def heatmap_Hepatitis_A():
Hepatitis_A = heatmap_disease_matrix('Hepatitis A')
Hepatitis_A = Hepatitis_A.drop([
'GUAM', 'PAC TRUST TERR', 'AMERICAN SAMOA', 'NORTHERN MARIANA ISLANDS'
],
axis=1)
fig, ax = plt.subplots(figsize=(15, 15))
flatui = [
'#ecf0f1', '#bdc3c7', '#95a5a6', '#7f8c8d', '#f1c40f', '#f39c12',
'#d35400', '#e74c3c'
]
sns.set_palette(flatui)
my_cmap = ListedColormap(flatui)
sns.set(font_scale=1.2)
sns.set_style({"savefig.dpi": 500})
ax = sns.heatmap(Hepatitis_A.T,
linewidths=.20,
cmap=my_cmap,
ax=ax,
vmin=0,
vmax=500,
xticklabels=5)
ax.set_title('Hepatitis A', fontsize=18, fontweight='bold')
ax.axvline(x=22, color='k', linewidth=2.5)
ax.text(22, 0.5, ' Vaccine introduced', fontsize=10, fontweight='bold')
plt.yticks(rotation='horizontal')
fig.tight_layout()
fig.savefig('Heatmap of Hepatitis_A.pdf')
def heatmap_Mumps():
Mumps = heatmap_disease_matrix('Mumps')
fig, ax = plt.subplots(figsize=(15, 15))
flatui = [
'#ecf0f1', '#bdc3c7', '#95a5a6', '#7f8c8d', '#f1c40f', '#f39c12',
'#d35400', '#e74c3c'
]
sns.set_palette(flatui)
my_cmap = ListedColormap(flatui)
sns.set(font_scale=1.2)
sns.set_style({"savefig.dpi": 500})
ax = sns.heatmap(Mumps.T,
linewidths=.20,
cmap=my_cmap,
ax=ax,
vmin=0,
vmax=2500,
xticklabels=5)
ax.set_title('Mumps', fontsize=18, fontweight='bold')
ax.axvline(x=10, color='k', linewidth=3)
ax.text(10.3, 0.5, ' Vaccine introduced', fontsize=10, fontweight='bold')
plt.yticks(rotation='horizontal')
fig.tight_layout()
fig.savefig('Heatmap of Mumps.pdf')
def heatmap_Smallpox():
Smallpox = heatmap_disease_matrix('Smallpox')
Smallpox = Smallpox.drop(Smallpox.index[list(range(27))])
fig, ax = plt.subplots(figsize=(15, 15))
flatui = [
'#ecf0f1', '#bdc3c7', '#95a5a6', '#7f8c8d', '#f1c40f', '#f39c12',
'#d35400', '#e74c3c'
]
sns.set_palette(flatui)
my_cmap = ListedColormap(flatui)
sns.set(font_scale=1.2)
sns.set_style({"savefig.dpi": 500})
ax = sns.heatmap(Smallpox.T,
linewidths=.20,
cmap=my_cmap,
ax=ax,
vmin=0,
vmax=500,
xticklabels=2)
ax.set_title('Smallpox', fontsize=18, fontweight='bold')
ax.axvline(x=12, color='k', linewidth=3)
ax.text(12, 0.3, ' Vaccine introduced', fontsize=10, fontweight='bold')
plt.yticks(rotation='horizontal')
fig.tight_layout()
fig.savefig('Heatmap of Smallpox.pdf')
def heatmap_Measles():
Measles = heatmap_disease_matrix('Measles')
Measles = Measles.loc[
1928:] #drop rows before 1928 for measles, since missing data
Measles = Measles.drop(
[
'GUAM', 'PAC TRUST TERR', 'AMERICAN SAMOA',
'NORTHERN MARIANA ISLANDS'
],
axis=1) #drop those states with no recording numbers
fig, ax = plt.subplots(figsize=(15, 15))
flatui = [
'#ecf0f1', '#bdc3c7', '#95a5a6', '#7f8c8d', '#f1c40f', '#f39c12',
'#d35400', '#e74c3c'
]
sns.set_palette(flatui)
my_cmap = ListedColormap(flatui)
sns.set(font_scale=1.2)
sns.set_style({"savefig.dpi": 100})
ax = sns.heatmap(Measles.T,
linewidths=.20,
cmap=my_cmap,
ax=ax,
vmin=0,
vmax=3000,
xticklabels=5)
ax.set_title('Measles', fontsize=18, fontweight='bold')
ax.axvline(x=36, color='k', linewidth=2.5)
ax.text(36, 0.1, ' Vaccine introduced', fontsize=10, fontweight='bold')
plt.yticks(rotation='horizontal')
fig.tight_layout()
fig.savefig('Heatmap of Measles.pdf')
def heatmap_Rubella():
Rubella = heatmap_disease_matrix('Rubella')
Rubella = Rubella.drop(['GUAM', 'PAC TRUST TERR', 'AMERICAN SAMOA'],
axis=1)
fig, ax = plt.subplots(figsize=(15, 15))
flatui = [
'#ecf0f1', '#bdc3c7', '#95a5a6', '#7f8c8d', '#f1c40f', '#f39c12',
'#d35400', '#e74c3c'
]
sns.set_palette(flatui)
my_cmap = ListedColormap(flatui)
sns.set(font_scale=1.2)
sns.set_style({"savefig.dpi": 500})
ax = sns.heatmap(Rubella.T,
linewidths=.20,
cmap=my_cmap,
ax=ax,
vmin=0,
vmax=1500,
xticklabels=5)
ax.set_title('Rubella', fontsize=18, fontweight='bold')
ax.axvline(x=4, color='k', linewidth=3)
ax.text(4, 0.3, ' Vaccine introduced', fontsize=10, fontweight='bold')
plt.yticks(rotation='horizontal')
fig.tight_layout()
fig.savefig('Heatmap of Rubella.pdf')
def __init__(self, disease):
self.name = disease
if self.name not in disease_list:
raise diseaseExceptioin()
else:
self.data = mt.heatmap_disease_matrix(disease)
self.lower = self.data.index.min()
self.upper = self.data.index.max()
def get_std_data_by_year(year, disease):
data = mt.heatmap_disease_matrix(disease).ix[year]
num_records = [
data[i.upper()] if i.upper() in data.index else 0 for i in state
] # to keep in the form of
max_num = np.max(num_records)
std_num_records = [i / max_num if max_num != 0 else 0 for i in num_records]
return std_num_records #so define a exception class here.
def get_mean(disease):
'''
Return the mean number of infected people before and after the year of vaccine invented,
Note: in some cases the mean number before vaccine invented is NaN since our dataset doesn't
have recorded data back to that time.
'''
valid_list = [
'measles', 'hepatitis_a', 'rubella', 'poliomyelitis', 'smallpox',
'mumps'
]
if disease not in valid_list:
raise InvalidDisease
df = heatmap_disease_matrix(disease)
df['sum_all_state'] = df.sum(axis=1)
df = df[['sum_all_state']]
if disease == 'measles':
mean_before_vc = np.mean(df.loc[:Measles_vaccine_year])
mean_after_vc = np.mean(df.loc[Measles_vaccine_year:])
elif disease == 'hepatitis_a':
mean_before_vc = np.mean(df.loc[:Hepatitis_A_vaccine_year])
mean_after_vc = np.mean(df.loc[Hepatitis_A_vaccine_year:])
elif disease == 'rubella':
mean_before_vc = np.mean(df.loc[:Rubella_vaccine_year])
mean_after_vc = np.mean(df.loc[Rubella_vaccine_year:])
elif disease == 'poliomyelitis':
mean_before_vc = np.mean(df.loc[:Poliomyelitis_vaccine_year])
mean_after_vc = np.mean(df.loc[Poliomyelitis_vaccine_year:])
elif disease == 'smallpox':
mean_before_vc = np.mean(df.loc[:Smallpox_vaccine_year])
mean_after_vc = np.mean(df.loc[Smallpox_vaccine_year:])
else:
mean_before_vc = np.mean(df.loc[:Mumps_vaccine_year])
mean_after_vc = np.mean(df.loc[Mumps_vaccine_year:])
return [mean_before_vc['sum_all_state'], mean_after_vc['sum_all_state']]
def detect_year(input_year, disease):
data = mt.heatmap_disease_matrix(disease)
if input_year in data.index:
return True
else:
return False
