WARNING: this package has not been updated in quite a while, since I have
switched to using ggplot. The still-relevant features from this packages will
at some point be migrated to ggplot.

StratPlot

The StratPlot function allows you to easily create depth and age profile plots
in R.

The files that you need are StratPlot.R, if you're plotting Magnetochron ages
Chronages.csv, and if you're plotting time GTS2012 time scales GTS_colours.csv.

Usage

Use your spreadsheat editing skills (or R) to create a .csv that holds one
sample per row with the variables of interest as separate columns. Make sure to
include depth or age information in one of the columns.

Get it into R using data <- read.csv("pathtofile.csv")

The simplest way to create a single plot is to give depth/age and var vectors of
equal length, and provide a value for xlab.

Note that if you want to use superscipts and subscripts in the x-axis label, you
can do so by providing xlab with a formula. For example:
Label~with~nice~formatting~(H[2]*O~m^{-2}~mu*M) will result in: Label with
nice formatting (H₂O m^-2 μM).

You can also provide var with a matrix or dataframe with the variables of
interst. The function tries to automatically find a column with depth or age
information and use that to plot the other variables. You can also specify it
with depthcol. They can be added to a single plot with oneplot = TRUE, can
be stacked with stacked = TRUE (useful for cumulative sum plots) or each
create a new plot (default). The function also tries to figure out whether it
should use "Age (Ma)" or "Age (ka)" based on the age variable.

When you create multiple plots, make sure there is room for the plots (via
par(mfrow = c(1,5)) for example). xlab and ylab can now also be entered as
vector of characters or a list of formulae. Otherwise it will use the variable
names in the dataframe.

Setting the pol and bar to TRUE adds a polygon and/or bar respectively.

Other configurations are also possible, just look at the function arguments and
see what they do :).

Example calls

# dinocyst data example
set.seed(1)
dinos <- data.frame(code = paste0("IJK", 1:10),
                    depth = seq(600, 800, length.out = 10),
	            age = 41:50,
                    Dinospecies1 = rnorm(10, 5, 3),
                    Dinospecies2 = rnorm(10, 10, 5),
                    Dinospecies3 = rnorm(10, 25, 20))
par(mfrow = c(1, 3))
StratPlot(dinos, pol = T, bar = T, xlim = c(0, 60))

# data with known error values
set.seed(1)
temp <- data.frame(age = 41:50, 
	           temp = rnorm(10, 30, 5),
		   error = rnorm(10, 2.5, 1))
StratPlot(temp$age, temp$temp, xlab = Temperature~(degree~C), 
          ylab = "Age (Ma)", error = temp$error)

example plot

The supplementary age-model plot to Cramwinckel et al. 2018¹
was created using (slightly different versions of) these plotting functions
(as well as some tweaking of colours in Inkscape).

1. Cramwinckel et al. Synchronous tropical and polar temperature evolution in the Eocene.
   Nature volume 559, pages382–386 (2018) doi:10.1038/s41586-018-0272-2