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CCRStable_Florida.R
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##########
##R CODE FOR COHORT CHANGE RATIO-BASED (HAMILTON-PERRY) WITH COMPONENTS AND STABLE POPULATION REVIEW SHINY APP - APPLIED TO FLORIDA COUNTIES
##
##EDDIE HUNSINGER, AUGUST 2019 (UPDATED JANUARY 2022)
##https://edyhsgr.github.io/eddieh/
##
##APPLIED DEMOGRAPHY TOOLBOX LISTING: https://applieddemogtoolbox.github.io/Toolbox/#CCRStable
##
##AN MS EXCEL SPREADSHEET THAT REPLICATES METHODS AND RESULTS (2010 to 2015 ratios for Alameda County, California, with any adjustments) IS AVAILABLE AT:
##https://github.com/edyhsgr/CCRStable/blob/master/Oct2020Presentation/CCRAdjustmentSheet_December2021.xlsx
##
####MORE INFORMATION IS AVAILABLE AT: https://github.com/edyhsgr/CCRStable/tree/master/Oct2020Presentation
##
##IF YOU WOULD LIKE TO USE, SHARE OR REPRODUCE THIS CODE, PLEASE CITE THE SOURCE
##This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 International License (more information: https://creativecommons.org/licenses/by-sa/3.0/igo/).
##
##THERE IS NO WARRANTY FOR THIS CODE
##THIS CODE HAS NOT BEEN PEER-REVIEWED OR CAREFULLY TESTED - QUESTIONS AND COMMENTS ARE WELCOME, OF COURSE ([email protected])
##########
#install.packages("shiny")
library(shiny)
ui<-fluidPage(
tags$h3("Cohort Change Ratio-Based Stable Population Review Shiny App - Florida Counties"),
p("Related information and ",
tags$a(href="https://www.r-project.org/", "R"),
"code available at: ",
tags$a(href="https://github.com/edyhsgr/CCRStable",
"CCRStable GitHub Repository")
),
hr(),
sidebarLayout(
sidebarPanel(
selectizeInput(inputId = "County", label = "County",
choices = c(
"Alachua"="Alachua County",
"Baker"="Baker County",
"Bay"="Bay County",
"Bradford"="Bradford County",
"Brevard"="Brevard County",
"Broward"="Broward County",
"Calhoun"="Calhoun County",
"Charlotte"="Charlotte County",
"Citrus"="Citrus County",
"Clay"="Clay County",
"Collier"="Collier County",
"Columbia"="Columbia County",
"DeSoto"="DeSoto County",
"Dixie"="Dixie County",
"Duval"="Duval County",
"Escambia"="Escambia County",
"Flagler"="Flagler County",
"Franklin"="Franklin County",
"Gadsden"="Gadsden County",
"Gilchrist"="Gilchrist County",
"Glades"="Glades County",
"Gulf"="Gulf County",
"Hamilton"="Hamilton County",
"Hardee"="Hardee County",
"Hendry"="Hendry County",
"Hernando"="Hernando County",
"Highlands"="Highlands County",
"Hillsborough"="Hillsborough County",
"Holmes"="Holmes County",
"Indian River"="Indian River County",
"Jackson"="Jackson County",
"Jefferson"="Jefferson County",
"Lafayette"="Lafayette County",
"Lake"="Lake County",
"Lee"="Lee County",
"Leon"="Leon County",
"Levy"="Levy County",
"Liberty"="Liberty County",
"Madison"="Madison County",
"Manatee"="Manatee County",
"Marion"="Marion County",
"Martin"="Martin County",
"Miami-Dade"="Miami-Dade County",
"Monroe"="Monroe County",
"Nassau"="Nassau County",
"Okaloosa"="Okaloosa County",
"Okeechobee"="Okeechobee County",
"Orange"="Orange County",
"Osceola"="Osceola County",
"Palm Beach"="Palm Beach County",
"Pasco"="Pasco County",
"Pinellas"="Pinellas County",
"Polk"="Polk County",
"Putnam"="Putnam County",
"St Johns"="St Johns County",
"St Lucie"="St Lucie County",
"Santa Rosa"="Santa Rosa County",
"Sarasota"="Sarasota County",
"Seminole"="Seminole County",
"Sumter"="Sumter County",
"Suwannee"="Suwannee County",
"Taylor"="Taylor County",
"Union"="Union County",
"Volusia"="Volusia County",
"Wakulla"="Wakulla County",
"Walton"="Walton County",
"Washington"="Washington County"
),
options = list(placeholder = "Type in a county to see graphs", multiple = TRUE, maxOptions = 5000, onInitialize = I('function() { this.setValue(""); }'))
),
selectInput("Sex", "Sex",
c(
"Total"="Total",
"Female"="Female",
"Male"="Male"
),
),
numericInput("STEP","Project to (year)",2030,2020,3000,step=5),
selectInput("RatiosFrom", "Using ratios from",
c(
"2014 to 2019"="7",
"2013 to 2018"="6",
"2012 to 2017"="5",
"2011 to 2016"="4",
"2010 to 2015"="3"
),
),
hr(),
selectInput("ImposeTFR", "Impose iTFR?",
c(
"No"="NO",
"Yes"="YES"
),
),
numericInput("ImposedTFR","If Yes, iTFR level",2.1,0,10,step=.1),
numericInput("ImposedTFR_ar","If Yes, iTFR AR(1)",.00,0,.99,step=.01),
hr(),
numericInput("SRB","Projected sex ratio at birth",round((1-.4886)/.4886,3),0,2,step=.005),
hr(),
numericInput("NetMigrationAdjustLevel","Net migration adjustment (annual, percent of population)",0,-25,25,step=.1),
numericInput("GrossMigrationAdjustLevel","Gross migration adjustment (percent of net migration ratios)",100,0,200,step=10),
selectInput("GrossMigrationProfile", "Gross migration age profile to use", selected="Florida",
c(
"California"="California",
"Florida"="Florida",
"Sarasota County, Florida"="SarasotaFlorida",
"Kentucky"="Kentucky"
),
),
hr(),
selectInput("ImputeMort", "Impute mortality?",
c(
"Yes"="YES",
"No"="NO"
),
),
numericInput("BAStart","If yes, Brass' model alpha for First projection step...",.03,-2,2,step=.03),
numericInput("BAEnd","...and Brass' model alpha for Last projection step",.12,-2,2,step=.03),
selectInput("LifeTable", "Life table standard to use", selected="Florida",
c(
"California"="California",
"Florida"="Florida",
"Kentucky"="Kentucky"
),
),
hr(),
p("This interface was made with ",
tags$a(href="https://shiny.rstudio.com/",
"Shiny for R."),
tags$a(href="https://edyhsgr.github.io/",
"Eddie Hunsinger,"),
"August 2019 (updated January 2022)."),
p("Information including ",
tags$a(href="https://github.com/edyhsgr/CCRStable/tree/master/Oct2020Presentation",
"formulas, a spreadsheet demonstration, and slides for a related talk, "),
"as well as ",
tags$a(href="https://www.r-project.org/",
"R"),
"code with input files for several examples, including a ",
tags$a(href="https://shiny.demog.berkeley.edu/eddieh/CCRUnc/",
"stochastic version, "),
"an ",
tags$a(href="https://edyhsgr.shinyapps.io/CCRStable_ValView_Florida/",
"errors review version"),
"and a ",
tags$a(href="https://shiny.demog.berkeley.edu/eddieh/CCRStable_StateSingle_Florida/",
"single-year-of-age version, "),
"is all available in the ",
tags$a(href="https://github.com/edyhsgr/CCRStable",
"related GitHub repository.")),
p("Population estimates inputs from ",
tags$a(href="https://www.census.gov/programs-surveys/popest.html",
"US Census Bureau Vintage 2019 Population Estimates.")),
p(" More information on cohort change ratios, including a chapter on stable population: ",
tags$a(href="https://www.worldcat.org/title/cohort-change-ratios-and-their-applications/oclc/988385033",
"Baker, Swanson, Tayman, and Tedrow (2017)."),
p("More information on iTFR: ",
tags$a(href="https://osf.io/adu98/",
"Hauer and Schmertmann (2019)"),
" and ",
tags$a(href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067226",
"Hauer, Baker, and Brown (2013).")),
p("Slides with background thoughts on adjusting net migration: ",
tags$a(href="https://edyhsgr.github.io/documents/ProjPresentation.pdf",
"Hunsinger (2007)."),
"Migration by age over time comparisons from Alaska data: ",
tags$a(href="http://shiny.demog.berkeley.edu/eddieh/AKPFDMigrationReview/",
"Hunsinger (2018)."),
"Interface with net migration adjustment examples and comparisons: ",
tags$a(href="http://shiny.demog.berkeley.edu/eddieh/NMAdjustCompare/",
"Hunsinger (2019)."),
"Migration adjustment profile was made from the US Census Bureau's 2013 to 2017
American Community Survey Public Use Microdata Sample, accessed via the ",
tags$a(href="https://usa.ipums.org/usa/",
"IPUMS USA, University of Minnesota.")),
tags$a(href="https://twitter.com/ApplDemogToolbx/status/1079286699941752832",
"Graph of e0 and Brass' relational life table alpha by US state."),
"Model life table (0.0 alpha) is the 5x5 2010 to 2014 life table for California from the ",
tags$a(href="https://usa.mortality.org/index.php",
"United States Mortality Database.")),
p(tags$a(href="https://applieddemogtoolbox.github.io/#CCRStable",
"Applied Demography Toolbox listing.")),
width=3
),
mainPanel(
plotOutput("plots")
))
)
##########
##READING EXTERNAL DATA IN
##########
##DATA (CENSUS BUREAU VINTAGE 2019 POPULATION ESTIMATES BY DEMOGRAPHIC CHARACTERISTICS)
##https://www2.census.gov/programs-surveys/popest/datasets/2010-2019/counties/asrh/cc-est2019-alldata-06.csv
##https://www2.census.gov/programs-surveys/popest/technical-documentation/file-layouts/2010-2019/
K<-data.frame(read.table(file="https://raw.githubusercontent.com/edyhsgr/CCRStable/master/InputData/PopEstimates/cc-est2019-alldata-12_Extract.csv",header=TRUE,sep=","))
server<-function(input, output) {
output$plots<-renderPlot({
par(mfrow=c(2,2))
##NUMBER FORMATTING
options(scipen=999)
##USMD CA SURVIVAL DATA (GENERIC)
if(input$LifeTable=="California") {lt<-read.table(file="https://raw.githubusercontent.com/edyhsgr/CCRStable/master/InputData/Mortality/lt_CA_USMD2010to2014.csv",header=TRUE,sep=",")
}
if(input$LifeTable=="Florida") {lt<-read.table(file="https://raw.githubusercontent.com/edyhsgr/CCRStable/master/InputData/Mortality/lt_FL_USMD2010to2014.csv",header=TRUE,sep=",")
}
if(input$LifeTable=="Kentucky") {lt<-read.table(file="https://raw.githubusercontent.com/edyhsgr/CCRStable/master/InputData/Mortality/lt_KY_USMD2010to2014.csv",header=TRUE,sep=",")
}
lxF<-lt$lx_Female/100000
lxM<-lt$lx_Male/100000
lxT<-lt$lx_Both/100000
lxF<-c(lxF[1],lxF[3:24])
lxM<-c(lxM[1],lxM[3:24])
lxT<-c(lxT[1],lxT[3:24])
##SELECT CENSUS ACS (via IPUMS) MIGRATION DATA
if(input$GrossMigrationProfile=="California") {
Migration<-data.frame(read.table(file="https://raw.githubusercontent.com/edyhsgr/CCRStable/master/InputData/Migration/AGenericMigrationProfile_CA_2013to2017ACS.csv",header=TRUE,sep=","))
Migration<-c(Migration$CA_F,Migration$CA_M)
}
if(input$GrossMigrationProfile=="Florida") {
Migration<-data.frame(read.table(file="https://raw.githubusercontent.com/edyhsgr/CCRStable/master/InputData/Migration/AGenericMigrationProfile_FL_2013to2017ACS.csv",header=TRUE,sep=","))
Migration<-c(Migration$FL_F,Migration$FL_M)
}
if(input$GrossMigrationProfile=="SarasotaFlorida") {
Migration<-data.frame(read.table(file="https://raw.githubusercontent.com/edyhsgr/CCRStable/master/InputData/Migration/AGenericMigrationProfile_SarasotaFL_2013to2017ACS.csv",header=TRUE,sep=","))
Migration<-c(Migration$SarasotaFL_F,Migration$SarasotaFL_M)
}
if(input$GrossMigrationProfile=="Kentucky") {
Migration<-data.frame(read.table(file="https://raw.githubusercontent.com/edyhsgr/CCRStable/master/InputData/Migration/AGenericMigrationProfile_KY_2013to2017ACS.csv",header=TRUE,sep=","))
Migration<-c(Migration$KY_F,Migration$KY_M)
}
##RUN ONLY IF COUNTY INPUTS ARE PROVIDED
if(input$County=="") {
plot.new()
legend("topleft",legend=c("Select a county with the panel to the left"),cex=2,bty="n")
}
if(input$County!="") {
##########
##SCRIPT INPUTS
##########
##DIMENSIONS
SIZE<-36
HALFSIZE<-SIZE/2
STEPS<-(input$STEP-2015)/5
STEPSSTABLE<-STEPS+1000
CURRENTSTEP<-0
CURRENTSTEPSTABLE<-0
PROJECTIONYEAR<-STEPS*5+2015
FERTWIDTH<-35
##SELECTING RATIOS BASIS
FirstYear<-strtoi(input$RatiosFrom)
SecondYear<-strtoi(input$RatiosFrom)+5
##IMPOSED TFR OPTION
ImposedTFR<-input$ImposedTFR
ffab<-1/(input$SRB+1)
UseImposedTFR<-input$ImposeTFR
##ADJUST BY MIGRATION OPTION
GrossMigrationAdjustLevel<-input$GrossMigrationAdjustLevel/100
NetMigrationAdjustLevel<-input$NetMigrationAdjustLevel/100
##IMPUTE MORTALITY OPTION
##"BA" IS THE BRASS RELATIONAL LOGIT MODEL ALPHA
if(input$ImputeMort=="YES") {
BA_start<-input$BAStart
BA_end<-input$BAEnd
BB<-1
}
if(input$ImputeMort=="NO") {
BA_start<-0
BA_end<-0
BB<-1
}
##SELECT BY SEX
SelectBySex<-input$Sex
##SELECT AREA
Name<-paste(input$County)
##SELECTING FROM THE INPUT POPULATION TABLE (K) BASED ON INPUTS
TMinusOneAgeInit_F<-subset(K,CTYNAME==input$County & YEAR==3 & AGEGRP>0)
TMinusOneAgeInit_F<-TMinusOneAgeInit_F$TOT_FEMALE
TMinusOneAge_F<-TMinusOneAgeInit_F
TMinusOneAgeInit_M<-subset(K,CTYNAME==input$County & YEAR==3 & AGEGRP>0)
TMinusOneAgeInit_M<-TMinusOneAgeInit_M$TOT_MALE
TMinusOneAge_M<-TMinusOneAgeInit_M
TMinusOneAge<-TMinusOneAgeInit<-c(TMinusOneAge_F,TMinusOneAge_M)
TMinusOneAgeInitRatios_F<-subset(K,CTYNAME==input$County & YEAR==FirstYear & AGEGRP>0)
TMinusOneAgeInitRatios_F<-TMinusOneAgeInitRatios_F$TOT_FEMALE
TMinusOneAgeRatios_F<-TMinusOneAgeInitRatios_F
TMinusOneAgeInitRatios_M<-subset(K,CTYNAME==input$County & YEAR==FirstYear & AGEGRP>0)
TMinusOneAgeInitRatios_M<-TMinusOneAgeInitRatios_M$TOT_MALE
TMinusOneAgeRatios_M<-TMinusOneAgeInitRatios_M
TMinusOneAgeRatios<-TMinusOneAgeInitRatios<-c(TMinusOneAgeRatios_F,TMinusOneAgeRatios_M)
TMinusZeroAgeInit_F<-subset(K,CTYNAME==input$County & YEAR==8 & AGEGRP>0)
TMinusZeroAgeInit_F<-TMinusZeroAgeInit_F$TOT_FEMALE
TMinusZeroAge_F<-TMinusZeroAgeInit_F
TMinusZeroAgeInit_M<-subset(K,CTYNAME==input$County & YEAR==8 & AGEGRP>0)
TMinusZeroAgeInit_M<-TMinusZeroAgeInit_M$TOT_MALE
TMinusZeroAge_M<-TMinusZeroAgeInit_M
TMinusZeroAge<-TMinusZeroAgeInit<-c(TMinusZeroAge_F,TMinusZeroAge_M)
TMinusZeroAgeInitRatios_F<-subset(K,CTYNAME==input$County & YEAR==SecondYear & AGEGRP>0)
TMinusZeroAgeInitRatios_F<-TMinusZeroAgeInitRatios_F$TOT_FEMALE
TMinusZeroAgeRatios_F<-TMinusZeroAgeInitRatios_F
TMinusZeroAgeInitRatios_M<-subset(K,CTYNAME==input$County & YEAR==SecondYear & AGEGRP>0)
TMinusZeroAgeInitRatios_M<-TMinusZeroAgeInitRatios_M$TOT_MALE
TMinusZeroAgeRatios_M<-TMinusZeroAgeInitRatios_M
TMinusZeroAgeRatios<-TMinusZeroAgeInitRatios<-c(TMinusZeroAgeRatios_F,TMinusZeroAgeRatios_M)
##########
##CALCULATIONS
##########
##COHORT CHANGE RATIOS
Ratios<-array(,length(TMinusOneAgeRatios))
for (i in 2:(HALFSIZE-1)) {Ratios[i]<-TMinusZeroAgeRatios[i]/TMinusOneAgeRatios[i-1]}
for (i in (HALFSIZE+2):(SIZE-1)) {Ratios[i]<-TMinusZeroAgeRatios[i]/TMinusOneAgeRatios[i-1]}
##PLACING COHORT CHANGE RATIOS (FEMALE)
S_F<-array(0,c(HALFSIZE,HALFSIZE))
S_F<-rbind(0,cbind(diag(Ratios[2:(HALFSIZE)]),0))
##OPEN-ENDED AGE GROUP (FEMALE)
S_F[HALFSIZE,HALFSIZE-1]<-TMinusZeroAgeRatios[HALFSIZE]/(TMinusOneAgeRatios[HALFSIZE-1]+TMinusOneAgeRatios[HALFSIZE])
Ratios[HALFSIZE]<-S_F[HALFSIZE,HALFSIZE]<-S_F[HALFSIZE,HALFSIZE-1]
##BIRTHS AND MATRIX PORTION CONSTRUCTION (FEMALE)
B_F<-0*S_F
B_F[1,4:10]<-Ratios[1]*ffab
A_F<-B_F+S_F
##PLACING COHORT CHANGE RATIOS (MALE)
S_M<-array(0,c(HALFSIZE,HALFSIZE))
S_M<-rbind(0,cbind(diag(Ratios[(HALFSIZE+2):SIZE]),0))
##OPEN-ENDED AGE GROUP (MALE)
S_M[HALFSIZE,HALFSIZE-1]<-TMinusZeroAgeRatios[SIZE]/(TMinusOneAgeRatios[SIZE-1]+TMinusOneAgeRatios[SIZE])
Ratios[SIZE]<-S_M[HALFSIZE,HALFSIZE]<-S_M[HALFSIZE,HALFSIZE-1]
##BIRTHS AND MATRIX PORTION CONSTRUCTION (MALE)
B_M<-0*S_M
B_M[1,4:10]<-Ratios[1]*(1-ffab)
##STRUCTURAL ZEROES
AEnd_Zero<-A_Zero<-array(0,c(HALFSIZE,HALFSIZE))
##MAKING FULL PROJECTION MATRIX (TWO-SEX)
Acolone<-cbind(A_F,A_Zero)
Acoltwo<-cbind(B_M,S_M)
A<-rbind(Acolone,Acoltwo)
##IMPLIED TFR CALCUATION
ImpliedTFR2010<-((TMinusOneAgeInit[1]+TMinusOneAgeInit[HALFSIZE+1])/5)/sum(TMinusZeroAgeInit[4:10])*FERTWIDTH
ImpliedTFR2015<-((TMinusZeroAgeInit[1]+TMinusZeroAgeInit[HALFSIZE+1])/5)/sum(TMinusZeroAgeInit[4:10])*FERTWIDTH
##########
##PROJECTION FUNCTION
##########
##MAX STEPS IN CASE USER (ESP ME) GETS CARRIED AWAY
if(STEPS<198){
##FUNCTION INPUTTING
CCRProject<-function(TMinusZeroAge,ImpliedTFR,BA_start,BA_end,CURRENTSTEP){
##CALCULATE SURVIVAL ADJUSTMENT (Yx, lx, Lx, Sx)
YxF<-YxM<-NULL
for (i in 1:length(lxF)){YxF[i]<-.5*log(lxF[i]/(1-lxF[i]))}
for (i in 1:length(lxM)){YxM[i]<-.5*log(lxM[i]/(1-lxM[i]))}
lxFStart<-array(0,length(lxF))
lxMStart<-array(0,length(lxM))
for (i in 1:length(lxFStart)){lxFStart[i]<-1/(1+exp(-2*BA_start-2*BB*YxF[i]))}
for (i in 1:length(lxMStart)){lxMStart[i]<-1/(1+exp(-2*BA_start-2*BB*YxM[i]))}
LxFStart<-array(,length(lxF))
LxMStart<-array(,length(lxM))
##**THIS IS A LITTLE OFF FOR THE FIRST AGE GROUP**
for (i in 1:length(LxFStart)){LxFStart[i]<-.5*(lxFStart[i]+lxFStart[i+1])}
for (i in 1:length(LxMStart)){LxMStart[i]<-.5*(lxMStart[i]+lxMStart[i+1])}
SxFStart<-array(,HALFSIZE)
SxMStart<-array(,HALFSIZE)
for (i in 2:HALFSIZE){SxFStart[i]<-(LxFStart[i]/LxFStart[i-1])}
for (i in 2:HALFSIZE){SxMStart[i]<-(LxMStart[i]/LxMStart[i-1])}
##(OPEN-ENDED AGE GROUP (FEMALE))
SxFStart[HALFSIZE]<-rev(cumsum(rev(LxFStart[HALFSIZE:(length(LxFStart)-1)])))[1]/rev(cumsum(rev(LxFStart[(HALFSIZE-1):(length(LxFStart)-1)])))[1]
##(OPEN-ENDED AGE GROUP (MALE))
SxMStart[HALFSIZE]<-rev(cumsum(rev(LxMStart[HALFSIZE:(length(LxMStart)-1)])))[1]/rev(cumsum(rev(LxMStart[(HALFSIZE-1):(length(LxMStart)-1)])))[1]
##INITIAL e0
e0FStart<-sum(LxFStart[1:(length(LxFStart)-1)]*5)
e0MStart<-sum(LxMStart[1:(length(LxFStart)-1)]*5)
lxFAdj<-array(0,length(lxF))
lxMAdj<-array(0,length(lxM))
##INTERPOLATING BRASS ALPHA BETWEEN FIRST AND LAST STEP
if(CURRENTSTEP<=STEPS){
for (i in 1:length(lxFAdj)){lxFAdj[i]<-1/(1+exp(-2*(BA_start*(1-CURRENTSTEP/STEPS)+BA_end*(CURRENTSTEP/STEPS))-2*BB*YxF[i]))}
for (i in 1:length(lxMAdj)){lxMAdj[i]<-1/(1+exp(-2*(BA_start*(1-CURRENTSTEP/STEPS)+BA_end*(CURRENTSTEP/STEPS))-2*BB*YxM[i]))}
}
##ALLOWING FOR LONG-TERM (STABLE POPULATION) SIMULATION
if(CURRENTSTEP>=STEPS){
for (i in 1:length(lxFAdj)){lxFAdj[i]<-1/(1+exp(-2*BA_end-2*BB*YxF[i]))}
for (i in 1:length(lxMAdj)){lxMAdj[i]<-1/(1+exp(-2*BA_end-2*BB*YxM[i]))}
}
##SURVIVAL ADJUSTMENTS (Lx, SX)
LxFAdj<-array(,length(lxF))
LxMAdj<-array(,length(lxM))
##**THIS IS A LITTLE OFF FOR THE FIRST AGE GROUP**
for (i in 1:length(LxFAdj)){LxFAdj[i]<-.5*(lxFAdj[i]+lxFAdj[i+1])}
for (i in 1:length(LxMAdj)){LxMAdj[i]<-.5*(lxMAdj[i]+lxMAdj[i+1])}
SxFAdj<-array(,HALFSIZE)
SxMAdj<-array(,HALFSIZE)
for (i in 2:length(SxFAdj)){SxFAdj[i]<-(LxFAdj[i]/LxFAdj[i-1])}
for (i in 2:length(SxMAdj)){SxMAdj[i]<-(LxMAdj[i]/LxMAdj[i-1])}
##(OPEN-ENDED AGE GROUP (FEMALE))
SxFAdj[HALFSIZE]<-rev(cumsum(rev(LxFAdj[HALFSIZE:(length(LxFAdj)-1)])))[1]/rev(cumsum(rev(LxFAdj[(HALFSIZE-1):(length(LxFAdj)-1)])))[1]
##(OPEN-ENDED AGE GROUP (MALE))
SxMAdj[HALFSIZE]<-rev(cumsum(rev(LxMAdj[HALFSIZE:(length(LxMAdj)-1)])))[1]/rev(cumsum(rev(LxMAdj[(HALFSIZE-1):(length(LxMAdj)-1)])))[1]
##ADJUSTED e0
e0FAdj<-sum(LxFAdj[1:(length(LxFStart)-1)]*5)
e0MAdj<-sum(LxMAdj[1:(length(LxFStart)-1)]*5)
##ADJUST GROSS MIGRATION OPTION
if(GrossMigrationAdjustLevel!=1){
RatiosGrossMigAdj<-Ratios
for (i in 2:HALFSIZE) {RatiosGrossMigAdj[i]<-(Ratios[i]-SxFStart[i])*GrossMigrationAdjustLevel+SxFStart[i]}
SGrossMigAdj_F<-array(0,c(HALFSIZE,HALFSIZE))
SGrossMigAdj_F<-rbind(0,cbind(diag(RatiosGrossMigAdj[2:HALFSIZE]),0))
##OPEN-ENDED AGE GROUP (FEMALE)
SGrossMigAdj_F[HALFSIZE,HALFSIZE]<-SGrossMigAdj_F[HALFSIZE,HALFSIZE-1]
S_F<-SGrossMigAdj_F
A_F<-B_F+S_F
for (i in (HALFSIZE+2):SIZE) {RatiosGrossMigAdj[i]<-(Ratios[i]-SxMStart[i-HALFSIZE])*GrossMigrationAdjustLevel+SxMStart[i-HALFSIZE]}
SGrossMigAdj_M<-array(0,c(HALFSIZE,HALFSIZE))
SGrossMigAdj_M<-rbind(0,cbind(diag(RatiosGrossMigAdj[(HALFSIZE+2):SIZE]),0))
##OPEN-ENDED AGE GROUP (MALE)
SGrossMigAdj_M[HALFSIZE,HALFSIZE]<-SGrossMigAdj_M[HALFSIZE,HALFSIZE-1]
S_M<-SGrossMigAdj_M
}
##CONSTRUCT PROJECTION MATRICES WITH SURVIVAL ADJUSTMENT
SAdj_F<-array(0,c(HALFSIZE,HALFSIZE))
SAdj_F<-rbind(0,cbind(diag(SxFAdj[2:HALFSIZE]-SxFStart[2:HALFSIZE]),0))
SAdj_F[HALFSIZE,HALFSIZE]<-SAdj_F[HALFSIZE,HALFSIZE-1]
SAdj_F<-SAdj_F+S_F
AAdj_F<-B_F+SAdj_F
SAdj_M<-array(0,c(HALFSIZE,HALFSIZE))
SAdj_M<-rbind(0,cbind(diag(SxMAdj[2:HALFSIZE]-SxMStart[2:HALFSIZE]),0))
SAdj_M[HALFSIZE,HALFSIZE]<-SAdj_M[HALFSIZE,HALFSIZE-1]
SAdj_M<-SAdj_M+S_M
AAdj_Zero<-A_Zero<-array(0,c(HALFSIZE,HALFSIZE))
Acolone<-cbind(A_F,A_Zero)
Acoltwo<-cbind(B_M,S_M)
A<-rbind(Acolone,Acoltwo)
AAdjcolone<-cbind(AAdj_F,AAdj_Zero)
AAdjcoltwo<-cbind(B_M,SAdj_M)
AAdj<-rbind(AAdjcolone,AAdjcoltwo)
##PROJECTION IMPLEMENTATION (WITH FERTILITY AND MIGRATION ADJUSTMENTS)
TMinusOneAgeNew<-data.frame(TMinusZeroAge)
if(CURRENTSTEP>0){
TMinusZeroAge<-AAdj%*%TMinusZeroAge
if(NetMigrationAdjustLevel!=0)
{TMinusZeroAge<-NetMigrationAdjustLevel*5*sum(TMinusOneAgeNew)*Migration+TMinusZeroAge}
if(UseImposedTFR=="YES")
{TMinusZeroAge[1]<-(ImpliedTFR*input$ImposedTFR_ar+ImposedTFR*(1-input$ImposedTFR_ar))*(sum(TMinusZeroAge[4:10])/FERTWIDTH)*5*ffab
TMinusZeroAge[HALFSIZE+1]<-(ImpliedTFR*input$ImposedTFR_ar+ImposedTFR*(1-input$ImposedTFR_ar))*(sum(TMinusZeroAge[4:10])/FERTWIDTH)*5*(1-ffab)}
if(UseImposedTFR=="NO")
{TMinusZeroAge[1]<-ImpliedTFR*(sum(TMinusZeroAge[4:10])/FERTWIDTH)*5*ffab
TMinusZeroAge[HALFSIZE+1]<-ImpliedTFR*(sum(TMinusZeroAge[4:10])/FERTWIDTH)*5*(1-ffab)}
}
TMinusZeroAge_NDF<-TMinusZeroAge
TMinusZeroAge<-data.frame(TMinusZeroAge)
##CALCULATE iTFR
ImpliedTFRNew<-((TMinusZeroAge_NDF[1]+TMinusZeroAge_NDF[HALFSIZE+1])/5)/sum(TMinusZeroAge_NDF[4:10])*FERTWIDTH
return(c(TMinusZeroAge=TMinusZeroAge,TMinusOneAge=TMinusOneAgeNew,ImpliedTFRNew=ImpliedTFRNew,e0FStart=e0FStart,e0MStart=e0MStart,e0FAdj=e0FAdj,e0MAdj=e0MAdj,CURRENTSTEP=CURRENTSTEP+1))
}
}
##APPLY PROJECTIONS
CCRNew<-CCRProject(TMinusZeroAge,ImpliedTFR2015,BA_start,BA_end,CURRENTSTEP)
while(CCRNew$CURRENTSTEP<STEPS+1) {CCRNew<-CCRProject(CCRNew$TMinusZeroAge,CCRNew$ImpliedTFRNew,BA_start,BA_end,CCRNew$CURRENTSTEP)}
##CALCULATE EFFECTIVE COHORT CHANGE RATIOS
CCRatios<-Ratios
for (i in 2:(HALFSIZE-1)) {CCRatios[i]<-CCRNew$TMinusZeroAge[i]/CCRNew$TMinusOneAge[i-1]}
for (i in (HALFSIZE+2):(SIZE-1)) {CCRatios[i]<-CCRNew$TMinusZeroAge[i]/CCRNew$TMinusOneAge[i-1]}
##OPEN-ENDED AGE GROUPS
CCRatios[HALFSIZE]<-CCRNew$TMinusZeroAge[HALFSIZE]/(CCRNew$TMinusOneAge[HALFSIZE-1]+CCRNew$TMinusOneAge[HALFSIZE])
CCRatios[SIZE]<-CCRNew$TMinusZeroAge[SIZE]/(CCRNew$TMinusOneAge[SIZE-1]+CCRNew$TMinusOneAge[SIZE])
##BY SEX
CCRatiosF<-CCRatios[2:HALFSIZE]
CCRatiosM<-CCRatios[2+HALFSIZE:(SIZE-2)]
##iTFR
ImpliedTFRNew<-CCRNew$ImpliedTFRNew
##ESTIMATE STABLE POPULATION BY SIMULATION
TMinusZeroAge<-TMinusZeroAgeInit
CCRStable<-CCRProject(TMinusZeroAge,ImpliedTFR2015,BA_start,BA_end,0)
while(CCRStable$CURRENTSTEP<STEPSSTABLE+1) {CCRStable<-CCRProject(CCRStable$TMinusZeroAge,CCRStable$ImpliedTFRNew,BA_start,BA_end,CCRStable$CURRENTSTEP)}
ImpliedTFRStable<-((CCRStable$TMinusZeroAge[1]+CCRStable$TMinusZeroAge[HALFSIZE+1])/5)/sum(CCRStable$TMinusZeroAge[4:10])*FERTWIDTH
##########
##TABLING DATA
##########
#JUST ALL POPULATIONS USED IN GRAPHS
NewAge_F<-CCRNew$TMinusZeroAge[1:HALFSIZE]
StableAge_F<-CCRStable$TMinusZeroAge[1:HALFSIZE]
TMinusOneAgeInit_F<-TMinusOneAgeInit[1:HALFSIZE]
TMinusZeroAgeInit_F<-TMinusZeroAgeInit[1:HALFSIZE]
NewAge_M<-CCRNew$TMinusZeroAge[(HALFSIZE+1):SIZE]
StableAge_M<-CCRStable$TMinusZeroAge[(HALFSIZE+1):SIZE]
TMinusOneAgeInit_M<-TMinusOneAgeInit[(HALFSIZE+1):SIZE]
TMinusZeroAgeInit_M<-TMinusZeroAgeInit[(HALFSIZE+1):SIZE]
NewAge_T<-NewAge_F+NewAge_M
StableAge_T<-StableAge_F+StableAge_M
TMinusOneAgeInit_T<-TMinusOneAgeInit_F+TMinusOneAgeInit_M
TMinusZeroAgeInit_T<-TMinusZeroAgeInit_F+TMinusZeroAgeInit_M
NewAge<-array(c(NewAge_T,NewAge_F,NewAge_M),c(HALFSIZE,3))
StableAge<-array(c(StableAge_T,StableAge_F,StableAge_M),c(HALFSIZE,3))
TMinusOneAgeInit<-array(c(TMinusOneAgeInit_T,TMinusOneAgeInit_F,TMinusOneAgeInit_M),c(HALFSIZE,3))
TMinusZeroAgeInit<-array(c(TMinusZeroAgeInit_T,TMinusZeroAgeInit_F,TMinusZeroAgeInit_M),c(HALFSIZE,3))
##########
##GRAPHING DATA (SOME ~HACKY LABELING SO MAY [LIKELY] NOT RENDER WELL)
##########
##FIRST GRAPH - MAJOR SUMMARY
agegroups<-c("0-4", "5-9", "10-14", "15-19", "20-24", "25-29", "30-34", "35-39", "40-44", "45-49", "50-54", "55-59", "60-64", "65-69", "70-74", "75-79", "80-84", "85+")
if(SelectBySex=="Total") {plot(TMinusOneAgeInit[,1]/sum(TMinusOneAgeInit[,1]),type="l",col="orange",main=paste(text=c(input$County,", ",input$Sex),collapse=""),ylim=c(0,.12),axes=FALSE,xlab="",ylab="Population (proportional)",lwd=4)}
if(SelectBySex=="Female") {plot(TMinusOneAgeInit[,2]/sum(TMinusOneAgeInit[,2]),type="l",col="orange",main=paste(text=c(input$County,", ",input$Sex),collapse=""),ylim=c(0,.12),axes=FALSE,xlab="",ylab="Population (proportional)",lwd=4)}
if(SelectBySex=="Male") {plot(TMinusOneAgeInit[,3]/sum(TMinusOneAgeInit[,3]),type="l",col="orange",main=paste(text=c(input$County,", ",input$Sex),collapse=""),ylim=c(0,.12),axes=FALSE,xlab="",ylab="Population (proportional)",lwd=4)}
if(SelectBySex=="Total") {lines(TMinusZeroAgeInit[,1]/sum(TMinusZeroAgeInit[,1]),col="blue",lwd=4)}
if(SelectBySex=="Female") {lines(TMinusZeroAgeInit[,2]/sum(TMinusZeroAgeInit[,2]),col="blue",lwd=4)}
if(SelectBySex=="Male") {lines(TMinusZeroAgeInit[,3]/sum(TMinusZeroAgeInit[,3]),col="blue",lwd=4)}
if(SelectBySex=="Total") {lines(NewAge[,1]/sum(NewAge[,1]),col="dark green",lty=1,lwd=4)}
if(SelectBySex=="Female") {lines(NewAge[,2]/sum(NewAge[,2]),col="dark green",lty=1,lwd=4)}
if(SelectBySex=="Male") {lines(NewAge[,3]/sum(NewAge[,3]),col="dark green",lty=1,lwd=4)}
if (min(StableAge)>=0) {
mtext(side=1,"Age groups",line=4,cex=.75)
axis(side=1,at=1:HALFSIZE,las=2,labels=agegroups,cex.axis=0.9)
axis(side=2)
legend(11.5, .12, legend=c("2010 (estimate)","2015 (estimate)",paste(c(PROJECTIONYEAR),"(projection)"),"Stable"),
col=c("orange","blue","dark green","black"), lty=c(1,1,1,3),lwd=c(4,4,4,1.5),cex=1.2)
}
if (min(StableAge)<0) {
mtext(side=1,"Age groups",line=4,cex=.75)
axis(side=1,at=1:HALFSIZE,las=2,labels=agegroups,cex.axis=0.9)
axis(side=2)
legend(11.5, .12, legend=c("2010 (estimate)","2015 (estimate)",paste(c(PROJECTIONYEAR),"(projection)")),
col=c("orange","blue","dark green"), lty=c(1,1,1),lwd=c(4,4,4),cex=1.2)
}
mtext(side=1,c("Sum 2010:"),line=-15,adj=.125,col="orange")
if(SelectBySex=="Total") {mtext(side=1,c(sum(TMinusOneAgeInit[,1])),line=-15,adj=.3,col="orange")}
if(SelectBySex=="Female") {mtext(side=1,c(sum(TMinusOneAgeInit[,2])),line=-15,adj=.3,col="orange")}
if(SelectBySex=="Male") {mtext(side=1,c(sum(TMinusOneAgeInit[,3])),line=-15,adj=.3,col="orange")}
mtext(side=1,c("Sum 2015:"),line=-14,adj=.125,col="blue")
if(SelectBySex=="Total") {mtext(side=1,c(sum(TMinusZeroAgeInit[,1])),line=-14,adj=.3,col="blue")}
if(SelectBySex=="Female") {mtext(side=1,c(sum(TMinusZeroAgeInit[,2])),line=-14,adj=.3,col="blue")}
if(SelectBySex=="Male") {mtext(side=1,c(sum(TMinusZeroAgeInit[,3])),line=-14,adj=.3,col="blue")}
mtext(side=1,c("Sum "),line=-13,adj=.117,col="dark green")
mtext(side=1,c(PROJECTIONYEAR),line=-13,adj=.18,col="dark green")
mtext(side=1,c(":"),line=-13,adj=.225,col="dark green")
if(SelectBySex=="Total") {mtext(side=1,c(round(sum(NewAge[,1]))),line=-13,adj=.3,col="dark green")}
if(SelectBySex=="Female") {mtext(side=1,c(round(sum(NewAge[,2]))),line=-13,adj=.3,col="dark green")}
if(SelectBySex=="Male") {mtext(side=1,c(round(sum(NewAge[,3]))),line=-13,adj=.3,col="dark green")}
mtext(side=1,c("iTFR 2010:"),line=-7,adj=.13,col="orange")
mtext(side=1,c(round(ImpliedTFR2010,2)),line=-7,adj=.29,col="orange")
mtext(side=1,c("iTFR 2015:"),line=-6,adj=.13,col="blue")
mtext(side=1,c(round(ImpliedTFR2015,2)),line=-6,adj=.29,col="blue")
mtext(side=1,c("iTFR"),line=-5,adj=.12,col="dark green")
mtext(side=1,c(PROJECTIONYEAR),line=-5,adj=.185,col="dark green")
mtext(side=1,c(":"),line=-5,adj=.23,col="dark green")
mtext(side=1,c(round(ImpliedTFRNew,2)),line=-5,adj=.29,col="dark green")
if(SelectBySex=="Total") {LASTGROWTHRATE<-paste(text=c("R (2010 to 2015): ", round(log(sum(TMinusZeroAgeInit[,1])/sum(TMinusOneAgeInit[,1]))/5*100,2)),collapse="")}
if(SelectBySex=="Male") {LASTGROWTHRATE<-paste(text=c("R (2010 to 2015): ", round(log(sum(TMinusZeroAgeInit[,1])/sum(TMinusOneAgeInit[,1]))/5*100,2)),collapse="")}
if(SelectBySex=="Female") {LASTGROWTHRATE<-paste(text=c("R (2010 to 2015): ", round(log(sum(TMinusZeroAgeInit[,1])/sum(TMinusOneAgeInit[,1]))/5*100,2)),collapse="")}
mtext(side=1,c(LASTGROWTHRATE),line=-11,adj=.15,col="blue")
if(SelectBySex=="Total") {GROWTHRATE<-paste(text=c("R (2015 to ",PROJECTIONYEAR,"): ", round(log(sum(NewAge[,1])/sum(TMinusZeroAgeInit[,1]))/(STEPS*5)*100,2)),collapse="")}
if(SelectBySex=="Female") {GROWTHRATE<-paste(text=c("R (2015 to ",PROJECTIONYEAR,"): ", round(log(sum(NewAge[,2])/sum(TMinusZeroAgeInit[,2]))/(STEPS*5)*100,2)),collapse="")}
if(SelectBySex=="Male") {GROWTHRATE<-paste(text=c("R (2015 to ",PROJECTIONYEAR,"): ", round(log(sum(NewAge[,3])/sum(TMinusZeroAgeInit[,3]))/(STEPS*5)*100,2)),collapse="")}
mtext(side=1,c(GROWTHRATE),line=-10,adj=.15,col="dark green")
if (min(StableAge)>=0) {
if(SelectBySex=="Total") {STABLEGROWTHRATE<-paste(text=c("~r (2015 forward): ", round(log(sum(StableAge[,1])/sum(TMinusZeroAgeInit[,1]))/(STEPSSTABLE*5)*100,2)),collapse="")}
if(SelectBySex=="Female") {STABLEGROWTHRATE<-paste(text=c("~r (2015 forward): ", round(log(sum(StableAge[,2])/sum(TMinusZeroAgeInit[,2]))/(STEPSSTABLE*5)*100,2)),collapse="")}
if(SelectBySex=="Male") {STABLEGROWTHRATE<-paste(text=c("~r (2015 forward): ", round(log(sum(StableAge[,3])/sum(TMinusZeroAgeInit[,3]))/(STEPSSTABLE*5)*100,2)),collapse="")}
mtext(side=1,c(STABLEGROWTHRATE),line=-9,adj=.15,col="black")
if(SelectBySex=="Total") {lines(StableAge[,1]/sum(StableAge[,1]),col="black",lty=3,lwd=1.5)}
if(SelectBySex=="Female") {lines(StableAge[,2]/sum(StableAge[,2]),col="black",lty=3,lwd=1.5)}
if(SelectBySex=="Male") {lines(StableAge[,3]/sum(StableAge[,3]),col="black",lty=3,lwd=1.5)}
}
if (min(StableAge)<0) {
if(SelectBySex=="Total") {STABLEGROWTHRATE<-paste(text=c("~r (2015 forward): ..."),collapse="")}
if(SelectBySex=="Female") {STABLEGROWTHRATE<-paste(text=c("~r (2015 forward): ..."),collapse="")}
if(SelectBySex=="Male") {STABLEGROWTHRATE<-paste(text=c("~r (2015 forward): ..."),collapse="")}
mtext(side=1,c(STABLEGROWTHRATE),line=-9,adj=.15,col="black")
}
if (input$ImputeMort=="YES" & SelectBySex=="Total") {
mtext(side=1,c("Imputed starting e0, female: "),line=-3,adj=.157,col="black")
mtext(side=1,c(round(CCRNew$e0FStart,1)),line=-3,adj=.455,col="black")
mtext(side=1,c("Imputed starting e0, male: "),line=-2,adj=.155,col="black")
mtext(side=1,c(round(CCRNew$e0MStart,1)),line=-2,adj=.4565,col="black")
}
if (input$ImputeMort=="YES" & SelectBySex=="Female") {
mtext(side=1,c("Imputed starting e0, female: "),line=-3,adj=.157,col="black")
mtext(side=1,c(round(CCRNew$e0FStart,1)),line=-3,adj=.455,col="black")
}
if (input$ImputeMort=="YES" & SelectBySex=="Male") {
mtext(side=1,c("Imputed starting e0, male: "),line=-3,adj=.155,col="black")
mtext(side=1,c(round(CCRNew$e0MStart,1)),line=-3,adj=.4565,col="black")
}
##SECOND GRAPH - COHORT CHANGE RATIOS WITH AND WITHOUT ADJUSTMENTS
agegroups2<-c("5-9", "10-14", "15-19", "20-24", "25-29", "30-34", "35-39", "40-44", "45-49", "50-54", "55-59", "60-64", "65-69", "70-74", "75-79", "80-84", "85+")
plot(Ratios[2:18],type="l",col="dodger blue",main=paste(text=c("Effective Cohort Change Ratios, ",PROJECTIONYEAR-5," to ",PROJECTIONYEAR),collapse=""),ylim=c(.25,1.75),axes=FALSE,xlab="",ylab="Ratio",lwd=4)
##OPEN-ENDED AGE GROUP OPTION
mtext(side=1,c("(Note: 85+ ratios are applied to full 80+ age groups)"),line=-42,adj=.50,col="black")
abline(a=NULL, b=NULL, h=1, v=NULL)
lines(Ratios[20:36],type="l",col="gold",lwd=4)
lines(CCRatiosF,type="l",col="dodger blue",lty=2,lwd=2)
lines(CCRatiosM,type="l",col="gold",lty=2,lwd=2)
mtext(side=1,"Age groups",line=4,cex=.75)
axis(side=1,at=1:(HALFSIZE-1),labels=agegroups2,las=2,cex.axis=0.9)
axis(side=2)
legend(7,1.75, legend=c("Female","Male", "Female, with migration and mortality adjustments","Male, with migration and mortality adjustments"),
col=c("dodger blue","gold","dodger blue","gold"), lty=c(1,1,2,2),lwd=c(4,4,2,2),cex=1.2)
if (input$ImputeMort=="YES") {
mtext(side=1,c("Imputed e0, female:"),line=-10,adj=.125,col="black")
mtext(side=1,c(round(CCRNew$e0FAdj,1)),line=-10,adj=.35,col="black")
mtext(side=1,c("Imputed e0, male:"),line=-9,adj=.122,col="black")
mtext(side=1,c(round(CCRNew$e0MAdj,1)),line=-9,adj=.35,col="black")
}
##THIRD GRAPH - PYRAMID (FEMALE PORTION)
barplot(NewAge_F,horiz=T,names=agegroups,space=0,xlim=c(max(NewAge_M)*2,0),col="dodger blue",las=1,main=paste(text=c("Female, ",PROJECTIONYEAR),collapse=""))
##FOURTH GRAPH - PYRAMID (MALE PORTION)
barplot(NewAge_M,horiz=T,names=FALSE,space=0,xlim=c(0,max(NewAge_M)*2),col="gold",main=paste(text=c("Male, ",PROJECTIONYEAR),collapse=""))
}
},height=1200,width=1200)
}
shinyApp(ui = ui, server = server)