Fix wrong data passed to non-parameteric bootstrap

nextpagesoft · Mar 26, 2023 · db7b3e1 · db7b3e1
1 parent 3f5cd0e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,9 @@
 ## 3.0.0
 
-###### _March 20 2023_
+###### _March 26 2023_
 
--  Set constraints and step in delta4Fac input
+- Set constraints and step in delta4Fac input
+- Fix wrong case-based data (non-bootstrap specific) passed to modelling
 
 
 ## 3.0.0

diff --git a/Client/package.json b/Client/package.json
@@ -28,10 +28,10 @@
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@mui/icons-material": "^5.11.11",
-    "@mui/lab": "5.0.0-alpha.123",
-    "@mui/material": "^5.11.13",
-    "@mui/system": "^5.11.13",
-    "echarts": "^5.4.1",
+    "@mui/lab": "5.0.0-alpha.124",
+    "@mui/material": "^5.11.14",
+    "@mui/system": "^5.11.14",
+    "echarts": "^5.4.2",
     "echarts-for-react": "^3.0.2",
     "file-saver": "^2.0.5",
     "jquery": "^3.6.4",
@@ -56,7 +56,7 @@
     "filemanager-webpack-plugin": "^8.0.0",
     "html-webpack-plugin": "^5.5.0",
     "terser-webpack-plugin": "^5.3.7",
-    "webpack": "^5.76.2",
+    "webpack": "^5.76.3",
     "webpack-bundle-analyzer": "^4.8.0",
     "webpack-cli": "^5.0.1",
     "webpack-dev-server": "^4.13.1",

diff --git a/Client/yarn.lock b/Client/yarn.lock
@@ -2239,9 +2239,9 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@mui/base@npm:5.0.0-alpha.121":
-  version: 5.0.0-alpha.121
-  resolution: "@mui/base@npm:5.0.0-alpha.121"
+"@mui/base@npm:5.0.0-alpha.122":
+  version: 5.0.0-alpha.122
+  resolution: "@mui/base@npm:5.0.0-alpha.122"
   dependencies:
     "@babel/runtime": ^7.21.0
     "@emotion/is-prop-valid": ^1.2.0
@@ -2258,14 +2258,14 @@ __metadata:
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+  checksum: 6d229f6f736074a41e0cf787cc5ef98eba23a52044d7edf22fcc42f03250275fd1b4bb4a7ab47fc1f1aec06bf777bde5474229cc381e515eefee8876f2d8cd5c
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-"@mui/core-downloads-tracker@npm:^5.11.13":
-  version: 5.11.13
-  resolution: "@mui/core-downloads-tracker@npm:5.11.13"
-  checksum: b8a32c9fc4beac4b596afe5fd3d2aecc2449e59d9e58a7ae6fbe528249fa6eabff3abf9195233eb7a46d523d6f1dc5c4ae95e1a69c287182c81311508c07c2c6
+"@mui/core-downloads-tracker@npm:^5.11.14":
+  version: 5.11.14
+  resolution: "@mui/core-downloads-tracker@npm:5.11.14"
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@@ -2285,13 +2285,13 @@ __metadata:
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   linkType: hard
 
-"@mui/lab@npm:5.0.0-alpha.123":
-  version: 5.0.0-alpha.123
-  resolution: "@mui/lab@npm:5.0.0-alpha.123"
+"@mui/lab@npm:5.0.0-alpha.124":
+  version: 5.0.0-alpha.124
+  resolution: "@mui/lab@npm:5.0.0-alpha.124"
   dependencies:
     "@babel/runtime": ^7.21.0
-    "@mui/base": 5.0.0-alpha.121
-    "@mui/system": ^5.11.13
+    "@mui/base": 5.0.0-alpha.122
+    "@mui/system": ^5.11.14
     "@mui/types": ^7.2.3
     "@mui/utils": ^5.11.13
     clsx: ^1.2.1
@@ -2311,18 +2311,18 @@ __metadata:
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     "@types/react":
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+  checksum: bc96ada0f2eec0bdb1ed0aa0ad03e7d8c41f50f3c0869114e5c21c4b428a7a1de476e6858b6d1d308cc70a587fd802b81fd2b6e890c5d9debdc6983ae5ff516e
   languageName: node
   linkType: hard
 
-"@mui/material@npm:^5.11.13":
-  version: 5.11.13
-  resolution: "@mui/material@npm:5.11.13"
+"@mui/material@npm:^5.11.14":
+  version: 5.11.14
+  resolution: "@mui/material@npm:5.11.14"
   dependencies:
     "@babel/runtime": ^7.21.0
-    "@mui/base": 5.0.0-alpha.121
-    "@mui/core-downloads-tracker": ^5.11.13
-    "@mui/system": ^5.11.13
+    "@mui/base": 5.0.0-alpha.122
+    "@mui/core-downloads-tracker": ^5.11.14
+    "@mui/system": ^5.11.14
     "@mui/types": ^7.2.3
     "@mui/utils": ^5.11.13
     "@types/react-transition-group": ^4.4.5
@@ -2344,7 +2344,7 @@ __metadata:
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     "@types/react":
       optional: true
-  checksum: 008e7e79bff7f193724c80308c9751151fc61dcaa76ce8f96d11473280ec6d78f61c9bdb8d23f0869e78b9359aa0bdd5164953d57a4e2f7160280f5d2a6b0b2d
+  checksum: 48fdd56ee55da6d551b8b716b8a080afe2276a62e0441efdd58be3b10ab1204d196a8ecc5f35ac23b8e9c7f5d6884ce37966cdcf8846771fe8ccc5ca626a8e1e
   languageName: node
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@@ -2386,9 +2386,9 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@mui/system@npm:^5.11.13":
-  version: 5.11.13
-  resolution: "@mui/system@npm:5.11.13"
+"@mui/system@npm:^5.11.14":
+  version: 5.11.14
+  resolution: "@mui/system@npm:5.11.14"
   dependencies:
     "@babel/runtime": ^7.21.0
     "@mui/private-theming": ^5.11.13
@@ -2410,7 +2410,7 @@ __metadata:
       optional: true
     "@types/react":
       optional: true
-  checksum: e6f1852ecf3dc901645c096f650950b858f5a5e53fc72ca68a7565e844d0841681c79402c3b63100574d1863b3af88d84b832bc680e8dae3a4a2147c7c9aee0f
+  checksum: a9df588ee7358438244ba5115f1f3bfe548b4c9077280204b6f6d4b98f20fd93f76bc36bf1430848b64e5c3a495ecb0e5000379932faa3dfb92360a34262f301
   languageName: node
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@@ -4192,13 +4192,13 @@ __metadata:
   languageName: node
   linkType: hard
 
-"echarts@npm:^5.4.1":
-  version: 5.4.1
-  resolution: "echarts@npm:5.4.1"
+"echarts@npm:^5.4.2":
+  version: 5.4.2
+  resolution: "echarts@npm:5.4.2"
   dependencies:
     tslib: 2.3.0
-    zrender: 5.4.1
-  checksum: 2868541087045d27691e99950a96896da48be2c758cb9cd6ab57244bfa40967edecc5a215e02f63a48fa9d56aa1dc91c8339982fdb8d2b1323b19852e91d9fa8
+    zrender: 5.4.3
+  checksum: 933c28dada362314f7c7a5fd4243b44b24f75adb233f7c87541ac9a81734cb380a9683c3f56c8e559dacfddd363879e95a96f0047e33820123cd8f5b95b60f8f
   languageName: node
   linkType: hard
 
@@ -4895,14 +4895,14 @@ fsevents@~2.3.2:
     "@emotion/react": ^11.10.6
     "@emotion/styled": ^11.10.6
     "@mui/icons-material": ^5.11.11
-    "@mui/lab": 5.0.0-alpha.123
-    "@mui/material": ^5.11.13
-    "@mui/system": ^5.11.13
+    "@mui/lab": 5.0.0-alpha.124
+    "@mui/material": ^5.11.14
+    "@mui/system": ^5.11.14
     "@types/webpack-merge": ^5.0.0
     babel-loader: ^9.1.2
     clean-webpack-plugin: ^4.0.0
     cross-env: ^7.0.3
-    echarts: ^5.4.1
+    echarts: ^5.4.2
     echarts-for-react: ^3.0.2
     file-loader: ^6.2.0
     file-saver: ^2.0.5
@@ -4917,7 +4917,7 @@ fsevents@~2.3.2:
     serializr: ^3.0.2
     terser-webpack-plugin: ^5.3.7
     tslib: ^2.5.0
-    webpack: ^5.76.2
+    webpack: ^5.76.3
     webpack-bundle-analyzer: ^4.8.0
     webpack-cli: ^5.0.1
     webpack-dev-server: ^4.13.1
@@ -7804,9 +7804,9 @@ resolve@^1.14.2:
   languageName: node
   linkType: hard
 
-"webpack@npm:^5.76.2":
-  version: 5.76.2
-  resolution: "webpack@npm:5.76.2"
+"webpack@npm:^5.76.3":
+  version: 5.76.3
+  resolution: "webpack@npm:5.76.3"
   dependencies:
     "@types/eslint-scope": ^3.7.3
     "@types/estree": ^0.0.51
@@ -7837,7 +7837,7 @@ resolve@^1.14.2:
       optional: true
   bin:
     webpack: bin/webpack.js
-  checksum: 86db98299a175c371031449c26077e87b33acd8f45de7f7945ed4b9b37c8ca11bc5169af9c44743efccd4d55e08042a3aa3a3bc42aff831309a0821ffbcd395e
+  checksum: 363f536b56971d056e34ab4cffa4cbc630b220e51be1a8c3adea87d9f0b51c49cfc7c3720d6614a1fd2c8c63f1ab3100db916fe8367c8bb9299327ff8c3f856d
   languageName: node
   linkType: hard
 
@@ -7962,11 +7962,11 @@ resolve@^1.14.2:
   languageName: node
   linkType: hard
 
-"zrender@npm:5.4.1":
-  version: 5.4.1
-  resolution: "zrender@npm:5.4.1"
+"zrender@npm:5.4.3":
+  version: 5.4.3
+  resolution: "zrender@npm:5.4.3"
   dependencies:
     tslib: 2.3.0
-  checksum: 9a50cc2cc42ef44a436cfca5a29d6378b92790f50755b4d54f513a55dc7dab9698cecbc5640d731b380ad282aab1c33ae8cc1d14b61c0d51f0e951085a1bf17c
+  checksum: ae89584fbe4256217e500a74183fd5870a2bed7e7b3234cd78fcbc0a1a82da8449596b2019105927069531b567ecf94425fb171abd6cedcbf517e52fdf438722
   languageName: node
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diff --git a/Server/DESCRIPTION b/Server/DESCRIPTION
@@ -2,7 +2,7 @@ Package: hivPlatform
 Type: Package
 Title: HIV Platform
 Version: 3.0.0
-Date: 2023-03-20
+Date: 2023-03-26
 Authors@R: c(person('Magdalena', 'Rosinska', email = '[email protected]',
     role = c('aut', 'cph')), person('Nikos', 'Pantazis', email =
     '[email protected]', role = c('aut')), person('Ard', 'van Sighem',

diff --git a/Server/R/HIVModelManager.R b/Server/R/HIVModelManager.R
@@ -498,7 +498,6 @@ HIVModelManager <- R6::R6Class( # nolint
 
             fits <- list()
             i <- 0
-
             for (imp in names(mainFitResult)) {
               i <- i + 1
               mainFit <- mainFitResult[[imp]]
@@ -518,24 +517,24 @@ HIVModelManager <- R6::R6Class( # nolint
 
               PrintH2('Main data set {.val {imp}}')
 
+              dataAfterMigr <- FALSE
               if (bsType == 'NON-PARAMETRIC') {
                 caseDataImp <- caseData[Imputation == as.integer(imp)]
+                dataAfterMigr <- 'ProbPre' %in% colnames(caseDataImp)
               } else {
                 bootData <- context$Data
               }
 
-              jSucc <- 1
+              jSucc <- 0
               j <- 0
               bootResults <- list()
-              while (jSucc <= bsCount) {
+              while (jSucc < bsCount) {
                 j <- j + 1
 
                 # Bootstrap data set
-                dataAfterMigr <- FALSE
+
                 if (bsType == 'NON-PARAMETRIC') {
-                  dataAfterMigr <- 'ProbPre' %in% colnames(caseDataImp)
                   bootCaseDataImp <- caseDataImp[sample.int(nrow(caseDataImp), replace = TRUE)]
-
                   if (dataAfterMigr && migrConnFlag) {
                     bootCaseDataImp[, MigrClass := data.table::fcase(
                       !is.na(DateOfArrival) & DateOfHIVDiagnosis < DateOfArrival, 'Diagnosed prior to arrival', # nolint
@@ -571,7 +570,7 @@ HIVModelManager <- R6::R6Class( # nolint
                       aggrData <- NULL
                     }
                   } else {
-                    caseDataAll <- PrepareDataSetsForModel(caseDataImp, splitBy = 'Imputation')
+                    caseDataAll <- PrepareDataSetsForModel(caseData, splitBy = 'Imputation')
                   }
                   bootData <- CombineData(caseDataAll, aggrData)[[1]]
                 }
@@ -616,11 +615,19 @@ HIVModelManager <- R6::R6Class( # nolint
                   dataAfterMigr
                 )
 
-                msgType <- ifelse(bootResult$Converged, 'success', 'danger')
+                if (bootResult$Converged) {
+                  msgType <- 'success'
+                  jSucc <- jSucc + 1
+                  progress <- (jSucc + (i - 1) * bsCount) / (mainCount * bsCount) * 100
+                } else {
+                  msgType <- 'danger'
+                }
+                jSuccRate <- jSucc / j
 
                 PrintAlert(
                   'Iteration {.val {jSucc}} done |',
-                  'Run time: {.timestamp {prettyunits::pretty_dt(runTime)}}',
+                  'Run time: {.timestamp {prettyunits::pretty_dt(runTime)}} |',
+                  'Success rate: {.val {jSuccRate * 100}}%',
                   type = msgType
                 )
 
@@ -632,11 +639,6 @@ HIVModelManager <- R6::R6Class( # nolint
                   DataSet = imp,
                   BootIteration = jSucc
                 )
-
-                if (bootResult$Converged) {
-                  jSucc <- jSucc + 1
-                  progress <- (jSucc - 1 + (i - 1) * bsCount) / (mainCount * bsCount) * 100
-                }
               }
 
               fits[[imp]] <- bootResults

diff --git a/Server/inst/app/www/js/main.js b/Server/inst/app/www/js/main.js
diff --git a/Server/inst/app/www/js/vendors.js b/Server/inst/app/www/js/vendors.js
diff --git a/Server/utils/Example.R b/Server/utils/Example.R
@@ -91,7 +91,7 @@ appMgr$CaseMgr$SetFilters(filters = list(
 # STEP 3 - Adjust case-based data ------------------------------------------------------------------
 adjustmentSpecs <- hivPlatform::GetAdjustmentSpecs(c(
   # "Multiple Imputation using Chained Equations - MICE",
-  "Reporting Delays with trend"
+  # "Reporting Delays with trend"
 ))
 
 result <- hivPlatform::RunAdjustments(
@@ -310,7 +310,6 @@ appMgr$HIVModelMgr$SetMigrConnFlag(TRUE)
 migrConnFlag <- appMgr$HIVModelMgr$MigrConnFlag
 randomSeed <- .Random.seed
 
-
 json <- ConvertObjToJSON(appMgr$HIVModelMgr$PlotData, dataframe = 'columns')
 writeLines(json, 'json.txt')
 
@@ -365,12 +364,13 @@ avgRunTime <- mean(sapply(appMgr$HIVModelMgr$MainFitResult, '[[', 'RunTime'))
 maxRunTime <- as.difftime(avgRunTime * maxRunTimeFactor, units = 'secs')
 prettyunits::pretty_dt(maxRunTime)
 mainFitResult <- isolate(appMgr$HIVModelMgr$MainFitResult)
+avgModelOutputs <- isolate(appMgr$HIVModelMgr$AvgModelOutputs)
 caseData <- isolate(appMgr$CaseMgr$Data)
 aggrData <- isolate(appMgr$AggrMgr$Data)
 popCombination <- isolate(appMgr$HIVModelMgr$PopCombination)
 aggrDataSelection <- isolate(appMgr$HIVModelMgr$AggrDataSelection)
 randomSeed <- .Random.seed
-migrConnFlag <- TRUE
+migrConnFlag <- FALSE
 
 # 3. Detailed HIV Model bootstrap results (rds)
 appMgr$HIVModelMgr$BootstrapFitResult