Merge pull request syounkin#11 from ITHIM/populationSize-#7

Population size syounkin#7
GHI-UW · Jun 9, 2017 · c7b3ae3 · c7b3ae3
2 parents 29f0ad2 + b5277b5
commit c7b3ae3
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Showing 4 changed files with 44 additions and 26 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ITHIM
 Type: Package
 Title: The Integrated Transport and Health Impacts Model
-Version: 0.5.2
-Date: 2017-05-22
+Version: 0.5.3
+Date: 2017-06-08
 Author: Samuel G. Younkin <syounkin@wisc.edu>
 Maintainer: Samuel G. Younkin <syounkin@wisc.edu>
 Description: Implements the Integrated Transport and Health Impacts

diff --git a/R/functions-ITHIM.R b/R/functions-ITHIM.R
@@ -23,7 +23,7 @@ createITHIMFunction <- function(roadInjuriesFile = system.file("roadInjuriesUS.c
                                 safetyInNumbersFile = system.file("SiN.csv", package = "ITHIM"),
                                 FFile = system.file("F.csv",package = "ITHIM"),
                                 meanType = "overall"){
-    
+
     new("ITHIM", parameters = parameters <- createParameterList(
                                   activeTransportTimeFile = activeTransportTimeFile,
                                   distRoadTypeFile = distRoadTypeFile,
@@ -83,25 +83,26 @@ createParameterList <- function(
     cvNonTravel <- 1 # coefficient of variation for leisure activity
     roadInjuries <- array()
     modeNames <- unlist(unique(lapply(roadInjuries, rownames)))
-    
+
     # read safetyInNumbers using helper function which converts "normalize" csv into array
 
     safetyInNumbers <- readSafetyInNumbers(file = safetyInNumbersFile)
-    
+
     # read distRoadType using helper function which converts "normalize" csv into array
-    
+
     distRoadType <- readDistByRoadType(file = distRoadTypeFile)
 
     GBD <- readGBD(filename = GBDFile)
 
-    F <- readF(filename = FFile)
+    N <- readF(filename = FFile)
+    P <- N/sum(N)
 
     if( meanType == "referent" ){
         muwt <- Mwt[3,2]
         muct <- Mct[3,2]
     }else if( meanType == "overall" ){
-        muwt <- sum(F*Mwt)
-        muct <- sum(F*Mct)
+        muwt <- sum(P*Mwt)
+        muct <- sum(P*Mct)
     }else{
         stop("Wrong meanType value.")
     }
@@ -120,7 +121,7 @@ createParameterList <- function(
         muNonTravel = muNonTravel,
         muNonTravelMatrix = muNonTravelMatrix,
         GBD = GBD,
-        F = F,
+        F = N,
         meanType = meanType,
         quantiles = quantiles,
         roadInjuries = roadInjuries,

diff --git a/inst/F-old.csv b/inst/F-old.csv
@@ -0,0 +1,17 @@
+ageClass,sex,value
+ageClass1,M,0.03535189
+ageClass2,M,0.06777091
+ageClass3,M,0.10827214
+ageClass4,M,0.10078132
+ageClass5,M,0.10124053
+ageClass6,M,0.04297974
+ageClass7,M,0.02363664
+ageClass8,M,0.01303553
+ageClass1,F,0.03373200
+ageClass2,F,0.06460902
+ageClass3,F,0.10256596
+ageClass4,F,0.09961365
+ageClass5,F,0.10519989
+ageClass6,F,0.04766630
+ageClass7,F,0.02974551
+ageClass8,F,0.02379898
diff --git a/inst/F.csv b/inst/F.csv
@@ -1,17 +1,17 @@
 ageClass,sex,value
-ageClass1,M,0.03535189
-ageClass2,M,0.06777091
-ageClass3,M,0.10827214
-ageClass4,M,0.10078132
-ageClass5,M,0.10124053
-ageClass6,M,0.04297974
-ageClass7,M,0.02363664
-ageClass8,M,0.01303553
-ageClass1,F,0.03373200
-ageClass2,F,0.06460902
-ageClass3,F,0.10256596
-ageClass4,F,0.09961365
-ageClass5,F,0.10519989
-ageClass6,F,0.04766630
-ageClass7,F,0.02974551
-ageClass8,F,0.02379898
+ageClass1,M,35351
+ageClass2,M,67770
+ageClass3,M,108272
+ageClass4,M,100781
+ageClass5,M,101240
+ageClass6,M,42979
+ageClass7,M,23636
+ageClass8,M,13035
+ageClass1,F,33732
+ageClass2,F,64609
+ageClass3,F,102565
+ageClass4,F,99613
+ageClass5,F,105199
+ageClass6,F,47666
+ageClass7,F,29745
+ageClass8,F,23798