def title_grid_legend(ax, title, grid, commaticks, setylim, legend_args, show_legend=True):
''' Plot styling -- set the plot title, add a legend, and optionally add gridlines'''
# Handle show_legend being in the legend args, since in some cases this is the only way it can get passed
if 'show_legend' in legend_args:
show_legend = legend_args.pop('show_legend')
popped = True
else:
popped = False
# Show the legend
if show_legend:
ax.legend(**legend_args)
# If we removed it from the legend_args dict, put it back now
if popped:
legend_args['show_legend'] = show_legend
# Set the title and gridlines
ax.set_title(title)
ax.grid(grid)
# Set the y axis style
if setylim:
ax.set_ylim(bottom=0)
if commaticks:
ylims = ax.get_ylim()
if ylims[1] >= 1000:
sc.commaticks(ax=ax)
return
def format_ax(ax, sim):
@ticker.FuncFormatter
def date_formatter(x, pos):
return (sim['start_day'] + dt.timedelta(days=x)).strftime('%b-%d')
ax.xaxis.set_major_formatter(date_formatter)
sc.commaticks()
# sc.boxoff()
return
def title_grid_legend(ax,
title,
grid,
commaticks,
setylim,
legend_args,
show_args,
show_legend=True):
''' Plot styling -- set the plot title, add a legend, and optionally add gridlines'''
# Handle show_legend being in the legend args, since in some cases this is the only way it can get passed
if 'show_legend' in legend_args:
show_legend = legend_args.pop('show_legend')
popped = True
else:
popped = False
# Show the legend
if show_legend and show_args[
'legend']: # It's pretty ugly, but there are multiple ways of controlling whether the legend shows
# Remove duplicate entries
handles, labels = ax.get_legend_handles_labels()
unique_inds = np.sort(np.unique(labels, return_index=True)[1])
handles = [handles[u] for u in unique_inds]
labels = [labels[u] for u in unique_inds]
# Actually make legend
ax.legend(handles=handles, labels=labels, **legend_args)
# If we removed it from the legend_args dict, put it back now
if popped:
legend_args['show_legend'] = show_legend
# Set the title, gridlines, and color
ax.set_title(title)
# Set the y axis style
if setylim and ax.yaxis.get_scale() != 'log':
ax.set_ylim(bottom=0)
if commaticks:
ylims = ax.get_ylim()
if ylims[1] >= 1000:
sc.commaticks(ax=ax)
# Optionally remove x-axis labels except on bottom plots -- don't use ax.label_outer() since we need to keep the y-labels
if show_args['outer']:
lastrow = ax.get_subplotspec().is_last_row()
if not lastrow:
for label in ax.get_xticklabels(which="both"):
label.set_visible(False)
ax.set_xlabel('')
return
def plot(self):
pl.figure()
pl.plot(self.t, self.S, label='S')
pl.plot(self.t, self.E, label='E')
pl.plot(self.t, self.I, label='I')
pl.plot(self.t, self.R, label='R')
pl.legend()
pl.xlabel('Day')
pl.ylabel('People')
sc.setylim() # Reset y-axis to start at 0
sc.commaticks() # Use commas in the y-axis labels
return
def format_ax(ax, sim, key=None):
''' Format the axes nicely '''
@ticker.FuncFormatter
def date_formatter(x, pos):
return (sim['start_day'] + dt.timedelta(days=x)).strftime('%b-%d')
ax.xaxis.set_major_formatter(date_formatter)
if key != 'r_eff':
sc.commaticks()
pl.xlim([0, sim['n_days']])
sc.boxoff()
return
def format_ax(ax, sim, key=None):
@ticker.FuncFormatter
def date_formatter(x, pos):
return (sim['start_day'] + dt.timedelta(days=int(x))).strftime('%b\n%y')
ax.xaxis.set_major_formatter(date_formatter)
if key != 'r_eff':
sc.commaticks()
pl.xlim([0, sim['n_days']])
pl.axvspan(lockdown1[0], lockdown1[1], color='steelblue', alpha=0.2, lw=0)
pl.axvspan(lockdown2[0], lockdown2[1], color='steelblue', alpha=0.2, lw=0)
pl.axvspan(lockdown3[0], lockdown3[1], color='lightblue', alpha=0.2, lw=0)
return
def format_axs(axs, key=None):
''' Format axes nicely '''
@ticker.FuncFormatter
def date_formatter(x, pos):
# print(x)
return (refsim['start_day'] + dt.timedelta(days=x)).strftime('%b-%d')
for i, ax in enumerate(axs):
bbox = None if i != 1 else (1.05, 1.05) # Move legend up a bit
day_stride = 21
xmin, xmax = ax.get_xlim()
ax.set_xticks(np.arange(xmin, xmax, day_stride))
ax.xaxis.set_major_formatter(date_formatter)
ax.legend(frameon=False, bbox_to_anchor=bbox)
sc.boxoff(ax=ax)
sc.setylim(ax=ax)
sc.commaticks(ax=ax)
return
def plot(self,
to_plot=None,
do_save=None,
fig_path=None,
fig_args=None,
plot_args=None,
axis_args=None,
fill_args=None,
legend_args=None,
as_dates=True,
dateformat=None,
interval=None,
n_cols=1,
font_size=18,
font_family=None,
grid=True,
commaticks=True,
do_show=True,
sep_figs=False,
verbose=None):
'''
Plot the results -- can supply arguments for both the figure and the plots.
Args:
to_plot (dict): Dict of results to plot; see default_scen_plots for structure
do_save (bool): Whether or not to save the figure
fig_path (str): Path to save the figure
fig_args (dict): Dictionary of kwargs to be passed to pl.figure()
plot_args (dict): Dictionary of kwargs to be passed to pl.plot()
axis_args (dict): Dictionary of kwargs to be passed to pl.subplots_adjust()
fill_args (dict): Dictionary of kwargs to be passed to pl.fill_between()
legend_args (dict): Dictionary of kwargs to be passed to pl.legend()
as_dates (bool): Whether to plot the x-axis as dates or time points
dateformat (str): Date string format, e.g. '%B %d'
interval (int): Interval between tick marks
n_cols (int): Number of columns of subpanels to use for subplot
font_size (int): Size of the font
font_family (str): Font face
grid (bool): Whether or not to plot gridlines
commaticks (bool): Plot y-axis with commas rather than scientific notation
do_show (bool): Whether or not to show the figure
sep_figs (bool): Whether to show separate figures for different results instead of subplots
verbose (bool): Display a bit of extra information
Returns:
fig: Figure handle
'''
if verbose is None:
verbose = self['verbose']
sc.printv('Plotting...', 1, verbose)
if to_plot is None:
to_plot = cvd.default_scen_plots
to_plot = sc.dcp(to_plot) # In case it's supplied as a dict
# Handle input arguments -- merge user input with defaults
fig_args = sc.mergedicts({'figsize': (16, 14)}, fig_args)
plot_args = sc.mergedicts({'lw': 3, 'alpha': 0.7}, plot_args)
axis_args = sc.mergedicts(
{
'left': 0.10,
'bottom': 0.05,
'right': 0.95,
'top': 0.90,
'wspace': 0.25,
'hspace': 0.25
}, axis_args)
fill_args = sc.mergedicts({'alpha': 0.2}, fill_args)
legend_args = sc.mergedicts({'loc': 'best'}, legend_args)
if sep_figs:
figs = []
else:
fig = pl.figure(**fig_args)
pl.subplots_adjust(**axis_args)
pl.rcParams['font.size'] = font_size
if font_family:
pl.rcParams['font.family'] = font_family
n_rows = np.ceil(len(to_plot) /
n_cols) # Number of subplot rows to have
for rk, reskey in enumerate(to_plot):
title = self.base_sim.results[
reskey].name # Get the name of this result from the base simulation
if sep_figs:
figs.append(pl.figure(**fig_args))
ax = pl.subplot(111)
else:
ax = pl.subplot(n_rows, n_cols, rk + 1)
resdata = self.results[reskey]
for scenkey, scendata in resdata.items():
pl.fill_between(self.tvec, scendata.low, scendata.high,
**fill_args)
pl.plot(self.tvec,
scendata.best,
label=scendata.name,
**plot_args)
pl.title(title)
if rk == 0:
pl.legend(**legend_args)
pl.grid(grid)
if commaticks:
sc.commaticks()
if self.base_sim.data is not None and reskey in self.base_sim.data:
data_t = np.array(
(self.base_sim.data.index - self.base_sim['start_day'])
/ np.timedelta64(1, 'D'))
pl.plot(data_t, self.base_sim.data[reskey], 'sk',
**plot_args)
# Optionally reset tick marks (useful for e.g. plotting weeks/months)
if interval:
xmin, xmax = ax.get_xlim()
ax.set_xticks(pl.arange(xmin, xmax + 1, interval))
# Set xticks as dates
if as_dates:
@ticker.FuncFormatter
def date_formatter(x, pos):
return (self.base_sim['start_day'] +
dt.timedelta(days=x)).strftime('%b-%d')
ax.xaxis.set_major_formatter(date_formatter)
if not interval:
ax.xaxis.set_major_locator(
ticker.MaxNLocator(integer=True))
# Ensure the figure actually renders or saves
if do_save:
if fig_path is None: # No figpath provided - see whether do_save is a figpath
fig_path = 'covasim_scenarios.png' # Just give it a default name
fig_path = sc.makefilepath(
fig_path) # Ensure it's valid, including creating the folder
pl.savefig(fig_path)
if do_show:
pl.show()
else:
pl.close(fig)
return fig
def plot(self, to_plot=None, do_save=None, fig_path=None, fig_args=None, plot_args=None,
axis_args=None, fill_args=None, as_dates=True, interval=None, dateformat=None,
font_size=18, font_family=None, grid=True, commaticks=True, do_show=True, sep_figs=False,
verbose=None):
'''
Plot the results -- can supply arguments for both the figure and the plots.
Args:
to_plot (dict): Dict of results to plot; see default_scen_plots for structure
do_save (bool): Whether or not to save the figure
fig_path (str): Path to save the figure
fig_args (dict): Dictionary of kwargs to be passed to pl.figure()
plot_args (dict): Dictionary of kwargs to be passed to pl.plot()
axis_args (dict): Dictionary of kwargs to be passed to pl.subplots_adjust()
fill_args (dict): Dictionary of kwargs to be passed to pl.fill_between()
as_dates (bool): Whether to plot the x-axis as dates or time points
interval (int): Interval between tick marks
dateformat (str): Date string format, e.g. '%B %d'
font_size (int): Size of the font
font_family (str): Font face
grid (bool): Whether or not to plot gridlines
commaticks (bool): Plot y-axis with commas rather than scientific notation
do_show (bool): Whether or not to show the figure
sep_figs (bool): Whether to show separate figures for different results instead of subplots
verbose (bool): Display a bit of extra information
Returns:
fig: Figure handle
'''
if verbose is None:
verbose = self['verbose']
sc.printv('Plotting...', 1, verbose)
if to_plot is None:
to_plot = default_scen_plots
to_plot = sc.odict(sc.dcp(to_plot)) # In case it's supplied as a dict
# Handle input arguments -- merge user input with defaults
fig_args = sc.mergedicts({'figsize': (16, 12)}, fig_args)
plot_args = sc.mergedicts({'lw': 3, 'alpha': 0.7}, plot_args)
axis_args = sc.mergedicts({'left': 0.10, 'bottom': 0.05, 'right': 0.95, 'top': 0.90, 'wspace': 0.5, 'hspace': 0.25}, axis_args)
fill_args = sc.mergedicts({'alpha': 0.2}, fill_args)
if sep_figs:
figs = []
else:
fig = pl.figure(**fig_args)
pl.subplots_adjust(**axis_args)
pl.rcParams['font.size'] = font_size
if font_family:
pl.rcParams['font.family'] = font_family
# %% Plotting
for rk,reskey,title in to_plot.enumitems():
if sep_figs:
figs.append(pl.figure(**fig_args))
ax = pl.subplot(111)
else:
ax = pl.subplot(len(to_plot), 1, rk + 1)
resdata = self.allres[reskey]
for scenkey, scendata in resdata.items():
pl.fill_between(self.tvec, scendata.low, scendata.high, **fill_args)
pl.plot(self.tvec, scendata.best, label=scendata.name, **plot_args)
pl.title(title)
if rk == 0:
pl.legend(loc='best')
pl.grid(grid)
if commaticks:
sc.commaticks()
# Optionally reset tick marks (useful for e.g. plotting weeks/months)
if interval:
xmin,xmax = ax.get_xlim()
ax.set_xticks(pl.arange(xmin, xmax+1, interval))
# Set xticks as dates
if as_dates:
xticks = ax.get_xticks()
xticklabels = self.base_sim.inds2dates(xticks, dateformat=dateformat)
ax.set_xticklabels(xticklabels)
# Ensure the figure actually renders or saves
if do_save:
if fig_path is None: # No figpath provided - see whether do_save is a figpath
fig_path = 'covasim_scenarios.png' # Just give it a default name
fig_path = sc.makefilepath(fig_path) # Ensure it's valid, including creating the folder
pl.savefig(fig_path)
if do_show:
pl.show()
else:
pl.close(fig)
return fig
def plot(self,
to_plot=None,
do_save=None,
fig_path=None,
fig_args=None,
plot_args=None,
scatter_args=None,
axis_args=None,
legend_args=None,
as_dates=True,
dateformat=None,
interval=None,
n_cols=1,
font_size=18,
font_family=None,
use_grid=True,
use_commaticks=True,
do_show=True,
verbose=None):
'''
Plot the results -- can supply arguments for both the figure and the plots.
Args:
to_plot (dict): Nested dict of results to plot; see default_sim_plots for structure
do_save (bool or str): Whether or not to save the figure. If a string, save to that filename.
fig_path (str): Path to save the figure
fig_args (dict): Dictionary of kwargs to be passed to pl.figure()
plot_args (dict): Dictionary of kwargs to be passed to pl.plot()
scatter_args (dict): Dictionary of kwargs to be passed to pl.scatter()
axis_args (dict): Dictionary of kwargs to be passed to pl.subplots_adjust()
legend_args (dict): Dictionary of kwargs to be passed to pl.legend()
as_dates (bool): Whether to plot the x-axis as dates or time points
dateformat (str): Date string format, e.g. '%B %d'
interval (int): Interval between tick marks
n_cols (int): Number of columns of subpanels to use for subplot
font_size (int): Size of the font
font_family (str): Font face
use_grid (bool): Whether or not to plot gridlines
use_commaticks (bool): Plot y-axis with commas rather than scientific notation
do_show (bool): Whether or not to show the figure
verbose (bool): Display a bit of extra information
Returns:
fig: Figure handle
'''
if verbose is None:
verbose = self['verbose']
sc.printv('Plotting...', 1, verbose)
if to_plot is None:
to_plot = cvd.default_sim_plots
to_plot = sc.odict(to_plot) # In case it's supplied as a dict
# Handle input arguments -- merge user input with defaults
fig_args = sc.mergedicts({'figsize': (16, 14)}, fig_args)
plot_args = sc.mergedicts({'lw': 3, 'alpha': 0.7}, plot_args)
scatter_args = sc.mergedicts({'s': 70, 'marker': 's'}, scatter_args)
axis_args = sc.mergedicts(
{
'left': 0.1,
'bottom': 0.05,
'right': 0.9,
'top': 0.97,
'wspace': 0.2,
'hspace': 0.25
}, axis_args)
legend_args = sc.mergedicts({'loc': 'best'}, legend_args)
fig = pl.figure(**fig_args)
pl.subplots_adjust(**axis_args)
pl.rcParams['font.size'] = font_size
if font_family:
pl.rcParams['font.family'] = font_family
res = self.results # Shorten since heavily used
# Plot everything
n_rows = np.ceil(len(to_plot) /
n_cols) # Number of subplot rows to have
for p, title, keylabels in to_plot.enumitems():
ax = pl.subplot(n_rows, n_cols, p + 1)
for key in keylabels:
label = res[key].name
this_color = res[key].color
y = res[key].values
pl.plot(res['t'], y, label=label, **plot_args, c=this_color)
if self.data is not None and key in self.data:
data_t = (
self.data.index - self['start_day']
) / np.timedelta64(
1, 'D'
) # Convert from data date to model output index based on model start date
pl.scatter(data_t,
self.data[key],
c=[this_color],
**scatter_args)
if self.data is not None and len(self.data):
pl.scatter(pl.nan,
pl.nan,
c=[(0, 0, 0)],
label='Data',
**scatter_args)
pl.legend(**legend_args)
pl.grid(use_grid)
sc.setylim()
if use_commaticks:
sc.commaticks()
pl.title(title)
# Optionally reset tick marks (useful for e.g. plotting weeks/months)
if interval:
xmin, xmax = ax.get_xlim()
ax.set_xticks(pl.arange(xmin, xmax + 1, interval))
# Set xticks as dates
if as_dates:
@ticker.FuncFormatter
def date_formatter(x, pos):
return (self['start_day'] +
dt.timedelta(days=x)).strftime('%b-%d')
ax.xaxis.set_major_formatter(date_formatter)
if not interval:
ax.xaxis.set_major_locator(
ticker.MaxNLocator(integer=True))
# Plot interventions
for intervention in self['interventions']:
intervention.plot(self, ax)
# Ensure the figure actually renders or saves
if do_save:
if fig_path is None: # No figpath provided - see whether do_save is a figpath
if isinstance(do_save, str):
fig_path = do_save # It's a string, assume it's a filename
else:
fig_path = 'covasim.png' # Just give it a default name
fig_path = sc.makefilepath(
fig_path) # Ensure it's valid, including creating the folder
pl.savefig(fig_path)
if do_show:
pl.show()
else:
pl.close(fig)
return fig
elinewidth=3,
capsize=0)
box_ax.set_xticks(x - 0.15)
#box_ax.set_xticklabels(labels)
@ticker.FuncFormatter
def date_formatter(x, pos):
return (cv.date('2021-01-12') + dt.timedelta(days=x * 7)).strftime('%d-%b')
box_ax.xaxis.set_major_formatter(date_formatter)
pl.ylabel('Estimated daily infections (000s)')
sc.boxoff(ax=box_ax)
sc.commaticks()
box_ax.legend(frameon=False)
# B. Cumulative total infections
width = 0.8 # the width of the bars
x = [0, 1, 2]
data = np.array([
msims[sn].results['cum_infections'].values[-1] -
msims[sn].results['cum_infections'].values[sim.day('2021-01-04')]
for sn in scenarios
])
bar_ax = pl.axes([xgapl + xgapm + dx1, ygapb, dx2, dy])
for sn, scen in enumerate(scenarios):
bar_ax.bar(x[sn], data[sn] / 1e3, width, color=colors[sn], alpha=1.0)
bar_ax.set_xticklabels(['', 'FNL', 'Primary-only\nPNL', 'Staggered\nPNL'])
def plot(self,
to_plot=None,
do_save=None,
fig_path=None,
fig_args=None,
plot_args=None,
scatter_args=None,
axis_args=None,
as_dates=True,
interval=None,
dateformat=None,
font_size=18,
font_family=None,
use_grid=True,
use_commaticks=True,
do_show=True,
verbose=None):
'''
Plot the results -- can supply arguments for both the figure and the plots.
Args:
to_plot (dict): Nested dict of results to plot; see default_sim_plots for structure
do_save (bool or str): Whether or not to save the figure. If a string, save to that filename.
fig_path (str): Path to save the figure
fig_args (dict): Dictionary of kwargs to be passed to pl.figure()
plot_args (dict): Dictionary of kwargs to be passed to pl.plot()
scatter_args (dict): Dictionary of kwargs to be passed to pl.scatter()
axis_args (dict): Dictionary of kwargs to be passed to pl.subplots_adjust()
as_dates (bool): Whether to plot the x-axis as dates or time points
interval (int): Interval between tick marks
dateformat (str): Date string format, e.g. '%B %d'
font_size (int): Size of the font
font_family (str): Font face
use_grid (bool): Whether or not to plot gridlines
use_commaticks (bool): Plot y-axis with commas rather than scientific notation
do_show (bool): Whether or not to show the figure
verbose (bool): Display a bit of extra information
Returns:
fig: Figure handle
'''
if verbose is None:
verbose = self['verbose']
sc.printv('Plotting...', 1, verbose)
if to_plot is None:
to_plot = default_sim_plots
to_plot = sc.odict(to_plot) # In case it's supplied as a dict
# Handle input arguments -- merge user input with defaults
fig_args = sc.mergedicts({'figsize': (16, 12)}, fig_args)
plot_args = sc.mergedicts({'lw': 3, 'alpha': 0.7}, plot_args)
scatter_args = sc.mergedicts({'s': 150, 'marker': 's'}, scatter_args)
axis_args = sc.mergedicts(
{
'left': 0.1,
'bottom': 0.05,
'right': 0.9,
'top': 0.97,
'wspace': 0.2,
'hspace': 0.25
}, axis_args)
fig = pl.figure(**fig_args)
pl.subplots_adjust(**axis_args)
pl.rcParams['font.size'] = font_size
if font_family:
pl.rcParams['font.family'] = font_family
res = self.results # Shorten since heavily used
# Plot everything
colors = sc.gridcolors(max([len(tp) for tp in to_plot.values()]))
# Define the data mapping. Must be here since uses functions
if self.data is not None and len(self.data):
data_mapping = {
'cum_exposed': pl.cumsum(self.data['new_infections']),
'cum_diagnosed': pl.cumsum(self.data['new_positives']),
'cum_tested': pl.cumsum(self.data['new_tests']),
'infections': self.data['new_infections'],
'tests': self.data['new_tests'],
'diagnoses': self.data['new_positives'],
}
else:
data_mapping = {}
for p, title, keylabels in to_plot.enumitems():
ax = pl.subplot(2, 1, p + 1)
for i, key, label in keylabels.enumitems():
this_color = colors[i]
y = res[key].values
pl.plot(res['t'], y, label=label, **plot_args, c=this_color)
if key in data_mapping:
pl.scatter(self.data['day'],
data_mapping[key],
c=[this_color],
**scatter_args)
if self.data is not None and len(self.data):
pl.scatter(pl.nan,
pl.nan,
c=[(0, 0, 0)],
label='Data',
**scatter_args)
pl.grid(use_grid)
cvu.fixaxis(self)
if use_commaticks:
sc.commaticks()
pl.title(title)
# Optionally reset tick marks (useful for e.g. plotting weeks/months)
if interval:
xmin, xmax = ax.get_xlim()
ax.set_xticks(pl.arange(xmin, xmax + 1, interval))
# Set xticks as dates
if as_dates:
xticks = ax.get_xticks()
xticklabels = self.inds2dates(xticks, dateformat=dateformat)
ax.set_xticklabels(xticklabels)
# Plot interventions
for intervention in self['interventions']:
intervention.plot(self, ax)
# Ensure the figure actually renders or saves
if do_save:
if fig_path is None: # No figpath provided - see whether do_save is a figpath
if isinstance(do_save, str):
fig_path = do_save # It's a string, assume it's a filename
else:
fig_path = 'covasim.png' # Just give it a default name
fig_path = sc.makefilepath(
fig_path) # Ensure it's valid, including creating the folder
pl.savefig(fig_path)
if do_show:
pl.show()
else:
pl.close(fig)
return fig
def plot(self,
do_save=None,
fig_args=None,
plot_args=None,
scatter_args=None,
fill_args=None,
axis_args=None,
font_size=None,
font_family=None,
use_grid=True,
do_show=True,
verbose=None):
'''
Plotting, copied from run_cdc_scenarios.
Args:
do_save (bool/str): whether or not to save the figure, if so, to this filename
fig_args (dict): options for styling the figure (e.g. size)
plot_args (dict): likewise, for the plot (e.g., line thickness)
scatter_args (dict): likewise, for scatter points (used for data)
fill_args (dict): likewise, for uncertainty bounds (e.g. alpha)
axis_args (dict): likewise, for axes (e.g. margins)
font_size (int): overall figure font size
font_family (str): what font to use (must exist on your system!)
use_grid (bool): whether or not to plot gridlines on the plot
verbose (bool): whether or not to print extra output
Returns:
fig: a matplotlib figure object
'''
if fig_args is None: fig_args = {'figsize': (16, 12)}
if plot_args is None: plot_args = {'lw': 3, 'alpha': 0.7}
if scatter_args is None: scatter_args = {'s': 150, 'marker': 's'}
if axis_args is None:
axis_args = {
'left': 0.1,
'bottom': 0.05,
'right': 0.9,
'top': 0.97,
'wspace': 0.2,
'hspace': 0.25
}
if fill_args is None: fill_args = {'alpha': 0.2}
if font_size is None: font_size = 18
if font_family is None: font_family = 'Proxima Nova'
fig = pl.figure(**fig_args)
pl.subplots_adjust(**axis_args)
pl.rcParams['font.size'] = font_size
pl.rcParams['font.family'] = font_family
xmin = self.startday
tvec = xmin + pl.arange(self.npts) # TODO: fix! With dates!
for rk, reskey in enumerate(self.reskeys):
pl.subplot(len(self.reskeys), 1, rk + 1)
resdata = self.beds[reskey]
for scenkey, scendata in resdata.items():
pl.fill_between(tvec, scendata.low, scendata.high, **fill_args)
# pl.plot(tvec, scendata.low, linestyle='--', **plot_args)
# pl.plot(tvec, scendata.high, linestyle='--', **plot_args)
pl.plot(tvec,
scendata.best,
label=self.scenlabels[scenkey],
**plot_args)
if rk == 0:
pl.legend()
pl.title(self.reslabels[rk])
# sc.setylim()
pl.grid(True)
# Set x-axis
xmax = xmin + self.npts # TODO: fix!!!
pl.gca().set_xticks(pl.arange(xmin, xmax + 1, 7))
xt = pl.gca().get_xticks()
lab = []
for t in xt:
tmp = dt.datetime(2020, 1, 1) + dt.timedelta(
days=int(t)) # + pars['day_0']
lab.append(tmp.strftime('%B %d'))
pl.gca().set_xticklabels(lab)
sc.commaticks(axis='y')
if do_show:
pl.show()
return fig
#%% Plotting
pl.figure(figsize=(18, 6), dpi=200)
# pl.rcParams['font.size'] = 18
pl.subplot(1, 3, 1)
colors = sc.vectocolor(pl.log10(popsizes), cmap='parula')
for k, key in enumerate(keys):
label = f'{int(float(key[1:]))/1000}k: {results[k][-1]:0.0f}'
pl.plot(results[k], label=label, lw=3, color=colors[k])
print(label)
# pl.legend()
pl.title('Total number of infections')
pl.xlabel('Day')
pl.ylabel('Number of infections')
sc.commaticks(axis='y')
pl.subplot(1, 3, 2)
for k, key in enumerate(keys):
label = f'{int(float(key[1:]))/1000}k: {results[k][-1]/popsizes[k]*100:0.1f}'
pl.plot(results[k] / popsizes[k] * 100, label=label, lw=3, color=colors[k])
print(label)
# pl.legend()
pl.title('Attack rate')
pl.xlabel('Day')
pl.ylabel('Attack rate (%)')
pl.subplot(1, 3, 3)
fres = [res[-1] for res in results]
pl.scatter(popsizes, fres, s=150, c=colors)
pl.title('Correlation')
for betakey in betadict.keys():
for scenkey in scenkeys:
tvec = sims[0].results['t']
average = np.zeros(sims[0].npts)
for seed in np.arange(n_seeds):
label = f'{betakey}_{scenkey}_{seed}'
res = sims[label].results
cum_infections = res['cum_infections'].values
a[betakey].plot(tvec, cum_infections, c=colors[scenkey], lw=3, alpha=0.2)
average += cum_infections/n_seeds
a[betakey].plot(tvec, average, '--', c=colors[scenkey], lw=3, alpha=1.0, zorder=10, label=scenmap[scenkey])
for betakey in betadict.keys():
ax = a[betakey]
sc.commaticks(ax=ax)
sc.setylim(ax=ax)
ax.set_xlim([0,150])
ax.set_ylabel('Cumulative infections')
betanorm = betadict[betakey]*100*3*0.78 # Normalized to match Fig. 1 beta
ax.set_title(rf'{betamap[betakey]} transmission, $\beta$ = {betanorm:0.1f}%')
sc.boxoff(ax=ax)
if betakey == 'best':
ax.legend(frameon=False)
if betakey == 'high':
ax.set_yticks(np.arange(8)*2e3)
ax.set_xlabel('Days since seed infections')
return fig
