Adjustments report
HIV Estimates Accuracy tool
14 October 2019, 22:43:44
1 Introduction
Input data:
- File name: ~/share/anastasiaHIVTest/anastasia.csv
- Filter on diagnosis year applied: [2000, 2010]
Adjustments:
- Multiple Imputation using Chained Equations - MICE
- Number of imputations: 2
- Number of mice iterations: 5
- Number of degrees of freedom for spline of diagnosis calendar year: 4
- Impute reporting delays inputs: TRUE
- Reporting Delays
- Diagnosis start year: 2008
- Notification end year: 2018
- Notification end quarter (integer between 1 and 4): 1
- Gender: FALSE
- Transmission: FALSE
- Migration: FALSE
Report options:
- Correction of count of cases for reporting delay.
- Original calendar time.
- CD4 plots with inter-quartile range.
2 Comparison of data by Gender
2.1 Number of diagnoses per year
Data stratified by gender is shown only for unadjusted data since there were no missing data on gender after pre-processing, which takes place before adjustments.
2.1.1 Before and after adjustments
| Year of diagnosis | Male [N (%)] | Female [N (%)] | Total [N (%)] |
|---|---|---|---|
| 2009 | 20728 (72) | 8080 (28) | 28808 (100) |
| 2010 | 23997 (73) | 8669 (27) | 32666 (100) |
| 2011 | 24277 (75) | 8272 (25) | 32549 (100) |
| 2012 | 25704 (76) | 8123 (24) | 33827 (100) |
| 2013 | 25777 (77) | 7820 (23) | 33597 (100) |
| 2014 | 25840 (77) | 7926 (23) | 33766 (100) |
| 2015 | 25676 (77) | 7606 (23) | 33282 (100) |
| 2016 | 24358 (77) | 7455 (23) | 31813 (100) |
| 2017 | 23006 (76) | 7184 (24) | 30190 (100) |
| 2018 | 19782 (76) | 6382 (24) | 26164 (100) |
| 2019 | 651 (65) | 345 (35) | 996 (100) |
| Total | 239796 (75) | 77862 (25) | 317658 (100) |
2.2 Median CD4 cell count (cells/µL)
2.2.1 Before adjustments
| Year of diagnosis | Male [Median (IQR)] | Female [Median (IQR)] | Overall [Median (IQR)] |
|---|---|---|---|
| 2009 | 357 (163, 547) | 317 (140, 523) | 347 (156, 540) |
| 2010 | 360 (160, 552) | 315 (137, 515) | 350 (153, 544) |
| 2011 | 362 (169, 551) | 325 (143, 529) | 353 (160, 546) |
| 2012 | 370 (170, 561) | 316 (136, 521) | 357 (160, 553) |
| 2013 | 379 (180, 570) | 334 (154, 540) | 368 (173, 564) |
| 2014 | 390 (188, 582) | 331 (148, 541) | 376 (178, 575) |
| 2015 | 385 (187, 580) | 337 (152, 550) | 376 (178, 575) |
| 2016 | 378 (181, 571) | 339 (146, 551) | 370 (173, 568) |
| 2017 | 368 (176, 570) | 340 (152, 543) | 360 (170, 563) |
| 2018 | 361 (167, 559) | 330 (148, 534) | 354 (162, 553) |
| 2019 | 364 (180, 534) | 326 (155, 489) | 353 (174, 529) |
| Overall | 371 (175, 565) | 328 (146, 535) | 361 (167, 560) |
2.2.2 After adjustments
| Year of diagnosis | Male [Median (IQR)] | Female [Median (IQR)] |
|---|---|---|
| 2009 | 356 (160, 549) | 321 (141, 526) |
| 2010 | 358 (159, 554) | 317 (140, 522) |
| 2011 | 363 (168, 556) | 327 (145, 532) |
| 2012 | 369 (169, 563) | 319 (140, 527) |
| 2013 | 380 (180, 568) | 334 (154, 538) |
| 2014 | 390 (190, 583) | 337 (153, 544) |
| 2015 | 390 (194, 583) | 345 (159, 552) |
| 2016 | 382 (189, 576) | 347 (160, 557) |
| 2017 | 372 (180, 568) | 343 (159, 550) |
| 2018 | 363 (170, 559) | 338 (153, 542) |
| 2019 | 378 (209, 555) | 380 (222, 572) |
3 Comparison of data by Transmission
3.1 Number of diagnoses per year
3.1.1 Before adjustments
| Year of diagnosis | Hetero [N (%)] | IDU [N (%)] | MSM [N (%)] | MTCT [N (%)] | Nosocomial [N (%)] | Transfusion [N (%)] | Missing [N (%)] | Overall [N (%)] |
|---|---|---|---|---|---|---|---|---|
| 2009 | 11259 (39) | 1588 (6) | 10866 (38) | 301 (1) | 14 (0) | 75 (0) | 4705 (16) | 28808 (100) |
| 2010 | 12889 (39) | 1729 (5) | 12641 (39) | 334 (1) | 12 (0) | 100 (0) | 4961 (15) | 32666 (100) |
| 2011 | 12267 (38) | 2006 (6) | 12705 (39) | 315 (1) | 13 (0) | 80 (0) | 5163 (16) | 32549 (100) |
| 2012 | 12038 (36) | 2232 (7) | 13909 (41) | 287 (1) | 8 (0) | 90 (0) | 5263 (16) | 33827 (100) |
| 2013 | 11548 (34) | 1867 (6) | 14205 (42) | 272 (1) | 11 (0) | 84 (0) | 5610 (17) | 33597 (100) |
| 2014 | 11618 (34) | 1487 (4) | 14704 (44) | 272 (1) | 16 (0) | 99 (0) | 5570 (16) | 33766 (100) |
| 2015 | 10955 (33) | 1432 (4) | 14424 (43) | 238 (1) | 9 (0) | 71 (0) | 6153 (18) | 33282 (100) |
| 2016 | 10589 (33) | 1204 (4) | 13344 (42) | 171 (1) | 17 (0) | 89 (0) | 6399 (20) | 31813 (100) |
| 2017 | 9996 (33) | 1134 (4) | 12380 (41) | 170 (1) | 12 (0) | 70 (0) | 6428 (21) | 30190 (100) |
| 2018 | 8580 (33) | 974 (4) | 10415 (40) | 177 (1) | 9 (0) | 83 (0) | 5926 (23) | 26164 (100) |
| 2019 | 297 (30) | 14 (1) | 262 (26) | 11 (1) | - (-) | 2 (0) | 410 (41) | 996 (100) |
| Overall | 112036 (35) | 15667 (5) | 129855 (41) | 2548 (1) | 121 (0) | 843 (0) | 56588 (18) | 317658 (100) |
3.1.2 After adjustments
| Year of diagnosis | Hetero [N (%)] | IDU [N (%)] | MSM [N (%)] | MTCT [N (%)] | Nosocomial [N (%)] | Transfusion [N (%)] | Overall [N (%)] |
|---|---|---|---|---|---|---|---|
| 2009 | 13573 (47) | 1880 (7) | 12927 (45) | 366 (1) | 14 (0) | 90 (0) | 28850 (100) |
| 2010 | 15367 (47) | 2060 (6) | 14844 (45) | 376 (1) | 13 (0) | 121 (0) | 32782 (100) |
| 2011 | 14769 (45) | 2413 (7) | 15064 (46) | 367 (1) | 14 (0) | 101 (0) | 32728 (100) |
| 2012 | 14526 (43) | 2658 (8) | 16445 (48) | 340 (1) | 10 (0) | 109 (0) | 34087 (100) |
| 2013 | 14246 (42) | 2251 (7) | 17007 (50) | 332 (1) | 13 (0) | 103 (0) | 33952 (100) |
| 2014 | 14380 (42) | 1828 (5) | 17608 (51) | 332 (1) | 18 (0) | 121 (0) | 34287 (100) |
| 2015 | 14003 (41) | 1782 (5) | 17856 (52) | 283 (1) | 12 (0) | 92 (0) | 34028 (100) |
| 2016 | 14053 (43) | 1542 (5) | 16904 (51) | 225 (1) | 24 (0) | 120 (0) | 32868 (100) |
| 2017 | 14296 (43) | 1542 (5) | 16783 (51) | 260 (1) | 16 (0) | 105 (0) | 33002 (100) |
| 2018 | 12997 (44) | 1431 (5) | 14828 (50) | 311 (1) | 12 (0) | 121 (0) | 29700 (100) |
| 2019 | 508 (51) | 35 (4) | 428 (43) | 21 (2) | - (-) | 4 (0) | 996 (100) |
| Overall | 142717 (44) | 19424 (6) | 160693 (49) | 3212 (1) | 146 (0) | 1087 (0) | 327279 (100) |
3.2 Median CD4 cell count (cells/µL)
3.2.1 Before adjustments
| Year of diagnosis | Hetero [Median (IQR)] | IDU [Median (IQR)] | MSM [Median (IQR)] | MTCT [Median (IQR)] | Nosocomial [Median (IQR)] | Transfusion [Median (IQR)] | Missing [Median (IQR)] | Overall [Median (IQR)] |
|---|---|---|---|---|---|---|---|---|
| 2009 | 290 (116, 488) | 308 (126, 516) | 412 (240, 590) | 544 (250, 891) | 246 (111, 481) | 340 (142, 466) | 240 (51, 450) | 347 (156, 540) |
| 2010 | 290 (110, 483) | 300 (108, 518) | 417 (243, 600) | 586 (331, 1120) | 190 (127, 339) | 306 (156, 508) | 236 (55, 463) | 350 (153, 544) |
| 2011 | 286 (111, 481) | 346 (151, 585) | 419 (249, 600) | 560 (275, 1020) | 315 (166, 328) | 358 (149, 568) | 256 (75, 475) | 353 (160, 546) |
| 2012 | 289 (112, 488) | 307 (131, 534) | 427 (252, 603) | 586 (336, 1061) | 154 (144, 452) | 334 (224, 497) | 247 (71, 460) | 357 (160, 553) |
| 2013 | 297 (117, 500) | 315 (124, 523) | 436 (260, 615) | 560 (314, 1091) | 578 (464, 680) | 296 (120, 495) | 282 (87, 494) | 368 (173, 564) |
| 2014 | 304 (119, 506) | 298 (95, 504) | 440 (264, 622) | 553 (243, 984) | 521 (129, 762) | 360 (168, 593) | 280 (88, 514) | 376 (178, 575) |
| 2015 | 300 (119, 506) | 303 (94, 518) | 438 (260, 625) | 642 (272, 1092) | 497 (334, 819) | 370 (200, 532) | 306 (110, 540) | 376 (178, 575) |
| 2016 | 300 (116, 502) | 360 (138, 547) | 430 (255, 610) | 510 (243, 951) | 632 (450, 695) | 342 (209, 570) | 314 (102, 520) | 370 (173, 568) |
| 2017 | 298 (121, 499) | 340 (134, 559) | 420 (244, 610) | 715 (361, 1331) | 436 (160, 530) | 253 (142, 556) | 289 (90, 508) | 360 (170, 563) |
| 2018 | 293 (115, 494) | 329 (131, 535) | 411 (237, 596) | 521 (216, 978) | 397 (197, 468) | 268 (133, 507) | 294 (101, 506) | 354 (162, 553) |
| 2019 | 304 (135, 478) | 175 (32, 326) | 403 (257, 579) | 333 (275, 447) | - (-, -) | 13 (13, 13) | 214 (80, 380) | 353 (174, 529) |
| Overall | 294 (116, 495) | 318 (124, 531) | 427 (251, 609) | 579 (275, 1040) | 380 (147, 633) | 326 (163, 530) | 276 (82, 498) | 361 (167, 560) |
3.2.2 After adjustments
| Year of diagnosis | Hetero [Median (IQR)] | IDU [Median (IQR)] | MSM [Median (IQR)] | MTCT [Median (IQR)] | Nosocomial [Median (IQR)] | Transfusion [Median (IQR)] |
|---|---|---|---|---|---|---|
| 2009 | 269 (269, 269) | 278 (278, 278) | 376 (376, 376) | 568 (568, 568) | 281 (281, 281) | 288 (288, 288) |
| 2010 | 267 (267, 267) | 278 (278, 278) | 381 (381, 381) | 642 (642, 642) | 279 (279, 279) | 286 (286, 286) |
| 2011 | 270 (270, 270) | 313 (313, 313) | 383 (383, 383) | 604 (604, 604) | 267 (267, 267) | 294 (294, 294) |
| 2012 | 269 (269, 269) | 299 (299, 299) | 387 (387, 387) | 637 (637, 637) | 262 (262, 262) | 306 (306, 306) |
| 2013 | 277 (277, 277) | 291 (291, 291) | 396 (396, 396) | 681 (681, 681) | 475 (475, 475) | 303 (303, 303) |
| 2014 | 283 (283, 283) | 286 (286, 286) | 403 (403, 403) | 669 (669, 669) | 378 (378, 378) | 340 (340, 340) |
| 2015 | 289 (289, 289) | 287 (287, 287) | 406 (406, 406) | 689 (689, 689) | 501 (501, 501) | 350 (350, 350) |
| 2016 | 287 (287, 287) | 320 (320, 320) | 399 (399, 399) | 651 (651, 651) | 404 (404, 404) | 339 (339, 339) |
| 2017 | 285 (285, 285) | 302 (302, 302) | 388 (388, 388) | 726 (726, 726) | 359 (359, 359) | 314 (314, 314) |
| 2018 | 283 (283, 283) | 297 (297, 297) | 377 (377, 377) | 571 (571, 571) | 429 (429, 429) | 285 (285, 285) |
| 2019 | 323 (323, 323) | 272 (272, 272) | 402 (402, 402) | 420 (420, 420) | - (-, -) | 288 (288, 288) |
4 Comparison of data by Migration
4.1 Number of diagnoses per year
4.1.1 Before adjustments
| Year of diagnosis | OTHER [N (%)] | REPCOUNTRY [N (%)] | Missing [N (%)] | Overall [N (%)] |
|---|---|---|---|---|
| 2009 | 10745 (37) | 14479 (50) | 3584 (12) | 28808 (100) |
| 2010 | 11904 (36) | 17034 (52) | 3728 (11) | 32666 (100) |
| 2011 | 11677 (36) | 17229 (53) | 3643 (11) | 32549 (100) |
| 2012 | 11752 (35) | 18649 (55) | 3426 (10) | 33827 (100) |
| 2013 | 10949 (33) | 19184 (57) | 3464 (10) | 33597 (100) |
| 2014 | 11600 (34) | 18973 (56) | 3193 (9) | 33766 (100) |
| 2015 | 11417 (34) | 17882 (54) | 3983 (12) | 33282 (100) |
| 2016 | 11125 (35) | 16549 (52) | 4139 (13) | 31813 (100) |
| 2017 | 10747 (36) | 15210 (50) | 4233 (14) | 30190 (100) |
| 2018 | 9543 (36) | 12817 (49) | 3804 (15) | 26164 (100) |
| 2019 | 338 (34) | 292 (29) | 366 (37) | 996 (100) |
| Overall | 111797 (35) | 168298 (53) | 37563 (12) | 317658 (100) |
4.1.2 After adjustments
| Year of diagnosis | OTHER [N (%)] | REPCOUNTRY [N (%)] | Overall [N (%)] |
|---|---|---|---|
| 2009 | 12312 (43) | 16538 (57) | 28850 (100) |
| 2010 | 13603 (41) | 19179 (59) | 32782 (100) |
| 2011 | 13243 (40) | 19484 (60) | 32728 (100) |
| 2012 | 13246 (39) | 20841 (61) | 34087 (100) |
| 2013 | 12459 (37) | 21493 (63) | 33952 (100) |
| 2014 | 13074 (38) | 21213 (62) | 34287 (100) |
| 2015 | 13303 (39) | 20725 (61) | 34028 (100) |
| 2016 | 13252 (40) | 19616 (60) | 32868 (100) |
| 2017 | 13703 (42) | 19299 (58) | 33002 (100) |
| 2018 | 12830 (43) | 16871 (57) | 29700 (100) |
| 2019 | 563 (57) | 433 (43) | 996 (100) |
| Overall | 131588 (40) | 195692 (60) | 327279 (100) |
4.2 Median CD4 cell count (cells/µL)
4.2.1 Before adjustments
| Year of diagnosis | OTHER [Median (IQR)] | REPCOUNTRY [Median (IQR)] | Missing [Median (IQR)] | Overall [Median (IQR)] |
|---|---|---|---|---|
| 2009 | 307 (139, 500) | 376 (174, 566) | 384 (179, 600) | 347 (156, 540) |
| 2010 | 320 (140, 508) | 378 (170, 570) | 308 (138, 485) | 350 (153, 544) |
| 2011 | 322 (145, 506) | 375 (174, 575) | 343 (159, 518) | 353 (160, 546) |
| 2012 | 326 (146, 518) | 380 (174, 574) | 352 (152, 550) | 357 (160, 553) |
| 2013 | 350 (172, 540) | 380 (173, 580) | 370 (180, 540) | 368 (173, 564) |
| 2014 | 357 (172, 560) | 390 (181, 583) | 380 (166, 580) | 376 (178, 575) |
| 2015 | 370 (180, 567) | 379 (177, 580) | 388 (180, 598) | 376 (178, 575) |
| 2016 | 365 (175, 563) | 376 (172, 570) | 366 (172, 570) | 370 (173, 568) |
| 2017 | 356 (180, 563) | 362 (160, 561) | 392 (207, 600) | 360 (170, 563) |
| 2018 | 352 (169, 552) | 353 (153, 552) | 383 (189, 591) | 354 (162, 553) |
| 2019 | 329 (180, 525) | 371 (175, 533) | 232 (99, 406) | 353 (174, 529) |
| Overall | 341 (160, 539) | 376 (171, 572) | 363 (170, 554) | 361 (167, 560) |
4.2.2 After adjustments
| Year of diagnosis | OTHER [Median (IQR)] | REPCOUNTRY [Median (IQR)] |
|---|---|---|
| 2009 | 317 (139, 510) | 371 (169, 565) |
| 2010 | 319 (139, 514) | 371 (168, 567) |
| 2011 | 328 (147, 520) | 371 (173, 572) |
| 2012 | 330 (146, 524) | 376 (172, 573) |
| 2013 | 349 (170, 540) | 381 (176, 575) |
| 2014 | 358 (171, 559) | 391 (187, 585) |
| 2015 | 373 (181, 570) | 384 (186, 582) |
| 2016 | 367 (177, 562) | 381 (184, 578) |
| 2017 | 357 (178, 560) | 370 (171, 567) |
| 2018 | 352 (168, 552) | 361 (164, 558) |
| 2019 | 380 (225, 569) | 380 (198, 552) |
5 Comparison of the reported and estimated number of diagnoses per year
| Diagnosis year |
Reported |
Weight estimated |
Weight not estimated |
Estimated unreported [N (95% CI)] |
Estimated total [N (95% CI)] |
|---|---|---|---|---|---|
| 2009 | 28808 | 18526 | 10282 | 42 (18, 66) | 28850 (28826, 28874) |
| 2010 | 32666 | 28657 | 4009 | 116 (75, 157) | 32782 (32741, 32823) |
| 2011 | 32549 | 28799 | 3750 | 178 (133, 223) | 32727 (32682, 32772) |
| 2012 | 33827 | 29803 | 4024 | 259 (208, 310) | 34086 (34035, 34137) |
| 2013 | 33597 | 29130 | 4467 | 352 (297, 408) | 33949 (33894, 34005) |
| 2014 | 33766 | 29277 | 4489 | 518 (455, 581) | 34284 (34221, 34347) |
| 2015 | 33282 | 29036 | 4246 | 743 (672, 814) | 34025 (33954, 34096) |
| 2016 | 31813 | 27427 | 4386 | 1053 (974, 1133) | 32866 (32787, 32946) |
| 2017 | 30190 | 26211 | 3979 | 2812 (2689, 2936) | 33002 (32879, 33126) |
| 2018 | 26164 | 6081 | 20083 | 3540 (3384, 3695) | 29704 (29548, 29859) |
| 2019 | 996 | 0 | 996 | 0 (0, 0) | 996 (996, 996) |
| Total | 317658 | 252947 | 64711 | 9612 (8904, 10321) | 327270 (326562, 327979) |