diff --git a/src/resource_use/resource_use_table_no_protected_country_split_MYS.py b/src/resource_use/resource_use_table_no_protected_country_split_MYS.py
new file mode 100644
index 0000000000000000000000000000000000000000..95373177799f13a97a35c667b46eb3e7c54bc104
--- /dev/null
+++ b/src/resource_use/resource_use_table_no_protected_country_split_MYS.py
@@ -0,0 +1,910 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jul 31 12:51:35 2017
+
+@author: mv39zilo
+script to make the table for the graph and the table
+# 0 - absence
+# 1 - plantation
+# 2 - deforestation
+# 3 - logging
+# 4 - primary forest < 750m
+# 5 - primary forest > 750
+# 6 - regrowth
+# 7 - plantations before 2000
+# 8 - other
+"""
+
+import numpy as np
+import MacPyver as mp
+import os
+
+year = 1999
+
+grid_layer_path = "/homes/mv39zilo/work/Borneo/data/resource_use/resource_use_grid.tif"
+resource_use = mp.tiff.read_tif(grid_layer_path, 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)
+np.unique(borneo)
+
+province_layer_path = "/homes/mv39zilo/work/Borneo/data/auxiliary_additional_data/Borneo_shape/cleaned_data/Borneo_province_repro_res.tif"
+borneo_province = mp.tiff.read_tif(province_layer_path, 1)
+np.unique(borneo_province)
+
+
+populations = mp.tiff.read_tif("/homes/mv39zilo/work/Borneo/data/populations_phva/meta_kalsarsab_20002015_diss_no_reintro_repro_res.tif", 1)
+
+#
+
+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)
+if 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"
+if year==2015:
+ 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) + "_2017-03-01_repro_res.tif"
+
+print abundance_path
+# read the data
+abundance_data = mp.tiff.read_tif(abundance_path, 1)
+
+
+# we want to know mean density of ou in plantation
+# so all pixels where no ou is 0, not na, also for absence
+
+abundance_data = np.where(populations != 0, abundance_data, 0)
+
+
+resource_use_MYS = np.where(borneo == 136, resource_use, 0)
+np.unique(resource_use_MYS)
+
+
+
+resource_use_SAB = np.where(borneo_province == 10, resource_use, 0)
+np.unique(resource_use_SAB)
+
+resource_use_SAW = np.where(borneo_province == 11, resource_use, 0)
+np.unique(resource_use_SAW)
+
+
+#IDN
+resource_use_IDN = np.where(borneo == 106, resource_use, 0)
+
+
+
+
+"""
+mp.tiff.write_tif(file_with_srid = grid_layer_path,
+ full_output_name = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use/test.tif",
+ data = resource_use_SAW ,
+ dtype = 4)
+
+"""
+
+
+
+
+#MYS
+
+file_path_table = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use/abundance_density_resource_use_" + str(year) + "no_absence.csv"
+resource_use = open(file_path_table, 'w')
+
+resource_use.write("type, country, abundance, percent_total, area, density \n")
+
+
+abundance_data_MYS = np.where(borneo == 136, abundance_data, 0 )
+count_abundance_MYS = np.count_nonzero(abundance_data_MYS)
+abundance_sum_MYS = np.sum(abundance_data_MYS)
+mean_abundance_MYS = abundance_sum_MYS/count_abundance_MYS
+
+resource_use.write( "total abundance" + "," + "MYS" + "," + str(abundance_sum_MYS) + "," +
+ str(abundance_sum_MYS/abundance_sum_MYS * 100 ) + "," +
+ str(count_abundance_MYS) +"," +
+ str(mean_abundance_MYS) + "\n")
+
+
+# planted
+planted_abundance_MYS = np.where(resource_use_MYS == 1, abundance_data_MYS, 0)
+abundance_count_MYS_planted = np.count_nonzero(planted_abundance_MYS)
+abundance_sum_MYS_planted = np.sum(planted_abundance_MYS)
+abundance_mean_MYS_planted = abundance_sum_MYS_planted / abundance_count_MYS_planted
+
+
+resource_use.write( "plantation" + "," + "MYS" + "," + str(abundance_sum_MYS_planted) + "," +
+ str(abundance_sum_MYS_planted/abundance_sum_MYS * 100 ) + "," +
+ str(abundance_count_MYS_planted) +"," +
+ str(abundance_mean_MYS_planted) + "\n")
+
+
+
+# deforested
+deforested_abundance_MYS = np.where(resource_use_MYS == 2, abundance_data_MYS, 0)
+abundance_count_MYS_deforested = np.count_nonzero(deforested_abundance_MYS)
+abundance_sum_MYS_deforested = np.sum(deforested_abundance_MYS)
+abundance_mean_MYS_deforested = abundance_sum_MYS_deforested/abundance_count_MYS_deforested
+
+resource_use.write( "deforestation" + "," + "MYS" + "," + str(abundance_sum_MYS_deforested) + "," +
+ str(abundance_sum_MYS_deforested/abundance_sum_MYS * 100 ) + "," +
+ str(abundance_count_MYS_deforested) +"," +
+ str(abundance_mean_MYS_deforested) + "\n")
+
+
+
+
+ # logged
+
+logged_abundance_MYS = np.where(resource_use_MYS == 3, abundance_data_MYS, 0)
+abundance_count_MYS_logged = np.count_nonzero(logged_abundance_MYS)
+abundance_sum_MYS_logged = np.sum(logged_abundance_MYS)
+abundance_mean_MYS_logged = abundance_sum_MYS_logged/abundance_count_MYS_logged
+
+resource_use.write( "logging" + "," + "MYS" + "," + str(abundance_sum_MYS_logged) + "," +
+ str(abundance_sum_MYS_logged/abundance_sum_MYS * 100 ) + "," +
+ str(abundance_count_MYS_logged) +"," +
+ str(abundance_mean_MYS_logged) + "\n")
+
+ # primary
+primary_abundance_MYS = np.where(resource_use_MYS == 4, abundance_data_MYS, 0)
+abundance_count_MYS_primary = np.count_nonzero(primary_abundance_MYS)
+abundance_sum_MYS_primary = np.sum(primary_abundance_MYS)
+abundance_mean_MYS_primary = abundance_sum_MYS_primary/abundance_count_MYS_primary
+
+
+resource_use.write( "primary forest" + "," + "MYS" + "," + str(abundance_sum_MYS_primary) + "," +
+ str(abundance_sum_MYS_primary/abundance_sum_MYS * 100 ) + "," +
+ str(abundance_count_MYS_primary) +"," +
+ str(abundance_mean_MYS_primary) + "\n")
+
+
+# primary montane
+primary_montane_abundance_MYS = np.where(resource_use_MYS == 5, abundance_data_MYS, 0)
+abundance_count_MYS_primary_montane = np.count_nonzero(primary_montane_abundance_MYS)
+abundance_sum_MYS_primary_montane = np.sum(primary_montane_abundance_MYS)
+abundance_mean_MYS_primary_montane = abundance_sum_MYS_primary_montane/abundance_count_MYS_primary_montane
+
+
+resource_use.write( "primary montane forest" + "," + "MYS" + "," + str(abundance_sum_MYS_primary_montane) + "," +
+ str(abundance_sum_MYS_primary_montane/abundance_sum_MYS * 100 ) + "," +
+ str(abundance_count_MYS_primary_montane) +"," +
+ str(abundance_mean_MYS_primary_montane) + "\n")
+
+
+ # regrowth
+regrowth_abundance_MYS = np.where(resource_use_MYS == 6, abundance_data_MYS, 0)
+abundance_count_MYS_regrowth = np.count_nonzero(regrowth_abundance_MYS)
+abundance_sum_MYS_regrowth = np.sum(regrowth_abundance_MYS)
+abundance_mean_MYS_regrowth = abundance_sum_MYS_regrowth/abundance_count_MYS_regrowth
+
+
+resource_use.write( "regrowth forest" + "," + "MYS" + "," + str(abundance_sum_MYS_regrowth) + "," +
+ str(abundance_sum_MYS_regrowth/abundance_sum_MYS * 100 ) + "," +
+ str(abundance_count_MYS_regrowth) +"," +
+ str(abundance_mean_MYS_regrowth) + "\n")
+
+
+# old plantations
+old_plantations_abundance_MYS = np.where(resource_use_MYS == 7, abundance_data_MYS, 0)
+abundance_count_MYS_old_plantations = np.count_nonzero(old_plantations_abundance_MYS)
+abundance_sum_MYS_old_plantations = np.sum(old_plantations_abundance_MYS)
+abundance_mean_MYS_old_plantations = abundance_sum_MYS_old_plantations/abundance_count_MYS_old_plantations
+
+
+resource_use.write( "old plantations" + "," + "MYS" + "," + str(abundance_sum_MYS_old_plantations) + "," +
+ str(abundance_sum_MYS_old_plantations/abundance_sum_MYS * 100 ) + "," +
+ str(abundance_count_MYS_old_plantations) +"," +
+ str(abundance_mean_MYS_old_plantations) + "\n")
+
+
+# nothing
+
+other_abundance_MYS = np.where(resource_use_MYS == 8, abundance_data_MYS, 0)
+abundance_count_MYS_other = np.count_nonzero(other_abundance_MYS)
+abundance_sum_MYS_other = np.sum(other_abundance_MYS)
+abundance_mean_MYS_other = abundance_sum_MYS_other/abundance_count_MYS_other
+
+
+resource_use.write( "other" + "," + "MYS" + "," + str(abundance_sum_MYS_other) + "," +
+ str(abundance_sum_MYS_other/abundance_sum_MYS * 100 ) + "," +
+ str(abundance_count_MYS_other) +"," +
+ str(abundance_mean_MYS_other) + "\n")
+
+
+#######
+# SAB #
+#######
+
+#SAB
+
+
+abundance_data_SAB = np.where(borneo_province == 10, abundance_data, 0 )
+count_abundance_SAB = np.count_nonzero(abundance_data_SAB)
+abundance_sum_SAB = np.sum(abundance_data_SAB)
+mean_abundance_SAB = abundance_sum_SAB/count_abundance_SAB
+
+resource_use.write( "total abundance" + "," + "SAB" + "," + str(abundance_sum_SAB) + "," +
+ str(abundance_sum_SAB/abundance_sum_SAB * 100 ) + "," +
+ str(count_abundance_SAB) +"," +
+ str(mean_abundance_SAB) + "\n")
+
+
+
+
+
+# planted
+planted_abundance_SAB = np.where(resource_use_SAB == 1, abundance_data_SAB, 0)
+abundance_count_SAB_planted = np.count_nonzero(planted_abundance_SAB)
+abundance_sum_SAB_planted = np.sum(planted_abundance_SAB)
+abundance_mean_SAB_planted = abundance_sum_SAB_planted / abundance_count_SAB_planted
+
+
+resource_use.write( "plantation" + "," + "SAB" + "," + str(abundance_sum_SAB_planted) + "," +
+ str(abundance_sum_SAB_planted/abundance_sum_SAB * 100 ) + "," +
+ str(abundance_count_SAB_planted) +"," +
+ str(abundance_mean_SAB_planted) + "\n")
+
+
+
+# deforested
+deforested_abundance_SAB = np.where(resource_use_SAB == 2, abundance_data_SAB, 0)
+abundance_count_SAB_deforested = np.count_nonzero(deforested_abundance_SAB)
+abundance_sum_SAB_deforested = np.sum(deforested_abundance_SAB)
+abundance_mean_SAB_deforested = abundance_sum_SAB_deforested/abundance_count_SAB_deforested
+
+resource_use.write( "deforestation" + "," + "SAB" + "," + str(abundance_sum_SAB_deforested) + "," +
+ str(abundance_sum_SAB_deforested/abundance_sum_SAB * 100 ) + "," +
+ str(abundance_count_SAB_deforested) +"," +
+ str(abundance_mean_SAB_deforested) + "\n")
+
+
+
+
+ # logged
+
+logged_abundance_SAB = np.where(resource_use_SAB == 3, abundance_data_SAB, 0)
+abundance_count_SAB_logged = np.count_nonzero(logged_abundance_SAB)
+abundance_sum_SAB_logged = np.sum(logged_abundance_SAB)
+abundance_mean_SAB_logged = abundance_sum_SAB_logged/abundance_count_SAB_logged
+
+resource_use.write( "logging" + "," + "SAB" + "," + str(abundance_sum_SAB_logged) + "," +
+ str(abundance_sum_SAB_logged/abundance_sum_SAB * 100 ) + "," +
+ str(abundance_count_SAB_logged) +"," +
+ str(abundance_mean_SAB_logged) + "\n")
+
+ # primary
+primary_abundance_SAB = np.where(resource_use_SAB == 4, abundance_data_SAB, 0)
+abundance_count_SAB_primary = np.count_nonzero(primary_abundance_SAB)
+abundance_sum_SAB_primary = np.sum(primary_abundance_SAB)
+abundance_mean_SAB_primary = abundance_sum_SAB_primary/abundance_count_SAB_primary
+
+
+resource_use.write( "primary forest" + "," + "SAB" + "," + str(abundance_sum_SAB_primary) + "," +
+ str(abundance_sum_SAB_primary/abundance_sum_SAB * 100 ) + "," +
+ str(abundance_count_SAB_primary) +"," +
+ str(abundance_mean_SAB_primary) + "\n")
+
+
+# primary montane
+primary_montane_abundance_SAB = np.where(resource_use_SAB == 5, abundance_data_SAB, 0)
+abundance_count_SAB_primary_montane = np.count_nonzero(primary_montane_abundance_SAB)
+abundance_sum_SAB_primary_montane = np.sum(primary_montane_abundance_SAB)
+abundance_mean_SAB_primary_montane = abundance_sum_SAB_primary_montane/abundance_count_SAB_primary_montane
+
+
+resource_use.write( "primary montane forest" + "," + "SAB" + "," + str(abundance_sum_SAB_primary_montane) + "," +
+ str(abundance_sum_SAB_primary_montane/abundance_sum_SAB * 100 ) + "," +
+ str(abundance_count_SAB_primary_montane) +"," +
+ str(abundance_mean_SAB_primary_montane) + "\n")
+
+
+ # regrowth
+regrowth_abundance_SAB = np.where(resource_use_SAB == 6, abundance_data_SAB, 0)
+abundance_count_SAB_regrowth = np.count_nonzero(regrowth_abundance_SAB)
+abundance_sum_SAB_regrowth = np.sum(regrowth_abundance_SAB)
+abundance_mean_SAB_regrowth = abundance_sum_SAB_regrowth/abundance_count_SAB_regrowth
+
+
+resource_use.write( "regrowth forest" + "," + "SAB" + "," + str(abundance_sum_SAB_regrowth) + "," +
+ str(abundance_sum_SAB_regrowth/abundance_sum_SAB * 100 ) + "," +
+ str(abundance_count_SAB_regrowth) +"," +
+ str(abundance_mean_SAB_regrowth) + "\n")
+
+
+# old plantations
+old_plantations_abundance_SAB = np.where(resource_use_SAB == 7, abundance_data_SAB, 0)
+abundance_count_SAB_old_plantations = np.count_nonzero(old_plantations_abundance_SAB)
+abundance_sum_SAB_old_plantations = np.sum(old_plantations_abundance_SAB)
+abundance_mean_SAB_old_plantations = abundance_sum_SAB_old_plantations/abundance_count_SAB_old_plantations
+
+
+resource_use.write( "old plantations" + "," + "SAB" + "," + str(abundance_sum_SAB_old_plantations) + "," +
+ str(abundance_sum_SAB_old_plantations/abundance_sum_SAB * 100 ) + "," +
+ str(abundance_count_SAB_old_plantations) +"," +
+ str(abundance_mean_SAB_old_plantations) + "\n")
+
+
+# nothing
+
+other_abundance_SAB = np.where(resource_use_SAB == 8, abundance_data_SAB, 0)
+abundance_count_SAB_other = np.count_nonzero(other_abundance_SAB)
+abundance_sum_SAB_other = np.sum(other_abundance_SAB)
+abundance_mean_SAB_other = abundance_sum_SAB_other/abundance_count_SAB_other
+
+
+resource_use.write( "other" + "," + "SAB" + "," + str(abundance_sum_SAB_other) + "," +
+ str(abundance_sum_SAB_other/abundance_sum_SAB * 100 ) + "," +
+ str(abundance_count_SAB_other) +"," +
+ str(abundance_mean_SAB_other) + "\n")
+
+#######
+# SAW #
+#######
+
+
+abundance_data_SAW = np.where(borneo_province == 11, abundance_data, 0 )
+count_abundance_SAW = np.count_nonzero(abundance_data_SAW)
+abundance_sum_SAW = np.sum(abundance_data_SAW)
+mean_abundance_SAW = abundance_sum_SAW/count_abundance_SAW
+
+resource_use.write( "total abundance" + "," + "SAW" + "," + str(abundance_sum_SAW) + "," +
+ str(abundance_sum_SAW/abundance_sum_SAW * 100 ) + "," +
+ str(count_abundance_SAW) +"," +
+ str(mean_abundance_SAW) + "\n")
+
+
+
+
+
+# planted
+planted_abundance_SAW = np.where(resource_use_SAW == 1, abundance_data_SAW, 0)
+abundance_count_SAW_planted = np.count_nonzero(planted_abundance_SAW)
+abundance_sum_SAW_planted = np.sum(planted_abundance_SAW)
+abundance_mean_SAW_planted = abundance_sum_SAW_planted / abundance_count_SAW_planted
+
+
+resource_use.write( "plantation" + "," + "SAW" + "," + str(abundance_sum_SAW_planted) + "," +
+ str(abundance_sum_SAW_planted/abundance_sum_SAW * 100 ) + "," +
+ str(abundance_count_SAW_planted) +"," +
+ str(abundance_mean_SAW_planted) + "\n")
+
+
+
+# deforested
+deforested_abundance_SAW = np.where(resource_use_SAW == 2, abundance_data_SAW, 0)
+abundance_count_SAW_deforested = np.count_nonzero(deforested_abundance_SAW)
+abundance_sum_SAW_deforested = np.sum(deforested_abundance_SAW)
+abundance_mean_SAW_deforested = abundance_sum_SAW_deforested/abundance_count_SAW_deforested
+
+resource_use.write( "deforestation" + "," + "SAW" + "," + str(abundance_sum_SAW_deforested) + "," +
+ str(abundance_sum_SAW_deforested/abundance_sum_SAW * 100 ) + "," +
+ str(abundance_count_SAW_deforested) +"," +
+ str(abundance_mean_SAW_deforested) + "\n")
+
+
+
+
+ # logged
+
+logged_abundance_SAW = np.where(resource_use_SAW == 3, abundance_data_SAW, 0)
+abundance_count_SAW_logged = np.count_nonzero(logged_abundance_SAW)
+abundance_sum_SAW_logged = np.sum(logged_abundance_SAW)
+abundance_mean_SAW_logged = abundance_sum_SAW_logged/abundance_count_SAW_logged
+
+resource_use.write( "logging" + "," + "SAW" + "," + str(abundance_sum_SAW_logged) + "," +
+ str(abundance_sum_SAW_logged/abundance_sum_SAW * 100 ) + "," +
+ str(abundance_count_SAW_logged) +"," +
+ str(abundance_mean_SAW_logged) + "\n")
+
+ # primary
+primary_abundance_SAW = np.where(resource_use_SAW == 4, abundance_data_SAW, 0)
+abundance_count_SAW_primary = np.count_nonzero(primary_abundance_SAW)
+abundance_sum_SAW_primary = np.sum(primary_abundance_SAW)
+abundance_mean_SAW_primary = abundance_sum_SAW_primary/abundance_count_SAW_primary
+
+
+resource_use.write( "primary forest" + "," + "SAW" + "," + str(abundance_sum_SAW_primary) + "," +
+ str(abundance_sum_SAW_primary/abundance_sum_SAW * 100 ) + "," +
+ str(abundance_count_SAW_primary) +"," +
+ str(abundance_mean_SAW_primary) + "\n")
+
+
+# primary montane
+primary_montane_abundance_SAW = np.where(resource_use_SAW == 5, abundance_data_SAW, 0)
+abundance_count_SAW_primary_montane = np.count_nonzero(primary_montane_abundance_SAW)
+abundance_sum_SAW_primary_montane = np.sum(primary_montane_abundance_SAW)
+abundance_mean_SAW_primary_montane = abundance_sum_SAW_primary_montane/abundance_count_SAW_primary_montane
+
+
+resource_use.write( "primary montane forest" + "," + "SAW" + "," + str(abundance_sum_SAW_primary_montane) + "," +
+ str(abundance_sum_SAW_primary_montane/abundance_sum_SAW * 100 ) + "," +
+ str(abundance_count_SAW_primary_montane) +"," +
+ str(abundance_mean_SAW_primary_montane) + "\n")
+
+
+ # regrowth
+regrowth_abundance_SAW = np.where(resource_use_SAW == 6, abundance_data_SAW, 0)
+abundance_count_SAW_regrowth = np.count_nonzero(regrowth_abundance_SAW)
+abundance_sum_SAW_regrowth = np.sum(regrowth_abundance_SAW)
+abundance_mean_SAW_regrowth = abundance_sum_SAW_regrowth/abundance_count_SAW_regrowth
+
+
+resource_use.write( "regrowth forest" + "," + "SAW" + "," + str(abundance_sum_SAW_regrowth) + "," +
+ str(abundance_sum_SAW_regrowth/abundance_sum_SAW * 100 ) + "," +
+ str(abundance_count_SAW_regrowth) +"," +
+ str(abundance_mean_SAW_regrowth) + "\n")
+
+
+# old plantations
+old_plantations_abundance_SAW = np.where(resource_use_SAW == 7, abundance_data_SAW, 0)
+abundance_count_SAW_old_plantations = np.count_nonzero(old_plantations_abundance_SAW)
+abundance_sum_SAW_old_plantations = np.sum(old_plantations_abundance_SAW)
+abundance_mean_SAW_old_plantations = abundance_sum_SAW_old_plantations/abundance_count_SAW_old_plantations
+
+
+resource_use.write( "old plantations" + "," + "SAW" + "," + str(abundance_sum_SAW_old_plantations) + "," +
+ str(abundance_sum_SAW_old_plantations/abundance_sum_SAW * 100 ) + "," +
+ str(abundance_count_SAW_old_plantations) +"," +
+ str(abundance_mean_SAW_old_plantations) + "\n")
+
+
+# nothing
+
+other_abundance_SAW = np.where(resource_use_SAW == 8, abundance_data_SAW, 0)
+abundance_count_SAW_other = np.count_nonzero(other_abundance_SAW)
+abundance_sum_SAW_other = np.sum(other_abundance_SAW)
+abundance_mean_SAW_other = abundance_sum_SAW_other/abundance_count_SAW_other
+
+
+resource_use.write( "other" + "," + "SAW" + "," + str(abundance_sum_SAW_other) + "," +
+ str(abundance_sum_SAW_other/abundance_sum_SAW * 100 ) + "," +
+ str(abundance_count_SAW_other) +"," +
+ str(abundance_mean_SAW_other) + "\n")
+
+
+
+########
+# IDN #
+#######
+
+
+abundance_data_IDN = np.where(borneo == 106, abundance_data, 0 )
+count_abundance_IDN = np.count_nonzero(abundance_data_IDN)
+abundance_data_IDN = np.where(borneo == 106, abundance_data, 0)
+abundance_sum_IDN = np.sum(abundance_data_IDN)
+mean_abundance_IDN = np.mean(abundance_data_IDN)
+
+count_abundance_IDN = np.count_nonzero(abundance_data_IDN)
+abundance_sum_IDN = np.sum(abundance_data_IDN)
+mean_abundance_IDN = abundance_sum_IDN/count_abundance_IDN
+
+resource_use.write( "total abundance" + "," + "IDN" + "," + str(abundance_sum_IDN) + "," +
+ str(abundance_sum_IDN/abundance_sum_IDN * 100 ) + "," +
+ str(count_abundance_IDN) +"," +
+ str(mean_abundance_IDN) + "\n")
+
+
+
+
+
+# planted
+planted_abundance_IDN = np.where(resource_use_IDN == 1, abundance_data_IDN, 0)
+abundance_count_IDN_planted = np.count_nonzero(planted_abundance_IDN)
+abundance_sum_IDN_planted = np.sum(planted_abundance_IDN)
+abundance_mean_IDN_planted = abundance_sum_IDN_planted / abundance_count_IDN_planted
+
+
+resource_use.write( "plantation" + "," + "IDN" + "," + str(abundance_sum_IDN_planted) + "," +
+ str(abundance_sum_IDN_planted/abundance_sum_IDN * 100 ) + "," +
+ str(abundance_count_IDN_planted) +"," +
+ str(abundance_mean_IDN_planted) + "\n")
+
+
+
+# deforested
+deforested_abundance_IDN = np.where(resource_use_IDN == 2, abundance_data_IDN, 0)
+abundance_count_IDN_deforested = np.count_nonzero(deforested_abundance_IDN)
+abundance_sum_IDN_deforested = np.sum(deforested_abundance_IDN)
+abundance_mean_IDN_deforested = abundance_sum_IDN_deforested/abundance_count_IDN_deforested
+
+resource_use.write( "deforestation" + "," + "IDN" + "," + str(abundance_sum_IDN_deforested) + "," +
+ str(abundance_sum_IDN_deforested/abundance_sum_IDN * 100 ) + "," +
+ str(abundance_count_IDN_deforested) +"," +
+ str(abundance_mean_IDN_deforested) + "\n")
+
+
+
+
+ # logged
+
+logged_abundance_IDN = np.where(resource_use_IDN == 3, abundance_data_IDN, 0)
+abundance_count_IDN_logged = np.count_nonzero(logged_abundance_IDN)
+abundance_sum_IDN_logged = np.sum(logged_abundance_IDN)
+abundance_mean_IDN_logged = abundance_sum_IDN_logged/abundance_count_IDN_logged
+
+resource_use.write( "logging" + "," + "IDN" + "," + str(abundance_sum_IDN_logged) + "," +
+ str(abundance_sum_IDN_logged/abundance_sum_IDN * 100 ) + "," +
+ str(abundance_count_IDN_logged) +"," +
+ str(abundance_mean_IDN_logged) + "\n")
+
+ # primary
+primary_abundance_IDN = np.where(resource_use_IDN == 4, abundance_data_IDN, 0)
+abundance_count_IDN_primary = np.count_nonzero(primary_abundance_IDN)
+abundance_sum_IDN_primary = np.sum(primary_abundance_IDN)
+abundance_mean_IDN_primary = abundance_sum_IDN_primary/abundance_count_IDN_primary
+
+
+resource_use.write( "primary forest" + "," + "IDN" + "," + str(abundance_sum_IDN_primary) + "," +
+ str(abundance_sum_IDN_primary/abundance_sum_IDN * 100 ) + "," +
+ str(abundance_count_IDN_primary) +"," +
+ str(abundance_mean_IDN_primary) + "\n")
+
+
+# primary montane
+primary_montane_abundance_IDN = np.where(resource_use_IDN == 5, abundance_data_IDN, 0)
+abundance_count_IDN_primary_montane = np.count_nonzero(primary_montane_abundance_IDN)
+abundance_sum_IDN_primary_montane = np.sum(primary_montane_abundance_IDN)
+abundance_mean_IDN_primary_montane = abundance_sum_IDN_primary_montane/abundance_count_IDN_primary_montane
+
+
+resource_use.write( "primary montane forest" + "," + "IDN" + "," + str(abundance_sum_IDN_primary_montane) + "," +
+ str(abundance_sum_IDN_primary_montane/abundance_sum_IDN * 100 ) + "," +
+ str(abundance_count_IDN_primary_montane) +"," +
+ str(abundance_mean_IDN_primary_montane) + "\n")
+
+
+ # regrowth
+regrowth_abundance_IDN = np.where(resource_use_IDN == 6, abundance_data_IDN, 0)
+abundance_count_IDN_regrowth = np.count_nonzero(regrowth_abundance_IDN)
+abundance_sum_IDN_regrowth = np.sum(regrowth_abundance_IDN)
+abundance_mean_IDN_regrowth = abundance_sum_IDN_regrowth/abundance_count_IDN_regrowth
+
+
+resource_use.write( "regrowth forest" + "," + "IDN" + "," + str(abundance_sum_IDN_regrowth) + "," +
+ str(abundance_sum_IDN_regrowth/abundance_sum_IDN * 100 ) + "," +
+ str(abundance_count_IDN_regrowth) +"," +
+ str(abundance_mean_IDN_regrowth) + "\n")
+
+
+# old plantations
+old_plantations_abundance_IDN = np.where(resource_use_IDN == 7, abundance_data_IDN, 0)
+abundance_count_IDN_old_plantations = np.count_nonzero(old_plantations_abundance_IDN)
+abundance_sum_IDN_old_plantations = np.sum(old_plantations_abundance_IDN)
+abundance_mean_IDN_old_plantations = abundance_sum_IDN_old_plantations/abundance_count_IDN_old_plantations
+
+
+resource_use.write( "old plantations" + "," + "IDN" + "," + str(abundance_sum_IDN_old_plantations) + "," +
+ str(abundance_sum_IDN_old_plantations/abundance_sum_IDN * 100 ) + "," +
+ str(abundance_count_IDN_old_plantations) +"," +
+ str(abundance_mean_IDN_old_plantations) + "\n")
+
+
+# nothing
+
+other_abundance_IDN = np.where(resource_use_IDN == 8, abundance_data_IDN, 0)
+abundance_count_IDN_other = np.count_nonzero(other_abundance_IDN)
+abundance_sum_IDN_other = np.sum(other_abundance_IDN)
+abundance_mean_IDN_other = abundance_sum_IDN_other/abundance_count_IDN_other
+
+
+resource_use.write( "other" + "," + "IDN" + "," + str(abundance_sum_IDN_other) + "," +
+ str(abundance_sum_IDN_other/abundance_sum_IDN * 100 ) + "," +
+ str(abundance_count_IDN_other) +"," +
+ str(abundance_mean_IDN_other) + "\n")
+
+"""
+mp.tiff.write_tif(file_with_srid = grid_layer_path,
+ full_output_name = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use/test.tif",
+ data = abundance_data_MYS ,
+ dtype = 4)
+np.max(planted_abundance)
+"""
+
+resource_use.close()
+# CONTINUE WITH R SCRIPT calculating_overlap_densities_country.R
+
+"""
+mp.tiff.write_tif(file_with_srid = grid_layer_path,
+ full_output_name = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use/resource_use_MYS.tif",
+ data = resource_use_MYS ,
+ dtype = 4)
+
+"""
+
+year = 1999
+
+
+if 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"
+
+print abundance_path
+# read the data
+abundance_data = mp.tiff.read_tif(abundance_path, 1)
+
+resource_use = mp.tiff.read_tif(grid_layer_path, 1)
+
+abundance_data = np.where(absence == 0, abundance_data, 0)
+#abundance_data = np.where(abundance_data > 0.1, abundance_data, 0)
+
+# there are some pixels in the outside shape of borneo,
+# where we have abundance but no grid, this we will clip
+abundance_data = np.where((resource_use == 0) &
+ (abundance_data > 0), 0, abundance_data)
+
+abundance_data_MYS = np.where(borneo == 136, abundance_data, 0 )
+abundance_data_SAB = np.where(borneo_province == 10, abundance_data, 0 )
+abundance_data_SAW = np.where(borneo_province == 11, abundance_data, 0 )
+abundance_data_IDN = np.where(borneo == 106, abundance_data, 0 )
+
+
+file_path_table_affected = "/homes/mv39zilo/work/Borneo/analysis/model_prep_and_running/results/resource_use/OU_area_affected_" + str(year) + ".csv"
+affected = open(file_path_table_affected, 'w')
+
+affected.write("type, country, ou_affected, perc_ou_affected, area_affected, perc_area_affected \n")
+
+
+# IT DOESNT MAKE A DIFFERENCE IF INCLUDING ONLY LARGER THAN 0.1
+
+# how many OU have been affected
+
+gone_ou_all = np.where(#(abundance_data > 0.1) &
+ ((resource_use == 1) |
+ (resource_use == 2) |
+ (resource_use == 3)), abundance_data, 0)
+
+ # # how much "area" was affected
+total_ae = np.where(abundance_data > 0, 1, 0)
+gone_ae_all = np.where(
+ # (abundance_data > 0.1) &
+ ((resource_use == 1) |
+ (resource_use == 2) |
+ (resource_use == 3)), 1, 0)
+
+affected.write( "all" + "," + "borneo" + "," +
+str(np.sum(gone_ou_all) ) + "," +
+str(np.sum(gone_ou_all)*100/np.sum(abundance_data)) + "," +
+str(np.sum(gone_ae_all) * 0.0001) + "," + str(np.sum(gone_ae_all)*100/ np.sum(total_ae)) + "\n")
+
+# how many OU have been affected
+gone_ou_defor = np.where(#(abundance_data > 0.1) &
+ ((resource_use == 1) |
+ (resource_use == 2) ), abundance_data, 0)
+
+ # # how much "area" was affected
+gone_ae_defor = np.where(
+ # (abundance_data > 0.1) &
+ ((resource_use == 1) |
+ (resource_use == 2) ), 1, 0)
+
+
+affected.write( "cover_change" + "," + "borneo" + "," +
+ str(np.sum(gone_ou_defor) ) + "," +
+ str(np.sum(gone_ou_defor)*100/np.sum(abundance_data)) + "," +
+ str(np.sum(gone_ae_defor)* 0.0001) + "," +
+ str(np.sum(gone_ae_defor)*100/ np.sum(total_ae)) + "\n")
+
+
+
+gone_ou_logging = np.where(#(abundance_data > 0.1) &
+ (resource_use == 3), abundance_data, 0)
+gone_ae_logging = np.where(#(abundance_data > 0.1) &
+ (resource_use == 3), 1, 0)
+
+
+affected.write( "logging" + "," + "borneo" + "," +
+ str(np.sum(gone_ou_logging) ) + "," +
+ str(np.sum(gone_ou_logging)*100/np.sum(abundance_data)) + "," +
+ str(np.sum(gone_ae_logging)* 0.0001) + "," +
+ str(np.sum(gone_ae_logging)*100/ np.sum(total_ae))+ "\n")
+
+
+gone_ou_IDN_all = np.where(#(abundance_data_IDN > 0.1) &
+ ((resource_use_IDN == 1) |
+ (resource_use_IDN == 2) |
+ (resource_use_IDN == 3)), abundance_data_IDN, 0)
+
+ # # how much "area" was affected
+total_ae_IDN = np.where(abundance_data_IDN > 0, 1, 0)
+gone_ae_IDN_all = np.where(
+ # (abundance_data_IDN > 0.1) &
+ ((resource_use_IDN == 1) |
+ (resource_use_IDN == 2) |
+ (resource_use_IDN == 3)), 1, 0)
+
+affected.write( "all" + "," + "IDN" + "," +
+str(np.sum(gone_ou_IDN_all) ) + "," +
+str(np.sum(gone_ou_IDN_all)*100/np.sum(abundance_data_IDN)) + "," +
+str(np.sum(gone_ae_IDN_all) * 0.0001) + "," + str(np.sum(gone_ae_IDN_all)*100/ np.sum(total_ae_IDN)) + "\n")
+
+# how many OU have been affected
+gone_ou_IDN_defor = np.where(#(abundance_data_IDN > 0.1) &
+ ((resource_use_IDN == 1) |
+ (resource_use_IDN == 2) ), abundance_data_IDN, 0)
+
+ # # how much "area" was affected
+gone_ae_IDN_defor = np.where(
+ # (abundance_data_IDN > 0.1) &
+ ((resource_use_IDN == 1) |
+ (resource_use_IDN == 2) ), 1, 0)
+
+
+affected.write( "cover_change" + "," + "IDN" + "," +
+ str(np.sum(gone_ou_IDN_defor) ) + "," +
+ str(np.sum(gone_ou_IDN_defor)*100/np.sum(abundance_data_IDN)) + "," +
+ str(np.sum(gone_ae_IDN_defor)* 0.0001) + "," +
+ str(np.sum(gone_ae_IDN_defor)*100/ np.sum(total_ae_IDN)) + "\n")
+
+
+
+gone_ou_IDN_logging = np.where(#(abundance_data_IDN > 0.1) &
+ (resource_use_IDN == 3), abundance_data_IDN, 0)
+gone_ae_IDN_logging = np.where(#(abundance_data_IDN > 0.1) &
+ (resource_use_IDN == 3), 1, 0)
+
+
+affected.write( "logging" + "," + "IDN" + "," +
+ str(np.sum(gone_ou_IDN_logging) ) + "," +
+ str(np.sum(gone_ou_IDN_logging)*100/np.sum(abundance_data_IDN)) + "," +
+ str(np.sum(gone_ae_IDN_logging)* 0.0001) + "," +
+ str(np.sum(gone_ae_IDN_logging)*100/ np.sum(total_ae_IDN))+ "\n")
+
+
+gone_ou_MYS_all = np.where(#(abundance_data_MYS > 0.1) &
+ ((resource_use_MYS == 1) |
+ (resource_use_MYS == 2) |
+ (resource_use_MYS == 3)), abundance_data_MYS, 0)
+
+ # # how much "area" was affected
+total_ae_MYS = np.where(abundance_data_MYS > 0, 1, 0)
+gone_ae_MYS_all = np.where(
+ # (abundance_data_MYS > 0.1) &
+ ((resource_use_MYS == 1) |
+ (resource_use_MYS == 2) |
+ (resource_use_MYS == 3)), 1, 0)
+
+affected.write( "all" + "," + "MYS" + "," +
+ str(np.sum(gone_ou_MYS_all) ) + "," +
+ str(np.sum(gone_ou_MYS_all)*100/np.sum(abundance_data_MYS)) + "," +
+ str(np.sum(gone_ae_MYS_all) * 0.0001) + "," +
+ str(np.sum(gone_ae_MYS_all)*100/ np.sum(total_ae_MYS)) + "\n")
+
+# how many OU have been affected
+gone_ou_MYS_defor = np.where(#(abundance_data_MYS > 0.1) &
+ ((resource_use_MYS == 1) |
+ (resource_use_MYS == 2)), abundance_data_MYS, 0)
+
+ # # how much "area" was affected
+gone_ae_MYS_defor = np.where(
+ # (abundance_data_MYS > 0.1) &
+ ((resource_use_MYS == 1) |
+ (resource_use_MYS == 2)), 1, 0)
+
+
+affected.write( "cover_change" + "," + "MYS" + "," +
+ str(np.sum(gone_ou_MYS_defor) ) + "," +
+ str(np.sum(gone_ou_MYS_defor)*100/np.sum(abundance_data_MYS)) + "," +
+ str(np.sum(gone_ae_MYS_defor) * 0.0001) + "," +
+ str(np.sum(gone_ae_MYS_defor)*100/ np.sum(total_ae_MYS)) + "\n")
+
+
+
+gone_ou_MYS_logging = np.where(#(abundance_data_MYS > 0.1) &
+ (resource_use_MYS == 3), abundance_data_MYS, 0)
+gone_ae_MYS_logging = np.where(#(abundance_data_MYS > 0.1) &
+ (resource_use_MYS == 3), 1, 0)
+
+
+affected.write( "logging" + "," + "MYS" + "," +
+ str(np.sum(gone_ou_MYS_logging) ) + "," +
+ str(np.sum(gone_ou_MYS_logging)*100/np.sum(abundance_data_MYS)) + "," +
+ str(np.sum(gone_ae_MYS_logging) * 0.0001) + "," +
+ str(np.sum(gone_ae_MYS_logging)*100/ np.sum(total_ae_MYS)) + "\n")
+
+# SAB
+
+gone_ou_SAB_all = np.where(#(abundance_data_SAB > 0.1) &
+ ((resource_use_SAB == 1) |
+ (resource_use_SAB == 2) |
+ (resource_use_SAB == 3)), abundance_data_SAB, 0)
+
+ # # how much "area" was affected
+total_ae_SAB = np.where(abundance_data_SAB > 0, 1, 0)
+gone_ae_SAB_all = np.where(
+ # (abundance_data_SAB > 0.1) &
+ ((resource_use_SAB == 1) |
+ (resource_use_SAB == 2) |
+ (resource_use_SAB == 3)), 1, 0)
+
+affected.write( "all" + "," + "SAB" + "," +
+ str(np.sum(gone_ou_SAB_all) ) + "," +
+ str(np.sum(gone_ou_SAB_all)*100/np.sum(abundance_data_SAB)) + "," +
+ str(np.sum(gone_ae_SAB_all) * 0.0001) + "," +
+ str(np.sum(gone_ae_SAB_all)*100/ np.sum(total_ae_SAB)) + "\n")
+
+# how many OU have been affected
+gone_ou_SAB_defor = np.where(#(abundance_data_SAB > 0.1) &
+ ((resource_use_SAB == 1) |
+ (resource_use_SAB == 2)), abundance_data_SAB, 0)
+
+ # # how much "area" was affected
+gone_ae_SAB_defor = np.where(
+ # (abundance_data_SAB > 0.1) &
+ ((resource_use_SAB == 1) |
+ (resource_use_SAB == 2)), 1, 0)
+
+
+affected.write( "cover_change" + "," + "SAB" + "," +
+ str(np.sum(gone_ou_SAB_defor) ) + "," +
+ str(np.sum(gone_ou_SAB_defor)*100/np.sum(abundance_data_SAB)) + "," +
+ str(np.sum(gone_ae_SAB_defor) * 0.0001) + "," +
+ str(np.sum(gone_ae_SAB_defor)*100/ np.sum(total_ae_SAB)) + "\n")
+
+
+
+gone_ou_SAB_logging = np.where(#(abundance_data_SAB > 0.1) &
+ (resource_use_SAB == 3), abundance_data_SAB, 0)
+gone_ae_SAB_logging = np.where(#(abundance_data_SAB > 0.1) &
+ (resource_use_SAB == 3), 1, 0)
+
+
+affected.write( "logging" + "," + "SAB" + "," +
+ str(np.sum(gone_ou_SAB_logging) ) + "," +
+ str(np.sum(gone_ou_SAB_logging)*100/np.sum(abundance_data_SAB)) + "," +
+ str(np.sum(gone_ae_SAB_logging) * 0.0001) + "," +
+ str(np.sum(gone_ae_SAB_logging)*100/ np.sum(total_ae_SAB)) + "\n")
+
+gone_ou_SAW_all = np.where(#(abundance_data_SAW > 0.1) &
+ ((resource_use_SAW == 1) |
+ (resource_use_SAW == 2) |
+ (resource_use_SAW == 3)), abundance_data_SAW, 0)
+
+ # # how much "area" was affected
+total_ae_SAW = np.where(abundance_data_SAW > 0, 1, 0)
+gone_ae_SAW_all = np.where(
+ # (abundance_data_SAW > 0.1) &
+ ((resource_use_SAW == 1) |
+ (resource_use_SAW == 2) |
+ (resource_use_SAW == 3)), 1, 0)
+
+affected.write( "all" + "," + "SAW" + "," +
+ str(np.sum(gone_ou_SAW_all) ) + "," +
+ str(np.sum(gone_ou_SAW_all)*100/np.sum(abundance_data_SAW)) + "," +
+ str(np.sum(gone_ae_SAW_all) * 0.0001) + "," +
+ str(np.sum(gone_ae_SAW_all)*100/ np.sum(total_ae_SAW)) + "\n")
+
+# how many OU have been affected
+gone_ou_SAW_defor = np.where(#(abundance_data_SAW > 0.1) &
+ ((resource_use_SAW == 1) |
+ (resource_use_SAW == 2)), abundance_data_SAW, 0)
+
+ # # how much "area" was affected
+gone_ae_SAW_defor = np.where(
+ # (abundance_data_SAW > 0.1) &
+ ((resource_use_SAW == 1) |
+ (resource_use_SAW == 2)), 1, 0)
+
+
+affected.write( "cover_change" + "," + "SAW" + "," +
+ str(np.sum(gone_ou_SAW_defor) ) + "," +
+ str(np.sum(gone_ou_SAW_defor)*100/np.sum(abundance_data_SAW)) + "," +
+ str(np.sum(gone_ae_SAW_defor) * 0.0001) + "," +
+ str(np.sum(gone_ae_SAW_defor)*100/ np.sum(total_ae_SAW)) + "\n")
+
+
+
+gone_ou_SAW_logging = np.where(#(abundance_data_SAW > 0.1) &
+ (resource_use_SAW == 3), abundance_data_SAW, 0)
+gone_ae_SAW_logging = np.where(#(abundance_data_SAW > 0.1) &
+ (resource_use_SAW == 3), 1, 0)
+
+
+affected.write( "logging" + "," + "SAW" + "," +
+ str(np.sum(gone_ou_SAW_logging) ) + "," +
+ str(np.sum(gone_ou_SAW_logging)*100/np.sum(abundance_data_SAW)) + "," +
+ str(np.sum(gone_ae_SAW_logging) * 0.0001) + "," +
+ str(np.sum(gone_ae_SAW_logging)*100/ np.sum(total_ae_SAW)) + "\n")
+
+
+
+
+affected.close()
+