fix: we were taking into account deaths not caused by covid-19 to plo…

…t cummulative deaths in figure 1, for the fatality ratios in figure 3 and for the death percentages in figure 4; this is no longer the case. I updated the plots/results_*.py files, as well as the rt script, for them to read the updated dataset and regenerated all figures.
ntorresd · Jun 21, 2023 · cbf050c · cbf050c
1 parent a970b7d
commit cbf050c
Show file tree

Hide file tree

Showing 10 changed files with 15 additions and 9 deletions.
diff --git a/plots/figure_4.py b/plots/figure_4.py
@@ -25,8 +25,8 @@
 fig, ax = plt.subplots(1,3, figsize=(12,5))
 plt.rcParams["savefig.pad_inches"] = 0.4
 
-# results_severe_outcomes.plot_percentage(ax)
-results_severe_outcomes.plot_percentage_err(ax)
+results_severe_outcomes.plot_percentage(ax)
+# results_severe_outcomes.plot_percentage_err(ax)
 
 ax[0].set_ylabel('Hospitalization percentage by age-group')
 ax[1].set_ylabel('ICU percentage by age-group')
@@ -40,5 +40,5 @@
 handles, labels = ax[2].get_legend_handles_labels()
 fig.legend(handles, labels, bbox_to_anchor = (0.79, -0.02), ncol = 6)
 
-# fig.savefig(FIG_PATH+'figure_4.png')
-fig.savefig(FIG_PATH+'figure_4_err.png')
+fig.savefig(FIG_PATH+'figure_4.png')
+# fig.savefig(FIG_PATH+'figure_4_err.png')
diff --git a/plots/figures/figure_1.png b/plots/figures/figure_1.png
diff --git a/plots/figures/figure_3.png b/plots/figures/figure_3.png
diff --git a/plots/figures/figure_4.png b/plots/figures/figure_4.png
diff --git a/plots/figures/figure_4_err.png b/plots/figures/figure_4_err.png
diff --git a/plots/figures/figure_5_v2.png b/plots/figures/figure_5_v2.png
diff --git a/plots/overview.py b/plots/overview.py
@@ -13,6 +13,7 @@
 config = yaml.load(open("config.yml", "r"))["default"]
 
 #Paths 
+UPDATE = config['UPDATE_DATES']['CONFIRMED_CASES']
 DATA_PATH = config['PATHS']['DATA_PATH']
 # WE NEED TO UNIFY THE UTILITIES
 UTILS_PATH = config['PATHS']['UTILS_PATH'].format(dir = 'severe_outcomes')
@@ -27,7 +28,7 @@
 import utilities_severity as ut
 
 # Read data
-df_confirmed_bogota = pd.read_csv(DATA_PATH + 'confirmed_cases.csv')
+df_confirmed_bogota = pd.read_csv(DATA_PATH + 'confirmed_cases_' + UPDATE + '.csv')
 df_confirmed_bogota = df_confirmed_bogota.astype({'age':int})
 
 df_confirmed_bogota['onset'] = pd.to_datetime(df_confirmed_bogota['onset'], errors='coerce')
@@ -70,7 +71,7 @@ def plot_pyramid(ax):
 
 ## Conditions
 mask_60p = (df['age_group']=='60+')
-mask_death = (df['death'].notnull())
+mask_death = (df['death'].notnull()) & ~(df_confirmed_bogota['condition'] =='Fallecido (No aplica No causa Directa)')
 
 df_cases_all = ut.counts(df, var='onset',columns=['date', 'cases'])
 df_cases_60p = ut.counts(df[mask_60p], var='onset', columns=['date', 'cases'])

diff --git a/plots/results_genomics.py b/plots/results_genomics.py
@@ -16,6 +16,7 @@
 
 config = yaml.load(open("config.yml", "r"))["default"]
 
+UPDATE = config['UPDATE_DATES']['CONFIRMED_CASES']
 DATA_PATH = config['PATHS']['DATA_PATH']
 OUT_PATH = config['PATHS']['OUT_PATH'].format(dir = 'genomics')
 DATE_GENOMICS = config['UPDATE_DATES']['GENOMICS']
@@ -41,7 +42,7 @@
 df_results['week_date'] = df_results.week_name.apply(lambda date: datetime.strptime(date + '-1', "%Y-%W-%w"))
 df_results = df_results.sort_values(by = 'week_date')
 ## Cases
-df_confirmed_bogota = pd.read_csv(DATA_PATH + 'confirmed_cases.csv')
+df_confirmed_bogota = pd.read_csv(DATA_PATH + 'confirmed_cases_' + UPDATE + '.csv')
 df_confirmed_bogota = df_confirmed_bogota.astype({'age':int})
 df_confirmed_bogota['onset'] = pd.to_datetime(df_confirmed_bogota['onset'], errors='coerce')
 df_confirmed_bogota['death'] = pd.to_datetime(df_confirmed_bogota['death'], errors='coerce')

diff --git a/plots/results_waves.py b/plots/results_waves.py
@@ -11,6 +11,7 @@
 
 config = yaml.load(open("config.yml", "r"))["default"]
 
+UPDATE = config['UPDATE_DATES']['CONFIRMED_CASES']
 DATA_PATH = config['PATHS']['DATA_PATH']
 OUT_PATH = config['PATHS']['OUT_PATH'].format(dir = 'waves')
 UTILS_PATH = config['PATHS']['UTILS_PATH'].format(dir = 'waves')
@@ -26,7 +27,7 @@
 import utilities_waves as ut
 
 # Read confirmed cases and waves information
-df_confirmed_bogota = pd.read_csv(DATA_PATH + 'confirmed_cases.csv')
+df_confirmed_bogota = pd.read_csv(DATA_PATH + 'confirmed_cases_' + UPDATE + '.csv')
 df_confirmed_bogota['onset'] = pd.to_datetime(df_confirmed_bogota['onset'], errors='coerce')
 
 df_waves = pd.read_csv(OUT_PATH + 'waves.csv')

diff --git a/rt/scripts/rt.R b/rt/scripts/rt.R
@@ -16,12 +16,15 @@ config <- config::get('PATHS')
 DATA_PATH = config$DATA_PATH
 OUT_PATH = config$OUT_PATH %>% str_replace('\\{dir\\}', 'rt')
 
+config <- config::get('UPDATE_DATES')
+UPDATE = config$CONFIRMED_CASES
+
 # parameters 
 incubation_period <- 5
 rt_window <- 14
 
 # read data
-df_confirmed_bogota <- read_csv(paste0(DATA_PATH, 'confirmed_cases.csv'))
+df_confirmed_bogota <- read_csv(paste0(DATA_PATH, 'confirmed_cases_', UPDATE,'.csv'))
 df_confirmed_bogota <- df_confirmed_bogota[, c('onset', 'age', 'age_unit', 'contagion_source')]
 df_confirmed_bogota$onset <- as.Date(df_confirmed_bogota$onset)
 df_confirmed_bogota$infection <- df_confirmed_bogota$onset - incubation_period