LexisPlotR is a tool to easily plot Lexis Diagrams within R. It is based on ggplot2 and wraps necessary steps like drawing the grid, highlighting certain areas or inserting lifelines in a couple of easy to use functions.
In demography a Lexis diagram (named after economist and social scientist Wilhelm Lexis) is a two dimensional diagram that is used to represent events (such as births or deaths) that occur to individuals belonging to different cohorts. Calendar time is usually represented on the horizontal axis, while age is represented on the vertical axis. (https://en.wikipedia.org/wiki/Lexis_diagram)
With v0.4 a complete rewrite of LexisPlotR started. To prevent existing code from failing, v0.4 still keeps functions from earlier versions, but only introduces new functionality in functions named using 'snake_case'. So if you are new to LexisPlotR do not use functions named using dot notation (e.g. lexis.grid()) but functions using snake_case (e.g. lexis_grid()). If you have existing code using functions from earlier versions of LexisPlotR please adapt new function names and syntax where necessary.
You can install the latest version of LexisPlotR by using install_github() from the devtools-package:
devtools::install_github("ottlngr/LexisPlotR")
library(LexisPlotR)
LexisPlotR (v0.4) is available on CRAN. Install v0.4 from CRAN:
install.packages("LexisPlotR")
LexisPlotR provides a couple of functions to draw Lexis Diagrams in R. Besides the ability to draw empty Lexis grids, LexisPlotR also offers some functionality to highlight certain areas of the grid or to add actual data to the Lexis Diagram.
A Lexis Diagram is basically determined by two measures: A range of years presented on the horizontal axis and a range of ages shown on the vertical axis. To plot an empty Lexis grid, use lexis_grid() which takes these measures as numeric inputs:
library(LexisPlotR)# Plot a Lexis grid from year 1900 to year 1905, representing the ages from 0 to 5
lexis_grid(year_start = 1900, year_end = 1905, age_start = 0, age_end = 5)
The aspect ratio of the axes is fixed to ensure right-angled triangles. So even non-square Lexis grids show right-angled triangles:
lexis_grid(year_start = 1900, year_end = 1905, age_start = 0, age_end = 8)
When using wide age and/or date ranges, it may be helpful to define a delta specifying the number of years to group in the grid:
lexis_grid(year_start = 1900, year_end = 1950, age_start = 0, age_end = 50, delta = 5)
Sometimes it is useful to highlight certain areas in the Lexis Diagram, like a certain age, year or cohort.
Highlighting a certain age in your grid is supported by lexis_age which will draw a coloured rectangle inside your grid marking all points in the grid belonging to a certain age group.
lexis <- lexis_grid(year_start = 1900, year_end = 1905, age_start = 0, age_end = 5)
lexis_age(lg = lexis, age = 2)
Next to lexis_age() there are also lexis_year() and lexis_cohort() which highlight a certain year or cohort, respectively:
lexis <- lexis_grid(year_start = 1900, year_end = 1905, age_start = 0, age_end = 5)
lexis_year(lg = lexis, year = 1903)
lexis <- lexis_grid(year_start = 1900, year_end = 1905, age_start = 0, age_end = 5)
lexis_cohort(lg = lexis, cohort = 1898)
The similar lexis_polygon() can be used to highlight arbitrary regions of the Lexis grid:
lexis <- lexis_grid(year_start = 1900, year_end = 1905, age_start = 0, age_end = 5)
polygons <- data.frame(group = c(1, 1, 1, 2, 2, 2),
x = c("1901-01-01", "1902-01-01", "1902-01-01", "1903-01-01", "1904-01-01", "1904-01-01"),
y = c(1, 1, 2, 1, 1, 2))
lexis_polygon(lg = lexis, x = polygons$x, y = polygons$y, group = polygons$group)
A life line is a simple tool to represent an individual's life in a Lexis Diagram.
The behaviour of lexis_lifeline() can be controlled by supplying an entry and/or exit date along with the individuals birthday:
lg <- lexis_grid(year_start = 1900, year_end = 1905, age_start = 0, age_end = 5)
lexis_lifeline(lg = lg, birth = "1901-09-23", lwd = 1.5)
lexis_lifeline(lg = lg, birth = "1901-09-23", entry = "1902-04-01", lwd = 1.5)
lexis_lifeline(lg = lg, birth = "1901-09-23", entry = "1902-04-01", exit = "1904-10-31", lwd = 1.5)
You can also use entry and death dates from a data.frame which is useful when plotting life lines of several individuals or hole populations. LexisPlotR comes with a random dataset of entry and exit dates for 300 Individuals from 1895 to 1905. Some of the deaths (or exits) are not observed or unknown. Take a look at the lifelines_sample dataset:
data("lifelines_sample")
lifelines_sample <- lifelines_sample[1:30,]
head(lifelines_sample, 10)## entry exit
## 1 1898-04-25 1898-07-30
## 2 1899-12-28 <NA>
## 3 1903-01-15 <NA>
## 4 1901-04-13 <NA>
## 5 1895-05-30 1900-03-29
## 6 1897-09-22 <NA>
## 7 1896-02-16 1896-04-24
## 8 1896-11-13 1902-10-30
## 9 1904-10-31 <NA>
## 10 1899-04-02 1902-04-11
To add all this data to your Lexis Diagram, use lexis.lifeline() and provide the respective columns of lifelines_sample as arguments:
lg <- lexis_grid(year_start = 1900, year_end = 1905, age_start = 0, age_end = 5)
lexis_lifeline(lg = lg, birth = lifelines_sample$entry, exit = lifelines_sample$exit, lwd = 1.5, lineends = TRUE)
LexisPlotR functions can be chained using the pipe operator %>% which can be imported from magrittr, dplyr and other packages.
library(magrittr)
lexis_grid(year_start = 1990, year_end = 2000, age_start = 0, age_end = 10) %>%
lexis_age(age = 3) %>%
lexis_cohort(cohort = 1988) %>%
lexis_year(year = 1998) %>%
lexis_lifeline(birth = "1991-09-23", lwd = 1.5)
LexisPlotR is actually just a collection of wrapper functions encapsulating ggplot2 logic. Therefore, each plot returned by LexisPlotR is an object of class ggplot and can be altered using well known ggplot2 functionalities.
library(magrittr)
library(ggplot2)
p <- lexis_grid(year_start = 1990, year_end = 2000, age_start = 0, age_end = 10) %>%
lexis_age(age = 3) %>%
lexis_cohort(cohort = 1988) %>%
lexis_year(year = 1998) %>%
lexis_lifeline(birth = "1991-09-23", lwd = 1.5)
p <- p + labs(x = "Age", y = "Year", "title" = "LexisPlotR")
p
Projects like the Human Mortality Database (HMD) provide demographic data for many countries in the world.
HMD's Lexis Triangle data can be visualized using LexisPlotR's lexis_polygon(). To fetch data from HMD, the HMDHFDplus package can be used:
library(LexisPlotR)
library(ggplot2)
library(HMDHFDplus)
triangles <- HMDHFDplus::readHMDweb(CNTRY = "RUS", "Deaths_lexis", Sys.getenv("HMD_USER"), Sys.getenv("HMD_PASSWORD"))
tidy_triangles <- tidy_triangle_data(triangles)
lg <- lexis_grid(1960, 2000, 30, 80, delta = 5)
lg + geom_polygon(data = tidy_triangles, aes(x = x, y = y, group = id, fill = Total))Besides HMD, there are other similar or related projects that provide demographic data that could be used within LexisPlotR. An incomplete list:
Until now, only HMD Lexis Triangles are supported natively by LexisPlotR.