#rcharts

[newpagodi]

So apparently with a slight modification to the HTML, you can post an rChart to tumblr

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[gchung05]

Micro-Stories on AIDS in the U.S. from 1982-2002

What can cause a 250% increase in the reported prevalence of AIDS in the U.S.? Turns out it’s not a wave of sexual emancipation, but a change in the medical definition of AIDS.

This and another micro-stories can be teased out with some patience from 20+ years of AIDS data. The kind folks from the Polaris Project provided me with 20 years of AIDS prevalence data (sourced from the CDC) to play with. A few hours of playtime uncovered the following tidbits…

Exploring & Understanding the Data

Describing the Data

By each year and major U.S. city, the CDC dataset provides the number of reported AIDS cases, an age category, and a country of birth. Here’s a detailed explanation:

Year. Years range from prior to 1982 (as a single category, denoted as 1981), to 2002, by year. Number of reported cases rise dramatically between 1982 and 1988. The cause may be increased reporting, increased disease incidence, or another factor.

Location. There are 110 locations available, typically major cities. Examples include San Jose, CA and Atlanta, GA.

Age. There are 14 age categories, examples include 1-12 years, 20-24 years, 40-44 years, and 65+ years. Reported cases increase dramatically between 12 and 20 years.

Country of Birth. Only two categories, born in the U.S./U.S. territories, or not.

Seeing Patterns Between Predictors

Relationships between predictors are very important. We explore them here.

Does the % of foreign born AIDS cases vary by age group?

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There’s a suggestive trend of increased foreign-borns among the early 20s and the 55+. Perhaps a generational relationship? Note: A good thing to do is to continue exploring predictor relationships. In the interest of brevity, I will move on.

Modeling and Visualizing the Data

AIDS Cases Over Time

How many AIDS cases were reported from 1981-2002, categorized by age group?

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Two primary points:

Clearly the 30s age group has the highest reporting rate.

A huge spike in reporting levels occurred in 1993, indicative of a shock in the system. UCSF indicates this is due to a change in the AIDS case definition.

The Top 7 AIDS Locations

Case Patterns by Location, Time, and Age Group Hint: Hit the Play button

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111, 426, 700, 766, 574, 339, 214, 142, 78, 71, 0, 3436 ], [ "Miami, FL", 1994, 0, 18, 92, 341, 607, 674, 475, 292, 184, 116, 86, 48, 0, 2933 ], [ "Miami, FL", 1995, 0, 10, 77, 259, 443, 518, 391, 236, 149, 101, 69, 43, 0, 2296 ], [ "Miami, FL", 1996, 0, 10, 60, 168, 410, 454, 374, 222, 117, 84, 51, 57, 0, 2007 ], [ "Miami, FL", 1997, 0, 8, 52, 168, 312, 352, 278, 188, 117, 80, 52, 46, 0, 1653 ], [ "Miami, FL", 1998, 0, 16, 41, 157, 261, 318, 295, 178, 97, 65, 41, 58, 0, 1527 ], [ "Miami, FL", 1999, 0, 8, 47, 121, 219, 313, 283, 167, 90, 59, 46, 48, 0, 1401 ], [ "Miami, FL", 2000, 0, 11, 48, 109, 188, 243, 259, 181, 106, 74, 38, 39, 0, 1296 ], [ "Miami, FL", 2001, 0, 19, 38, 100, 151, 257, 240, 183, 91, 73, 28, 30, 0, 1210 ], [ "Miami, FL", 2002, 0, 12, 26, 94, 143, 233, 216, 173, 98, 67, 37, 47, 0, 1146 ], [ "New York, NY", 1981, 0, 0, 2, 11, 24, 22, 17, 5, 6, 1, 0, 0, 0, 88 ], [ "New York, NY", 1982, 0, 0, 12, 58, 81, 63, 43, 25, 16, 6, 1, 1, 0, 306 ], [ "New York, NY", 1983, 0, 3, 26, 126, 195, 154, 112, 67, 41, 27, 7, 0, 0, 758 ], [ "New York, NY", 1984, 0, 7, 43, 222, 350, 323, 211, 121, 67, 42, 15, 7, 0, 1408 ], [ "New York, NY", 1985, 0, 6, 73, 333, 549, 508, 325, 168, 116, 59, 24, 16, 0, 2177 ], [ "New York, NY", 1986, 0, 11, 138, 462, 847, 793, 460, 285, 150, 103, 51, 23, 0, 3323 ], [ "New York, NY", 1987, 0, 6, 111, 468, 843, 815, 489, 300, 179, 108, 48, 26, 0, 3393 ], [ "New York, NY", 1988, 0, 7, 189, 797, 1433, 1395, 849, 494, 281, 178, 81, 56, 0, 5760 ], [ "New York, NY", 1989, 0, 11, 137, 590, 1139, 1194, 739, 424, 224, 153, 70, 59, 0, 4740 ], [ "New York, NY", 1990, 0, 14, 198, 837, 1577, 1706, 1171, 695, 418, 200, 98, 69, 0, 6983 ], [ "New York, NY", 1991, 0, 14, 149, 748, 1451, 1722, 1242, 660, 390, 193, 127, 86, 0, 6782 ], [ "New York, NY", 1992, 0, 15, 141, 695, 1314, 1699, 1336, 763, 408, 216, 114, 127, 0, 6828 ], [ "New York, NY", 1993, 0, 40, 319, 1384, 2588, 3386, 2993, 1571, 812, 465, 223, 174, 0, 13955 ], [ "New York, NY", 1994, 0, 45, 259, 1244, 2398, 2970, 2549, 1488, 779, 449, 234, 206, 0, 12621 ], [ "New York, NY", 1995, 0, 36, 205, 917, 1875, 2293, 2250, 1287, 647, 355, 216, 129, 0, 10210 ], [ "New York, NY", 1996, 0, 41, 194, 922, 1852, 2315, 2087, 1303, 641, 385, 176, 170, 0, 10086 ], [ "New York, NY", 1997, 0, 51, 193, 825, 1777, 2106, 1935, 1365, 690, 354, 180, 148, 0, 9624 ], [ "New York, NY", 1998, 0, 47, 171, 572, 1253, 1528, 1409, 1055, 602, 332, 155, 127, 0, 7251 ], [ "New York, NY", 1999, 0, 57, 143, 449, 1063, 1324, 1261, 875, 509, 281, 152, 138, 0, 6252 ], [ "New York, NY", 2000, 0, 42, 130, 396, 860, 1163, 1052, 791, 463, 234, 143, 106, 0, 5380 ], [ "New York, NY", 2001, 0, 89, 161, 415, 865, 1241, 1256, 915, 571, 307, 158, 246, 0, 6224 ], [ "New York, NY", 2002, 0, 104, 177, 406, 781, 1170, 1118, 835, 503, 287, 142, 139, 0, 5662 ], [ "Northeast, pediatric or not in MSA", 1981, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 3 ], [ "Northeast, pediatric or not in MSA", 1982, 3, 0, 2, 4, 4, 2, 0, 0, 1, 0, 0, 0, 5, 21 ], [ "Northeast, pediatric or not in MSA", 1983, 7, 0, 1, 7, 16, 10, 3, 4, 1, 0, 0, 0, 8, 57 ], [ "Northeast, pediatric or not in MSA", 1984, 11, 0, 4, 17, 30, 17, 7, 1, 3, 1, 2, 0, 25, 118 ], [ "Northeast, pediatric or not in MSA", 1985, 45, 2, 5, 32, 49, 42, 22, 16, 6, 3, 3, 0, 36, 261 ], [ "Northeast, pediatric or not in MSA", 1986, 55, 0, 18, 47, 73, 74, 29, 19, 8, 7, 6, 1, 51, 388 ], [ "Northeast, pediatric or not in MSA", 1987, 82, 4, 11, 85, 141, 105, 49, 39, 17, 12, 10, 3, 88, 646 ], [ "Northeast, pediatric or not in MSA", 1988, 179, 4, 27, 123, 226, 193, 108, 44, 27, 22, 6, 14, 116, 1089 ], [ "Northeast, pediatric or not in MSA", 1989, 165, 4, 42, 154, 264, 236, 117, 70, 39, 13, 5, 17, 101, 1227 ], [ "Northeast, pediatric or not in MSA", 1990, 217, 5, 43, 145, 238, 227, 161, 74, 31, 27, 9, 10, 116, 1303 ], [ "Northeast, pediatric or not in MSA", 1991, 179, 5, 30, 155, 257, 234, 170, 76, 42, 16, 15, 13, 87, 1279 ], [ "Northeast, pediatric or not in MSA", 1992, 180, 1, 28, 114, 236, 239, 160, 89, 51, 21, 10, 7, 109, 1245 ], [ "Northeast, pediatric or not in MSA", 1993, 250, 22, 68, 290, 557, 573, 462, 229, 87, 40, 24, 23, 134, 2759 ], [ "Northeast, pediatric or not in MSA", 1994, 287, 14, 45, 214, 415, 480, 357, 157, 81, 27, 28, 15, 126, 2246 ], [ "Northeast, pediatric or not in MSA", 1995, 202, 9, 44, 212, 398, 475, 352, 187, 93, 47, 16, 19, 80, 2134 ], [ "Northeast, pediatric or not in MSA", 1996, 194, 6, 42, 198, 382, 440, 355, 202, 77, 35, 19, 14, 74, 2038 ], [ "Northeast, pediatric or not in MSA", 1997, 154, 16, 57, 230, 523, 544, 447, 251, 95, 49, 18, 18, 40, 2442 ], [ "Northeast, pediatric or not in MSA", 1998, 141, 5, 27, 85, 199, 234, 194, 118, 61, 34, 14, 15, 36, 1163 ], [ "Northeast, pediatric or not in MSA", 1999, 67, 6, 28, 110, 252, 299, 242, 160, 81, 38, 9, 10, 29, 1331 ], [ "Northeast, pediatric or not in MSA", 2000, 42, 5, 22, 70, 167, 215, 199, 136, 81, 35, 9, 12, 16, 1009 ], [ "Northeast, pediatric or not in MSA", 2001, 53, 10, 28, 69, 165, 258, 201, 149, 73, 33, 17, 17, 12, 1085 ], [ "Northeast, pediatric or not in MSA", 2002, 32, 10, 20, 50, 136, 196, 193, 129, 88, 37, 18, 15, 8, 932 ], [ "San Francisco, CA", 1981, 0, 0, 1, 2, 1, 2, 1, 3, 0, 0, 0, 0, 0, 10 ], [ "San Francisco, CA", 1982, 0, 0, 1, 4, 4, 5, 2, 1, 0, 0, 0, 0, 0, 17 ], [ "San Francisco, CA", 1983, 0, 0, 2, 26, 47, 39, 23, 7, 7, 3, 1, 2, 0, 157 ], [ "San Francisco, CA", 1984, 0, 2, 13, 59, 125, 112, 77, 36, 24, 12, 7, 1, 0, 468 ], [ "San Francisco, CA", 1985, 0, 2, 17, 80, 190, 197, 104, 61, 38, 27, 7, 11, 0, 734 ], [ "San Francisco, CA", 1986, 0, 0, 11, 91, 184, 230, 146, 78, 53, 28, 9, 2, 0, 832 ], [ "San Francisco, CA", 1987, 0, 0, 31, 157, 359, 402, 272, 158, 89, 44, 19, 14, 0, 1545 ], [ "San Francisco, CA", 1988, 0, 1, 42, 180, 369, 427, 307, 181, 84, 44, 22, 30, 0, 1687 ], [ "San Francisco, CA", 1989, 0, 2, 29, 186, 377, 422, 331, 212, 92, 57, 30, 17, 0, 1755 ], [ "San Francisco, CA", 1990, 0, 1, 43, 191, 427, 514, 432, 229, 88, 78, 41, 32, 0, 2076 ], [ "San Francisco, CA", 1991, 0, 4, 22, 197, 409, 471, 391, 196, 122, 62, 41, 28, 0, 1943 ], [ "San Francisco, CA", 1992, 0, 0, 35, 171, 439, 496, 425, 246, 128, 66, 37, 29, 0, 2072 ], [ "San Francisco, CA", 1993, 0, 3, 107, 499, 962, 1032, 901, 526, 271, 115, 70, 42, 0, 4528 ], [ "San Francisco, CA", 1994, 0, 6, 46, 287, 553, 562, 485, 309, 145, 82, 35, 31, 0, 2541 ], [ "San Francisco, CA", 1995, 0, 2, 47, 198, 459, 488, 413, 258, 113, 55, 24, 16, 0, 2073 ], [ "San Francisco, CA", 1996, 0, 1, 21, 139, 324, 376, 282, 186, 104, 47, 19, 22, 0, 1521 ], [ "San Francisco, CA", 1997, 0, 2, 31, 136, 265, 313, 221, 151, 80, 38, 16, 17, 0, 1270 ], [ "San Francisco, CA", 1998, 0, 3, 12, 81, 205, 185, 207, 141, 65, 39, 13, 4, 0, 955 ], [ "San Francisco, CA", 1999, 0, 0, 17, 70, 174, 210, 160, 112, 59, 28, 11, 3, 0, 844 ], [ "San Francisco, CA", 2000, 0, 2, 14, 54, 137, 184, 131, 113, 59, 33, 12, 13, 0, 752 ], [ "San Francisco, CA", 2001, 0, 3, 11, 38, 108, 135, 111, 94, 51, 24, 9, 11, 0, 595 ], [ "San Francisco, CA", 2002, 0, 1, 12, 39, 96, 118, 101, 84, 57, 31, 10, 10, 0, 559 ], [ "South, pediatric or not in MSA", 1981, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1 ], [ "South, pediatric or not in MSA", 1982, 0, 0, 0, 2, 5, 2, 0, 0, 1, 0, 0, 0, 1, 11 ], [ "South, pediatric or not in MSA", 1983, 1, 2, 2, 9, 17, 5, 4, 6, 2, 2, 0, 1, 8, 59 ], [ "South, pediatric or not in MSA", 1984, 3, 0, 9, 19, 23, 23, 18, 10, 9, 2, 3, 1, 3, 123 ], [ "South, pediatric or not in MSA", 1985, 23, 4, 25, 56, 78, 54, 32, 20, 10, 7, 6, 8, 17, 340 ], [ "South, pediatric or not in MSA", 1986, 31, 5, 48, 115, 126, 99, 36, 25, 17, 10, 18, 11, 27, 568 ], [ "South, pediatric or not in MSA", 1987, 47, 9, 81, 174, 280, 211, 120, 68, 43, 27, 38, 47, 45, 1190 ], [ "South, pediatric or not in MSA", 1988, 101, 12, 142, 344, 392, 338, 184, 97, 61, 40, 37, 56, 71, 1875 ], [ "South, pediatric or not in MSA", 1989, 123, 25, 142, 474, 551, 416, 249, 141, 77, 56, 46, 43, 88, 2431 ], [ "South, pediatric or not in MSA", 1990, 150, 33, 205, 613, 697, 569, 384, 196, 96, 87, 59, 85, 130, 3304 ], [ "South, pediatric or not in MSA", 1991, 158, 25, 159, 594, 763, 596, 424, 224, 144, 80, 53, 71, 121, 3412 ], [ "South, pediatric or not in MSA", 1992, 171, 34, 190, 670, 890, 796, 502, 269, 161, 81, 61, 72, 153, 4050 ], [ "South, pediatric or not in MSA", 1993, 192, 89, 456, 1430, 1906, 1578, 1052, 552, 295, 177, 112, 103, 155, 8097 ], [ "South, pediatric or not in MSA", 1994, 245, 58, 344, 1041, 1495, 1345, 884, 479, 257, 149, 88, 104, 143, 6632 ], [ "South, pediatric or not in MSA", 1995, 182, 50, 362, 981, 1457, 1325, 933, 482, 318, 157, 95, 96, 119, 6557 ], [ "South, pediatric or not in MSA", 1996, 188, 54, 293, 916, 1484, 1338, 1001, 532, 270, 180, 86, 99, 80, 6521 ], [ "South, pediatric or not in MSA", 1997, 114, 53, 238, 736, 1218, 1254, 875, 503, 257, 160, 73, 82, 56, 5619 ], [ "South, pediatric or not in MSA", 1998, 88, 39, 185, 574, 1020, 1014, 810, 492, 265, 144, 92, 96, 45, 4864 ], [ "South, pediatric or not in MSA", 1999, 64, 42, 233, 583, 995, 1139, 905, 560, 291, 141, 101, 104, 34, 5192 ], [ "South, pediatric or not in MSA", 2000, 47, 40, 196, 499, 866, 1050, 786, 456, 305, 160, 84, 78, 31, 4598 ], [ "South, pediatric or not in MSA", 2001, 44, 40, 210, 453, 889, 1084, 887, 618, 327, 160, 112, 98, 23, 4945 ], [ "South, pediatric or not in MSA", 2002, 53, 54, 207, 447, 792, 1049, 958, 648, 382, 189, 107, 97, 23, 5006 ], [ "Washington, DC", 1982, 0, 0, 1, 0, 0, 2, 2, 0, 0, 0, 0, 0, 0, 5 ], [ "Washington, DC", 1983, 0, 0, 1, 9, 11, 7, 6, 3, 0, 0, 0, 1, 0, 38 ], [ "Washington, DC", 1984, 0, 0, 6, 24, 37, 35, 15, 14, 8, 1, 2, 1, 0, 143 ], [ "Washington, DC", 1985, 0, 3, 18, 47, 69, 76, 42, 25, 13, 6, 6, 3, 0, 308 ], [ "Washington, DC", 1986, 0, 0, 23, 54, 73, 88, 54, 37, 17, 12, 10, 7, 0, 375 ], [ "Washington, DC", 1987, 0, 3, 41, 136, 188, 178, 95, 50, 29, 23, 8, 12, 0, 763 ], [ "Washington, DC", 1988, 0, 0, 36, 132, 216, 174, 117, 65, 33, 18, 5, 16, 0, 812 ], [ "Washington, DC", 1989, 0, 1, 46, 157, 201, 179, 121, 61, 42, 25, 13, 10, 0, 856 ], [ "Washington, DC", 1990, 0, 4, 60, 213, 303, 285, 204, 102, 53, 32, 12, 17, 0, 1285 ], [ "Washington, DC", 1991, 0, 3, 51, 206, 309, 298, 199, 126, 52, 33, 18, 14, 0, 1309 ], [ "Washington, DC", 1992, 0, 3, 47, 200, 293, 310, 246, 120, 65, 42, 17, 17, 0, 1360 ], [ "Washington, DC", 1993, 0, 12, 85, 361, 652, 587, 485, 290, 140, 75, 31, 19, 0, 2737 ], [ "Washington, DC", 1994, 0, 6, 83, 278, 503, 556, 440, 234, 109, 55, 31, 26, 0, 2321 ], [ "Washington, DC", 1995, 0, 16, 69, 260, 439, 483, 376, 221, 105, 55, 43, 20, 0, 2087 ], [ "Washington, DC", 1996, 0, 20, 73, 245, 456, 438, 431, 253, 97, 61, 20, 18, 0, 2112 ], [ "Washington, DC", 1997, 0, 10, 49, 182, 378, 369, 351, 202, 113, 46, 35, 22, 0, 1757 ], [ "Washington, DC", 1998, 0, 14, 69, 181, 299, 365, 276, 170, 105, 52, 18, 23, 0, 1572 ], [ "Washington, DC", 1999, 0, 7, 36, 142, 315, 330, 277, 199, 116, 51, 22, 24, 0, 1519 ], [ "Washington, DC", 2000, 0, 11, 47, 166, 308, 323, 292, 209, 91, 35, 26, 26, 0, 1534 ], [ "Washington, DC", 2001, 0, 6, 61, 150, 295, 372, 300, 209, 134, 63, 31, 20, 0, 1641 ], [ "Washington, DC", 2002, 0, 14, 67, 173, 293, 410, 339, 280, 133, 59, 36, 21, 0, 1825 ] ]; data.addColumn('string','Location'); data.addColumn('number','Year'); data.addColumn('number','Cases | Age 1-12'); data.addColumn('number','Cases | Age 13-19'); data.addColumn('number','Cases | Age 20-24'); data.addColumn('number','Cases | Age 25-29'); data.addColumn('number','Cases | Age 30-34'); data.addColumn('number','Cases | Age 35-39 or missing'); data.addColumn('number','Cases | Age 40-44'); data.addColumn('number','Cases | Age 45-49'); data.addColumn('number','Cases | Age 50-54'); data.addColumn('number','Cases | Age 55-59'); data.addColumn('number','Cases | Age 60-64'); data.addColumn('number','Cases | Age 65+'); data.addColumn('number','Cases | Age <1'); data.addColumn('number','Cases | All Ages'); data.addRows(datajson); return(data); } // 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My presets compare New York and Los Angeles over time. The axes compare cases between the 20-24 and 30-34 year old cohorts. Additionally, the bubble size indicates cases for all ages. There are many interpretations to make, but here is one: We can visually verify the assumption that reporting rates between the 20-24 and 30-34 cohorts remain the same over time. If they do, all the bubbles should lie on the same line. It appears, however, that in 2001-2002 in New York, 20-24 year olds were more likely than 30-34 year olds to report an AIDS infection. Play around with the graph to see what you can find out.

Credits & Copyright

Data: All data were provided by the Polaris Project and the CDC. Visualization: googleVis-0.5.5 • R version 3.1.1 (2014-07-10) • Google Terms of Use • Documentation and Data Policy Copyright: All rights reserved.