requirements and figures

iezqrom · Jan 2, 2023 · 5561a4d · 5561a4d
1 parent cd3b265
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Showing 76 changed files with 55 additions and 32 deletions.
diff --git a/code/n_pubhs_per_drug.py b/code/n_pubhs_per_drug.py
@@ -148,7 +148,7 @@ def fig_2_indv(data, sch_color, max_y, steps, dict_params):
     ax.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
     plt.tight_layout()
 
-    plt.savefig(f'./../figures/dev_write_up/sched_2_{data.lower()}.png'.format(), transparent = True, bbox_inches='tight')
+    plt.savefig(f'./../figures/writeup/sched_2_{data.lower()}.png'.format(), transparent = True, bbox_inches='tight')
 
     return dict_params
 
@@ -230,7 +230,7 @@ def fig_2_indv(data, sch_color, max_y, steps, dict_params):
                 labelleft=False,
                 labelbottom=False)
 
-plt.savefig(f'./../figures/dev_write_up/solo_legend.png', transparent = True, bbox_inches='tight')
+plt.savefig(f'./../figures/writeup/solo_legend.png', transparent = True, bbox_inches='tight')
 
 # %% Figure 2 fitting by schedule
 def fig_2_sche(data, color, lineswag, name_file, max_y, steps, dict_params):
@@ -280,7 +280,7 @@ def fig_2_sche(data, color, lineswag, name_file, max_y, steps, dict_params):
     ax.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
     plt.tight_layout()
 
-    plt.savefig(f'./../figures/dev_write_up/{name_file}.png'.format(), transparent = True, bbox_inches='tight')
+    plt.savefig(f'./../figures/writeup/{name_file}.png'.format(), transparent = True, bbox_inches='tight')
 
     return dict_params
 
@@ -349,7 +349,7 @@ def fig_2_drug_cat(data, color, title, name_file, max_y, steps, dict_params):
     ax.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
     plt.tight_layout()
 
-    plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+    plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
     return dict_params
 
@@ -391,7 +391,7 @@ def fig_2_drug_cat(data, color, title, name_file, max_y, steps, dict_params):
 #### Figure 3 Rs, Grs and table
 # %% Save R^2, a_init, g_rate as csv for table
 file_table = 'table_params_exp'
-table_exp_params = open('./../figures/dev_write_up/{}.csv'.format(file_table), 'a')
+table_exp_params = open('./../figures/writeup/{}.csv'.format(file_table), 'a')
 
 data_writer = csv.writer(table_exp_params)
 header_pure = dict_params['Alcohol'].keys()
@@ -491,7 +491,7 @@ def fig_2_drug_cat(data, color, title, name_file, max_y, steps, dict_params):
 # # name_file = 'heatmap_r_values'
 plt.tight_layout(pad=1.6)
 name_file = 'hbars_r_values_ORD_sched'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %%
 order_sched = ['Psilocybin', 'Cannabis', 'Khat', 'LSD', 'Heroin', 'MDMA',
@@ -540,7 +540,7 @@ def fig_2_drug_cat(data, color, title, name_file, max_y, steps, dict_params):
 
 plt.tight_layout(pad=1.6)
 name_file = 'exp_hbars_sched_ORD'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %% R-square values coloured by schedule ORDERED MAX TO LOW
 sort_orders_r2 = sorted(rs_ds.items(), key=lambda x: x[1][0], reverse=True)
@@ -602,7 +602,7 @@ def fig_2_drug_cat(data, color, title, name_file, max_y, steps, dict_params):
 # # name_file = 'heatmap_r_values'
 plt.tight_layout(pad=1.6)
 name_file = 'hbars_r_values_sched'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %% PLOT R squares
 zs = np.reshape(r_squares, (16, 1))
@@ -647,7 +647,7 @@ def fig_2_drug_cat(data, color, title, name_file, max_y, steps, dict_params):
 # # name_file = 'heatmap_r_values'
 plt.tight_layout(pad=1.6)
 name_file = 'hbars_r_values'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %% GROWTH RATE by SCHEDULE
 
@@ -698,7 +698,7 @@ def fig_2_drug_cat(data, color, title, name_file, max_y, steps, dict_params):
 
 plt.tight_layout(pad=1.6)
 name_file = 'exp_hbars_sched'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 
 # %%
@@ -735,7 +735,7 @@ def fig_2_drug_cat(data, color, title, name_file, max_y, steps, dict_params):
 
 plt.tight_layout(pad=1.6)
 name_file = 'exp_hbars'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 
 # %% Initial value
@@ -849,7 +849,7 @@ def fig_3_sched(data, color, name_file):
     leg.get_frame().set_linewidth(0.0)
 
     # plt.tight_layout()
-    plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+    plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %% Schedule I
 fig_3_sched(sched_Irgr[:3], ['#235f74', '#3388a6', '#99c3d2'], 'sched_I_lsd_md_hero')
@@ -921,7 +921,7 @@ def fig_3_rgr(data, color, title, name_file):
     leg.get_frame().set_linewidth(0.0)
 
     # plt.tight_layout()
-    plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+    plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %% Depressants
 fig_3_rgr(depressants, blue_moon, 'Relative Growth Rate.\n Excluding alcohol', 'rgr_depressants_excl_alc')
@@ -1055,9 +1055,9 @@ def fig_3_rgr(data, color, title, name_file):
 leg.get_frame().set_linewidth(0.0)
 
 name_file = 'time_pie_chart_sched_indv'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
-name_file = 'figure5_time_pie_chart_sched_indv'
-plt.savefig('./../figures/final_paper/{}.pdf'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+# name_file = 'figure5_time_pie_chart_sched_indv'
+# plt.savefig('./../figures/final_paper/{}.pdf'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %%
 
@@ -1104,9 +1104,8 @@ def fig_3_rgr(data, color, title, name_file):
 # plt.tight_layout()
 
 name_file = 'time_pie_chart_inset'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
-plt.savefig('./../figures/final_paper/{}.pdf'.format(name_file), transparent = True, bbox_inches='tight')
-
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+# plt.savefig('./../figures/final_paper/{}.pdf'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %%
 
@@ -1163,9 +1162,9 @@ def fig_3_rgr(data, color, title, name_file):
 # plt.tight_layout()
 
 name_file = 'time_pie_chart_by_schedule'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
-name_file = 'figure5_time_pie_chart_by_schedule'
-plt.savefig('./../figures/final_paper/{}.pdf'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+# name_file = 'figure5_time_pie_chart_by_schedule'
+# plt.savefig('./../figures/final_paper/{}.pdf'.format(name_file), transparent = True, bbox_inches='tight')
 
 # %%
 
@@ -1223,9 +1222,9 @@ def fig_3_rgr(data, color, title, name_file):
 # plt.tight_layout()
 
 name_file = 'time_pie_chart_by_cat'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
-name_file = 'figure5_time_pie_chart_by_cat'
-plt.savefig('./../figures/final_paper/{}.pdf'.format(name_file), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+# name_file = 'figure5_time_pie_chart_by_cat'
+# plt.savefig('./../figures/final_paper/{}.pdf'.format(name_file), transparent = True, bbox_inches='tight')
 
 
 # %% Figure 5 Per countries
@@ -1317,7 +1316,7 @@ def fig_5_countries(dat, years, title, color, y_max, steps, name_file):
     leg.get_frame().set_linewidth(0.0)
     plt.tight_layout()
 
-    plt.savefig('./../figures/dev_write_up/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
+    plt.savefig('./../figures/writeup/{}.png'.format(name_file), transparent = True, bbox_inches='tight')
 
 
 # %% Figure 5 Alcohol
@@ -1609,7 +1608,7 @@ def test(x, a, b):
 ax.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
 
 name = 'all'
-# plt.savefig('./../figures/dev_write_up/{}.png'.format(name), transparent = True, bbox_inches='tight')
+# plt.savefig('./../figures/writeup/{}.png'.format(name), transparent = True, bbox_inches='tight')
 
 # %% ############# Figure 2 all no alcohol
 drugs = raw.iloc[:,2:16]
@@ -1637,7 +1636,7 @@ def test(x, a, b):
 ax.legend(loc='center left', bbox_to_anchor=(1, 0.5))
 ax.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
 
-plt.savefig('./../figures/dev_write_up/all_no_alc.png', transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/all_no_alc.png', transparent = True, bbox_inches='tight')
 
 # %% ############ Figure 2 number pubs selected_two_axes
 drugs_two = ['Cannabis', 'Ketamine', 'MDMA', 'Psilocybin']
@@ -1686,7 +1685,7 @@ def test(x, a, b):
 ax.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
 ax2.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
 
-plt.savefig('./../figures/dev_write_up/selected_two_axes.png', transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/selected_two_axes.png', transparent = True, bbox_inches='tight')
 
 
 # %% ############ Figure 2 WoS
@@ -1715,7 +1714,7 @@ def test(x, a, b):
 ax.legend(loc='center left', bbox_to_anchor=(1, 0.5))
 ax.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
 
-plt.savefig('./../figures/dev_write_up/WoS.png', transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/WoS.png', transparent = True, bbox_inches='tight')
 
 
 # %% ############ Figure 2 LSD, Psilocybin, alcohol
@@ -1765,7 +1764,7 @@ def test(x, a, b):
 ax2.yaxis.label.set_color('b')
 ax2.spines['right'].set_color('b')
 
-plt.savefig('./../figures/dev_write_up/psyche_alc.png', transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/psyche_alc.png', transparent = True, bbox_inches='tight')
 
 # %%############ Figure 2 Depressants
 fig, ax = plt.subplots(figsize = (20, 10))
@@ -1805,4 +1804,4 @@ def test(x, a, b):
 ax.yaxis.set_major_formatter(mpl.ticker.StrMethodFormatter('{x:,.0f}'))
 
 name = 'depressants'
-plt.savefig('./../figures/dev_write_up/{}.png'.format(name), transparent = True, bbox_inches='tight')
+plt.savefig('./../figures/writeup/{}.png'.format(name), transparent = True, bbox_inches='tight')
diff --git a/figures/final_paper/submission/figure1.pdf → figures/submission/figure1.pdf b/figures/final_paper/submission/figure1.pdf → figures/submission/figure1.pdf
diff --git a/figures/final_paper/submission/figure2.pdf → figures/submission/figure2.pdf b/figures/final_paper/submission/figure2.pdf → figures/submission/figure2.pdf
diff --git a/figures/final_paper/submission/figure3.pdf → figures/submission/figure3.pdf b/figures/final_paper/submission/figure3.pdf → figures/submission/figure3.pdf
diff --git a/figures/final_paper/submission/figure4.pdf → figures/submission/figure4.pdf b/figures/final_paper/submission/figure4.pdf → figures/submission/figure4.pdf
diff --git a/figures/final_paper/submission/figure5.pdf → figures/submission/figure5.pdf b/figures/final_paper/submission/figure5.pdf → figures/submission/figure5.pdf
diff --git a/figures/final_paper/submission/figure6.pdf → figures/submission/figure6.pdf b/figures/final_paper/submission/figure6.pdf → figures/submission/figure6.pdf
diff --git a/figures/writeup/alcohol.png b/figures/writeup/alcohol.png
diff --git a/figures/writeup/alcohol_countries.png b/figures/writeup/alcohol_countries.png
diff --git a/figures/writeup/amphetamine_countries.png b/figures/writeup/amphetamine_countries.png
diff --git a/figures/writeup/benzos_countries.png b/figures/writeup/benzos_countries.png
diff --git a/figures/writeup/cannabis.png b/figures/writeup/cannabis.png
diff --git a/figures/writeup/cannabis_countries.png b/figures/writeup/cannabis_countries.png
diff --git a/figures/writeup/cocaine_countries.png b/figures/writeup/cocaine_countries.png
diff --git a/figures/writeup/codeine_countries.png b/figures/writeup/codeine_countries.png
diff --git a/figures/writeup/depressants_excl_alc.png b/figures/writeup/depressants_excl_alc.png
diff --git a/figures/writeup/disso.png b/figures/writeup/disso.png
diff --git a/figures/writeup/exp_hbars.png b/figures/writeup/exp_hbars.png
diff --git a/figures/writeup/exp_hbars_sched.png b/figures/writeup/exp_hbars_sched.png
diff --git a/figures/writeup/exp_hbars_sched_ORD.png b/figures/writeup/exp_hbars_sched_ORD.png
diff --git a/figures/writeup/ghb_countries.png b/figures/writeup/ghb_countries.png
diff --git a/figures/writeup/hbars_r_values.png b/figures/writeup/hbars_r_values.png
diff --git a/figures/writeup/hbars_r_values_ORD_sched.png b/figures/writeup/hbars_r_values_ORD_sched.png
diff --git a/figures/writeup/hbars_r_values_sched.png b/figures/writeup/hbars_r_values_sched.png
diff --git a/figures/writeup/heroin_countries.png b/figures/writeup/heroin_countries.png
diff --git a/figures/writeup/ketamine_countries.png b/figures/writeup/ketamine_countries.png
diff --git a/figures/writeup/khat_countries.png b/figures/writeup/khat_countries.png
diff --git a/figures/writeup/legal.png b/figures/writeup/legal.png
diff --git a/figures/writeup/lsd_countries.png b/figures/writeup/lsd_countries.png
diff --git a/figures/writeup/mdma.png b/figures/writeup/mdma.png
diff --git a/figures/writeup/mdma_countries.png b/figures/writeup/mdma_countries.png
diff --git a/figures/writeup/methadone_countries.png b/figures/writeup/methadone_countries.png
diff --git a/figures/writeup/methamphetamine_countries.png b/figures/writeup/methamphetamine_countries.png
diff --git a/figures/writeup/opioids.png b/figures/writeup/opioids.png
diff --git a/figures/writeup/psilo_countries.png b/figures/writeup/psilo_countries.png
diff --git a/figures/writeup/psychedelics.png b/figures/writeup/psychedelics.png
diff --git a/figures/writeup/rgr_alcohol.png b/figures/writeup/rgr_alcohol.png
diff --git a/figures/writeup/rgr_cannabis.png b/figures/writeup/rgr_cannabis.png
diff --git a/figures/writeup/rgr_depressants_excl_alc.png b/figures/writeup/rgr_depressants_excl_alc.png
diff --git a/figures/writeup/rgr_disso.png b/figures/writeup/rgr_disso.png
diff --git a/figures/writeup/rgr_mdma.png b/figures/writeup/rgr_mdma.png
diff --git a/figures/writeup/rgr_opioids.png b/figures/writeup/rgr_opioids.png
diff --git a/figures/writeup/rgr_psychedelics.png b/figures/writeup/rgr_psychedelics.png
diff --git a/figures/writeup/rgr_stimulants.png b/figures/writeup/rgr_stimulants.png
diff --git a/figures/writeup/sched_2_alcohol.png b/figures/writeup/sched_2_alcohol.png
diff --git a/figures/writeup/sched_2_amphetamines.png b/figures/writeup/sched_2_amphetamines.png
diff --git a/figures/writeup/sched_2_benzodiazepines.png b/figures/writeup/sched_2_benzodiazepines.png
diff --git a/figures/writeup/sched_2_cannabis.png b/figures/writeup/sched_2_cannabis.png
diff --git a/figures/writeup/sched_2_cocaine.png b/figures/writeup/sched_2_cocaine.png
diff --git a/figures/writeup/sched_2_codeine.png b/figures/writeup/sched_2_codeine.png
diff --git a/figures/writeup/sched_2_ghb.png b/figures/writeup/sched_2_ghb.png
diff --git a/figures/writeup/sched_2_heroin.png b/figures/writeup/sched_2_heroin.png
diff --git a/figures/writeup/sched_2_ketamine.png b/figures/writeup/sched_2_ketamine.png
diff --git a/figures/writeup/sched_2_khat.png b/figures/writeup/sched_2_khat.png
diff --git a/figures/writeup/sched_2_lsd.png b/figures/writeup/sched_2_lsd.png
diff --git a/figures/writeup/sched_2_mdma.png b/figures/writeup/sched_2_mdma.png
diff --git a/figures/writeup/sched_2_methadone.png b/figures/writeup/sched_2_methadone.png
diff --git a/figures/writeup/sched_2_methamphetamines.png b/figures/writeup/sched_2_methamphetamines.png
diff --git a/figures/writeup/sched_2_psilocybin.png b/figures/writeup/sched_2_psilocybin.png
diff --git a/figures/writeup/sched_2_wos.png b/figures/writeup/sched_2_wos.png
diff --git a/figures/writeup/sched_II.png b/figures/writeup/sched_II.png
diff --git a/figures/writeup/sched_III.png b/figures/writeup/sched_III.png
diff --git a/figures/writeup/sched_IV.png b/figures/writeup/sched_IV.png
diff --git a/figures/writeup/sched_I_lsd_md_hero.png b/figures/writeup/sched_I_lsd_md_hero.png
diff --git a/figures/writeup/sched_I_psilo_khat_cann.png b/figures/writeup/sched_I_psilo_khat_cann.png
diff --git a/figures/writeup/sched_V.png b/figures/writeup/sched_V.png
diff --git a/figures/writeup/solo_legend.png b/figures/writeup/solo_legend.png
diff --git a/figures/writeup/stimulants.png b/figures/writeup/stimulants.png
diff --git a/figures/writeup/table_params_exp.csv b/figures/writeup/table_params_exp.csv
@@ -0,0 +1,17 @@
+Drugs,r_square,a_init,g_rate
+Benzodiazepines,0.66,292.16651926784664,0.02815790196273298
+GHB,0.75,6.842647843781876,0.050659040932815674
+Khat,0.95,0.7573195888486924,0.08433647660996227
+WoS,0.96,372992.76088430115,0.03569500846588188
+Ketamine,0.98,24.47362488980567,0.06950411985704238
+LSD,0.85,10.094979754268229,0.06229877229509308
+Psilocybin,0.92,0.00492157881490633,0.17299473920184968
+MDMA,0.84,21.25269365573248,0.05509322680872568
+Heroin,0.97,41.891593093546476,0.0557433756755348
+Methadone,0.96,35.9703138806572,0.057031237068768934
+Codeine,0.94,18.141177640385344,0.046405073422656644
+Alcohol,0.99,1093.572415688869,0.06360406994539172
+Cannabis,0.97,35.03599976981951,0.08452446892719857
+Methamphetamines,0.97,17.046746758139676,0.07131789289344002
+Cocaine,0.86,176.3232388877336,0.047814290740857066
+Amphetamines,0.82,166.1616081082101,0.03599289697473994
diff --git a/figures/writeup/time_pie_chart_by_cat.png b/figures/writeup/time_pie_chart_by_cat.png
diff --git a/figures/writeup/time_pie_chart_by_schedule.png b/figures/writeup/time_pie_chart_by_schedule.png
diff --git a/figures/writeup/time_pie_chart_inset.png b/figures/writeup/time_pie_chart_inset.png
diff --git a/figures/writeup/time_pie_chart_sched_indv.png b/figures/writeup/time_pie_chart_sched_indv.png
diff --git a/figures/writeup/wos_pubs.png b/figures/writeup/wos_pubs.png
diff --git a/figures/writeup/wos_rgr.png b/figures/writeup/wos_rgr.png
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,7 @@
+matplotlib==3.6.1
+matplotlib-inline==0.1.6
+scikit-learn==1.2.0
+scipy==1.9.3
+pandas==1.5.1
+numpy==1.23.4
+scipy==1.9.3