From 49a28121ecd816f44267f1baa769a5adc878093c Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Tue, 10 Dec 2024 22:35:11 +0200 Subject: [PATCH 01/19] initial commit --- DESCRIPTION | 2 +- NEWS.md | 5 + R/input-comparison.R | 29 ++-- R/inputs-spectrum.R | 80 +++++++++-- tests/testthat/refdata/ART_adjustment_test.DP | 134 ++++++++++++++++++ tests/testthat/test-input-comparison.R | 3 + tests/testthat/test-spectrum.R | 22 +++ 7 files changed, 257 insertions(+), 18 deletions(-) create mode 100644 tests/testthat/refdata/ART_adjustment_test.DP diff --git a/DESCRIPTION b/DESCRIPTION index 2bfcb9f2..4299d4c5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: naomi Title: Naomi Model for Subnational HIV Estimates -Version: 2.10.4 +Version: 2.10.5 Authors@R: person(given = "Jeff", family = "Eaton", diff --git a/NEWS.md b/NEWS.md index 424d65fb..5ba5e1ae 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# naomi 2.10.5 +* Update `read_dp_art_dec31()` with new .DP file flags to ensure ART adjustment factor and ART patient reallocation counts are applied to number on ART extracted from Spectrum. +* Ensure adjusted Spectrum number on ART is used in Spectrum-Naomi comparison table. +* Add ART adjustment factor and ART patient reallocation counts to Spectrum-Naomi comparison table. + # naomi 2.10.4 * If users upload multiple quarters in ART programme data, return only the last quarter per year for input comparison data. diff --git a/R/input-comparison.R b/R/input-comparison.R index f073a888..0aa153a8 100644 --- a/R/input-comparison.R +++ b/R/input-comparison.R @@ -39,15 +39,26 @@ prepare_art_spectrum_comparison <- function(art, shape, pjnz) { if(identical(unique(art_single_cq$sex), c("both"))) { # If no sex aggregated data present in ART data, aggregate Spectrum by age spec_aggreagted <- pjnz$art_dec31 |> - dplyr::count(spectrum_region_code, year, age_group, - wt = art_dec31, name = "value_spectrum") |> - dplyr::mutate(sex = "both") - + dplyr::mutate(calendar_quarter = paste0("CY", year, "Q4")) |> + dplyr::group_by(spectrum_region_code, calendar_quarter, year, age_group) |> + dplyr::summarise( + value_spectrum = sum(art_dec31), + artadj_factor = sum(artadj_factor), + artadj_absolute = sum(artadj_absolute), + .groups = "drop") |> + dplyr::mutate( + value_spectrum_adjusted = (value_spectrum + artadj_absolute) * artadj_factor, + artadj_factor = dplyr::if_else(age_group == "Y000_014",artadj_factor, artadj_factor/2), + sex = "both") |> + dplyr::select(spectrum_region_code, calendar_quarter, year, age_group, sex, value_spectrum, + value_spectrum_adjusted, artadj_absolute, artadj_factor) } else { # If sex aggregated data present in ART data, aggregate Spectrum by age and sex spec_aggreagted <- pjnz$art_dec31 |> - dplyr::count(spectrum_region_code, year, sex, age_group, - wt = art_dec31, name = "value_spectrum") + dplyr::mutate(calendar_quarter = paste0("CY", year, "Q4"), + value_spectrum_adjusted = (art_dec31 + artadj_absolute) * artadj_factor) |> + dplyr::select(spectrum_region_code, calendar_quarter,year, age_group, sex, + value_spectrum = art_dec31, value_spectrum_adjusted, artadj_absolute, artadj_factor) } # Get spectrum level to select correct area names @@ -69,9 +80,11 @@ prepare_art_spectrum_comparison <- function(art, shape, pjnz) { indicator = "number_on_art", group = dplyr::if_else(age_group == "Y000_014", "art_children", paste0("art_adult_", sex)), - difference = value_spectrum - value_naomi) |> + difference = value_naomi - value_spectrum_adjusted, + prop_difference = 1 - abs((value_naomi - value_spectrum_adjusted) / value_spectrum_adjusted)) |> dplyr::select(indicator, area_name, year, group, - value_spectrum, value_naomi, difference) + value_spectrum = value_spectrum_adjusted, artadj_factor, + artadj_absolute, value_naomi, difference, prop_difference) } ##' Compare aggregated subnational ART inputs + spectrum totals for comparison table diff --git a/R/inputs-spectrum.R b/R/inputs-spectrum.R index 242a70f7..3919d4a1 100644 --- a/R/inputs-spectrum.R +++ b/R/inputs-spectrum.R @@ -195,7 +195,6 @@ read_dp_art_dec31 <- function(dp) { art15plus_need <- rbind(male_15plus_needart, female_15plus_needart) dimnames(art15plus_need) <- list(sex = c("male", "female"), year = proj.years) - if (any(art15plus_num[art15plus_isperc == 1] < 0 | art15plus_num[art15plus_isperc == 1] > 100)) { stop("Invalid percentage on ART entered for adult ART") @@ -208,27 +207,73 @@ read_dp_art_dec31 <- function(dp) { ## * Enabled / disabled by checkbox flag ("") ## * Scaling factor only applies to number inputs, not percentages (John Stover email, 20 Feb 2023) ## -> Even if scaling factor specified in a year with percentage input, ignore it. + ## ** UPDATE Spectrum 6.37 beta 18 ** + ## + ## Two changes to the adult ART adjustment were implemented in Spectrum 6.37 beta 18: + ## + ## * ART adjustments were moved the main Spectrum editor and the flag variable + ## "" was removed from the .DP file. + ## * New tag "" was added allowing for input + ## of absolute count adjustment + ## + ## New logic to account for these changes: + ## * Initialise values to defaults 1.0 for relative adjustment and 0.0 + ## for absolute adjustment. + ## * Only check flag variable if it exists. If adjustment variable exists + ## but flag variable does not exist, use the adjustment. + + ## Initialise + adult_artadj_factor <- array(1.0, dim(art15plus_num)) + dimnames(adult_artadj_factor) <- list(sex = c("male", "female"), year = proj.years) - if (exists_dptag("") && - dpsub("", 2, 4) == 1) { + adult_artadj_absolute <- array(0.0, dim(art15plus_num)) + dimnames(adult_artadj_absolute) <- list(sex = c("male", "female"), year = proj.years) + + ## Flag to use adjustment + use_artadj <- exists_dptag("") && + (!exists_dptag("") || + (exists_dptag("") && + dpsub("", 2, 4) == 1)) + + if (use_artadj) { adult_artadj_factor <- sapply(dpsub("", 3:4, timedat.idx), as.numeric) + if(exists_dptag("")) { + adult_artadj_absolute <- sapply(dpsub("", 3:4, timedat.idx), as.numeric) + } + ## Only apply if is number (! is percentage) adult_artadj_factor <- adult_artadj_factor ^ as.numeric(!art15plus_isperc) + adult_artadj_absolute <- adult_artadj_absolute * as.numeric(!art15plus_isperc) + + ## First add absolute adjustment, then apply scalar adjustment (Spectrum procedure) + art15plus_num_adj <- art15plus_num + adult_artadj_absolute + art15plus_num_adj <- art15plus_num * adult_artadj_factor - art15plus_num <- art15plus_num * adult_artadj_factor } + # Covert percentage coverage to absolute numbers on ART art15plus_num[art15plus_isperc == 1] <- art15plus_need[art15plus_isperc == 1] * art15plus_num[art15plus_isperc == 1] / 100 + # Adjusted number on ART art15plus <- as.data.frame.table(art15plus_num, responseName = "art_dec31", stringsAsFactors = FALSE) + # ART adjustment factor + art15plus_adjfactor <- as.data.frame.table(adult_artadj_factor, + responseName = "artadj_factor", + stringsAsFactors = FALSE) + # ART reallocation + art15plus_adjabsolute <- as.data.frame.table(adult_artadj_absolute, + responseName = "artadj_absolute", + stringsAsFactors = FALSE) + + art15plus$artadj_factor <- art15plus_adjfactor$artadj_factor + art15plus$artadj_absolute <- art15plus_adjabsolute$artadj_absolute art15plus$age_group <- "Y015_999" art15plus$year <- utils::type.convert(art15plus$year, as.is = TRUE) - ## # Child number on ART ## ## - If age-stratified entered, use sum of three age categories @@ -284,18 +329,33 @@ read_dp_art_dec31 <- function(dp) { ## ## * Implemented same as adult adjustment factor above - if (exists_dptag("") && - dpsub("", 2, 4) == 1) { + ## Initialise + child_artadj_factor <- rep(1.0, length(child_art)) + child_artadj_absolute <- rep(0.0, length(child_art)) + + ## Flag to use adjustment + use_child_artadj <- exists_dptag("") && + (!exists_dptag("") || + (exists_dptag("") && + dpsub("", 2, 4) == 1)) + + if (use_child_artadj) { child_artadj_factor <- as.numeric(dpsub("", 2, timedat.idx)) + if(exists_dptag("")) { + child_artadj_absolute <- as.numeric(dpsub("", 2, timedat.idx)) + } + ## Only apply if is number (! is percentage) child_artadj_factor <- child_artadj_factor ^ !child_art_isperc + child_artadj_absolute <- child_artadj_absolute ^ !child_art_isperc + ## First add absolute adjustment, then apply scalar adjustment (Spectrum procedure) + child_art <- child_art + child_artadj_absolute child_art <- child_art * child_artadj_factor } - if (any(is.na(child_art))) { stop("Something has gone wrong extracting child ART inputs; please seek troubleshooting.") } @@ -303,7 +363,9 @@ read_dp_art_dec31 <- function(dp) { child_art <- data.frame(sex = "both", age_group = "Y000_014", year = proj.years, - art_dec31 = child_art) + art_dec31 = child_art, + artadj_factor = child_artadj_factor, + artadj_absolute = child_artadj_absolute) art_dec31 <- rbind(child_art, art15plus) diff --git a/tests/testthat/refdata/ART_adjustment_test.DP b/tests/testthat/refdata/ART_adjustment_test.DP new file mode 100644 index 00000000..3a38b078 --- /dev/null +++ b/tests/testthat/refdata/ART_adjustment_test.DP @@ -0,0 +1,134 @@ 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+,,,0,0.02053,0.05205,0.11291,0.22853,0.44765,1.17651,2.47959,4.95046,9.53093,17.75856,31.85637,54.30983,87.55202,132.39396,187.80076,250.66741,316.8199,382.63346,445.47955,503.07219,553.48528,595.97832,629.99429,655.81469,674.09107,685.68577,691.55986,692.77418,690.52357,686.0442,682.26505,682.28684,687.22573,709.61071,759.70352,822.02725,888.25776,970.89056,1060.5841,1188.29931,1485.72767,1570.31035,1863.36432,2058.20541,2244.21273,2504.12289,2887.50867,3255.32538,3649.26559,4046.79682,4446.13687,4855.04841,5292.99053,5787.68832,6351.17,7013.91311,7780.74452,8641.59699,9588.6103,10618.63776,,,,,,,,,,,,,,,,,,,, +,,,0,0.01513,0.03727,0.07774,0.15021,0.27995,0.67974,1.36595,2.61398,4.83513,8.68389,15.0899,25.04311,39.46462,58.60814,81.99065,108.28433,135.77026,162.92951,188.64344,211.88547,231.8272,248.16214,260.66419,269.45268,274.83358,277.24428,277.22064,275.3505,272.30228,268.69818,265.82579,264.98323,266.4296,275.21374,295.76984,321.82499,349.46832,383.82769,421.73939,474.3315,589.26172,618.71133,723.80791,795.35654,867.75505,969.06408,1120.60562,1267.0317,1424.14837,1582.80263,1742.85275,1907.69064,2084.57375,2284.08109,2509.3135,2778.36225,3090.74324,3442.2181,3830.39048,4254.89504,,,,,,,,,,,,,,,,,,,, +,,,0,0.0054,0.01478,0.03517,0.07832,0.1677,0.49677,1.11364,2.33648,4.69579,9.07467,16.76647,29.26673,48.0874,73.78582,105.81011,142.38308,181.04964,219.70394,256.83612,291.18671,321.65808,347.81619,369.33009,386.362,399.25749,408.44149,414.33921,417.42368,418.22129,417.34602,416.43926,417.30361,420.79613,434.39696,463.93367,500.20226,538.78944,587.06287,638.84471,713.96781,896.46595,951.59903,1139.55641,1262.84886,1376.45768,1535.05881,1766.90305,1988.29368,2225.11723,2463.99419,2703.28412,2947.35777,3208.41679,3503.60723,3841.8565,4235.55087,4690.00128,5199.37889,5758.21983,6363.74272,,,,,,,,,,,,,,,,,,,, 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+,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1066,2132,3198,4264,5330,6396,7462,8532,13413,17673,49470,60994,63881,42145,48752,47677,54077,59173,62079,36769,40166,37369,38633,35418,90,90,90,90,90,90,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1066,2132,3198,4264,5330,6396,7462,8532,13413,17673,21763,24735,35453,43525,54680,60029,63936,65134,67131,66203,-9999,-9999,-9999,-9999,-9999,90,91,92,93,94,95,,,,,,,,,,,,,,,,,,,, +,,,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,10352,9564,8900,8346,7998,-9999,-9999,-9999,-9999,-9999,-9999,,,,,,,,,,,,,,,,,,,, +,,,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,22736,21710,19898,17800,16947,-9999,-9999,-9999,-9999,-9999,-9999,,,,,,,,,,,,,,,,,,,, +,,,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,-9999,28657,28579,30579,28833,29156,-9999,-9999,-9999,-9999,-9999,-9999,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0.9,0.9,0.9,0.9,0.9,1,1,1,1,1,1,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5000,5000,5000,5000,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,Children needing cotrimoxazole (0-14),,0,3.36469,12.18701,27.87784,60.41272,128.37535,359.38112,880.31488,1831.75677,3650.01746,7067.84131,13108.21875,23005.43066,37714.49219,57212.8457,79913.99609,103193.1797,124183.4414,140964.7031,158045.0547,166574.2578,172450.8359,176187.2188,178293.75,178645.8125,178071.8672,178154.2344,177646.1953,176929.7109,176177.4141,175445.125,174463.3984,172871.7969,171755.6797,171484.4453,172123.3984,172841.7891,172240.7734,171986.0313,170808.9297,169196.3672,180170.7734,177112.6875,173144.3047,216372.1328,206312.6641,197712.9141,192730.3125,186546.3828,179011.1172,170342.5156,164820.0938,159976.6484,153783.7734,148511.6172,143153.8594,137139.5469,129362.9336,123105.4414,117403.875,111558.8828,,,,,,,,,,,,,,,,,,,, +,,,0,1.70687,6.17935,14.13323,30.62651,65.07931,182.21779,446.30133,928.60406,1850.32178,3582.84326,6644.59619,11660.75684,19114.53125,28992.2168,40485.36719,52258.89844,62857.40625,71310.66406,79909.86719,84163.92188,87066.97656,88883.45312,89879.53906,90000.38281,89664.58594,89671.77344,89385.39062,88994.5,88589.65625,88206.57031,87717.71875,86938.38281,86410.28906,86317.41406,86693.05469,87109.97656,86857.28906,86778.84375,86242.92188,85489.38281,90933.33594,89462.10156,87539.10938,109182.8281,104240.0703,99995.83594,97559.60938,94485.78125,90711.85938,86351.24219,83570.89062,81131.90625,78009.07812,75345.03906,72632.8125,69583.17969,65637.73438,62462.90234,59569.90625,56604.15234,,,,,,,,,,,,,,,,,,,, +,,,0,1.65781,6.00766,13.74461,29.78621,63.29604,177.16333,434.01355,903.15271,1799.69568,3484.99805,6463.62256,11344.67383,18599.96094,28220.62891,39428.62891,50934.28125,61326.03516,69654.03906,78135.1875,82410.33594,85383.85938,87303.76562,88414.21094,88645.42969,88407.28125,88482.46094,88260.80469,87935.21094,87587.75781,87238.55469,86745.67969,85933.41406,85345.39062,85167.03125,85430.34375,85731.8125,85383.48438,85207.1875,84566.00781,83706.98438,89237.4375,87650.58594,85605.19531,107189.3047,102072.5938,97717.07812,95170.70312,92060.60156,88299.25781,83991.27344,81249.20312,78844.74219,75774.69531,73166.57812,70521.04688,67556.36719,63725.19922,60642.53906,57833.96875,54954.73047,,,,,,,,,,,,,,,,,,,, +,Children receiving cotrimoxazole (0-14),,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1066,2132,3198,4264,5330,6396,7462,8532,13413,17673,49470,60994,63881,42145,48752,47677,54077,59173,62079,36769,40166,37369,38633,35418,128838.4766,123425.5938,116426.6406,110794.8906,105663.4844,100402.9922,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,535.96964,1072.19706,1608.91385,2146.30236,2684.55053,3223.49958,3762.92471,4304.9839,6772.34065,8929.58766,24967.82274,30808.92453,32297.25404,21266.65018,24632.08996,24113.25371,27373.64418,29971.13792,31457.82989,18639.20356,20365.893,18951.62879,19597.15576,17968.7657,65369.53284,62624.86251,59073.95935,56216.61052,53612.91404,50943.73592,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,530.03032,1059.80294,1589.086,2117.69783,2645.44923,3172.5007,3699.07496,4227.0161,6640.65873,8743.41152,24502.17512,30185.07547,31583.74308,20878.35134,24119.91189,23563.74817,26703.35582,29201.86456,30621.1674,18129.79644,19800.107,18417.36938,19035.84227,17449.23244,63468.94373,60800.73124,57352.67776,54578.28362,52050.57034,49459.25627,,,,,,,,,,,,,,,,,,,, +,Children needing ART (0-14),,0,0.88841,2.09747,4.74571,10.50568,22.43291,70.80359,151.90424,311.86383,624.90027,1206.79724,2207.49512,3811.7019,6162.92285,9222.48633,12795.63965,16564.57812,20190.04102,23438.86914,26541.88867,29149.97266,31392.61914,33501.39844,35429.72656,37050.23438,38516.88281,39831.4375,40872.49219,41637.28906,42140.76172,42338.91223,42393.16388,42494.33067,42585.8551,42582.80848,42554.44848,42568.0816,53648.35396,51682.85735,51263.47704,71659.85199,70246.58768,66202.37294,126633.4855,122510.6222,118873.1137,115643.8674,112033.5157,106654.638,101241.9202,95398.61364,89452.41426,84297.91672,78647.32804,72096.67355,66854.47616,63015.09145,60260.48266,56972.05983,53762.86857,50610.57088,,,,,,,,,,,,,,,,,,,, +,,,0,0.45058,1.06214,2.40292,5.31895,11.3571,35.86704,76.90902,157.88348,316.33969,610.86346,1117.26257,1928.79858,3117.72363,4663.44824,6465.77686,8362.07617,10179.62207,11801.17383,13344.5957,14632.57812,15731.9502,16760.625,17697.85156,18482.70508,19192.74609,19828.62305,20328.51953,20690.5918,20924.45508,21011.81804,21034.36148,21085.40814,21134.38674,21138.36315,21131.89768,21151.3858,26790.17162,25815.59957,25629.6945,35794.47068,35135.4142,33145.70598,63440.05625,61496.79426,59774.93791,58238.95015,56493.34848,53838.02258,51155.5314,48247.07698,45277.5986,42700.4383,39863.82088,36564.72716,33921.41103,31982.32361,30588.68516,28918.24545,27287.26491,25685.454,,,,,,,,,,,,,,,,,,,, +,,,0,0.43783,1.03533,2.34278,5.18673,11.07582,34.93655,74.99521,153.98036,308.56055,595.93378,1090.23242,1882.90332,3045.19922,4559.03809,6329.86279,8202.50098,10010.41895,11637.69531,13197.29297,14517.39551,15660.66895,16740.77539,17731.87305,18567.53125,19324.13477,20002.8125,20543.97266,20946.69531,21216.30664,21327.09615,21358.8024,21408.92252,21451.46641,21444.44532,21422.5508,21416.69581,26858.18234,25867.25974,25633.78254,35865.38132,35111.17348,33056.66696,63193.42921,61013.82792,59098.17579,57404.9172,55540.16916,52816.61742,50086.38689,47151.53666,44174.81371,41597.47744,38783.50618,35531.94542,32933.06561,31032.76809,29671.7975,28053.81437,26475.60366,24925.117,,,,,,,,,,,,,,,,,,,, +,Children receiving ART (0-14),,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,454.93567,1421.89826,2454.50645,3496.38635,4536.61707,5565.60864,6617.3277,7613.69381,10233.31047,14439.89111,18776.60199,22512.94315,29108.30263,38683.68077,48279.54406,56680.71526,61757.87907,64493.48443,66085.02087,66513.83431,61944.84801,56518.14864,54711.17453,51589.06632,48710.29465,53378.66561,55350.06997,54945.1101,53084.22755,50872.88468,48439.35164,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,225.1989,703.20718,1212.94134,1726.85158,2239.88268,2749.61643,3272.27447,3773.08959,5088.61324,7203.98747,9381.07224,11266.18959,14595.66106,19421.43906,24279.41926,28547.52775,31136.90523,32545.37191,33376.01868,33618.80484,31333.83284,28607.8818,27708.74397,26142.9869,24700.65196,27083.46963,28092.33044,27890.97617,26945.19016,25820.79823,24583.86929,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,229.73677,718.69107,1241.5651,1769.53477,2296.73439,2815.99221,3345.05323,3840.60422,5144.69724,7235.90364,9395.52975,11246.75356,14512.64157,19262.24171,24000.1248,28133.18751,30620.97384,31948.11252,32709.00219,32895.02947,30611.01518,27910.26684,27002.43057,25446.07942,24009.64269,26295.19599,27257.73953,27054.13393,26139.03739,25052.08645,23855.48235,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,Number of adults receiving ART,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,Male+Female,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4368,10052,15736,44960.99999,82604,81731,102700,143381,168300,215193,250892,342626,468903,590434,653376.2364,858265,1005571,1100973,1169899,1217321,1260305,1308793,1351380,1405893,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, +,Males,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2065.85988,4700.42997,7288.82816,20674.72831,37784.71481,37216.66378,46630.34566,64654,75887,96998,112237,126253,151244,195731,217341.5188,286814,343237,379316,405140,425804,436479,450799,462976,485372,95,95,95,95,95,95,,,,,,,,,,,,,,,,,,,, +,Females,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2302.14012,5351.57003,8447.17184,24286.27168,44819.28519,44514.33622,56069.65434,78727,92413,118195,138655,216373,317659,394703,436034.7176,571451,662334,721657,764759,791517,823826,857994,888404,920521,98,98,98,98,98,98,,,,,,,,,,,,,,,,,,,, +,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + diff --git a/tests/testthat/test-input-comparison.R b/tests/testthat/test-input-comparison.R index 64571708..37bb2af1 100644 --- a/tests/testthat/test-input-comparison.R +++ b/tests/testthat/test-input-comparison.R @@ -30,6 +30,9 @@ test_that("ART data is properly aggreagted for Spectrum comparison table", { expect_equal(unique(x$group), c("art_children", "art_adult_both")) expect_equal(unique(x$area_name), c("Malawi - Demo")) + # TO DO: Ensure ART adjustments in Spectrum are applied + # Make a test "pjnz" file + }) test_that("ANC data is properly aggreagted for Spectrum comparison table", { diff --git a/tests/testthat/test-spectrum.R b/tests/testthat/test-spectrum.R index 55c38d8f..4f6d53ba 100644 --- a/tests/testthat/test-spectrum.R +++ b/tests/testthat/test-spectrum.R @@ -191,3 +191,25 @@ Using file: Malawi.zip.shiny90") expect_equal(w$shiny90new, "Malawi.zip.shiny90") }) + +test_that("ART adjustments properly extracted from Spectrum", { + + dp_path <- file.path("refdata/ART_adjustment_test.DP") + dp <- as.data.frame( + readr::read_csv(dp_path, + name_repair = "minimal", + col_types = readr::cols(.default = "c"))) + + spec_art <- read_dp_art_dec31(dp) + rownames(spec_art) <- seq_len(nrow(spec_art)) + + # Test ART adjustments correctly read from test file with + expect_equal(colnames(spec_art), c("sex", "age_group", "year", + "art_dec31", "artadj_factor","artadj_absolute")) + # Adults + expect_setequal(spec_art[166,], c("male", "Y015_999", "2022", "450799", "0.88", "10000")) + expect_setequal(spec_art[167,], c("female", "Y015_999", "2022", "857994", "0.85", "12000")) + # Children + expect_setequal(spec_art[52,], c("both", "Y000_014", "2021", "58367.7", "0.9", "5000")) + +}) From 59fa41c30822aff6789f33ce048d84a35f721f30 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Tue, 10 Dec 2024 22:37:35 +0200 Subject: [PATCH 02/19] bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4299d4c5..ebd39ef4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: naomi Title: Naomi Model for Subnational HIV Estimates -Version: 2.10.5 +Version: 2.10.6 Authors@R: person(given = "Jeff", family = "Eaton", From b1eb11a597dbf81eea53ca7b4fbbf087fc1787b1 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 11:17:00 +0200 Subject: [PATCH 03/19] update function to report adjusted attending and residing ART numbers from Spectrum --- R/input-comparison.R | 39 ++++++----- R/inputs-spectrum.R | 64 +++++++++++-------- tests/testthat/refdata/ART_adjustment_test.DP | 6 +- tests/testthat/test-spectrum.R | 9 +-- 4 files changed, 64 insertions(+), 54 deletions(-) diff --git a/R/input-comparison.R b/R/input-comparison.R index 0aa153a8..c5dc1a97 100644 --- a/R/input-comparison.R +++ b/R/input-comparison.R @@ -38,29 +38,28 @@ prepare_art_spectrum_comparison <- function(art, shape, pjnz) { if(identical(unique(art_single_cq$sex), c("both"))) { # If no sex aggregated data present in ART data, aggregate Spectrum by age - spec_aggreagted <- pjnz$art_dec31 |> - dplyr::mutate(calendar_quarter = paste0("CY", year, "Q4")) |> - dplyr::group_by(spectrum_region_code, calendar_quarter, year, age_group) |> + spec <- pjnz$art_dec31 |> + dplyr::group_by(spectrum_region_code, year, age_group) |> dplyr::summarise( - value_spectrum = sum(art_dec31), - artadj_factor = sum(artadj_factor), - artadj_absolute = sum(artadj_absolute), + value_spectrum_reported = round(sum(art_dec31_reported)), + art_dec31_attend = round(sum(art_dec31_attend)), + art_dec31_reside = round(sum(art_dec31_reside)), .groups = "drop") |> - dplyr::mutate( - value_spectrum_adjusted = (value_spectrum + artadj_absolute) * artadj_factor, - artadj_factor = dplyr::if_else(age_group == "Y000_014",artadj_factor, artadj_factor/2), - sex = "both") |> - dplyr::select(spectrum_region_code, calendar_quarter, year, age_group, sex, value_spectrum, - value_spectrum_adjusted, artadj_absolute, artadj_factor) + dplyr::mutate(sex = "both") } else { # If sex aggregated data present in ART data, aggregate Spectrum by age and sex - spec_aggreagted <- pjnz$art_dec31 |> - dplyr::mutate(calendar_quarter = paste0("CY", year, "Q4"), - value_spectrum_adjusted = (art_dec31 + artadj_absolute) * artadj_factor) |> - dplyr::select(spectrum_region_code, calendar_quarter,year, age_group, sex, - value_spectrum = art_dec31, value_spectrum_adjusted, artadj_absolute, artadj_factor) + spec <- pjnz$art_dec31 |> + dplyr::select(value_spectrum_reported = art_dec31_reported, dplyr::everything()) } + spec_aggreagted <- spec |> + dplyr::mutate( + value_spectrum_adjusted = art_dec31_attend, + value_spectrum_reallocated = art_dec31_reside - art_dec31_attend, + value_spectrum_adj_factor = value_spectrum_adjusted/ (value_spectrum_reported + value_spectrum_reallocated)) |> + dplyr::select(spectrum_region_code, year, age_group, sex, value_spectrum_reported, + value_spectrum_adjusted, value_spectrum_reallocated, value_spectrum_adjusted, value_spectrum_adj_factor) + # Get spectrum level to select correct area names spectrum_region_code <- unique(shape$spectrum_region_code) @@ -82,9 +81,9 @@ prepare_art_spectrum_comparison <- function(art, shape, pjnz) { "art_children", paste0("art_adult_", sex)), difference = value_naomi - value_spectrum_adjusted, prop_difference = 1 - abs((value_naomi - value_spectrum_adjusted) / value_spectrum_adjusted)) |> - dplyr::select(indicator, area_name, year, group, - value_spectrum = value_spectrum_adjusted, artadj_factor, - artadj_absolute, value_naomi, difference, prop_difference) + dplyr::select(indicator, area_name, year, group, value_naomi, + value_spectrum_reported, value_spectrum_adjusted, + value_spectrum_reallocated, value_spectrum_adjusted, value_spectrum_adj_factor) } ##' Compare aggregated subnational ART inputs + spectrum totals for comparison table diff --git a/R/inputs-spectrum.R b/R/inputs-spectrum.R index 3919d4a1..fa5b4d00 100644 --- a/R/inputs-spectrum.R +++ b/R/inputs-spectrum.R @@ -246,31 +246,38 @@ read_dp_art_dec31 <- function(dp) { ## Only apply if is number (! is percentage) adult_artadj_factor <- adult_artadj_factor ^ as.numeric(!art15plus_isperc) adult_artadj_absolute <- adult_artadj_absolute * as.numeric(!art15plus_isperc) - - ## First add absolute adjustment, then apply scalar adjustment (Spectrum procedure) - art15plus_num_adj <- art15plus_num + adult_artadj_absolute - art15plus_num_adj <- art15plus_num * adult_artadj_factor - } + ## First add absolute adjustment, then apply scalar adjustment (Spectrum procedure) + art15plus_attend <- art15plus_num + adult_artadj_absolute + art15plus_attend <- art15plus_attend * adult_artadj_factor + art15plus_reside <- art15plus_attend + adult_artadj_absolute + # Covert percentage coverage to absolute numbers on ART art15plus_num[art15plus_isperc == 1] <- art15plus_need[art15plus_isperc == 1] * art15plus_num[art15plus_isperc == 1] / 100 + art15plus_attend[art15plus_isperc == 1] <- art15plus_need[art15plus_isperc == 1] * art15plus_attend[art15plus_isperc == 1] / 100 + art15plus_reside[art15plus_isperc == 1] <- art15plus_need[art15plus_isperc == 1] * art15plus_reside[art15plus_isperc == 1] / 100 - # Adjusted number on ART - art15plus <- as.data.frame.table(art15plus_num, - responseName = "art_dec31", + # Reported number on ART + art_dec31_reported <- as.data.frame.table(art15plus_num, + responseName = "art_dec31_reported", stringsAsFactors = FALSE) - # ART adjustment factor - art15plus_adjfactor <- as.data.frame.table(adult_artadj_factor, - responseName = "artadj_factor", + + # Adjusted number on ART (attending) + art_dec31_attend <- as.data.frame.table(art15plus_attend, + responseName = "art_dec31_attend", stringsAsFactors = FALSE) - # ART reallocation - art15plus_adjabsolute <- as.data.frame.table(adult_artadj_absolute, - responseName = "artadj_absolute", + + # Adjusted number on ART (residing) + art_dec31_reside <- as.data.frame.table(art15plus_reside, + responseName = "art_dec31_reside", stringsAsFactors = FALSE) - art15plus$artadj_factor <- art15plus_adjfactor$artadj_factor - art15plus$artadj_absolute <- art15plus_adjabsolute$artadj_absolute + art15plus <- purrr::reduce(list(art_dec31_reported, + art_dec31_attend, + art_dec31_reside), dplyr::left_join, + by = dplyr::join_by(sex, year)) + art15plus$age_group <- "Y015_999" art15plus$year <- utils::type.convert(art15plus$year, as.is = TRUE) @@ -325,6 +332,11 @@ read_dp_art_dec31 <- function(dp) { child_art_isperc == 1 ~ child_art_need * child_art_0to14 / 100) names(child_art) <- proj.years + if (any(is.na(child_art))) { + stop("Something has gone wrong extracting child ART inputs; please seek troubleshooting.") + } + + ## # Child on ART adjustment factor ## ## * Implemented same as adult adjustment factor above @@ -350,24 +362,22 @@ read_dp_art_dec31 <- function(dp) { ## Only apply if is number (! is percentage) child_artadj_factor <- child_artadj_factor ^ !child_art_isperc child_artadj_absolute <- child_artadj_absolute ^ !child_art_isperc - - ## First add absolute adjustment, then apply scalar adjustment (Spectrum procedure) - child_art <- child_art + child_artadj_absolute - child_art <- child_art * child_artadj_factor } - if (any(is.na(child_art))) { - stop("Something has gone wrong extracting child ART inputs; please seek troubleshooting.") - } + ## First add absolute adjustment, then apply scalar adjustment (Spectrum procedure) + child_art_attend <- child_art + child_artadj_absolute + child_art_attend <- child_art_attend * child_artadj_factor + child_art_reside <- child_art_attend + child_artadj_absolute child_art <- data.frame(sex = "both", age_group = "Y000_014", year = proj.years, - art_dec31 = child_art, - artadj_factor = child_artadj_factor, - artadj_absolute = child_artadj_absolute) + art_dec31_reported = child_art, + art_dec31_attend = child_art_attend, + art_dec31_reside = child_art_reside) - art_dec31 <- rbind(child_art, art15plus) + art_dec31 <- rbind(child_art, art15plus) |> + dplyr::mutate(dplyr::across(where(is.numeric), ~ round(., 0))) art_dec31 } diff --git a/tests/testthat/refdata/ART_adjustment_test.DP b/tests/testthat/refdata/ART_adjustment_test.DP index 3a38b078..f1949488 100644 --- a/tests/testthat/refdata/ART_adjustment_test.DP +++ b/tests/testthat/refdata/ART_adjustment_test.DP @@ -24,8 +24,8 @@ Tag,Description,Notes,Data,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -,Males,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10000,10000,10000,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, -,Females,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,12000,12000,12000,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, +,Males,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-10000,-10000,-10000,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, +,Females,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-12000,-12000,-12000,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @@ -98,7 +98,7 @@ Tag,Description,Notes,Data,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5000,5000,5000,5000,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, +,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-5000,-5000,-5000,-5000,0,0,0,0,0,0,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, diff --git a/tests/testthat/test-spectrum.R b/tests/testthat/test-spectrum.R index 4f6d53ba..6bad1152 100644 --- a/tests/testthat/test-spectrum.R +++ b/tests/testthat/test-spectrum.R @@ -195,6 +195,7 @@ Using file: Malawi.zip.shiny90") test_that("ART adjustments properly extracted from Spectrum", { dp_path <- file.path("refdata/ART_adjustment_test.DP") + dp <- as.data.frame( readr::read_csv(dp_path, name_repair = "minimal", @@ -205,11 +206,11 @@ test_that("ART adjustments properly extracted from Spectrum", { # Test ART adjustments correctly read from test file with expect_equal(colnames(spec_art), c("sex", "age_group", "year", - "art_dec31", "artadj_factor","artadj_absolute")) + "art_dec31_reported", "art_dec31_attend","art_dec31_reside")) # Adults - expect_setequal(spec_art[166,], c("male", "Y015_999", "2022", "450799", "0.88", "10000")) - expect_setequal(spec_art[167,], c("female", "Y015_999", "2022", "857994", "0.85", "12000")) + expect_setequal(spec_art[166,], c("male", "Y015_999", "2022", "450799", "387903.12", "377903.12")) + expect_setequal(spec_art[167,], c("female", "Y015_999", "2022", "857994", "719094.9", "707094.9")) # Children - expect_setequal(spec_art[52,], c("both", "Y000_014", "2021", "58367.7", "0.9", "5000")) + expect_setequal(spec_art[52,], c("both", "Y000_014", "2021", "59853", "49367.7", "44367.7")) }) From 25e6565450d14371f3724beeefdf6a1e880c6e71 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 11:22:18 +0200 Subject: [PATCH 04/19] update tests --- tests/testthat/test-spectrum.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/testthat/test-spectrum.R b/tests/testthat/test-spectrum.R index 6bad1152..30a3c0ab 100644 --- a/tests/testthat/test-spectrum.R +++ b/tests/testthat/test-spectrum.R @@ -208,9 +208,9 @@ test_that("ART adjustments properly extracted from Spectrum", { expect_equal(colnames(spec_art), c("sex", "age_group", "year", "art_dec31_reported", "art_dec31_attend","art_dec31_reside")) # Adults - expect_setequal(spec_art[166,], c("male", "Y015_999", "2022", "450799", "387903.12", "377903.12")) - expect_setequal(spec_art[167,], c("female", "Y015_999", "2022", "857994", "719094.9", "707094.9")) + expect_setequal(spec_art[166,], c("male", "Y015_999", "2022", "450799", "387903", "377903")) + expect_setequal(spec_art[167,], c("female", "Y015_999", "2022", "857994", "719095", "707095")) # Children - expect_setequal(spec_art[52,], c("both", "Y000_014", "2021", "59853", "49367.7", "44367.7")) + expect_setequal(spec_art[52,], c("both", "Y000_014", "2021", "59853", "49368", "44368")) }) From d07a38f9b902dfc249cdf7cafb17e0e60f362ee5 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 11:42:38 +0200 Subject: [PATCH 05/19] remove naomi-spectrum comparison check from navigator code --- R/model.R | 65 ++--------------------------------- R/unaids-navigator.R | 4 --- tests/testthat/test-outputs.R | 4 +-- 3 files changed, 3 insertions(+), 70 deletions(-) diff --git a/R/model.R b/R/model.R index a21d8f6e..7a1a5650 100644 --- a/R/model.R +++ b/R/model.R @@ -570,7 +570,7 @@ naomi_model_frame <- function(area_merged, spec_unaware_untreated_prop_t4 = unaware_untreated_prop, asfr_t4 = asfr, frr_plhiv_t4 = frr_plhiv, - frr_already_art_t4 = frr_already_art + frr_already_art_t4 = frr_already_art ), by = c("spectrum_region_code", "sex", "age_group") ) %>% @@ -881,65 +881,6 @@ select_naomi_data <- function( stopifnot(methods::is(naomi_mf, "naomi_mf")) - ## Check anc_testing and art_number against Spectrum inputs. - ## Return NA if spec_program_data not provided - anc_testing_spectrum_aligned <- NA - art_number_spectrum_aligned <- NA - - if (!is.null(spec_program_data)) { - stopifnot(methods::is(spec_program_data, "spec_program_data")) - - if (!is.null(anc_testing)) { - - anc_merged <- anc_testing %>% - dplyr::left_join( - dplyr::select(naomi_mf$mf_areas, area_id, spectrum_region_code), - by = "area_id" - ) %>% - tidyr::pivot_longer(dplyr::starts_with("anc"), - names_to = "indicator", - values_to = "value_naomi") %>% - dplyr::count(spectrum_region_code, year, indicator, - wt = value_naomi, name = "value_naomi") %>% - dplyr::inner_join( - spec_program_data$anc_testing %>% - dplyr::rename("value_spectrum" = "value"), - by = c("spectrum_region_code", "indicator", "year") - ) - - anc_testing_spectrum_aligned <- all(anc_merged$value_naomi == anc_merged$value_spectrum) - - } else { - ## If no ANC testing data, return TRUE - anc_testing_spectrum_aligned <- TRUE - } - - if (!is.null(art_number)) { - - art_merged <- art_number %>% - dplyr::left_join( - dplyr::select(naomi_mf$mf_areas, area_id, spectrum_region_code), - by = "area_id" - ) %>% - dplyr::count(spectrum_region_code, sex, age_group, calendar_quarter, - wt = art_current, name = "art_current_naomi") %>% - dplyr::inner_join( - spec_program_data$art_dec31 %>% - dplyr::mutate( - calendar_quarter = paste0("CY", year, "Q4"), - year = NULL - ), - by = c("spectrum_region_code", "sex", "age_group", "calendar_quarter") - ) - - art_number_spectrum_aligned <- all(art_merged$art_current_naomi == art_merged$art_dec31) - - } else { - ## If no ANC testing data, return TRUE - art_number_spectrum_aligned <- TRUE - } - } - common_surveys <- intersect(artcov_survey_ids, vls_survey_ids) if (length(common_surveys)) { stop(t_("ART_COV_AND_VLS_SAME_SURVEY", @@ -1101,9 +1042,7 @@ select_naomi_data <- function( artnum_calendar_quarter_t1 = artnum_calendar_quarter_t1, artnum_calendar_quarter_t2 = artnum_calendar_quarter_t2, anc_prev_year_t1 = anc_artcov_year_t1, - anc_prev_year_t2 = anc_artcov_year_t2, - art_number_spectrum_aligned = art_number_spectrum_aligned, - anc_testing_spectrum_aligned = anc_testing_spectrum_aligned) + anc_prev_year_t2 = anc_artcov_year_t2) naomi_mf$data_options <- data_options diff --git a/R/unaids-navigator.R b/R/unaids-navigator.R index dfc4292d..e538d453 100644 --- a/R/unaids-navigator.R +++ b/R/unaids-navigator.R @@ -91,10 +91,6 @@ write_navigator_checklist <- function(naomi_output, if (!is.null(data_options)) { - ## Compare aggregated naomi inputs to national Spectrum totals - v$TrueFalse[v$NaomiCheckPermPrimKey == "ART_is_Spectrum"] <- data_options$art_number_spectrum_aligned - v$TrueFalse[v$NaomiCheckPermPrimKey == "ANC_is_Spectrum"] <- data_options$anc_testing_spectrum_aligned - ## Check that all surveys used are from most recent quarter available most_recent_survey_available <- max(data_options$prev_survey_available_quarters) v$TrueFalse[v$NaomiCheckPermPrimKey == "Opt_recent_survey_only"] <- diff --git a/tests/testthat/test-outputs.R b/tests/testthat/test-outputs.R index 2bcf7ad8..afb75217 100644 --- a/tests/testthat/test-outputs.R +++ b/tests/testthat/test-outputs.R @@ -165,7 +165,7 @@ test_that("subset_output_package() saves expected output package", { ## Test that can **drop** selected indicators (rather than keep) - + sub_drop_file <- tempfile(fileext = ".zip") expect_warning( @@ -328,8 +328,6 @@ test_that("navigator checklist returns expected results", { adj_output$fit$data_options$prev_survey_ids <- "DEMO2020PHIA" adj_output$fit$data_options$prev_survey_quarters <- "CY2020Q3" - adj_output$fit$data_options$art_number_spectrum_aligned <- TRUE - adj_output$fit$data_options$anc_testing_spectrum_aligned <- TRUE adj_output$fit$calibration_options$spectrum_population_calibration <- "subnational" adj_output$fit$calibration_options$spectrum_artnum_calibration_level <- "subnational" From e1de628ad066c3412dbe6ac6b6eb34497b9eb1f2 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 12:48:58 +0200 Subject: [PATCH 06/19] update comparison table output structure and warnings --- R/input-comparison.R | 27 ++++++++---------- R/run-model.R | 4 +-- R/warnings.R | 39 +++++++++++++++++++++++--- tests/testthat/test-input-comparison.R | 2 +- 4 files changed, 49 insertions(+), 23 deletions(-) diff --git a/R/input-comparison.R b/R/input-comparison.R index c5dc1a97..bb30d6c7 100644 --- a/R/input-comparison.R +++ b/R/input-comparison.R @@ -55,10 +55,9 @@ prepare_art_spectrum_comparison <- function(art, shape, pjnz) { spec_aggreagted <- spec |> dplyr::mutate( value_spectrum_adjusted = art_dec31_attend, - value_spectrum_reallocated = art_dec31_reside - art_dec31_attend, - value_spectrum_adj_factor = value_spectrum_adjusted/ (value_spectrum_reported + value_spectrum_reallocated)) |> + value_spectrum_reallocated = art_dec31_reside - art_dec31_attend ) |> dplyr::select(spectrum_region_code, year, age_group, sex, value_spectrum_reported, - value_spectrum_adjusted, value_spectrum_reallocated, value_spectrum_adjusted, value_spectrum_adj_factor) + value_spectrum_adjusted, value_spectrum_reallocated) # Get spectrum level to select correct area names spectrum_region_code <- unique(shape$spectrum_region_code) @@ -78,12 +77,10 @@ prepare_art_spectrum_comparison <- function(art, shape, pjnz) { dplyr::mutate( indicator = "number_on_art", group = dplyr::if_else(age_group == "Y000_014", - "art_children", paste0("art_adult_", sex)), - difference = value_naomi - value_spectrum_adjusted, - prop_difference = 1 - abs((value_naomi - value_spectrum_adjusted) / value_spectrum_adjusted)) |> - dplyr::select(indicator, area_name, year, group, value_naomi, + "art_children", paste0("art_adult_", sex))) |> + dplyr::select(indicator, area_name, year, group, value_spectrum_reported, value_spectrum_adjusted, - value_spectrum_reallocated, value_spectrum_adjusted, value_spectrum_adj_factor) + value_naomi, value_spectrum_reallocated) } ##' Compare aggregated subnational ART inputs + spectrum totals for comparison table @@ -153,13 +150,10 @@ prepare_anc_spectrum_comparison <- function(anc, shape, pjnz) { ##' @export prepare_spectrum_naomi_comparison <- function(art, anc, shape, pjnz){ - null_df <- setNames(data.frame(matrix(ncol = 7, nrow = 0)), - c("indicator", "area_name", "year", "group","value_spectrum", "value_naomi", "difference")) - if(is.null(art) & is.null(anc) ){ # Empty data frame if no programme data - comparison_df <- null_df + comparison_table <- list(art = NULL, anc = NULL) } else { @@ -175,18 +169,19 @@ prepare_spectrum_naomi_comparison <- function(art, anc, shape, pjnz){ if (!is.null(art)) { art_comparison <- prepare_art_spectrum_comparison(art, shape, pjnz) } else { - art_comparison <- null_df + art_comparison <- NULL } # Create ANC comparison or empty data frame if no ART supplied if (!is.null(anc)) { anc_comparison <- prepare_anc_spectrum_comparison(anc, shape, pjnz) } else { - anc_comparison <- null_df + anc_comparison <- NULL } - comparison_df <- rbind(art_comparison, anc_comparison) + comparison_table <- list(art = art_comparison, + anc = anc_comparison) } - comparison_df + comparison_table } diff --git a/R/run-model.R b/R/run-model.R index 05e791c1..f95553b1 100644 --- a/R/run-model.R +++ b/R/run-model.R @@ -324,14 +324,14 @@ naomi_prepare_data <- function(data, options) { if (!is.null(data$art_number)) { art_number <- read_art_number(data$art_number$path) art_spectrum_comparison <- prepare_art_spectrum_comparison(art_number, area_merged, spec_program_data) - programme_data_warning(art_spectrum_comparison) + art_programme_data_warning(art_spectrum_comparison) } else { art_number <- NULL } if (!is.null(data$anc_testing)) { anc_testing <- read_anc_testing(data$anc_testing$path) anc_spectrum_comparison <- prepare_anc_spectrum_comparison(anc_testing, area_merged, spec_program_data) - programme_data_warning(anc_spectrum_comparison) + anc_programme_data_warning(anc_spectrum_comparison) } else { anc_testing <- NULL } diff --git a/R/warnings.R b/R/warnings.R index 76f996c7..f141bb23 100644 --- a/R/warnings.R +++ b/R/warnings.R @@ -76,14 +76,45 @@ output_naomi_warning <- function(naomi_output, ind, threshold, locations) { ##' ##' @param naomi_spectrum_comparison Comparison table of aggregated subnational ##' Naomi and national Spectrum programme data created by -##' prepare_art_spectrum_comparison() or prepare_anc_spectrum_comparison() +##' prepare_art_spectrum_comparison() +##' +##' @keywords internal +art_programme_data_warning <- function(art_naomi_spectrum_comparison) { + + df <- art_naomi_spectrum_comparison |> + dplyr::group_by(year, indicator) |> + dplyr::summarise( + value_naomi = sum(value_naomi), + value_spectrum_adjusted = sum(value_spectrum_adjusted), .groups = "drop") |> + dplyr::mutate(total_diff = value_naomi - value_spectrum_adjusted) |> + dplyr::filter(total_diff > 0) |> + dplyr::group_by(indicator) |> + dplyr::summarise(years = paste0(year, collapse = ";"), .groups = "drop") |> + dplyr::mutate(text = paste(indicator, years, sep = ": ")) + + + if(nrow(df) > 0) { + msg <- t_("WARNING_PROGRAMME_DATA_NOT_EQUAL_TO_SPECTRUM", list(years = paste(df$text, collapse = "\n"))) + naomi_warning(msg, c("model_calibrate", "review_output")) + } + +} + +##' Warning for aggregated subnational data input snot equal to spectrum totals +##' +##' Generate warning if aggregated subnational totals do not match spectrum totals +##' +##' @param naomi_spectrum_comparison Comparison table of aggregated subnational +##' Naomi and national Spectrum programme data created by +##' prepare_art_spectrum_comparison() ##' ##' @keywords internal -programme_data_warning <- function(naomi_spectrum_comparison) { +anc_programme_data_warning <- function(anc_naomi_spectrum_comparison) { - df <- naomi_spectrum_comparison |> + df <- anc_naomi_spectrum_comparison |> dplyr::group_by(year, indicator) |> - dplyr::summarise(total_diff = sum(abs(difference)), .groups = "drop") |> + dplyr::summarise( + total_diff = sum(abs(difference)), .groups = "drop") |> dplyr::filter(total_diff > 0) |> dplyr::group_by(indicator) |> dplyr::summarise(years = paste0(year, collapse = ";"), .groups = "drop") |> diff --git a/tests/testthat/test-input-comparison.R b/tests/testthat/test-input-comparison.R index 37bb2af1..a329667e 100644 --- a/tests/testthat/test-input-comparison.R +++ b/tests/testthat/test-input-comparison.R @@ -63,7 +63,7 @@ test_that("ANC data is properly aggreagted for Spectrum comparison table", { }) -test_that("Comparisoon wrapper function works with missing programme data", { +test_that("Comparison wrapper function works with missing programme data", { # Test wrapper function with all programme data supplied shape <- a_hintr_data$shape From bdd332a6334f6aebefbec1b1f5f4b663f5190662 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 13:45:20 +0200 Subject: [PATCH 07/19] Assign adjusted ART value from Spectrum to "art_dec31" used in model fit --- R/inputs-spectrum.R | 3 ++- man/anc_programme_data_warning.Rd | 17 +++++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 man/anc_programme_data_warning.Rd diff --git a/R/inputs-spectrum.R b/R/inputs-spectrum.R index fa5b4d00..01635777 100644 --- a/R/inputs-spectrum.R +++ b/R/inputs-spectrum.R @@ -377,7 +377,8 @@ read_dp_art_dec31 <- function(dp) { art_dec31_reside = child_art_reside) art_dec31 <- rbind(child_art, art15plus) |> - dplyr::mutate(dplyr::across(where(is.numeric), ~ round(., 0))) + dplyr::mutate(dplyr::across(where(is.numeric), ~ round(., 0)), + art_dec31 = art_dec31_attend) art_dec31 } diff --git a/man/anc_programme_data_warning.Rd b/man/anc_programme_data_warning.Rd new file mode 100644 index 00000000..f52efa0b --- /dev/null +++ b/man/anc_programme_data_warning.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/warnings.R +\name{anc_programme_data_warning} +\alias{anc_programme_data_warning} +\title{Warning for aggregated subnational data input snot equal to spectrum totals} +\usage{ +anc_programme_data_warning(anc_naomi_spectrum_comparison) +} +\arguments{ +\item{naomi_spectrum_comparison}{Comparison table of aggregated subnational +Naomi and national Spectrum programme data created by +prepare_art_spectrum_comparison()} +} +\description{ +Generate warning if aggregated subnational totals do not match spectrum totals +} +\keyword{internal} From 044a6d31e4da6f98e48e68f4c07cf52386b735c4 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 13:45:29 +0200 Subject: [PATCH 08/19] update warnings --- ...amme_data_warning.Rd => art_programme_data_warning.Rd} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename man/{programme_data_warning.Rd => art_programme_data_warning.Rd} (70%) diff --git a/man/programme_data_warning.Rd b/man/art_programme_data_warning.Rd similarity index 70% rename from man/programme_data_warning.Rd rename to man/art_programme_data_warning.Rd index d0f71c3c..8a9be428 100644 --- a/man/programme_data_warning.Rd +++ b/man/art_programme_data_warning.Rd @@ -1,15 +1,15 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/warnings.R -\name{programme_data_warning} -\alias{programme_data_warning} +\name{art_programme_data_warning} +\alias{art_programme_data_warning} \title{Warning for aggregated subnational data input snot equal to spectrum totals} \usage{ -programme_data_warning(naomi_spectrum_comparison) +art_programme_data_warning(art_naomi_spectrum_comparison) } \arguments{ \item{naomi_spectrum_comparison}{Comparison table of aggregated subnational Naomi and national Spectrum programme data created by -prepare_art_spectrum_comparison() or prepare_anc_spectrum_comparison()} +prepare_art_spectrum_comparison()} } \description{ Generate warning if aggregated subnational totals do not match spectrum totals From c7cc5f0de43c0905cc2c2b5023718016e9f36c24 Mon Sep 17 00:00:00 2001 From: Rob Ashton Date: Wed, 11 Dec 2024 13:40:40 +0000 Subject: [PATCH 09/19] Remove difference, calculate this in the front end --- R/input-comparison.R | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/R/input-comparison.R b/R/input-comparison.R index bb30d6c7..c7645cc0 100644 --- a/R/input-comparison.R +++ b/R/input-comparison.R @@ -134,10 +134,9 @@ prepare_anc_spectrum_comparison <- function(anc, shape, pjnz) { dat |> dplyr::mutate( sex = "female", age_group = "Y015_049", - group = "anc_adult_female", - difference = value_spectrum - value_naomi) |> + group = "anc_adult_female") dplyr::select(indicator, area_name, year, group, - value_spectrum, value_naomi, difference) + value_spectrum, value_naomi) } From 16b38d6bdb4326a8a6f47ec2785803b28977ccc8 Mon Sep 17 00:00:00 2001 From: Rob Ashton Date: Wed, 11 Dec 2024 13:46:21 +0000 Subject: [PATCH 10/19] Add back deleted pipe --- R/input-comparison.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/input-comparison.R b/R/input-comparison.R index c7645cc0..50b49804 100644 --- a/R/input-comparison.R +++ b/R/input-comparison.R @@ -134,7 +134,7 @@ prepare_anc_spectrum_comparison <- function(anc, shape, pjnz) { dat |> dplyr::mutate( sex = "female", age_group = "Y015_049", - group = "anc_adult_female") + group = "anc_adult_female") |> dplyr::select(indicator, area_name, year, group, value_spectrum, value_naomi) From e4e4152649d3d18f117ee2706c2f4cfe81e2194e Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 16:41:09 +0200 Subject: [PATCH 11/19] fix anc programme warning --- R/warnings.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/warnings.R b/R/warnings.R index f141bb23..4ef1ffc7 100644 --- a/R/warnings.R +++ b/R/warnings.R @@ -113,6 +113,7 @@ anc_programme_data_warning <- function(anc_naomi_spectrum_comparison) { df <- anc_naomi_spectrum_comparison |> dplyr::group_by(year, indicator) |> + dplyr::mutate(difference = value_naomi - value_spectrum) |> dplyr::summarise( total_diff = sum(abs(difference)), .groups = "drop") |> dplyr::filter(total_diff > 0) |> From b0e60e4d7b7704767aa1e825519884b719342a3d Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 16:41:27 +0200 Subject: [PATCH 12/19] remove remaining navigator code --- R/unaids-navigator.R | 8 ++------ tests/testthat/test-outputs.R | 4 ++-- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/R/unaids-navigator.R b/R/unaids-navigator.R index e538d453..171fe1e2 100644 --- a/R/unaids-navigator.R +++ b/R/unaids-navigator.R @@ -14,9 +14,7 @@ write_navigator_checklist <- function(naomi_output, path <- paste0(path, ".csv") } - key <- c("ART_is_Spectrum", - "ANC_is_Spectrum", - "Package_created", + key <- c("Package_created", "Package_has_all_data", "Opt_recent_qtr", "Opt_future_proj_qtr", @@ -35,9 +33,7 @@ write_navigator_checklist <- function(naomi_output, "Cal_new_infections", "Cal_method") - label <- c(t_("NAVIGATOR_ART_IS_SPECTRUM_DESC"), - t_("NAVIGATOR_ANC_IS_SPECTRUM_DESC"), - t_("NAVIGATOR_PACKAGE_CREATED_DESC"), + label <- c(t_("NAVIGATOR_PACKAGE_CREATED_DESC"), t_("NAVIGATOR_PACKAGE_HAS_ALL_DATA_DESC"), t_("NAVIGATOR_OPT_RECENT_QTR_DESC"), t_("NAVIGATOR_OPT_FUTURE_PROJ_QTR_DESC"), diff --git a/tests/testthat/test-outputs.R b/tests/testthat/test-outputs.R index afb75217..8205d9d2 100644 --- a/tests/testthat/test-outputs.R +++ b/tests/testthat/test-outputs.R @@ -290,8 +290,8 @@ test_that("navigator checklist returns expected results", { model_output <- read_hintr_output(a_hintr_output_calibrated$model_output_path) - expected_checklist <- c("ART_is_Spectrum" = FALSE, - "ANC_is_Spectrum" = FALSE, + expected_checklist <- c("ART_is_Spectrum" = NA, + "ANC_is_Spectrum" = NA, "Package_created" = TRUE, "Package_has_all_data" = TRUE, "Opt_recent_qtr" = FALSE, From 5c7ec602831985e49f1739282664f5981793bfde Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 16:41:56 +0200 Subject: [PATCH 13/19] fix navigator tests --- tests/testthat/test-outputs.R | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/tests/testthat/test-outputs.R b/tests/testthat/test-outputs.R index 8205d9d2..2cb310fe 100644 --- a/tests/testthat/test-outputs.R +++ b/tests/testthat/test-outputs.R @@ -353,9 +353,7 @@ test_that("navigator checklist returns results if options lists missing", { no_data_opts_output$fit$data_options <- NULL - expect_chklst_no_data_opts<- c("ART_is_Spectrum" = NA, - "ANC_is_Spectrum" = NA, - "Package_created" = TRUE, + expect_chklst_no_data_opts<- c("Package_created" = TRUE, "Package_has_all_data" = TRUE, "Opt_recent_qtr" = FALSE, "Opt_future_proj_qtr" = FALSE, @@ -387,9 +385,7 @@ test_that("navigator checklist returns results if options lists missing", { no_model_opts_output$fit$model_options <- NULL - expect_chklst_no_model_opts <- c("ART_is_Spectrum" = FALSE, - "ANC_is_Spectrum" = FALSE, - "Package_created" = TRUE, + expect_chklst_no_model_opts <- c("Package_created" = TRUE, "Package_has_all_data" = TRUE, "Opt_recent_qtr" = NA, "Opt_future_proj_qtr" = NA, @@ -421,9 +417,7 @@ test_that("navigator checklist returns results if options lists missing", { no_calib_opts_output$fit$calibration_options <- NULL - expect_chklst_no_calib_opts <- c("ART_is_Spectrum" = FALSE, - "ANC_is_Spectrum" = FALSE, - "Package_created" = TRUE, + expect_chklst_no_calib_opts <- c( "Package_created" = TRUE, "Package_has_all_data" = TRUE, "Opt_recent_qtr" = FALSE, "Opt_future_proj_qtr" = FALSE, @@ -567,7 +561,7 @@ test_that("one input and output for each area_id/age/sex/indicator/period combin dups <- inputs_outputs %>% dplyr::group_by(area_id, sex, age_group, calendar_quarter, indicator) %>% - dplyr::summarise(n = dplyr::n()) %>% + dplyr::summarise(n = dplyr::n(), .groups = "drop") %>% dplyr::filter(indicator != "prevalence", n != 2) expect_equal(nrow(dups), 0) From 6adbfbccf128f111e600b352f5b17134b18e02d1 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 17:31:11 +0200 Subject: [PATCH 14/19] fix failing tests --- tests/testthat/test-01-run-model.R | 2 +- tests/testthat/test-downloads.R | 6 ++---- tests/testthat/test-warning.R | 2 +- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/tests/testthat/test-01-run-model.R b/tests/testthat/test-01-run-model.R index 3a2229ff..11910edc 100644 --- a/tests/testthat/test-01-run-model.R +++ b/tests/testthat/test-01-run-model.R @@ -205,7 +205,7 @@ test_that("exceeding max_iterations raises convergence warning", { expect_length(out$warnings, 3) expect_equal(out$warnings[[1]]$text, - paste0("Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2011;2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023")) + paste0("Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2019;2021;2022;2023")) expect_equal(out$warnings[[3]]$text, paste0("Convergence error: iteration limit reached without convergence (10)")) diff --git a/tests/testthat/test-downloads.R b/tests/testthat/test-downloads.R index 0849cdd2..2b774264 100644 --- a/tests/testthat/test-downloads.R +++ b/tests/testthat/test-downloads.R @@ -27,8 +27,7 @@ test_that("spectrum download can be created", { expect_equal(names(navigator_checklist), c("NaomiCheckPermPrimKey", "NaomiCheckDes", "TrueFalse")) - checklist_primkeys <- c( "ART_is_Spectrum","ANC_is_Spectrum","Package_created", - "Package_has_all_data","Opt_recent_qtr","Opt_future_proj_qtr", + checklist_primkeys <- c( "Package_created", "Package_has_all_data","Opt_recent_qtr","Opt_future_proj_qtr", "Opt_area_ID_selected","Opt_calendar_survey_match","Opt_recent_survey_only", "Opt_ART_coverage","Opt_ANC_data","Opt_ART_data", "Opt_ART_attendance_yes","Model_fit","Cal_Population", @@ -257,8 +256,7 @@ test_that("spectrum download can be created", { expect_equal(names(navigator_checklist), c("NaomiCheckPermPrimKey", "NaomiCheckDes", "TrueFalse")) - checklist_primkeys <- c( "ART_is_Spectrum","ANC_is_Spectrum","Package_created", - "Package_has_all_data","Opt_recent_qtr","Opt_future_proj_qtr", + checklist_primkeys <- c( "Package_has_all_data","Opt_recent_qtr","Opt_future_proj_qtr", "Opt_area_ID_selected","Opt_calendar_survey_match","Opt_recent_survey_only", "Opt_ART_coverage","Opt_ANC_data","Opt_ART_data", "Opt_ART_attendance_yes","Model_fit","Cal_Population", diff --git a/tests/testthat/test-warning.R b/tests/testthat/test-warning.R index 6ef9ebd4..d3306dfc 100644 --- a/tests/testthat/test-warning.R +++ b/tests/testthat/test-warning.R @@ -61,7 +61,7 @@ test_that("warning raised after false convergence", { expect_length(out$warnings, 3) expect_match(out$warnings[[1]]$text, - "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2011;2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023") + "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2019;2021;2022;2023") expect_match(out$warnings[[2]]$text, "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nanc_already_art: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_clients: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_known_neg: 2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_known_pos: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_tested: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023") expect_equal(out$warnings[[3]]$text, From 6fcb1cb0f5c65ebdf8c238216a9456222861af7d Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 17:43:40 +0200 Subject: [PATCH 15/19] fix failing spectrum test --- tests/testthat/test-spectrum.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/testthat/test-spectrum.R b/tests/testthat/test-spectrum.R index 30a3c0ab..bcdb9e6b 100644 --- a/tests/testthat/test-spectrum.R +++ b/tests/testthat/test-spectrum.R @@ -206,7 +206,8 @@ test_that("ART adjustments properly extracted from Spectrum", { # Test ART adjustments correctly read from test file with expect_equal(colnames(spec_art), c("sex", "age_group", "year", - "art_dec31_reported", "art_dec31_attend","art_dec31_reside")) + "art_dec31_reported", "art_dec31_attend", + "art_dec31_reside", "art_dec31")) # Adults expect_setequal(spec_art[166,], c("male", "Y015_999", "2022", "450799", "387903", "377903")) expect_setequal(spec_art[167,], c("female", "Y015_999", "2022", "857994", "719095", "707095")) @@ -214,3 +215,4 @@ test_that("ART adjustments properly extracted from Spectrum", { expect_setequal(spec_art[52,], c("both", "Y000_014", "2021", "59853", "49368", "44368")) }) + From 130a99469bcca2f368bf9c4346c7a188081fbbfe Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 18:40:59 +0200 Subject: [PATCH 16/19] update (more) failing tests --- R/warnings.R | 22 ++++++++++++++++++---- tests/testthat/test-input-comparison.R | 24 ++++++++++++++++-------- tests/testthat/test-warning.R | 10 +++++----- 3 files changed, 39 insertions(+), 17 deletions(-) diff --git a/R/warnings.R b/R/warnings.R index 4ef1ffc7..d69a6f30 100644 --- a/R/warnings.R +++ b/R/warnings.R @@ -87,7 +87,7 @@ art_programme_data_warning <- function(art_naomi_spectrum_comparison) { value_naomi = sum(value_naomi), value_spectrum_adjusted = sum(value_spectrum_adjusted), .groups = "drop") |> dplyr::mutate(total_diff = value_naomi - value_spectrum_adjusted) |> - dplyr::filter(total_diff > 0) |> + dplyr::filter(abs(total_diff) > 0) |> dplyr::group_by(indicator) |> dplyr::summarise(years = paste0(year, collapse = ";"), .groups = "drop") |> dplyr::mutate(text = paste(indicator, years, sep = ": ")) @@ -134,13 +134,27 @@ anc_programme_data_warning <- function(anc_naomi_spectrum_comparison) { ##' This can throw validation errors or warnings which will be shown to user ##' in naomi web app ##' -##' @param naomi_spectrum_comparison Comparison table of aggregated subnational +##' @param art_naomi_spectrum_comparison Comparison table of aggregated subnational +##' Naomi and national Spectrum programme data created by +##' prepare_art_spectrum_comparison() or prepare_anc_spectrum_comparison() +##' +##' @export +hintr_validate_art_programme_data <- function(art_naomi_spectrum_comparison) { + handle_naomi_warnings(art_programme_data_warning(art_naomi_spectrum_comparison)) +} + +##' Run validation for subnational programme data input +##' +##' This can throw validation errors or warnings which will be shown to user +##' in naomi web app +##' +##' @param anc_naomi_spectrum_comparison Comparison table of aggregated subnational ##' Naomi and national Spectrum programme data created by ##' prepare_art_spectrum_comparison() or prepare_anc_spectrum_comparison() ##' ##' @export -hintr_validate_programme_data <- function(naomi_spectrum_comparison) { - handle_naomi_warnings(programme_data_warning(naomi_spectrum_comparison)) +hintr_validate_anc_programme_data <- function(anc_naomi_spectrum_comparison) { + handle_naomi_warnings(anc_programme_data_warning(anc_naomi_spectrum_comparison)) } diff --git a/tests/testthat/test-input-comparison.R b/tests/testthat/test-input-comparison.R index a329667e..d0df4386 100644 --- a/tests/testthat/test-input-comparison.R +++ b/tests/testthat/test-input-comparison.R @@ -73,18 +73,23 @@ test_that("Comparison wrapper function works with missing programme data", { x <- prepare_spectrum_naomi_comparison(art, anc, shape, pjnz) - expect_equal(unique(x$indicator), c("number_on_art", "anc_already_art", "anc_clients", - "anc_known_neg", "anc_known_pos", "anc_tested" , "anc_tested_pos")) - expect_equal(unique(x$group), c("art_children", "art_adult_both", "anc_adult_female")) + expect_equal(unique(x$art$indicator), c("number_on_art")) + expect_equal(unique(x$anc$indicator), c("anc_already_art", "anc_clients", + "anc_known_neg", "anc_known_pos", + "anc_tested" , "anc_tested_pos")) + expect_equal(unique(x$art$group), c("art_children", "art_adult_both")) + expect_equal(unique(x$anc$group), c("anc_adult_female")) # Test wrapper function with no ART art <- NULL x <- prepare_spectrum_naomi_comparison(art, anc, shape, pjnz) - expect_equal(unique(x$indicator), c("anc_already_art", "anc_clients", "anc_known_neg", + expect_equal(x$art, NULL) + + expect_equal(unique(x$anc$indicator), c("anc_already_art", "anc_clients", "anc_known_neg", "anc_known_pos", "anc_tested" , "anc_tested_pos")) - expect_equal(unique(x$group), c("anc_adult_female")) + expect_equal(unique(x$anc$group), c("anc_adult_female")) # Test wrapper function with no ANC art <- a_hintr_data$art_number @@ -92,14 +97,17 @@ test_that("Comparison wrapper function works with missing programme data", { x <- prepare_spectrum_naomi_comparison(art, anc, shape, pjnz) - expect_equal(unique(x$indicator), c("number_on_art")) - expect_equal(unique(x$group), c("art_children", "art_adult_both")) + expect_equal(x$anc, NULL) + + expect_equal(unique(x$art$indicator), c("number_on_art")) + expect_equal(unique(x$art$group), c("art_children", "art_adult_both")) # Test wrapper function with no programme data art <- NULL x <- prepare_spectrum_naomi_comparison(art, anc, shape, pjnz) - expect_equal(nrow(x), 0) + expect_equal(x$art, NULL) + expect_equal(x$anc, NULL) }) diff --git a/tests/testthat/test-warning.R b/tests/testthat/test-warning.R index d3306dfc..2692df5a 100644 --- a/tests/testthat/test-warning.R +++ b/tests/testthat/test-warning.R @@ -61,7 +61,7 @@ test_that("warning raised after false convergence", { expect_length(out$warnings, 3) expect_match(out$warnings[[1]]$text, - "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2019;2021;2022;2023") + "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2011;2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023") expect_match(out$warnings[[2]]$text, "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nanc_already_art: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_clients: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_known_neg: 2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_known_pos: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_tested: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023") expect_equal(out$warnings[[3]]$text, @@ -130,8 +130,8 @@ test_that("ART warning raised if spectrum totals do not match naomi data", { ) # National warnings for national pjnz file - spec_comparison <- prepare_art_spectrum_comparison(data$art_number, data$shape, data$pjnz) - art <- hintr_validate_programme_data(spec_comparison) + art_spec_comparison <- prepare_art_spectrum_comparison(data$art_number, data$shape, data$pjnz) + art <- hintr_validate_art_programme_data(art_spec_comparison) expect_length(art$warnings, 1) expect_equal(art$warnings[[1]]$locations, @@ -151,8 +151,8 @@ test_that("ANC warning raised if spectrum totals do not match naomi data", { ) # National warnings for national pjnz file - spec_comparison <- prepare_anc_spectrum_comparison(data$anc_testing, data$shape, data$pjnz) - anc <- hintr_validate_programme_data(spec_comparison) + anc_spec_comparison <- prepare_anc_spectrum_comparison(data$anc_testing, data$shape, data$pjnz) + anc <- hintr_validate_anc_programme_data(anc_spec_comparison) expect_length(anc$warnings, 1) expect_equal(anc$warnings[[1]]$locations, From e2f820301c0f62f1ac383725cf3eabe40741b467 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 18:47:10 +0200 Subject: [PATCH 17/19] update roxygen docs --- NAMESPACE | 3 ++- ....Rd => hintr_validate_anc_programme_data.Rd} | 8 ++++---- man/hintr_validate_art_programme_data.Rd | 17 +++++++++++++++++ 3 files changed, 23 insertions(+), 5 deletions(-) rename man/{hintr_validate_programme_data.Rd => hintr_validate_anc_programme_data.Rd} (63%) create mode 100644 man/hintr_validate_art_programme_data.Rd diff --git a/NAMESPACE b/NAMESPACE index a5e29c55..02abd71e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -54,7 +54,8 @@ export(hintr_prepare_datapack_download) export(hintr_prepare_spectrum_download) export(hintr_prepare_summary_report_download) export(hintr_run_model) -export(hintr_validate_programme_data) +export(hintr_validate_anc_programme_data) +export(hintr_validate_art_programme_data) export(interpolate_population_agesex) export(log_linear_interp) export(map_outputs) diff --git a/man/hintr_validate_programme_data.Rd b/man/hintr_validate_anc_programme_data.Rd similarity index 63% rename from man/hintr_validate_programme_data.Rd rename to man/hintr_validate_anc_programme_data.Rd index bf3a1c3b..f5153437 100644 --- a/man/hintr_validate_programme_data.Rd +++ b/man/hintr_validate_anc_programme_data.Rd @@ -1,13 +1,13 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/warnings.R -\name{hintr_validate_programme_data} -\alias{hintr_validate_programme_data} +\name{hintr_validate_anc_programme_data} +\alias{hintr_validate_anc_programme_data} \title{Run validation for subnational programme data input} \usage{ -hintr_validate_programme_data(naomi_spectrum_comparison) +hintr_validate_anc_programme_data(anc_naomi_spectrum_comparison) } \arguments{ -\item{naomi_spectrum_comparison}{Comparison table of aggregated subnational +\item{anc_naomi_spectrum_comparison}{Comparison table of aggregated subnational Naomi and national Spectrum programme data created by prepare_art_spectrum_comparison() or prepare_anc_spectrum_comparison()} } diff --git a/man/hintr_validate_art_programme_data.Rd b/man/hintr_validate_art_programme_data.Rd new file mode 100644 index 00000000..983612d9 --- /dev/null +++ b/man/hintr_validate_art_programme_data.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/warnings.R +\name{hintr_validate_art_programme_data} +\alias{hintr_validate_art_programme_data} +\title{Run validation for subnational programme data input} +\usage{ +hintr_validate_art_programme_data(art_naomi_spectrum_comparison) +} +\arguments{ +\item{art_naomi_spectrum_comparison}{Comparison table of aggregated subnational +Naomi and national Spectrum programme data created by +prepare_art_spectrum_comparison() or prepare_anc_spectrum_comparison()} +} +\description{ +This can throw validation errors or warnings which will be shown to user +in naomi web app +} From f92bd306a5e4f43fae1fdf8040dcaf3389e8f574 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Wed, 11 Dec 2024 23:05:40 +0200 Subject: [PATCH 18/19] fix (one more) failing test --- tests/testthat/test-01-run-model.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-01-run-model.R b/tests/testthat/test-01-run-model.R index 11910edc..3a2229ff 100644 --- a/tests/testthat/test-01-run-model.R +++ b/tests/testthat/test-01-run-model.R @@ -205,7 +205,7 @@ test_that("exceeding max_iterations raises convergence warning", { expect_length(out$warnings, 3) expect_equal(out$warnings[[1]]$text, - paste0("Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2019;2021;2022;2023")) + paste0("Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2011;2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023")) expect_equal(out$warnings[[3]]$text, paste0("Convergence error: iteration limit reached without convergence (10)")) From 9bffe8f1aa78d637e37ca131d95ff7613c599350 Mon Sep 17 00:00:00 2001 From: Rob Ashton Date: Wed, 11 Dec 2024 21:14:48 +0000 Subject: [PATCH 19/19] Remove failing navigator checklist test --- tests/testthat/test-downloads.R | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/tests/testthat/test-downloads.R b/tests/testthat/test-downloads.R index 2b774264..1e9f94c8 100644 --- a/tests/testthat/test-downloads.R +++ b/tests/testthat/test-downloads.R @@ -248,26 +248,6 @@ test_that("spectrum download can be created", { expect_equal(dir(tmp), "info") expect_equal(dir(file.path(tmp, "info")), names(info)) - - ## # UNAIDS Navigator Checklist checks - navigator_checklist <- utils::read.csv(unz(out$path, "info/unaids_navigator_checklist.csv")) - - - expect_equal(names(navigator_checklist), - c("NaomiCheckPermPrimKey", "NaomiCheckDes", "TrueFalse")) - - checklist_primkeys <- c( "Package_has_all_data","Opt_recent_qtr","Opt_future_proj_qtr", - "Opt_area_ID_selected","Opt_calendar_survey_match","Opt_recent_survey_only", - "Opt_ART_coverage","Opt_ANC_data","Opt_ART_data", - "Opt_ART_attendance_yes","Model_fit","Cal_Population", - "Cal_PLHIV","Cal_ART","Cal_KOS", - "Cal_new_infections","Cal_method" ) - expect_equal(navigator_checklist$NaomiCheckPermPrimKey, checklist_primkeys) - expect_true(all(navigator_checklist$TrueFalse %in% c(TRUE, FALSE))) - ## Check tradiure translation hooks worked - expect_true("Calibration - method is logistic" %in% navigator_checklist$NaomiCheckDes) - - outputs <- read_output_package(out$path) expect_true( all(c("area_level", "area_level_label", "area_id", "area_name", "parent_area_id",