Tycho
#Plotting Tycho Data
"Project Tycho ( https://www.tycho.pitt.edu/ ) is a project at the University of Pittsburgh to advance the availability and use of public health data for science and policy making. Currently, the Project Tycho database includes data from all weekly notifiable disease reports for the United States dating back to 1888."
register Tycho , and download the data level 2. It's a CSV file looking like this
"Weekly Measles Cases, 1909-2001"
"Data provided by Project Tycho, Data Version 1.0.0, released 28 November 2013."
"YEAR","WEEK","ALABAMA","ALASKA","AMERICAN SAMOA","ARIZONA","ARKANSAS","CALIFORNIA","COLORADO","CONNECTICUT","DELAWARE","DISTRICT OF COLUMBIA","FLORIDA","GEORGIA","GUAM","HAWAII","IDAHO","ILLINOIS","INDIANA","IOWA","KANSAS","KENTUCKY","LOUISIANA","MAINE","MARYLAND","MASSACHUSETTS","MICHIGAN","MINNESOTA","MISSISSIPPI","MISSOURI","MONTANA","NEBRASKA","NEVADA","NEW HAMPSHIRE","NEW JERSEY","NEW MEXICO","NEW YORK","NEW YORK CITY","NORTH CAROLINA","NORTH DAKOTA","NORTHERN MARIANA ISLANDS","OHIO","OKLAHOMA","OREGON","PAC TRUST TERR","PENNSYLVANIA","PUERTO RICO","RHODE ISLAND","SOUTH CAROLINA","SOUTH DAKOTA","TENNESSEE","TEXAS","UPSTATE NEW YORK","UTAH","VERMONT","VIRGIN ISLANDS","VIRGINIA","WASHINGTON","WEST VIRGINIA","WISCONSIN","WYOMING",""
1954,1,87,14,-,50,52,621,20,21,1,7,139,115,-,2,156,413,410,80,9,334,26,130,174,27,523,15,39,2,224,7,2,3,55,37,692,-,120,41,-,204,5,44,-,534,46,1,94,34,208,579,-,251,2,-,108,266,167,55,80
1954,2,94,30,-,93,13,685,37,17,1,12,119,79,-,2,142,315,425,201,18,188,42,78,124,31,815,3,30,20,104,1,2,4,39,56,819,-,32,71,-,444,10,67,-,438,12,2,84,15,43,606,-,199,10,-,90,351,169,101,32
1954,3,188,40,-,88,37,715,17,11,7,33,186,93,-,1,125,417,471,162,37,381,95,119,185,16,648,12,55,23,97,6,1,7,61,33,997,-,144,54,-,449,13,42,-,554,29,-,176,11,247,677,-,241,4,-,325,301,123,99,58
1954,4,152,16,-,69,91,841,29,35,15,22,164,210,-,5,217,377,685,432,21,556,88,139,208,23,728,19,78,35,56,37,1,4,52,24,1105,-,425,66,-,168,14,66,-,590,54,11,164,3,121,872,-,250,10,-,404,297,121,155,24
1954,6,166,25,-,131,132,888,55,12,2,29,149,212,-,4,129,457,417,152,21,589,49,207,322,28,719,10,193,56,99,80,2,4,79,49,1560,-,356,85,-,281,12,96,-,659,66,2,290,21,206,1412,-,251,19,-,368,757,109,194,49
1954,8,510,19,-,109,124,1569,96,21,13,75,309,220,-,10,184,750,959,118,101,10402,272,230,485,83,995,17,81,87,129,187,4,1,72,115,2242,-,395,38,-,1120,116,79,-,877,131,-,595,11,814,2084,-,264,36,-,592,675,129,292,37
1954,9,351,7,-,127,90,1593,44,20,30,135,450,164,-,10,362,936,1099,114,31,1226,145,206,631,95,1097,70,146,40,84,166,-,10,183,82,2727,-,730,102,-,1066,32,109,-,892,133,2,483,7,754,2886,-,388,41,-,725,713,114,208,36
- we first convert the CSV data to RDF with awk: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/tycho/tycho-csv2rdf.awk
<?xml version="1.0"?>
<rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:t="https://www.tycho.pitt.edu/">
<rdf:Description rdf:about="">
<dc:title>"Weekly Measles Cases, 1909-2001"</dc:title>
<dc:description>"Data provided by Project Tycho, Data Version 1.0.0, released 28 November 2013."</dc:description>
</rdf:Description>
<t:State rdf:about="https://www.tycho.pitt.edu/state/ALABAMA">
<dc:title>ALABAMA</dc:title>
</t:State>
<t:State rdf:about="https://www.tycho.pitt.edu/state/ALASKA">
<dc:title>ALASKA</dc:title>
</t:State>
(...)
<t:Data>
<t:state rdf:resource="https://www.tycho.pitt.edu/state/DISTRICT_OF_COLUMBIA"/>
<t:year rdf:resource="https://www.tycho.pitt.edu/year/1909"/>
<t:week>13</t:week>
<t:count>12</t:count>
</t:Data>
<t:Data>
<t:state rdf:resource="https://www.tycho.pitt.edu/state/VIRGINIA"/>
<t:year rdf:resource="https://www.tycho.pitt.edu/year/1921"/>
<t:week>20</t:week>
<t:count>1</t:count>
</t:Data>
<t:Data>
<t:state rdf:resource="https://www.tycho.pitt.edu/state/VIRGINIA"/>
<t:year rdf:resource="https://www.tycho.pitt.edu/year/1922"/>
<t:week>42</t:week>
<t:count>2</t:count>
</t:Data>
(...)- the RDF document is converted to SVG using xsltproc and the following XSLT stylesheet : https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/tycho/tycho-rdf2svg.xsl
(...)
<g title="1923" transform="translate(60,0)">
<text y="0" x="0" transform="translate(15,-2) rotate(-90) ">1923</text>
<rect x="0" title="VIRGINIA (1923) N=2" y="1080" width="20" height="20" style="fill:rgb(15,0,240);stroke:gray;"/>
</g>
<g title="1927" transform="translate(80,0)">
<text y="0" x="0" transform="translate(15,-2) rotate(-90) ">1927</text>
<rect x="0" title="ALABAMA (1927) N=323" y="0" width="20" height="20" style="fill:rgb(128,0,127);stroke:gray;"/>
<rect x="0" title="ARIZONA (1927) N=32" y="60" width="20" height="20" style="fill:rgb(77,0,178);stroke:gray;"/>
<rect x="0" title="ARKANSAS (1927) N=134" y="80" width="20" height="20" style="fill:rgb(108,0,147);stroke:gray;"/>
<rect x="0" title="CALIFORNIA (1927) N=174" y="100" width="20" height="20" style="fill:rgb(114,0,141);stroke:gray;"/>
<rect x="0" title="COLORADO (1927) N=50" y="120" width="20" height="20" style="fill:rgb(87,0,168);stroke:gray;"/>
(...)
the command line:
awk -f tycho-csv2rdf.awk MEASLES_Cases_1909-2001.csv |\
xsltproc tycho-rdf2svg.xsl - > output.svg
