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R - Mortality Tables
Commit beeaa415 authored by Reinhold Kainhofer's avatar Reinhold Kainhofer
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Add log and aes arguments to plotMortalityTables 

Implement dimensional factors in the plot functions for table comparisons and for the trend
parent 7b3171b1
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Showing with 122 additions and 85 deletions
R/plotMortalityTableComparisons.R
View file @ beeaa415
......@@ -26,6 +26,7 @@
#' @export
plotMortalityTableComparisons = function(
data, ...,
aes = NULL,
ages = NULL,
xlim = NULL, ylim = NULL,
xlab = NULL, ylab = NULL,
......@@ -56,7 +57,11 @@ plotMortalityTableComparisons = function(
env=list(refname=reference@name));
}
pl = ggplot(data, aes(x = x, y = y, color = group)) +
pl = ggplot(data, aes(x = x, y = y, color = group))
if (!is.null(aes)) {
pl = pl + aes
}
pl = pl +
theme_bw() +
theme(
plot.title = element_text(size=18, face="bold"),
......
R/plotMortalityTables.R
View file @ beeaa415
......@@ -4,6 +4,7 @@
#'
#' @param data First life table to be plotted. Either a \code{data.frame} generated by \code{makeQxDataFrame} or a \code{mortalityTable} object
#' @param ... Additional life tables to be plotted (if \code{data} is a \code{mortalityTable} object)
#' @param aes Optional aesthetics to append or override the default. The default aesthetics will always be applied first and provide defaults for x, y and color. This argument can be used to override the defaults or append other aesthetics.
#' @param xlim X-axis limitatation (as a two-element vector)
#' @param ylim Y-axis limitatation (as a two-element vector)
#' @param xlab X-axis label (default: "Alter")
......@@ -14,6 +15,7 @@
#' @param legend.key.width The keywith of the lines in the legend (default is \code{unit(25,"mm")})
#' @param legend.title Title of the legend (\code{NULL} to hide)
#' @param ages Plot only the given ages
#' @param log Display y axes in logarithmic scale (default: TRUE)
#'
#' @examples
#' # Load the Austrian census data
......@@ -40,13 +42,15 @@
#' @export
plotMortalityTables = function(
data, ...,
aes = NULL,
ages = NULL,
legend.title = "Sterbetafel",
xlim=NULL, ylim=NULL,
xlab=NULL, ylab=NULL,
title = "",
legend.position = c(0.9,0.1), legend.justification = c(1, 0),
legend.key.width = unit(25, "mm")
legend.key.width = unit(25, "mm"),
log = TRUE
) {
if (!is.data.frame(data)) {
data = makeQxDataFrame(data, ...);
......@@ -58,40 +62,47 @@ plotMortalityTables = function(
if (!is.null(ages)) {
data = data[data$x %in% ages,]
}
pl = ggplot(subset(data, y > 0), aes(x = x, y = y, colour = group)) +
theme_bw() +
theme(
plot.title = element_text(size = 18, face = "bold"),
legend.title = element_text(size = 14, face = "bold.italic"),
# legend in bottom right corner of the plot
legend.justification = legend.justification, legend.position = legend.position,
# No box around legend entries
legend.key = element_blank(),
legend.key.width = legend.key.width,
legend.background = element_rect(colour = "gray50", linetype = "solid")
) +
geom_line(na.rm = TRUE) +
scale_y_log10(
name = ylab,
breaks = scales::trans_breaks('log10', function(x) 10^x),
labels = scales::trans_format('log10', scales::math_format(10^.x))
#minor_breaks = log(c(sapply(x, function(x) seq(0, x, x/10))), 10)
) +
scale_x_continuous(
name = xlab,
#breaks = function (limits) scales::trans_breaks('', function(x) 10^x),
# breaks = function (limits) seq(max(min(limits),0),max(limits),5),
minor_breaks = function(limits) seq(max(round(min(limits)), 0), round(max(limits)), 1)
#labels = scales::trans_format('log10', scales::math_format(10^.x))
pl = ggplot(subset(data, y > 0), aes(x = x, y = y, color = group))
if (!is.null(aes)) {
pl = pl + aes
}
pl = pl +
theme_bw() +
theme(
plot.title = element_text(size = 14, face = "bold"),
legend.title = element_text(size = 12, face = "plain"),
# legend in bottom right corner of the plot
legend.justification = legend.justification, legend.position = legend.position,
# No box around legend entries
legend.key = element_blank(),
legend.key.width = legend.key.width,
legend.background = element_rect(colour = "gray50", linetype = "solid")
) +
geom_line(na.rm = TRUE)
if (log) {
pl = pl + scale_y_log10(
name = ylab,
breaks = scales::trans_breaks('log10', function(x) 10^x),
labels = scales::trans_format('log10', scales::math_format(10^.x))
#minor_breaks = log(c(sapply(x, function(x) seq(0, x, x/10))), 10)
) +
annotation_logticks(sides = "lr")
}
pl = pl + scale_x_continuous(
name = xlab,
minor_breaks = function(limits) seq(max(round(min(limits)), 0), round(max(limits)), 1)
) +
coord_cartesian(xlim = xlim, ylim = ylim) +
annotation_logticks(sides = "lr") +
xlab("Alter") + labs(colour = legend.title, shape = legend.title);
if (title != "") {
pl = pl + ggtitle(title);
}
pl
coord_cartesian(xlim = xlim, ylim = ylim) +
xlab("Alter") +
labs(colour = legend.title);
if (title != "") {
pl = pl + ggtitle(title);
}
pl
}
globalVariables(c("x", "y", ".x", "group"))
......
R/plotMortalityTrend.R
View file @ beeaa415
......@@ -6,6 +6,7 @@
#'
#' @param data First life table to be plotted. Either a \code{data.frame} generated by \code{makeQxDataFrame} or a \code{mortalityTable} object
#' @param ... Additional life tables to be plotted (if \code{data} is a \code{mortalityTable} object)
#' @param aes Optional aesthetics to append or override the default. The default aesthetics will always be applied first and provide defaults for x, y and color. This argument can be used to override the defaults or append other aesthetics.
#' @param xlim X-axis limitatation (as a two-element vector)
#' @param ylim Y-axis limitatation (as a two-element vector)
#' @param xlab X-axis label (default: "Alter")
......@@ -39,6 +40,7 @@
#' @export
plotMortalityTrend = function(
data, ...,
aes = NULL,
ages = NULL,
xlim=NULL, ylim=NULL,
xlab=NULL, ylab=NULL,
......@@ -56,60 +58,70 @@ plotMortalityTrend = function(
if (missing(xlab)) xlab = "Alter";
if (missing(ylab)) ylab = expression(paste("Sterblichkeitstrend ", lambda[x]));
pl = ggplot(data, aes(x = x, y = y, colour = data$group)) +
theme_bw() +
theme(
plot.title = element_text(size = 18, face = "bold"),
legend.title = element_text(size = 14, face = "bold.italic"),
# legend in bottom right corner of the plot
legend.justification = legend.justification, legend.position = legend.position,
# No box around legend entries
legend.key = element_blank(),
legend.key.width = legend.key.width,
legend.background = element_rect(colour = "gray50", linetype = "solid")
) +
geom_line() +
scale_y_continuous(
name = ylab,
# breaks = scales::trans_breaks('log10', function(x) 10^x),
# labels = scales::trans_format('log10', scales::math_format(10^.x))
#minor_breaks = log(c(sapply(x, function(x) seq(0, x, x/10))), 10)
) +
scale_x_continuous(
name = xlab,
#breaks = function (limits) scales::trans_breaks('', function(x) 10^x),
breaks = function(limits) seq(max(min(limits), 0), max(limits), 5),
minor_breaks = function(limits) seq(max(round(min(limits)), 0), round(max(limits)), 1)
#labels = scales::trans_format('log10', scales::math_format(10^.x))
) +
coord_cartesian(xlim = xlim, ylim = ylim) +
annotation_logticks(sides = "lr") +
xlab("Alter") + labs(colour = legend.title);
if (title != "") {
pl = pl + ggtitle(title);
}
pl
pl = ggplot(data, aes(x = x, y = y, color = group))
if (!is.null(aes)) {
pl = pl + aes
}
pl = pl +
theme_bw() +
theme(
plot.title = element_text(size = 18, face = "bold"),
legend.title = element_text(size = 14, face = "bold.italic"),
# legend in bottom right corner of the plot
legend.justification = legend.justification, legend.position = legend.position,
# No box around legend entries
legend.key = element_blank(),
legend.key.width = legend.key.width,
legend.background = element_rect(colour = "gray50", linetype = "solid")
) +
geom_line() +
scale_y_continuous(
name = ylab,
# breaks = scales::trans_breaks('log10', function(x) 10^x),
# labels = scales::trans_format('log10', scales::math_format(10^.x))
#minor_breaks = log(c(sapply(x, function(x) seq(0, x, x/10))), 10)
) +
scale_x_continuous(
name = xlab,
#breaks = function (limits) scales::trans_breaks('', function(x) 10^x),
breaks = function(limits) seq(max(min(limits), 0), max(limits), 5),
minor_breaks = function(limits) seq(max(round(min(limits)), 0), round(max(limits)), 1)
#labels = scales::trans_format('log10', scales::math_format(10^.x))
) +
coord_cartesian(xlim = xlim, ylim = ylim) +
xlab("Alter") + labs(colour = legend.title);
if (title != "") {
pl = pl + ggtitle(title);
}
pl
}
makeMortalityTrendDataFrame = function(..., YOB = 1972, Period = NULL) {
# If reference is given, normalize all probabilities by that table!
data = unlist(list(...));
names(data) = lapply(data, function(t) t@name);
if (is.null(data)) return(data.frame(x = double(), y = double(), group = character()))
# names(data) = lapply(data, function(t) t@name);
if (missing(Period) || is.null(Period)) {
data = lapply(data, function(t) {
cbind(x = ages(t), y = mortalityImprovement(t, YOB = YOB))
if (is.data.frame(t@data$dim) || is.list(t@data$dim)) {
data.frame(x = ages(t), y = `names<-`(mortalityImprovement(t, YOB = YOB), NULL), group = t@name, as.data.frame(t@data$dim))
} else {
data.frame(x = ages(t), y = `names<-`(mortalityImprovement(t, YOB = YOB), NULL), group = t@name)
}
});
} else {
data = lapply(data, function(t) {
cbind(x = ages(t), y = mortalityImprovement(t, Period = Period))
if (is.data.frame(t@data$dim) || is.list(t@data$dim)) {
data.frame(x = ages(t), y = `names<-`(mortalityImprovement(t, Period = Period), NULL), group = t@name, as.data.frame(t@data$dim))
} else {
data.frame(x = ages(t), y = `names<-`(mortalityImprovement(t, Period = Period), NULL), group = t@name)
}
});
}
list.names = names(data)
lns <- sapply(data, nrow)
data <- as.data.frame(do.call("rbind", data))
data$group <- rep(list.names, lns)
names(data) = NULL
data <- as.data.frame(do.call("rbind.expand", data))
data
}
......@@ -120,7 +132,7 @@ globalVariables(c("x", "y", ".x"))
# mortalityTables.load("Austria_*")
# plotMortalityTrend(AVOe1996R.male, AVOe1996R.female, AVOe2005R.male, AVOe2005R.female, YOB=1972, title="Austrian Annuity Tables, YOB=1972 (for cohort tables)")
#
# plotMortalityTables(mort.AT.census.2001.male, AVOe2005R.male, YOB=1972, title="Comparison Austrian Tables")
# plotMortalityTables(mort.AT.census.2001.male, AVOe2005R.male, AVOe2005R.female, YOB=1972, title="Comparison Austrian Tables")
# plotMortalityTables(getCohortTable(AVOe2005R.male, YOB=1972), getCohortTable(AVOe2005R.male, YOB=2016), title="Comparison Austrian Tables")
# plotMortalityTrend(EttlPagler.male@qx, AVOe1999P.male@qx, AVOe2008P.male@qx, YOB = 2003, title="Sterblichkeitstrends der Pagler-Tafeln")
man/plotMortalityTableComparisons.Rd
View file @ beeaa415
......@@ -4,8 +4,8 @@
\alias{plotMortalityTableComparisons}
\title{Plot multiple mortality tables (life tables) in one plot, relative to a given reference table}
\usage{
plotMortalityTableComparisons(data, ..., ages = NULL, xlim = NULL,
ylim = NULL, xlab = NULL, ylab = NULL, title = "",
plotMortalityTableComparisons(data, ..., aes = NULL, ages = NULL,
xlim = NULL, ylim = NULL, xlab = NULL, ylab = NULL, title = "",
legend.position = c(0.9, 0.1), legend.justification = c(1, 0),
legend.title = "Sterbetafel", legend.key.width = unit(25, "mm"),
reference = NULL)
......@@ -15,6 +15,8 @@ plotMortalityTableComparisons(data, ..., ages = NULL, xlim = NULL,
\item{...}{Additional life tables to be plotted (if \code{data} is a \code{mortalityTable} object)}
\item{aes}{Optional aesthetics to append or override the default. The default aesthetics will always be applied first and provide defaults for x, y and color. This argument can be used to override the defaults or append other aesthetics.}
\item{ages}{Plot only the given ages}
\item{xlim}{X-axis limitatation (as a two-element vector)}
......
man/plotMortalityTables.Rd
View file @ beeaa415
......@@ -4,16 +4,19 @@
\alias{plotMortalityTables}
\title{Plot multiple mortality tables (life tables) in one plot}
\usage{
plotMortalityTables(data, ..., ages = NULL, legend.title = "Sterbetafel",
xlim = NULL, ylim = NULL, xlab = NULL, ylab = NULL, title = "",
legend.position = c(0.9, 0.1), legend.justification = c(1, 0),
legend.key.width = unit(25, "mm"))
plotMortalityTables(data, ..., aes = NULL, ages = NULL,
legend.title = "Sterbetafel", xlim = NULL, ylim = NULL, xlab = NULL,
ylab = NULL, title = "", legend.position = c(0.9, 0.1),
legend.justification = c(1, 0), legend.key.width = unit(25, "mm"),
log = TRUE)
}
\arguments{
\item{data}{First life table to be plotted. Either a \code{data.frame} generated by \code{makeQxDataFrame} or a \code{mortalityTable} object}
\item{...}{Additional life tables to be plotted (if \code{data} is a \code{mortalityTable} object)}
\item{aes}{Optional aesthetics to append or override the default. The default aesthetics will always be applied first and provide defaults for x, y and color. This argument can be used to override the defaults or append other aesthetics.}
\item{ages}{Plot only the given ages}
\item{legend.title}{Title of the legend (\code{NULL} to hide)}
......@@ -33,6 +36,8 @@ plotMortalityTables(data, ..., ages = NULL, legend.title = "Sterbetafel",
\item{legend.justification}{The justification of the legend (default is \code{c(1,)})}
\item{legend.key.width}{The keywith of the lines in the legend (default is \code{unit(25,"mm")})}
\item{log}{Display y axes in logarithmic scale (default: TRUE)}
}
\description{
\code{plotMortalityTables} prints multiple life tables (objects of child classes of \code{mortalityTable}) in one log-linear plot, with a legend showing the names of the tables.
......
man/plotMortalityTrend.Rd
View file @ beeaa415
......@@ -4,16 +4,18 @@
\alias{plotMortalityTrend}
\title{Plot the trends of multiple mortality tables (life tables) in one chart}
\usage{
plotMortalityTrend(data, ..., ages = NULL, xlim = NULL, ylim = NULL,
xlab = NULL, ylab = NULL, title = "", legend.position = c(0.9, 0.9),
legend.justification = c(1, 1), legend.title = "Sterbetafel",
legend.key.width = unit(25, "mm"))
plotMortalityTrend(data, ..., aes = NULL, ages = NULL, xlim = NULL,
ylim = NULL, xlab = NULL, ylab = NULL, title = "",
legend.position = c(0.9, 0.9), legend.justification = c(1, 1),
legend.title = "Sterbetafel", legend.key.width = unit(25, "mm"))
}
\arguments{
\item{data}{First life table to be plotted. Either a \code{data.frame} generated by \code{makeQxDataFrame} or a \code{mortalityTable} object}
\item{...}{Additional life tables to be plotted (if \code{data} is a \code{mortalityTable} object)}
\item{aes}{Optional aesthetics to append or override the default. The default aesthetics will always be applied first and provide defaults for x, y and color. This argument can be used to override the defaults or append other aesthetics.}
\item{ages}{Plot only the given ages}
\item{xlim}{X-axis limitatation (as a two-element vector)}
......
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