x)]=0
sum(x*abundMod_results$w_aic)
})
SEs=apply(abundMod_results [, grepl(x=colnames(abundMod_results ), pattern="SE")], 2, function(x){
x[is.na(x)]=0
- sum(x*abundMod_results$w_aic)
+ sum(x*abundMod_results$w_ai)c
})
SEs=SEs[-length(SEs)]
names(ests)=gsub(x=names(ests), pattern="coeff_", replacement="", fixed=T)