-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
9 changed files
with
208 additions
and
122 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,12 @@ | ||
| Package: bayesMig | ||
| Version: 0.4-6.9004 | ||
| Date: 2024-06-07 | ||
| Version: 0.4-6.9005 | ||
| Date: 2024-11-07 | ||
| Title: Bayesian Projection of Migration | ||
| Authors@R: c(person("Jon", "Azose", role = "aut"), | ||
| person("Hana", "Sevcikova", email = "[email protected]", role = c("aut", "cre")), | ||
| person("Adrian", "Raftery", role = c("aut"))) | ||
| Depends: R (>= 3.5.0), bayesTFR | ||
| Imports: coda, truncnorm, wpp2019 | ||
| Imports: coda, truncnorm, wpp2019, data.table | ||
| Suggests: | ||
| Description: Producing probabilistic projections of net migration rate for all countries of the world | ||
| or for subnational units using a Bayesian hierarchical model by Azose an Raftery (2015) <doi:10.1007/s13524-015-0415-0>. | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -12,7 +12,7 @@ | |
| #' Maintainer: Hana Sevcikova <[email protected]> | ||
| #' | ||
| #' @docType package | ||
| #' @import coda truncnorm wpp2019 | ||
| #' @import coda truncnorm wpp2019 data.table | ||
| #' @import grDevices graphics stats utils bayesTFR | ||
| #' @importFrom utils data | ||
| #' | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,175 @@ | ||
| #' @title Adjusting the Projection Medians | ||
| #' | ||
| #' @description These functions are to be used by expert analysts. They allow to | ||
| #' change the projection medians either to specific values, or shift the medians | ||
| #' by a given constant or align one projection object with another. | ||
| #' | ||
| #' @param sim.dir Directory containing the prediction object. | ||
| #' @param country Name or numerical code of a country. | ||
| #' @param values Vector of the new median values. | ||
| #' @param years Numeric vector giving years for which to change the median. | ||
| #' In \code{mig.median.set} it gives years which \code{values} correspond to. | ||
| #' Ideally it should be of the same length as \code{values}. If it is \code{NULL}, | ||
| #' \code{values} are set starting from the first prediction time period. | ||
| #' If \code{values} correspond to consecutive years, only the first year might be given here. | ||
| #' In \code{mig.align.predictions} it gives years for which the medians should be aligned. | ||
| #' @param \dots Additional arguments passed to the underlying adjustment functions, such as | ||
| #' \code{verbose} to show/hide the progress of the adjustment. | ||
| #' For \code{mig.shift.prediction.to.wpp} it can be \code{stat} with values \dQuote{median} (default) | ||
| #' or \dQuote{mean} to specify which statistics should be adjusted; | ||
| #' \code{wpp.year} to adjust it to if it differs from the wpp year of the simulation. | ||
| #' | ||
| #' @details The function \code{mig.median.set} can be used to set the medians of the | ||
| #' given country to specific values. | ||
| #' | ||
| #' @return All functions return an updated object of class \code{\link{bayesMig.prediction}}. | ||
| #' @export | ||
| #' @rdname mig.adjust | ||
| mig.median.set <- function(sim.dir, country, values, years=NULL, ...) { | ||
| pred <- get.mig.prediction(sim.dir) | ||
| new.pred <- bayesTFR:::.bdem.median.set(pred, type='mig', country=country, | ||
| values=values, years=years, ...) | ||
| store.bayesMig.prediction(new.pred) | ||
| invisible(new.pred) | ||
| } | ||
|
|
||
| #' @export | ||
| #' @keywords internal | ||
| #' @rdname internal | ||
| #' | ||
| get.mig.shift <- function(country.code, pred) return(bayesTFR::get.tfr.shift(country.code, pred)) | ||
|
|
||
| #' @param reset Logical. If \code{TRUE} medians in a range of \code{from} and \code{to} are | ||
| #' reset to their original values. | ||
| #' @param shift Constant by which the medians should be offset. It is not used if \code{reset} is \code{TRUE}. | ||
| #' @param from Year from which the offset/reset should start. By default, it starts at the first prediction period. | ||
| #' @param to Year until which the offset/reset should be done. By default, it is set to the last prediction period. | ||
| #' | ||
| #' @details Function \code{mig.median.shift} can be used to offset the medians by a specific constant, or to reset | ||
| #' the medians to their original values. | ||
| #' @export | ||
| #' @rdname mig.adjust | ||
| mig.median.shift <- function(sim.dir, country, reset = FALSE, shift = 0, | ||
| from = NULL, to = NULL) { | ||
| pred <- get.mig.prediction(sim.dir) | ||
| new.pred <- bayesTFR:::.bdem.median.shift(pred, type='mig', country=country, reset=reset, | ||
| shift=shift, from=from, to=to) | ||
| store.bayesMig.prediction(new.pred) | ||
| invisible(new.pred) | ||
| } | ||
|
|
||
| #' @param countries Vector of country names or codes. If this argument is \code{NULL} (default), | ||
| #' the reset is done for all countries. | ||
| #' | ||
| #' @details Function \code{mig.median.reset} resets medians of the given countries | ||
| #' to the original values. By default it deletes adjustments for all countries. | ||
| #' @export | ||
| #' @rdname mig.adjust | ||
| mig.median.reset <- function(sim.dir, countries = NULL) { | ||
| if(is.null(countries)) { | ||
| pred <- get.mig.prediction(sim.dir) | ||
| pred$median.shift <- NULL | ||
| store.bayesMig.prediction(pred) | ||
| cat('\nMedians for all countries reset.\n') | ||
| } else | ||
| for(country in countries) pred <- mig.median.shift(sim.dir, country, reset=TRUE) | ||
| invisible(pred) | ||
| } | ||
|
|
||
| #' @param sim.dir1 Directory with the bayesMig prediction object to be adjusted. | ||
| #' @param sim.dir2 Directory with the bayesMig prediction object used to align the medians from \code{sim.dir1} to. | ||
| #' @param country.codes Numerical codes of countries to adjust. By default all countries | ||
| #' found in \code{sim.dir2} are adjusted in \code{sim.dir1}. | ||
| #' @details Function \code{mig.align.predictions} shifts medians stored in \code{sim.dir1} to match | ||
| #' the medians in \code{sim.dir1}. | ||
| #' | ||
| #' In all cases, if a median is modified, the corresponding offset is stored in the prediction object | ||
| #' (element \code{median.shift}). All functions write the updated prediction object back to disk. All | ||
| #' functions in the package that use trajectories and trajectory statistics use the \code{median.shift} | ||
| #' values to offset the results correspondingly, i.e. trajectories are shifted the same way as the | ||
| #' medians. | ||
| #' @export | ||
| #' @rdname mig.adjust | ||
| mig.align.predictions <- function(sim.dir1, sim.dir2, country.codes = NULL, | ||
| years = NULL, ...){ | ||
| pred1 <- get.mig.prediction(sim.dir1) | ||
| pred2 <- get.mig.prediction(sim.dir2) | ||
| cntries1 <- if(is.null(country.codes)) get.countries.table(pred1)$code else country.codes | ||
| cntries2 <- get.countries.table(pred2)$code | ||
| avail.years <- dimnames(pred2$quantiles)[[3]] | ||
| if(is.null(years)) | ||
| years <- avail.years | ||
| else years <- intersect(as.character(years), avail.years) | ||
| for(cntry in cntries1){ | ||
| cidx <- which(cntries2 == cntry) | ||
| if(length(cidx) == 0){ | ||
| warning("Country ", cntry, " not found in sim.dir2. No adjustment for this country.") | ||
| next | ||
| } | ||
| adjust.to <- get.median.from.prediction(pred2, cidx, cntry)[years] | ||
| pred <- mig.median.set(sim.dir1, cntry, values = adjust.to, | ||
| years = as.integer(names(adjust.to)), ...) | ||
| } | ||
| invisible(pred) | ||
| } | ||
|
|
||
| .do.mig.shift.prediction.to.wpp <- function(pred, stat = "median", wpp.year = NULL, verbose = TRUE){ | ||
| country_code <- year <- NULL # for CRAN check not to complain | ||
| meta <- pred$mcmc.set$meta | ||
| wpp.year <- if(!is.null(wpp.year)) wpp.year else meta$wpp.year | ||
| countries <- get.countries.table(pred$mcmc.set)$code | ||
| if(wpp.year < 2024) stop("Function not implemented for WPP < 2024.") | ||
| n <- if(meta$annual.simulation) "1" else "5" | ||
| migcounts.wpp <- bayesTFR:::load.bdem.dataset(paste0("migproj", n, "dt"), wpp.year = wpp.year, verbose = verbose) | ||
| popcounts.wpp <- bayesTFR:::load.bdem.dataset(paste0("popproj", n, "dt"), wpp.year = wpp.year, verbose = verbose) | ||
| if(!meta$annual.simulation) migcounts.wpp[, year := year + 2] # align migration and pop years | ||
|
|
||
| migrates.wpp <- merge(migcounts.wpp[, c("country_code", "name", "year", "mig"), with = FALSE], | ||
| popcounts.wpp[, c("country_code", "name", "year", "pop"), with = FALSE], | ||
| by = c("country_code", "name", "year") | ||
| ) | ||
| migrates.wpp$wpp <- migrates.wpp$mig / (migrates.wpp$pop - migrates.wpp$mig) | ||
| if(!meta$annual.simulation) migrates.wpp[, year := year - 2] | ||
|
|
||
| pred.years <- as.numeric(dimnames(pred$quantiles)[[3]]) | ||
| pred$median.shift <- NULL | ||
|
|
||
| if(verbose) cat("\n") | ||
| for(icntry in seq_along(countries)) { | ||
| if (verbose) { | ||
| if(interactive()) cat("\rAdjusting countries' prediction to wpp", wpp.year, " ... ", round(icntry/length(countries) * 100), ' %') | ||
| else { | ||
| if (icntry == 1) | ||
| cat("Adjusting countries' prediction to wpp", wpp.year, " ... ") | ||
| cat(icntry, ", ") | ||
| } | ||
| } | ||
| cntry <- countries[icntry] | ||
| if(!stat %in% c("median", "mean")) stop("Argument 'stat' must be 'median' or 'mean', but is ", stat, ".") | ||
| to.match <- merge(data.table::data.table(year = pred.years, median = pred$quantiles[icntry, "0.5", ]), | ||
| migrates.wpp[country_code == cntry, c("year", "wpp"), with = FALSE], | ||
| by = "year", all.x = TRUE) | ||
| if(stat == "mean") to.match[["median"]] <- to.match[["median"]] + pred$traj.mean.sd[icntry, 1, ] - to.match[["median"]] # difference between the mean and median | ||
| to.match$wpp[is.na(to.match$wpp)] <- to.match$median[is.na(to.match$wpp)] # no shift for years that don't match | ||
| to.match$shift <- to.match$wpp - to.match$median | ||
| if(sum(to.match$shift) != 0) | ||
| pred$median.shift[[as.character(cntry)]] <- to.match$shift | ||
| } | ||
| if(verbose) cat("\n") | ||
| return(pred) | ||
| } | ||
|
|
||
| #' @details Function \code{mig.shift.prediction.to.wpp} shifts the projected medians or means | ||
| #' (if \code{stat} is \dQuote{mean}), so that they correspond to the values found in the \code{migproj1dt} or \code{migproj5dt} | ||
| #' datasets of the \pkg{wpp} package that either corresponds to the package used for the simulation itself | ||
| #' or is given by the \code{wpp.year} argument. Currently, the function only works for \pkg{wpp2024}. | ||
| #' Note that regardless if it is an adjustment of the median or mean, the corresponding offset is always | ||
| #' converted to a shift of the median. | ||
| #' @export | ||
| #' @rdname mig.adjust | ||
| mig.shift.prediction.to.wpp <- function(sim.dir, ...){ | ||
| pred <- get.mig.prediction(sim.dir) | ||
| new.pred <- .do.mig.shift.prediction.to.wpp(pred, ...) | ||
| store.bayesMig.prediction(new.pred) | ||
| invisible(new.pred) | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Oops, something went wrong.
Oops, something went wrong.