extract_shiny90_age_sex.RdExport estimates for proportion aware of status from a Shiny90 output file to five-year age groups 15-19 to 50+.
extract_shiny90_age_sex(shiny90_path, pjnz_path = NULL, years = NULL)A data frame consisting of the number of PLHIV, aware of status
and on ART by sex and five year age group 15-49 and age 50+ for
specified years.
The 'artnum' divided by 'plhiv' columns in the output will give a different ART coverage than Spectrum output for the same year because these outputs are based on the internal mid-year ART coverage in Spectrum, while Spectrum reports an end of year (Dec 31) ART coverage.
pjnz <- system.file("extdata/demo_mwi2019.PJNZ", package = "naomi")
shiny90dir <- tempfile()
utils::unzip(pjnz, "malawi.zip.shiny90", exdir = shiny90dir)
shiny90_path <- file.path(shiny90dir, "malawi.zip.shiny90")
extract_shiny90_age_sex(shiny90_path, pjnz, year = 2010:2019)
#> area year sex agegr hivstatus plhiv aware artnum
#> 1 Malawi 2010 female 15-19 positive 27683.72 15266.408 4381.599
#> 2 Malawi 2011 female 15-19 positive 28183.36 16279.563 6122.000
#> 3 Malawi 2012 female 15-19 positive 28603.07 17260.667 8396.273
#> 4 Malawi 2013 female 15-19 positive 28882.68 17452.191 10490.296
#> 5 Malawi 2014 female 15-19 positive 29064.81 18012.046 12282.135
#> 6 Malawi 2015 female 15-19 positive 29187.39 18559.369 13619.078
#> 7 Malawi 2016 female 15-19 positive 29244.18 19362.446 15466.313
#> 8 Malawi 2017 female 15-19 positive 29053.52 21266.472 17402.425
#> 9 Malawi 2018 female 15-19 positive 28656.27 22357.327 18884.849
#> 10 Malawi 2019 female 15-19 positive 28070.55 22596.591 19479.052
#> 11 Malawi 2010 male 15-19 positive 11749.82 6131.658 3320.775
#> 12 Malawi 2011 male 15-19 positive 12767.52 7009.456 4271.046
#> 13 Malawi 2012 male 15-19 positive 13654.40 7776.337 5311.768
#> 14 Malawi 2013 male 15-19 positive 14406.60 8448.882 6313.194
#> 15 Malawi 2014 male 15-19 positive 15040.15 9241.806 7272.166
#> 16 Malawi 2015 male 15-19 positive 15594.00 10028.171 8179.690
#> 17 Malawi 2016 male 15-19 positive 16052.38 10805.027 9069.360
#> 18 Malawi 2017 male 15-19 positive 16358.26 11850.914 10097.032
#> 19 Malawi 2018 male 15-19 positive 16540.43 12780.792 11120.259
#> 20 Malawi 2019 male 15-19 positive 16622.07 13417.919 11518.660
#> 21 Malawi 2010 female 20-24 positive 55619.65 37479.252 7398.818
#> 22 Malawi 2011 female 20-24 positive 56161.13 39921.811 10925.906
#> 23 Malawi 2012 female 20-24 positive 56371.46 41643.686 15691.178
#> 24 Malawi 2013 female 20-24 positive 56138.36 41811.447 20227.533
#> 25 Malawi 2014 female 20-24 positive 55595.22 42086.372 23792.162
#> 26 Malawi 2015 female 20-24 positive 54945.18 42227.077 26439.041
#> 27 Malawi 2016 female 20-24 positive 54330.57 42768.444 29937.306
#> 28 Malawi 2017 female 20-24 positive 53637.89 44891.748 33784.134
#> 29 Malawi 2018 female 20-24 positive 52809.09 45973.971 36742.602
#> 30 Malawi 2019 female 20-24 positive 51777.23 45970.899 38154.877
#> 31 Malawi 2010 male 20-24 positive 19441.86 8893.872 1765.231
#> 32 Malawi 2011 male 20-24 positive 20491.95 9714.336 2500.187
#> 33 Malawi 2012 male 20-24 positive 21460.42 10424.568 3355.655
#> 34 Malawi 2013 male 20-24 positive 22218.18 10930.351 4224.123
#> 35 Malawi 2014 male 20-24 positive 22793.39 11613.465 5392.836
#> 36 Malawi 2015 male 20-24 positive 23251.61 12314.176 6431.330
#> 37 Malawi 2016 male 20-24 positive 23649.79 13191.923 7868.122
#> 38 Malawi 2017 male 20-24 positive 23921.54 14793.458 9594.242
#> 39 Malawi 2018 male 20-24 positive 24045.37 16117.992 11221.598
#> 40 Malawi 2019 male 20-24 positive 24017.19 16965.905 11736.147
#> 41 Malawi 2010 female 25-29 positive 72711.24 55680.031 15202.328
#> 42 Malawi 2011 female 25-29 positive 72166.53 58092.235 19631.225
#> 43 Malawi 2012 female 25-29 positive 72459.45 60229.755 25984.353
#> 44 Malawi 2013 female 25-29 positive 73420.73 61605.896 32335.536
#> 45 Malawi 2014 female 25-29 positive 74681.21 63410.863 38040.260
#> 46 Malawi 2015 female 25-29 positive 75780.35 65032.802 42777.997
#> 47 Malawi 2016 female 25-29 positive 76322.18 66548.629 48102.378
#> 48 Malawi 2017 female 25-29 positive 76003.17 68839.440 53441.662
#> 49 Malawi 2018 female 25-29 positive 74868.61 69481.267 57163.604
#> 50 Malawi 2019 female 25-29 positive 73166.72 68728.162 58657.654
#> 51 Malawi 2010 male 25-29 positive 37543.01 23623.900 4349.519
#> 52 Malawi 2011 male 25-29 positive 37192.65 23730.526 5361.153
#> 53 Malawi 2012 male 25-29 positive 37369.49 23773.915 6501.972
#> 54 Malawi 2013 male 25-29 positive 37952.27 23784.395 7595.678
#> 55 Malawi 2014 male 25-29 positive 38773.95 24424.362 9289.791
#> 56 Malawi 2015 male 25-29 positive 39606.63 25284.539 10858.342
#> 57 Malawi 2016 male 25-29 positive 40237.33 26483.871 13078.175
#> 58 Malawi 2017 male 25-29 positive 40424.61 28888.282 15890.509
#> 59 Malawi 2018 male 25-29 positive 40146.24 30566.350 18512.385
#> 60 Malawi 2019 male 25-29 positive 39512.87 31263.827 19126.693
#> 61 Malawi 2010 female 30-34 positive 85675.62 69574.758 23432.959
#> 62 Malawi 2011 female 30-34 positive 84748.91 72492.640 28992.573
#> 63 Malawi 2012 female 30-34 positive 83579.92 73862.844 36121.084
#> 64 Malawi 2013 female 30-34 positive 82392.45 73807.049 42389.454
#> 65 Malawi 2014 female 30-34 positive 81408.85 73755.557 47572.814
#> 66 Malawi 2015 female 30-34 positive 80865.28 73862.349 51741.930
#> 67 Malawi 2016 female 30-34 positive 80987.56 74709.511 56762.190
#> 68 Malawi 2017 female 30-34 positive 81741.95 77114.737 62556.001
#> 69 Malawi 2018 female 30-34 positive 82964.66 79422.855 67795.021
#> 70 Malawi 2019 female 30-34 positive 84240.22 81241.453 71563.235
#> 71 Malawi 2010 male 30-34 positive 56351.93 40788.883 9543.201
#> 72 Malawi 2011 male 30-34 positive 54948.73 40975.010 11384.250
#> 73 Malawi 2012 male 30-34 positive 53496.78 40289.383 13145.395
#> 74 Malawi 2013 male 30-34 positive 52112.31 39084.437 14485.785
#> 75 Malawi 2014 male 30-34 positive 50939.25 38282.026 16106.459
#> 76 Malawi 2015 male 30-34 positive 50142.89 37841.964 17534.407
#> 77 Malawi 2016 male 30-34 positive 49863.71 38152.746 19684.917
#> 78 Malawi 2017 male 30-34 positive 50055.50 40177.991 22910.885
#> 79 Malawi 2018 male 30-34 positive 50592.26 42298.341 26389.802
#> 80 Malawi 2019 male 30-34 positive 51222.08 43956.982 27830.450
#> 81 Malawi 2010 female 35-39 positive 78133.65 57835.978 26516.958
#> 82 Malawi 2011 female 35-39 positive 80836.15 65034.880 33638.712
#> 83 Malawi 2012 female 35-39 positive 83273.44 70832.107 42732.434
#> 84 Malawi 2013 female 35-39 positive 85296.75 74893.820 51043.136
#> 85 Malawi 2014 female 35-39 positive 86693.60 77851.545 57490.090
#> 86 Malawi 2015 female 35-39 positive 87361.80 79662.356 62556.840
#> 87 Malawi 2016 female 35-39 positive 87300.20 80648.931 67278.436
#> 88 Malawi 2017 female 35-39 positive 86629.41 81530.930 71534.178
#> 89 Malawi 2018 female 35-39 positive 85654.83 81776.143 74375.324
#> 90 Malawi 2019 female 35-39 positive 84703.13 81591.778 75657.429
#> 91 Malawi 2010 male 35-39 positive 60904.67 39791.190 14434.121
#> 92 Malawi 2011 male 35-39 positive 61180.39 42883.782 17634.101
#> 93 Malawi 2012 male 35-39 positive 61371.24 44890.742 20856.227
#> 94 Malawi 2013 male 35-39 positive 61412.19 46007.304 23553.123
#> 95 Malawi 2014 male 35-39 positive 61161.82 46662.582 25862.877
#> 96 Malawi 2015 male 35-39 positive 60555.19 46835.348 27788.419
#> 97 Malawi 2016 male 35-39 positive 59580.64 46772.999 29903.901
#> 98 Malawi 2017 male 35-39 positive 58323.36 47198.631 32741.623
#> 99 Malawi 2018 male 35-39 positive 56984.78 47566.818 35341.333
#> 100 Malawi 2019 male 35-39 positive 55777.67 47686.551 35623.029
#> 101 Malawi 2010 female 40-44 positive 54769.49 39257.773 20768.439
#> 102 Malawi 2011 female 40-44 positive 58779.68 46146.204 26986.167
#> 103 Malawi 2012 female 40-44 positive 62948.50 52703.645 35105.190
#> 104 Malawi 2013 female 40-44 positive 67225.34 58507.832 43227.139
#> 105 Malawi 2014 female 40-44 positive 71581.10 64139.224 50604.495
#> 106 Malawi 2015 female 40-44 positive 76272.92 69761.517 57888.121
#> 107 Malawi 2016 female 40-44 positive 79732.02 74161.925 64654.012
#> 108 Malawi 2017 female 40-44 positive 82643.17 78406.212 71136.194
#> 109 Malawi 2018 female 40-44 positive 84885.45 81677.939 76239.528
#> 110 Malawi 2019 female 40-44 positive 86346.63 83814.202 79378.492
#> 111 Malawi 2010 male 40-44 positive 49441.20 31535.131 14129.315
#> 112 Malawi 2011 male 40-44 positive 51464.88 35537.967 17831.782
#> 113 Malawi 2012 male 40-44 positive 53383.71 38920.647 21756.509
#> 114 Malawi 2013 male 40-44 positive 55180.37 41722.828 25403.768
#> 115 Malawi 2014 male 40-44 positive 56886.97 44331.852 28637.564
#> 116 Malawi 2015 male 40-44 positive 58890.71 46977.426 31980.672
#> 117 Malawi 2016 male 40-44 positive 59828.19 48764.145 35073.581
#> 118 Malawi 2017 male 40-44 positive 60462.24 50830.156 38882.922
#> 119 Malawi 2018 male 40-44 positive 60765.70 52527.532 42394.651
#> 120 Malawi 2019 male 40-44 positive 60692.99 53549.573 43418.543
#> 121 Malawi 2010 female 45-49 positive 34093.41 24158.991 14860.199
#> 122 Malawi 2011 female 45-49 positive 37469.61 29185.968 19267.035
#> 123 Malawi 2012 female 45-49 positive 41192.48 34317.923 25154.355
#> 124 Malawi 2013 female 45-49 positive 45143.00 39169.341 31219.996
#> 125 Malawi 2014 female 45-49 positive 49085.89 43942.991 36693.329
#> 126 Malawi 2015 female 45-49 positive 52544.39 48126.252 41762.551
#> 127 Malawi 2016 female 45-49 positive 56888.85 53099.345 47898.055
#> 128 Malawi 2017 female 45-49 positive 61188.47 58306.015 54221.943
#> 129 Malawi 2018 female 45-49 positive 65408.73 63236.374 60093.254
#> 130 Malawi 2019 female 45-49 positive 69595.73 67886.274 65169.885
#> 131 Malawi 2010 male 45-49 positive 33729.01 21546.671 11840.175
#> 132 Malawi 2011 male 45-49 positive 36022.05 25032.048 14991.448
#> 133 Malawi 2012 male 45-49 positive 38566.28 28432.537 18586.620
#> 134 Malawi 2013 male 45-49 positive 41226.37 31686.668 22218.768
#> 135 Malawi 2014 male 45-49 positive 43735.04 34830.218 25409.381
#> 136 Malawi 2015 male 45-49 positive 45560.10 37338.402 28304.910
#> 137 Malawi 2016 male 45-49 positive 47960.89 40322.588 31795.962
#> 138 Malawi 2017 male 45-49 positive 50085.82 43447.281 35879.111
#> 139 Malawi 2018 male 45-49 positive 51946.06 46283.143 39762.953
#> 140 Malawi 2019 male 45-49 positive 53678.76 48747.443 41860.854
#> 141 Malawi 2010 female 50-99 positive 46406.36 30046.911 21775.700
#> 142 Malawi 2011 female 50-99 positive 50615.39 36712.216 27697.882
#> 143 Malawi 2012 female 50-99 positive 55466.83 43678.183 35457.632
#> 144 Malawi 2013 female 50-99 positive 61008.03 50580.910 43642.910
#> 145 Malawi 2014 female 50-99 positive 67234.06 57997.977 51625.714
#> 146 Malawi 2015 female 50-99 positive 74149.61 65936.089 60194.392
#> 147 Malawi 2016 female 50-99 positive 81755.93 74573.836 70060.592
#> 148 Malawi 2017 female 50-99 positive 89984.38 84267.800 80831.020
#> 149 Malawi 2018 female 50-99 positive 98750.53 94289.740 91692.658
#> 150 Malawi 2019 female 50-99 positive 107891.05 104309.792 101935.179
#> 151 Malawi 2010 male 50-99 positive 43512.14 25676.657 17249.662
#> 152 Malawi 2011 male 50-99 positive 47091.63 30790.732 22014.533
#> 153 Malawi 2012 male 50-99 positive 51166.08 36056.086 27495.354
#> 154 Malawi 2013 male 50-99 positive 55722.89 41493.886 33340.062
#> 155 Malawi 2014 male 50-99 positive 60701.77 47352.344 38987.425
#> 156 Malawi 2015 male 50-99 positive 66094.16 53542.045 45180.230
#> 157 Malawi 2016 male 50-99 positive 71892.19 60216.575 52212.482
#> 158 Malawi 2017 male 50-99 positive 78028.16 67747.150 60625.676
#> 159 Malawi 2018 male 50-99 positive 84400.52 75519.233 69331.520
#> 160 Malawi 2019 male 50-99 positive 90880.78 83099.996 75898.624