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Mapping Infant Botulism Cases in the US from 1975-2017
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"description" : "The CDC Botulism Consultation Service, the Alaska Division of Public Health, and the California Department of Public Health provide clinical consultations on suspected cases of all types of botulism except infant botulism. These agencies are the only sources of antitoxin for non-infant botulism in the United States. The California Infant Botulism Treatment and Prevention provides clinical consultations on suspected infant botulism cases; it is the only source of antitoxin for infant botulism in the United States. Together, these clinical consultations provide expert guidance to clinicians and support the collection of epidemiologic and medical information for all suspected botulism cases reported in the United States.", | |
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, [ "row-d73h~vhan_77ct", "00000000-0000-0000-3BC1-B976BB6C950B", 0, 1558625993, null, 1558625993, null, "{ }", "California", "2005", "Wound", "A", "21" ] | |
, [ "row-qaqd_asn6.k8di", "00000000-0000-0000-0E29-7264E5E7B6AD", 0, 1558625993, null, 1558625993, null, "{ }", "California", "2005", "Wound", "B", "2" ] | |
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, [ "row-xwqz_uq2a~mgz9", "00000000-0000-0000-3F9F-652090A60359", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1995", "Infant", "B", "1" ] | |
, [ "row-ihzf_paeg~hsiy", "00000000-0000-0000-97AB-ED013B83E68E", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1997", "Infant", "A", "2" ] | |
, [ "row-viq8-ng9d.ywrq", "00000000-0000-0000-DC01-F1631D5F692C", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1997", "Infant", "B", "1" ] | |
, [ "row-qnvz_99c9.ie8e", "00000000-0000-0000-43B2-E1557A595E42", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1998", "Infant", "B", "1" ] | |
, [ "row-p6x8_2hwm.td7b", "00000000-0000-0000-6042-58F1AA50EFAC", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "1999", "Infant", "A", "1" ] | |
, [ "row-fuay-n4nq_gkbu", "00000000-0000-0000-184B-5150941BF63D", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "2000", "Other", "A", "1" ] | |
, [ "row-xg25-pndj_5y9t", "00000000-0000-0000-FC40-D21EE2D3CF0E", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "2007", "Foodborne", "A", "1" ] | |
, [ "row-n993_xbbu~gj9z", "00000000-0000-0000-0399-46EC932CB96E", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "2009", "Infant", "B", "1" ] | |
, [ "row-b9hs_2y8s.rwvb", "00000000-0000-0000-7529-6E91D7CF875F", 0, 1558625993, null, 1558625993, null, "{ }", "Wisconsin", "2014", "Infant", "B", "1" ] | |
, [ "row-9xwz.dmjg_zs2g", "00000000-0000-0000-6DEF-D79758327F89", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1940", "Foodborne", "Unknown", "3" ] | |
, [ "row-sya8~rs8q-4vnb", "00000000-0000-0000-6505-A69B7003F2CF", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1963", "Foodborne", "B", "1" ] | |
, [ "row-493t.jibj-gygh", "00000000-0000-0000-C387-13E9393E951E", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1972", "Wound", "Unknown", "1" ] | |
, [ "row-f544~xk44_hw9f", "00000000-0000-0000-F996-E7382F860FAB", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1973", "Foodborne", "B", "6" ] | |
, [ "row-ni6v_cv39.8qrx", "00000000-0000-0000-731D-7AA4AFFB127B", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1981", "Infant", "B", "2" ] | |
, [ "row-9xbn.7cvj.54z5", "00000000-0000-0000-068F-C9BF65D67112", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1982", "Foodborne", "B", "1" ] | |
, [ "row-8p49.dbwm_7skg", "00000000-0000-0000-0838-D08BD6E4EBE6", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1984", "Infant", "B", "1" ] | |
, [ "row-q7ja-m5mh.ibve", "00000000-0000-0000-704D-79842FE64BE5", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1991", "Infant", "B", "1" ] | |
, [ "row-bdiy~9fdf_irrc", "00000000-0000-0000-D752-DD33D89C2272", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1997", "Infant", "A", "1" ] | |
, [ "row-ixvk-ugpp~xrfa", "00000000-0000-0000-8B80-DB85E30BE8A8", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "1997", "Infant", "B", "1" ] | |
, [ "row-5vuf_7hkr.qwjb", "00000000-0000-0000-3556-5A8BB6437234", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2001", "Infant", "B", "1" ] | |
, [ "row-sr7r~3ix9~jwx3", "00000000-0000-0000-30CA-3E10A60B2F99", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2004", "Infant", "B", "2" ] | |
, [ "row-y7h8.vh7u_sjjp", "00000000-0000-0000-F507-767E6E78BCFC", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2006", "Infant", "B", "1" ] | |
, [ "row-c96k.fwak-vfnu", "00000000-0000-0000-728D-84DC85A27F60", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2007", "Infant", "A", "1" ] | |
, [ "row-k9p9~6wh6-j5zd", "00000000-0000-0000-8E21-A595C5AD6CC0", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2008", "Foodborne", "A", "1" ] | |
, [ "row-76f5_3etf.khmg", "00000000-0000-0000-1462-D40142340D7F", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2008", "Infant", "B", "1" ] | |
, [ "row-558f~3s3i~swew", "00000000-0000-0000-E71F-33D4FDAA436F", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2010", "Infant", "A", "1" ] | |
, [ "row-mxfh.ppdg-vqst", "00000000-0000-0000-8ABD-CFF6870D1602", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2010", "Infant", "B", "2" ] | |
, [ "row-4a48.ukt4_5ehu", "00000000-0000-0000-8D12-70E61C2B39E6", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2013", "Infant", "B", "1" ] | |
, [ "row-h6e5-hkqw~a7y2", "00000000-0000-0000-A0BF-2920E6BB340F", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2015", "Infant", "B", "1" ] | |
, [ "row-8v3i_zz9a-dmbk", "00000000-0000-0000-87CB-DD6F71AE075F", 0, 1558625993, null, 1558625993, null, "{ }", "West Virginia", "2016", "Infant", "B", "2" ] | |
, [ "row-54zi_677w_6t98", "00000000-0000-0000-D1B1-94A9AB56E07A", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1924", "Foodborne", "A", "7" ] | |
, [ "row-96xz~giwm-xcpi", "00000000-0000-0000-547C-DCFB7641E54C", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1925", "Foodborne", "B", "4" ] | |
, [ "row-j85n.4ndn-st8u", "00000000-0000-0000-A7FC-A7ED21594450", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1926", "Foodborne", "Unknown", "3" ] | |
, [ "row-st2q~s6bj~xw3g", "00000000-0000-0000-D0D9-6E96B9A33A13", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1929", "Foodborne", "A", "6" ] | |
, [ "row-bji5~d5nb_mpyy", "00000000-0000-0000-7376-EA9F60272A59", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1936", "Foodborne", "A", "3" ] | |
, [ "row-tgnk-jec8.g923", "00000000-0000-0000-2263-A3C45AE7DDDB", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1936", "Foodborne", "Unknown", "5" ] | |
, [ "row-p6i7_9ysn~3a5v", "00000000-0000-0000-D827-A236FE109FDC", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1975", "Foodborne", "A", "1" ] | |
, [ "row-gza9.k2vf_msna", "00000000-0000-0000-97DD-726E8DEDC90B", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1982", "Foodborne", "A", "1" ] | |
, [ "row-v3ft-5hun.a4wk", "00000000-0000-0000-9599-21AC1FD98D02", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1984", "Infant", "A", "1" ] | |
, [ "row-tfw9~r9kc~jump", "00000000-0000-0000-5130-3656E0E0CA2D", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1986", "Wound", "Unknown", "1" ] | |
, [ "row-hmpb-ejpu_mkkh", "00000000-0000-0000-1840-23D8F330B9C2", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "1990", "Foodborne", "A", "1" ] | |
, [ "row-zkuq.khjr_8tm3", "00000000-0000-0000-1B1B-344F55CD96E4", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2006", "Infant", "A", "1" ] | |
, [ "row-kp45-p65a_pk5a", "00000000-0000-0000-3E10-37DFCBF93812", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2008", "Infant", "A", "1" ] | |
, [ "row-97dy.efpn_p399", "00000000-0000-0000-F31C-F9ACFDCAAE11", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2012", "Infant", "A", "2" ] | |
, [ "row-4jn5.zbyj_e7b5", "00000000-0000-0000-CFED-417272A70C53", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2015", "Infant", "A", "1" ] | |
, [ "row-ddyu_e8zf~iczt", "00000000-0000-0000-EDE1-D95C542445C9", 0, 1558625993, null, 1558625993, null, "{ }", "Wyoming", "2016", "Infant", "A", "1" ] | |
] | |
} |
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#!/usr/bin/env python | |
# -*- coding: utf-8 -*- | |
import numpy as np | |
import matplotlib.pyplot as plt | |
import matplotlib.animation as ani | |
from matplotlib.collections import PatchCollection | |
from mpl_toolkits.basemap import Basemap | |
from matplotlib.patches import Polygon | |
import json | |
COLOR_COUNT = 5 | |
def divide_chunks(l, n): | |
# looping till length l | |
for i in range(0, len(l), n): | |
yield l[i:i + n] | |
# Get data from exported json from CDC site | |
# https://data.cdc.gov/Foodborne-Waterborne-and-Related-Diseases/Botulism/66i6-hisz/data | |
with open("".join("botulism.json")) as file: | |
json_data = json.load(file) | |
# Sort by year | |
json_data = sorted(json_data["data"], key=lambda k: k[9]) | |
year_data = {} | |
counts = [] | |
# Pull data to be worked | |
for row in json_data: | |
if row[10].lower() == "infant" and row[8] != "NA": | |
if not year_data.get(row[9]): | |
year_data[row[9]] = {} | |
year_data[row[9]].update({row[8]: int(row[12])}) | |
else: | |
if year_data[row[9]].get(row[8]): | |
year_data[row[9]][row[8]] += int(row[12]) | |
else: | |
year_data[row[9]].update({row[8]: int(row[12])}) | |
# Find year range from data | |
years = [year for year in year_data.keys()] | |
first_last = years[::len(years)-1] | |
# Create figure | |
fig = plt.figure(figsize=(10, 12)) | |
plt.suptitle("Infant Botulism Cases in the US from {}".format("-".join(first_last)), x=0.475, | |
size=25) | |
# Create subplots | |
map_ax = plt.subplot2grid((2, 3), (0, 0), colspan=3) | |
# Draw map before creating bargraph subplot | |
bmap = Basemap(llcrnrlon=-119,llcrnrlat=22,urcrnrlon=-64,urcrnrlat=49, | |
projection='lcc',lat_1=33,lat_2=45,lon_0=-95) | |
bmap.drawcoastlines() | |
# Load the shapefile, use the name 'states' | |
bmap.readshapefile('st99_d00', name='states', drawbounds=True) | |
# Create list of State names | |
state_names = [] | |
for shape_dict in bmap.states_info: | |
state_names.append(shape_dict['NAME']) | |
# Set color map to red | |
patches = [] | |
reds = plt.get_cmap('Reds', COLOR_COUNT) | |
# Work through data collect to create state polygon and red mappings | |
year_totals = {} | |
year_poly = {} | |
for year, data in year_data.items(): | |
yearly_counts = [] | |
year_poly.update({year: []}) | |
for state, count in data.items(): | |
seg = bmap.states[state_names.index(state)] | |
color = reds(float(count / (10 * COLOR_COUNT))) | |
poly = Polygon(seg, facecolor=color, edgecolor=color) | |
patches.append(poly) | |
counts.append(count) | |
yearly_counts.append(count) | |
year_poly[year].append({"state": state, | |
"count": count, | |
"poly": poly, | |
"color": color}) | |
year_totals[year] = sum(yearly_counts) | |
# Gether information for colorbar for map legend | |
clean_counts = list(set(counts)) | |
count_max = clean_counts[-1] | |
clean_range = list(range(count_max)) | |
range_array = np.array(clean_range) | |
# Compute the indices to split on for colorbar for map legend | |
splits = np.array_split(range_array, COLOR_COUNT) | |
clean_labels = ["> {}".format(splits[0][-1])] | |
for chunk in splits[1:-1]: | |
clean_labels.append("{}-{}".format(chunk[0], chunk[-1])) | |
clean_labels.append("< {}".format(splits[-1][0])) | |
# Create colorbar for map legend | |
pathcollection = PatchCollection(patches, cmap=reds) | |
pathcollection.set_array(np.array(clean_counts)) | |
pathcollection.set_clim(-0.5, COLOR_COUNT+0.5) | |
colorbar = fig.colorbar(pathcollection, ax=map_ax, orientation='vertical') | |
colorbar.set_ticks(np.linspace(0, COLOR_COUNT, COLOR_COUNT)) | |
colorbar.set_ticklabels(range(COLOR_COUNT)) | |
colorbar.ax.tick_params(labelsize=15) | |
colorbar.ax.set_yticklabels(clean_labels) | |
map_ax.set_aspect('auto') | |
# Create bar chart for top states | |
bar_ax = plt.subplot2grid((2, 3), (1, 0)) | |
bar_ax.set_xlim(0, count_max + 5) | |
# Create line graph for yearly occurrences | |
line_ax = plt.subplot2grid((2, 3), (1, 1), colspan=2) | |
xlim = [int(x) for x in first_last] | |
ylim = [0, max(year_totals.values())] | |
xlim[1] += 2 | |
ylim[1] += 5 | |
year_dates = [int(year)for year in years] | |
line_ax.set_xticks(year_dates) | |
# Create writer for creating gif | |
ImageWriter = ani.writers['imagemagick'] | |
metadata = dict(title='Ani CDC Infant Botulism', artist='Matplotlib', | |
comment='Gif support!') | |
writer = ImageWriter(fps=1, metadata=metadata) | |
counts_lst = [] | |
years_lst = [] | |
# Start writing | |
with writer.saving(fig, 'infant_botulism_results.gif', 60): | |
for year, data in year_poly.items(): | |
state_totals = {} | |
state_colors = {} | |
# Update states map | |
for d in data: | |
map_ax.add_patch(d["poly"]) | |
state_totals.update({d["state"]: d["count"]}) | |
state_colors.update({d["state"]: d["color"]}) | |
# Find top 3 states with most cases | |
top_counts = sorted(state_totals.items(), key=lambda kv: kv[1], reverse=True) | |
top_list = list(top_counts)[:3] | |
top_counts = [] | |
top_states = [] | |
top_colors = [] | |
for state, count in top_list: | |
top_states.append(state) | |
top_counts.append(count) | |
top_colors.append(state_colors.get(state)) | |
x_pos = list(reversed([i for i, _ in enumerate(top_states)])) | |
# Clear bar chart each year and create | |
bar_ax.cla() | |
bar_ax.barh(x_pos, count_max, align='center', color="white", edgecolor="white", height=0.9) | |
rects = bar_ax.barh(x_pos, top_counts, align='center', color=top_colors, edgecolor="black") | |
bar_ax.set_yticklabels(top_states) | |
bar_ax.set_yticks(x_pos) | |
plt.cla() | |
year_total = sum(state_totals.values()) | |
years_lst.append(int(year)) | |
counts_lst.append(year_total) | |
# Plot to line graph | |
line_ax.plot(years_lst, counts_lst, color="r") | |
line_ax.set_xlim(xlim) | |
line_ax.set_ylim(ylim) | |
# Set updating yearly totals | |
bar_ax.set_title('Top 3 States', size=20, loc='left') | |
line_ax.set_title("{} Total: {}".format(year, year_total), size=20, loc='left') | |
# plt.show() | |
writer.grab_frame() | |
writer.grab_frame() |
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