This tutorial provides a brief overview of options for plotting results, printing objects, and saving results.
Click here to open an interactive version of this notebook.
HPVsim allows the user to set various options that apply to all plots. You can change the font size, default DPI, whether plots should be shown by default, etc. (for the full list, see hpv.options.help()
). For example, we might want higher resolution, to turn off automatic figure display, close figures after they're rendered, and to turn off the messages that print when a simulation is running. We can do this using built-in defaults for Jupyter notebooks (and then run a sim) with:
import hpvsim as hpv
hpv.options(jupyter=True, verbose=0) # Standard options for Jupyter notebook
sim = hpv.Sim()
sim.run()
There are three levels of detail available for most objects (sims, multisims, scenarios, and people). The shortest is brief()
:
sim.brief()
You can get more detail with summarize()
:
sim.summarize()
Finally, to show the full object, including all methods and attributes, use disp()
:
sim.disp()
While a sim can be plotted using default settings simply by sim.plot()
, this is just a small fraction of what's available. First, note that results can be plotted directly using e.g. Matplotlib. You can see what quantities are available for plotting with sim.results.keys()
(remember, it's just a dict). A simple example of plotting using Matplotlib is:
import pylab as plt # Shortcut for import matplotlib.pyplot as plt
plt.plot(sim.results['year'], sim.results['infections']);
However, as you can see, this isn't ideal since the default formatting is...not great. (Also, note that each result is a Result
object, not a simple Numpy array; like a pandas dataframe, you can get the array of values directly via e.g. sim.results.infections.values
.)
An alternative, you can also select one or more quantities to plot with the first (to_plot
) argument, e.g.
sim.plot(to_plot=['infections', 'hpv_incidence']);
While we can save this figure using Matplotlib's built-in savefig()
, if we use HPVsim's hpv.savefig()
we get a couple of advantages:
hpv.savefig('my-fig.png')
First, it saves the figure at higher resolution by default (which you can adjust with the dpi
argument). But second, it stores information about the code that was used to generate the figure as metadata, which can be loaded later. Made an awesome plot but can't remember even what script you ran to generate it, much less what version of the code? You'll never have to worry about that again.
hpv.get_png_metadata('my-fig.png')
We saw above how to set default plot configuration options for Jupyter. HPVsim provides a lot of flexibility in customizing the appearance of plots as well. There are three different levels at which you can set plotting options: global, just for HPVsim, or just for the current plot. To give an example with changing the figure DPI:
sc.options(dpi=150)
or pl.rc('figure', dpi=150)
(where sc
is import sciris as sc
)hpv.options(dpi=150)
sim.plot(dpi=150)
The easiest way to change the style of HPVsim plots is with the style
argument. For example, to plot using a built-in Matplotlib style would simply be:
sim.plot(style='ggplot');
In addition to the default style ('hpvsim'
), there is also a "simple" style. You can combine built-in styles with additional overrides, including any valid Matplotlib commands:
sim.plot(style='simple', legend_args={'frameon':True}, style_args={'ytick.direction':'in'});
Although most style handling is done automatically, you can also use it yourself in a with block, e.g.:
import numpy as np
with hpv.options.with_style(fontsize=6):
sim.plot() # This will have 6 point font
plt.figure(); plt.plot(np.random.rand(20), 'o') # So will this
Saving sims is also pretty simple. The simplest way to save is simply
sim.save('my-sim.sim')
Technically, this saves as a gzipped pickle file (via sc.saveobj()
using the Sciris library). By default this does not save the people in the sim since they are very large (and since, if the random seed is saved, they can usually be regenerated). If you want to save the people as well, you can use the keep_people
argument. For example, here's what it would look like to create a sim, run it halfway, save it, load it, change the overall transmissibility (beta), and finish running it:
sim_orig = hpv.Sim(start=2000, end=2030, label='Load & save example')
sim_orig.run(until='2015')
sim_orig.save('my-half-finished-sim.sim') # Note: HPVsim always saves the people if the sim isn't finished running yet
sim = hpv.load('my-half-finished-sim.sim')
sim['beta'] *= 0.3
sim.run()
sim.plot(['infections', 'hpv_incidence', 'cancer_incidence']);
Aside from saving the entire simulation, there are other export options available. You can export the results and parameters to a JSON file (using sim.to_json()
), but probably the most useful is to export the results to an Excel workbook, where they can easily be stored and processed with e.g. Pandas:
import pandas as pd
sim.to_excel('my-sim.xlsx')
df = pd.read_excel('my-sim.xlsx')
print(df)