implement absolute ART adjustment

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: eppasm
 Title: Age-structured EPP Model for HIV Epidemic Estimates
-Version: 0.8.2
+Version: 0.8.3
 Authors@R: person("Jeff", "Eaton", email = "[email protected]", role = c("aut", "cre"))
 Description: What the package does (one paragraph).
 Depends: R (>= 3.1.0),

NEWS.md

@@ -1,3 +1,22 @@
+## eppasm 0.8.3
+
+* Implement Spectrum adult ART adjustment by absolute count. This is a user 
+  input that adjust the number on ART count by an absolute value. It is
+  intended to be used to account for clients receiving services in or
+  from another region; typically with subnational Spectrum files.
+
+  If both absolute count and ratio adjustments are specified in the same
+  year, the absolute count is applied first and then ratio is applied. 
+  If ART is specified as a percentage, then adjustments do not have any 
+  influence.
+
+  Previously entered ART adjustments were applied or not via a checkbox in
+  Spectrum. The checkbox has been removed in Spectrum 6.38 beta 18. For 
+  backward compatability with previously simulated Spectrum outputs, if the 
+  checkbox flag exists in the .DP file, it is still used to determine 
+  application of the ratios; if the .DP file does not contain the checkbox 
+  flag, then the ratio is applied.
+
 ## eppasm 0.8.2
 
 Implement new excess non-AIDS mortality among PLHIV implemented in 

R/read-spectrum-files.R

@@ -653,20 +653,50 @@ read_hivproj_param <- function(pjnz, use_ep5=FALSE){
   ## * Enabled / disabled by checkbox flag ("<AdultARTAdjFactorFlag>")
   ## * 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.
+  ##
   ## 
-
-  if (exists_dptag("<AdultARTAdjFactorFlag>") &&
-        dpsub("<AdultARTAdjFactorFlag>", 2, 4) == 1) {
-
+  ## ** 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
+  ##   "<AdultARTAdjFactorFlag>" was removed from the .DP file.
+  ## * New tag "<AdultPatsAllocToFromOtherRegion>" 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))
+  adult_artadj_absolute <- array(0.0, dim(art15plus_num))
+
+  ## Flag to use adjustment
+  use_artadj <- exists_dptag("<AdultARTAdjFactor>") &&
+    (!exists_dptag("<AdultARTAdjFactorFlag>") ||
+        (exists_dptag("<AdultARTAdjFactorFlag>") &&
+           dpsub("<AdultARTAdjFactorFlag>", 2, 4) == 1))
+
+  if (use_artadj) {
+
     adult_artadj_factor <- sapply(dpsub("<AdultARTAdjFactor>", 3:4, timedat.idx), as.numeric)
 
+    if(exists_dptag("<AdultPatsAllocToFromOtherRegion>")) {
+      adult_artadj_absolute <- sapply(dpsub("<AdultPatsAllocToFromOtherRegion>", 3:4, timedat.idx), as.numeric)
+    }
+
     ## Only apply if is number (! is percentage)
     adult_artadj_factor <- adult_artadj_factor ^ as.numeric(!art15plus_numperc)
+    adult_artadj_absolute <- adult_artadj_absolute * as.numeric(!art15plus_numperc)
 
+    ## First add absolute adjustment, then apply scalar adjustment (Spectrum procedure)
+    art15plus_num <- art15plus_num + adult_artadj_absolute
     art15plus_num <- art15plus_num * adult_artadj_factor
-  } else {
-    adult_artadj_factor <- array(1.0, dim(art15plus_num))
-  }
+  } 
 
 
   if(exists_dptag("<NewARTPatAllocationMethod MV2>"))