R Under development (unstable) (2023-09-29 r85235 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> start.test <- function(name) cat('\n<=== Starting test of', name,'====\n')
> test.ok <- function(name) cat('\n==== Test of', name, 'OK.===>\n')
> 
> test.run.annual.simulation <- function(parallel = FALSE) {
+     # run MCMC
+     test.name <- 'running annual migration MCMC for US states'
+     if(parallel) test.name <- paste(test.name, "(in parallel)")
+     start.test(test.name)
+     us.mig.file <- file.path(find.package("bayesMig"), "extdata", "USmigrates.txt")
+     sim.dir <- tempfile()
+     m <- run.mig.mcmc(nr.chains = 2, iter = 30, thin = 1, my.mig.file = us.mig.file, 
+              output.dir = sim.dir, present.year = 2017, annual = TRUE, parallel = parallel)
+     stopifnot(m$mcmc.list[[1]]$finished.iter == 30)
+     stopifnot(get.total.iterations(m$mcmc.list, 0) == 60)
+     
+     par.values <- get.mig.parameter.traces(m$mcmc.list, burnin = 5)
+     stopifnot(all(dim(par.values) == c(50, 4)))
+     par.values.cs <- get.mig.parameter.traces.cs(m$mcmc.list, 
+                         country.obj = get.country.object("California", meta = m$meta),
+                         burnin = 5, par.names = "phi_c")
+     stopifnot(all(dim(par.values.cs) == c(50, 1)))
+     test.ok(test.name)
+     
+     # Prediction
+     test.name <- 'running annual projections'
+     start.test(test.name)
+     pred <- mig.predict(sim.dir = sim.dir, burnin = 10, end.year = 2050)
+     spred <- summary(pred)
+     stopifnot(spred$nr.traj == 40)
+     stopifnot(nrow(get.countries.table(pred))== 52)
+     stopifnot(dim(pred$quantiles)[3] == length(2017:2050))
+     test.ok(test.name)
+     
+     # output
+     test.name <- 'analyzing output of annual projections'
+     start.test(test.name)
+     tab <- mig.trajectories.table(pred, "Hawaii")
+     years <- as.integer(rownames(tab))
+     should.be.years <- 2001:2050
+     stopifnot(length(years) == length(should.be.years))
+     stopifnot(all(years == should.be.years))
+     stopifnot(all(dim(tab) == c(length(should.be.years), 5)))
+     test.ok(test.name)
+     
+     unlink(sim.dir, recursive=TRUE)
+ }
> 
> test.run.national.simulation <- function(parallel = FALSE) {
+     # run MCMC
+     test.name <- 'running national migration MCMC'
+     if(parallel) test.name <- paste(test.name, "(in parallel)")
+     start.test(test.name)
+ 
+     sim.dir <- tempfile()
+     m <- run.mig.mcmc(nr.chains = 2, iter = 60, thin = 2, output.dir = sim.dir, parallel = parallel,
+                       wpp.year = 2019)
+     stopifnot(m$mcmc.list[[1]]$finished.iter == 60)
+     stopifnot(get.total.iterations(m$mcmc.list, 0) == 120)
+     test.ok(test.name)
+     
+     # Prediction
+     test.name <- 'running national projections'
+     start.test(test.name)
+     pred <- mig.predict(sim.dir = sim.dir, burnin = 10, end.year = 2050)
+     spred <- summary(pred)
+     stopifnot(spred$nr.traj == 50)
+     stopifnot(nrow(get.countries.table(pred))== 201)
+     stopifnot(dim(pred$quantiles)[3] == length(seq(2018, 2048, by = 5)))
+     test.ok(test.name)
+     
+     # output
+     test.name <- 'analyzing output of national projections'
+     start.test(test.name)
+     tab <- mig.trajectories.table(pred, "France")
+     years <- as.integer(rownames(tab))
+     should.be.years <- seq(1953, 2048, by = 5)
+     stopifnot(length(years) == length(should.be.years))
+     stopifnot(all(years == should.be.years))
+     test.ok(test.name)
+     
+     unlink(sim.dir, recursive=TRUE)
+ }
> 
> test.run.annual.national.simulation <- function(parallel = FALSE) {
+     # run MCMC using wpp2022
+     test.name <- 'running annual national migration MCMC'
+     if(parallel) test.name <- paste(test.name, "(in parallel)")
+     start.test(test.name)
+     
+     sim.dir <- tempfile()
+     
+     # find small countries to be excluded (take it from bayesTFR include dataset)
+     data(include_2022, package = "bayesTFR")
+     small.countries <- subset(include_2022, include_code == 1)$country_code
+     
+     m <- run.mig.mcmc(nr.chains = 2, iter = 60, thin = 2, output.dir = sim.dir, 
+                       parallel = parallel, annual = TRUE, wpp.year = 2022,
+                       present.year = 2021, exclude.from.world = small.countries,
+                       use.cummulative.threshold = TRUE)
+     
+     stopifnot(m$meta$nr.countries.est == 203)
+     stopifnot(m$meta$nr.countries == 236)
+     stopifnot(m$mcmc.list[[1]]$finished.iter == 60)
+     stopifnot(get.total.iterations(m$mcmc.list, 0) == 120)
+     test.ok(test.name)
+     
+     # Prediction
+     test.name <- 'running annual national projections'
+     start.test(test.name)
+     pred <- mig.predict(sim.dir = sim.dir, burnin = 10, end.year = 2050)
+     spred <- summary(pred)
+     stopifnot(spred$nr.traj == 50)
+     stopifnot(nrow(get.countries.table(pred))== 236)
+     stopifnot(dim(pred$quantiles)[3] == length(seq(2021, 2050, by = 1)))
+     test.ok(test.name)
+     
+     # output
+     test.name <- 'analyzing output of annual national projections'
+     start.test(test.name)
+     tab <- mig.trajectories.table(pred, "Ireland")
+     years <- as.integer(rownames(tab))
+     should.be.years <- seq(1951, 2050, by = 1)
+     stopifnot(length(years) == length(should.be.years))
+     stopifnot(all(years == should.be.years))
+     test.ok(test.name)
+     
+     unlink(sim.dir, recursive=TRUE)
+ }
> 
> 
> test.run.annual.national.simulation.with.interpolation <- function(parallel = FALSE) {
+     # run MCMC
+     test.name <- 'running annual national migration MCMC with interpolated data'
+     if(parallel) test.name <- paste(test.name, "(in parallel)")
+     start.test(test.name)
+     
+     sim.dir <- tempfile()
+     m <- run.mig.mcmc(nr.chains = 2, iter = 60, thin = 2, output.dir = sim.dir, 
+                       parallel = parallel, annual = TRUE, wpp.year = 2019)
+     
+     stopifnot(m$mcmc.list[[1]]$finished.iter == 60)
+     stopifnot(get.total.iterations(m$mcmc.list, 0) == 120)
+     test.ok(test.name)
+     
+     # Prediction
+     test.name <- 'running annual national projections with interpolated data'
+     start.test(test.name)
+     pred <- mig.predict(sim.dir = sim.dir, burnin = 10, end.year = 2050)
+     spred <- summary(pred)
+     stopifnot(spred$nr.traj == 50)
+     stopifnot(nrow(get.countries.table(pred))== 201)
+     stopifnot(dim(pred$quantiles)[3] == length(seq(2020, 2050, by = 1)))
+     test.ok(test.name)
+     
+     # output
+     test.name <- 'analyzing output of annual national projections with interpolated data'
+     start.test(test.name)
+     tab <- mig.trajectories.table(pred, "Ireland")
+     years <- as.integer(rownames(tab))
+     should.be.years <- seq(1950, 2050, by = 1)
+     stopifnot(length(years) == length(should.be.years))
+     stopifnot(all(years == should.be.years))
+     test.ok(test.name)
+     
+     unlink(sim.dir, recursive=TRUE)
+ }
> 
> test.include.code.and.last.observed <- function(parallel = FALSE) {
+     # run MCMC
+     test.name <- 'running annual migration MCMC with states excluded and missing data'
+     if(parallel) test.name <- paste(test.name, "(in parallel)")
+     start.test(test.name)
+     us.mig.file <- file.path(find.package("bayesMig"), "extdata", "USmigrates.txt")
+     mig <- bayesTFR:::read.tfr.file(file = us.mig.file)
+     mig$include_code <- 2
+     mig$last.observed <- 2017
+     mig[mig$name %in% c("Rhode Island", "District of Columbia"), "include_code"] <- 1 # used only for prediction
+     mig[mig$name == "Hawaii", "include_code"] <- 0 # excluded
+     mig[mig$name == "Washington", "last.observed"] <- 2015 # 2 data points will be imputed
+     mig[mig$name == "Idaho", "2017"] <- NA # 1 data point missing without changing last.observed
+     migfile <- tempfile()
+     write.table(mig, file = migfile, sep='\t', row.names=FALSE)
+     
+     sim.dir <- tempfile()
+     m <- run.mig.mcmc(nr.chains = 2, iter = 30, thin = 1, my.mig.file = migfile, 
+                       output.dir = sim.dir, present.year = 2017, annual = TRUE, parallel = parallel,
+                       exclude.from.world = 29) # also exclude Nevada
+ 
+     stopifnot((m$meta$nr.countries - m$meta$nr.countries.est) == 3) # 3 countries excluded from estimation
+     stopifnot(! "Hawaii" %in% m$meta$regions$country_name) # Hawaii is not included at all
+     stopifnot(all(is.na(m$meta$mig.rates[m$meta$regions$country_name == "Washington", c("2016", "2017")]))) # missing data
+     test.ok(test.name)
+     
+     # Prediction
+     test.name <- 'running annual projections with data imputation'
+     start.test(test.name)
+     pred <- mig.predict(sim.dir = sim.dir, burnin = 10, end.year = 2050)
+     
+     imputed <- pred$mig.rates.reconstructed[m$meta$regions$country_name == "Washington", c("2016", "2017")]
+     orig <- m$meta$mig.rates.all[m$meta$regions$country_name == "Washington", c("2016", "2017")]
+     stopifnot(all(!is.na(imputed))) # was it imputed
+     stopifnot(all.equal(imputed, orig)  > 0.1) # relative difference is big
+     stopifnot(nrow(get.countries.table(pred))== 51) # 51 states included
+     stopifnot(!is.na(pred$mig.rates.reconstructed[m$meta$regions$country_name == "Idaho", "2017"])) # Idaho was imputed
+     stopifnot(dim(pred$quantiles)[3] == length(2017:2050))
+     test.ok(test.name)
+     
+     unlink(migfile)
+     unlink(sim.dir, recursive=TRUE)
+ }
> 
> proc.time()
   user  system elapsed 
   0.18    0.01    0.20