final tidying

InstituteforDiseaseModeling · Jan 17, 2022 · d9019ea · d9019ea
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -34,12 +34,12 @@ Version 3.1.2 (2021-01-16)
 Highlights
 ^^^^^^^^^^
 - **New styles**: Plots have gotten a complete revamp.
-- **More options**: There is now many more options to control plot styles, warnings, etc.
+- **More options**: There are now many more options to control plot styles, warnings, etc.
 - **Populations**: It is now easier to work with pre-generated populations and contacts.
 
 Plotting
 ^^^^^^^^
-- Default plotting styles have been updated. Run e.g. ``cv.Sim(n_days=365).run().plot()`` to see most of the changes. Major changes include: a new date formatter, grid lines à la Seaborn, new bundled fonts (`Mulish <https://fonts.google.com/specimen/Mulish>`_) and `Rosario <https://fonts.google.com/specimen/Rosario>`_), finer control of style options, and better defaults for Jupyter.
+- Default plotting styles have been updated. Run e.g. ``cv.Sim(n_days=365).run().plot()`` to see most of the changes. Major changes include: a new date formatter, grid lines à la Seaborn, new bundled fonts (`Mulish <https://fonts.google.com/specimen/Mulish>`_ and `Rosario <https://fonts.google.com/specimen/Rosario>`_), finer control of style options, and better defaults for Jupyter.
 - Changing styles is now much easier, e.g. ``sim.plot(style='seaborn-whitegrid')`` will use the named Matplotlib style. See ``cv.options.help()`` for more information.
 - Covasim now uses Sciris' default date formatter, which is similar to Plotly's. You can change this using the ``dateformat`` argument, e.g. ``sim.plot(dateformat='sciris')`` vs. ``sim.plot(dateformat='concise')``.
 - ``cv.savefig()`` can now save multiple figures simultaneously via the (new) ``fig`` argument.

diff --git a/docs/tutorials/tut_immunity.ipynb b/docs/tutorials/tut_immunity.ipynb
@@ -306,7 +306,7 @@
     "sim_booster.run()\n",
     "\n",
     "# Plot the sims with and without boosters together\n",
-    "cv.MultiSim([sim, sim_booster]).plot(to_plot=['cum_infections', 'cum_severe', 'cum_deaths','pop_nabs'])\n",
+    "cv.MultiSim([sim, sim_booster]).plot(['cum_infections', 'cum_severe', 'cum_deaths','pop_nabs'])\n",
     "\n",
     "# Plot doses again\n",
     "pl.figure()\n",

diff --git a/docs/tutorials/tut_interventions.ipynb b/docs/tutorials/tut_interventions.ipynb
@@ -186,7 +186,7 @@
     "\n",
     "# Run and plot results\n",
     "msim = cv.parallel(sim1, sim2, sim3)\n",
-    "msim.plot(to_plot=['new_infections', 'new_tests', 'new_diagnoses', 'cum_diagnoses'])"
+    "msim.plot(['new_infections', 'new_tests', 'new_diagnoses', 'cum_diagnoses'])"
    ]
   },
   {

diff --git a/docs/tutorials/tut_intro.ipynb b/docs/tutorials/tut_intro.ipynb
@@ -183,7 +183,7 @@
     "s2 = cv.Sim(pars, interventions=protect_elderly, label='Protect the elderly')\n",
     "msim = cv.MultiSim([s1, s2])\n",
     "msim.run()\n",
-    "fig = msim.plot(to_plot=['cum_deaths', 'cum_infections'])"
+    "fig = msim.plot(['cum_deaths', 'cum_infections'])"
    ]
   }
  ],

diff --git a/docs/tutorials/tut_people.ipynb b/docs/tutorials/tut_people.ipynb
@@ -149,7 +149,7 @@
     ")\n",
     "sim = cv.Sim(pars=pars, datafile='example_data.csv', interventions=cv.test_num(daily_tests='data'))\n",
     "sim.run()\n",
-    "sim.plot(to_plot=['cum_tests', 'cum_diagnoses', 'cum_deaths'])"
+    "sim.plot(['cum_tests', 'cum_diagnoses', 'cum_deaths'])"
    ]
   },
   {

diff --git a/docs/tutorials/tut_plotting.ipynb b/docs/tutorials/tut_plotting.ipynb
@@ -134,7 +134,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You can also select one or more quantities to plot with the `to_plot` argument, e.g."
+    "You can also select one or more quantities to plot with the first (`to_plot`) argument, e.g."
    ]
   },
   {
@@ -159,7 +159,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim.plot(to_plot='overview', n_cols=5, figsize=(20,20), dateformat='concise', dpi=50) # NB: dateformat='concise' is already the default for >2 columns"
+    "sim.plot('overview', n_cols=5, figsize=(20,20), dateformat='concise', dpi=50) # NB: dateformat='concise' is already the default for >2 columns"
    ]
   },
   {

diff --git a/docs/tutorials/tut_running.ipynb b/docs/tutorials/tut_running.ipynb
@@ -165,7 +165,7 @@
     "pars = {'start_day':'2021-03-01', 'n_days':120}\n",
     "s1 = cv.Sim(pars, label='Default')\n",
     "s2 = cv.Sim(pars, label='Protect the elderly', interventions=protect_elderly)\n",
-    "cv.parallel(s1, s2).plot(to_plot=['cum_deaths', 'cum_infections'])"
+    "cv.parallel(s1, s2).plot(['cum_deaths', 'cum_infections'])"
    ]
   },
   {