From b2c901fa9645fe61c92c3a5ab4ce423751bc81ee Mon Sep 17 00:00:00 2001
From: Hana Sevcikova <hanas@uw.edu>
Date: Thu, 7 Nov 2024 13:34:07 -0800
Subject: [PATCH] documentation

---
 man/get.mig.trajectories.Rd | 28 +++++++++++
 man/mig.adjust.Rd           | 93 +++++++++++++++++++++++++++++++++++++
 2 files changed, 121 insertions(+)
 create mode 100644 man/get.mig.trajectories.Rd
 create mode 100644 man/mig.adjust.Rd

diff --git a/man/get.mig.trajectories.Rd b/man/get.mig.trajectories.Rd
new file mode 100644
index 0000000..8fc5d4c
--- /dev/null
+++ b/man/get.mig.trajectories.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_outputs.R
+\name{get.mig.trajectories}
+\alias{get.mig.trajectories}
+\title{Accessing Trajectories of Net Migration Rate}
+\usage{
+get.mig.trajectories(mig.pred, country)
+}
+\arguments{
+\item{mig.pred}{Object of class \code{\link{bayesMig.prediction}}.}
+
+\item{country}{Name or numerical code of a country. It can also be given as
+ISO-2 or ISO-3 characters.}
+}
+\value{
+Array of size the number of projection periods (including the present year) times the number of trajectories.
+}
+\description{
+Function for accessing all future trajectories of the net migration rate 
+    from a prediction object in a form of an array.
+}
+\details{
+The function loads projected trajectories of net migration rate for the given country from disk
+    and returns it as a matrix.
+}
+\seealso{
+\code{\link{bayesMig.prediction}}, \code{\link{get.mig.prediction}}, \code{\link{mig.trajectories.table}}
+}
diff --git a/man/mig.adjust.Rd b/man/mig.adjust.Rd
new file mode 100644
index 0000000..78c8a48
--- /dev/null
+++ b/man/mig.adjust.Rd
@@ -0,0 +1,93 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/predict_mig.R
+\name{mig.median.set}
+\alias{mig.median.set}
+\alias{mig.median.shift}
+\alias{mig.median.reset}
+\alias{mig.align.predictions}
+\title{Adjusting the Projection Medians}
+\usage{
+mig.median.set(sim.dir, country, values, years = NULL, ...)
+
+mig.median.shift(
+  sim.dir,
+  country,
+  reset = FALSE,
+  shift = 0,
+  from = NULL,
+  to = NULL
+)
+
+mig.median.reset(sim.dir, countries = NULL)
+
+mig.align.predictions(
+  sim.dir1,
+  sim.dir2,
+  country.codes = NULL,
+  years = NULL,
+  ...
+)
+}
+\arguments{
+\item{sim.dir}{Directory containing the prediction object.}
+
+\item{country}{Name or numerical code of a country.}
+
+\item{values}{Vector of the new median values.}
+
+\item{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.}
+
+\item{\dots}{Additional arguments passed to the underlying adjustment function. 
+It can be \code{verbose} to show/hide the progress of the adjustment.}
+
+\item{reset}{Logical. If \code{TRUE} medians in a range of \code{from} and \code{to} are
+reset to their original values.}
+
+\item{shift}{Constant by which the medians should be offset. It is not used if \code{reset} is \code{TRUE}.}
+
+\item{from}{Year from which the offset/reset should start. By default, it starts at the first prediction period.}
+
+\item{to}{Year until which the offset/reset should be done. By default, it is set to the last prediction period.}
+
+\item{countries}{Vector of country names or codes. If this argument is \code{NULL} (default), 
+the reset is done for all countries.}
+
+\item{sim.dir1}{Directory with the bayesMig prediction object to be adjusted.}
+
+\item{sim.dir2}{Directory with the bayesMig prediction object used to align the medians from \code{sim.dir1} to.}
+
+\item{country.codes}{Numerical codes of countries to adjust. By default all countries 
+found in \code{sim.dir2} are adjusted in \code{sim.dir1}.}
+}
+\value{
+All functions return an updated object of class \code{\link{bayesMig.prediction}}.
+}
+\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.
+}
+\details{
+The function \code{mig.median.set} can be used to set the medians of the
+    given country to specific values.
+
+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.
+
+Function \code{mig.median.reset} resets medians of the given countries
+    to the original values. By default it deletes adjustments for all countries.
+
+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.
+}