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Merge pull request #346 from amath-idm/fix-docs
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updating requirements
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@dinacmistry
dinacmistry committed Feb 27, 2021
2 parents 1258354 + 06d73f6 commit bbf55c8
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Showing 4 changed files with 85 additions and 107 deletions.
3 changes: 2 additions & 1 deletion setup.py
View file
Expand Up @@ -45,7 +45,8 @@
include_package_data=True,
install_requires=[
"sciris>=1.0.0",
"matplotlib>=3.3.0",
"covasim>=2.0.0",
"matplotlib>=3.3.0, <=3.3.4",
"numpy",
"scipy",
"pandas",
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174 changes: 77 additions & 97 deletions synthpops/plotting.py
View file
Expand Up @@ -274,25 +274,22 @@ def plot_contact_matrix(matrix, age_count, aggregate_age_count, age_brackets, ag
for aggregated age brackets.
Args:
matrix (np.array) : symmetric contact matrix, element ij is the contact for an average individual in age group i with all of their contacts in age group j
age_count (dict) : dictionary with the count of individuals in the population for each age
aggregate_age_count (dict) : dictionary with the count of individuals in the population in each age bracket
age_brackets (dict) : dictionary mapping age bracket keys to age bracket range
age_by_brackets_dic (dict) : dictionary mapping age to the age bracket range it falls in
Other Parameters:
**kwargs:
layer (str) : name of the physial contact layer: H for households, S for schools, W for workplaces, C for community, etc.
density_or_frequency (str) : Default value is 'density', see notes for more details.
logcolors_flag (bool) : If True, plot heatmap in logscale
aggregate_flag (bool) : If True, plot the contact matrix for aggregate age brackets, else single year age contact matrix.
cmap(str or matplotlib colormap) : colormap
fontsize (int) : base font size
rotation (int) : rotation for x axis labels
title_prefix(str) : optional title prefix for the figure
fig (Figure) : if supplied, use this figure instead of generating one
ax (Axes) : if supplied, use these axes instead of generating one
titles (dict) : dictionary of titles to be used for different layers
matrix (np.array) : symmetric contact matrix, element ij is the contact for an average individual in age group i with all of their contacts in age group j
age_count (dict) : dictionary with the count of individuals in the population for each age
aggregate_age_count (dict) : dictionary with the count of individuals in the population in each age bracket
age_brackets (dict) : dictionary mapping age bracket keys to age bracket range
age_by_brackets_dic (dict) : dictionary mapping age to the age bracket range it falls in
**layer (str) : name of the physial contact layer: H for households, S for schools, W for workplaces, C for community, etc.
**density_or_frequency (str) : Default value is 'density', see notes for more details.
**logcolors_flag (bool) : If True, plot heatmap in logscale
**aggregate_flag (bool) : If True, plot the contact matrix for aggregate age brackets, else single year age contact matrix.
**cmap(str or matplotlib colormap) : colormap
**fontsize (int) : base font size
**rotation (int) : rotation for x axis labels
**title_prefix(str) : optional title prefix for the figure
**fig (Figure) : if supplied, use this figure instead of generating one
**ax (Axes) : if supplied, use these axes instead of generating one
**titles (dict) : dictionary of titles to be used for different layers
Returns:
Matplotlib figure and axes.
Expand Down Expand Up @@ -432,24 +429,21 @@ def plot_contacts(pop, **kwargs):
Plot the age mixing matrix for a specific contact layer.
Args:
pop (pop object): population, either synthpops.pop.Pop or dict
Other Parameters:
**kwargs:
layer (str) : name of the physial contact layer: H for households, S for schools, W for workplaces, C for community or other
aggregate_flag (bool) : If True, plot the contact matrix for aggregate age brackets, else single year age contact matrix.
logcolors_flag (bool) : If True, plot heatmap in logscale
density_or_frequency (str) : If 'density', then each contact counts for 1/(group size -1) of a person's contact in a group, elif 'frequency' then count each contact. This means that more people in a group leads to higher rates of contact/exposure.
state_location (string) : name of the state the location is in
country_location (string) : name of the country the location is in
cmap (str or matplotlib cmap) : colormap
fontsize (int) : base font size
rotation (int) : rotation for x axis labels
title_prefix(str) : optional title prefix for the figure
fig (matplotlib.figure) : If supplied, use this figure instead of generating one
ax (matplotlib.axes) : If supplied, use these axes instead of generating one
do_show (bool) : If True, show the plot
do_save (bool) : If True, save the plot to disk
pop (pop object) : population, either synthpops.pop.Pop or dict
**layer (str) : name of the physial contact layer: H for households, S for schools, W for workplaces, C for community or other
**aggregate_flag (bool) : If True, plot the contact matrix for aggregate age brackets, else single year age contact matrix.
**logcolors_flag (bool) : If True, plot heatmap in logscale
**density_or_frequency (str) : If 'density', then each contact counts for 1/(group size -1) of a person's contact in a group, elif 'frequency' then count each contact. This means that more people in a group leads to higher rates of contact/exposure.
**state_location (string) : name of the state the location is in
**country_location (string) : name of the country the location is in
**cmap (str or matplotlib cmap) : colormap
**fontsize (int) : base font size
**rotation (int) : rotation for x axis labels
**title_prefix(str) : optional title prefix for the figure
**fig (matplotlib.figure) : If supplied, use this figure instead of generating one
**ax (matplotlib.axes) : If supplied, use these axes instead of generating one
**do_show (bool) : If True, show the plot
**do_save (bool) : If True, save the plot to disk
Returns:
Matplotlib figure.
Expand Down Expand Up @@ -508,21 +502,18 @@ def plot_array(expected, fig=None, ax=None, **kwargs):
expected (array) : Array of expected values
fig (matplotlib.figure) : Matplotlib.figure object
ax (matplotlib.axis) : Matplotlib.axes object
Other Parameters:
**kwargs:
generated (array) : Array of values generated using a model
names (list or dict) : names to display on x-axis, default is set to the indexes of data
figname (str) : name to save figure to disk
figdir (str) : directory to save the plot if provided
prefix (str) : used to prefix the title of the plot
fontsize (float) : default fontsize
color_1 (str) : color for expected data
color_2 (str) : color for generated data
expect_label (str) : Label to show in the plot, default to "expected"
value_text (bool) : If True, display the values on top of the bar if specified
rotation (float) : rotation angle for xticklabels
binned (bool) : If True, data are binned. Else, if False, plot a simple histogram for expected data.
**generated (array) : Array of values generated using a model
**names (list or dict) : names to display on x-axis, default is set to the indexes of data
**figname (str) : name to save figure to disk
**figdir (str) : directory to save the plot if provided
**prefix (str) : used to prefix the title of the plot
**fontsize (float) : default fontsize
**color_1 (str) : color for expected data
**color_2 (str) : color for generated data
**expect_label (str) : Label to show in the plot, default to "expected"
**value_text (bool) : If True, display the values on top of the bar if specified
**rotation (float) : rotation angle for xticklabels
**binned (bool) : If True, data are binned. Else, if False, plot a simple histogram for expected data.
Returns:
Matplotlib figure and axes.
Expand Down Expand Up @@ -587,14 +578,11 @@ def autolabel(ax, rects, h_offset=0, v_offset=0.3, **kwargs):
Attach a text label above each bar in *rects*, displaying its height.
Args:
ax : Matplotlib.axes object
rects : Matplotlib.container.BarContainer
h_offset (float) : The position x to place the text at.
v_offset (float) : The position y to place the text at.
Other Parameters:
**kwargs:
fontsize (float) : Default fontsize
ax : Matplotlib.axes object
rects : Matplotlib.container.BarContainer
h_offset (float) : The position x to place the text at.
v_offset (float) : The position y to place the text at.
**fontsize (float) : Default fontsize
Returns:
None.
Expand All @@ -614,28 +602,25 @@ def autolabel(ax, rects, h_offset=0, v_offset=0.3, **kwargs):
text.set_fontsize(kwargs.fontsize)


def plot_ages(pop, *args, **kwargs):
def plot_ages(pop, **kwargs):
"""
Plot a comparison of the expected and generated age distribution.
Args:
pop (pop object): population, either synthpops.pop.Pop, covasim.people.People, or dict
pop (pop object) : population, either synthpops.pop.Pop, covasim.people.People, or dict
**left (float) : Matplotlib.figure.subplot.left
**right (float) : Matplotlib.figure.subplot.right
**top (float) : Matplotlib.figure.subplot.top
**bottom (float) : Matplotlib.figure.subplot.bottom
**color_1 (str) : color for expected data
**color_2 (str) : color for data from generated population
**fontsize (float) : Matplotlib.figure.fontsize
**figname (str) : name to save figure to disk
**comparison (bool) : If True, plot comparison to the generated population
Returns:
Matplotlib figure and axes.
Other Parameters:
**kwargs:
left (float) : Matplotlib.figure.subplot.left
right (float) : Matplotlib.figure.subplot.right
top (float) : Matplotlib.figure.subplot.top
bottom (float) : Matplotlib.figure.subplot.bottom
color_1 (str) : color for expected data
color_2 (str) : color for data from generated population
fontsize (float) : Matplotlib.figure.fontsize
figname (str) : name to save figure to disk
comparison (bool) : If True, plot comparison to the generated population
Note:
If using pop with type covasim.people.Pop or dict, args must be supplied
for the location parameters to get the expected distribution.
Expand Down Expand Up @@ -717,38 +702,33 @@ def plot_ages(pop, *args, **kwargs):
return fig, ax


def plot_school_sizes(pop, *args, **kwargs):
def plot_school_sizes(pop, **kwargs):
"""
Plot a comparison of the expected and generated school size distribution for
each type of school expected.
Args:
pop (pop object): population, either synthpops.pop.Pop, or dict
args (list): list of arguments to pass to data methods and plotting (see below)
kwargs (dict) : keyword arguments to pass to data methods and plotting (see below).
pop (pop object) : population, either synthpops.pop.Pop, or dict
**with_school_types (type) : If True, plot school size distributions by type, else plot overall school size distributions
**keys_to_exclude (str or list) : school types to exclude
**left (float) : Matplotlib.figure.subplot.left
**right (float) : Matplotlib.figure.subplot.right
**top (float) : Matplotlib.figure.subplot.top
**bottom (float) : Matplotlib.figure.subplot.bottom
**hspace (float) : Matplotlib.figure.subplot.hspace
**subplot_height (float) : height of subplot in inches
**subplot_width (float) : width of subplot in inches
**screen_height_factor (float) : fraction of the screen height to use for display
**location_text_y (float) : height to add location text to figure
**fontsize (float) : Matplotlib.figure.fontsize
**rotation (float) : rotation angle for xticklabels
**cmap (str) : colormap
**figname (str) : name to save figure to disk
**comparison (bool) : If True, plot comparison to the generated population
Returns:
Matplotlib figure and axes.
Other Parameters:
**kwargs:
with_school_types (type) : If True, plot school size distributions by type, else plot overall school size distributions
keys_to_exclude (str or list) : school types to exclude
left (float) : Matplotlib.figure.subplot.left
right (float) : Matplotlib.figure.subplot.right
top (float) : Matplotlib.figure.subplot.top
bottom (float) : Matplotlib.figure.subplot.bottom
hspace (float) : Matplotlib.figure.subplot.hspace
subplot_height (float) : height of subplot in inches
subplot_width (float) : width of subplot in inches
screen_height_factor (float) : fraction of the screen height to use for display
location_text_y (float) : height to add location text to figure
fontsize (float) : Matplotlib.figure.fontsize
rotation (float) : rotation angle for xticklabels
cmap (str) : colormap
figname (str) : name to save figure to disk
comparison (bool) : If True, plot comparison to the generated population
Note:
If using pop with type covasim.people.Pop or dict, args must be supplied
for the location parameters to get the expected distribution.
Expand Down
11 changes: 4 additions & 7 deletions synthpops/schools.py
View file
Expand Up @@ -1236,17 +1236,14 @@ def send_students_to_school(school_sizes, uids_in_school, uids_in_school_by_age,
return syn_schools, syn_school_uids, syn_school_types


def get_enrollment_by_school_type(popdict, *args, **kwargs):
def get_enrollment_by_school_type(popdict, **kwargs):
"""
Get enrollment sizes by school types in popdict.
Args:
popdict (dict): population dictionary
Other Parameters:
**kwargs:
with_school_types (bool) : If True, return enrollment by school types as defined in the popdict. Otherwise, combine all enrollment sizes for a school type of None.
keys_to_exclude (list) : school types to exclude
popdict (dict) : population dictionary
**with_school_types (bool) : If True, return enrollment by school types as defined in the popdict. Otherwise, combine all enrollment sizes for a school type of None.
**keys_to_exclude (list) : school types to exclude
Returns:
dict: Dictionary of generated enrollment sizes by school type.
Expand Down
4 changes: 2 additions & 2 deletions synthpops/version.py
View file
@@ -1,2 +1,2 @@
__version__ = '1.5.0'
__versiondate__ = '2021-02-13'
__version__ = '1.5.1'
__versiondate__ = '2021-02-26'

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