| Type: | Package |
| Title: | Geological Time Scale Plotting |
| Version: | 2.0.1 |
| Date: | 2015-05-12 |
| Author: | Mark A. Bell <mark.bell521@gmail.com>. |
| Maintainer: | Mark A. Bell <mark.bell521@gmail.com> |
| Description: | Functionality for adding the geological timescale to bivariate plots. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| LazyData: | yes |
| LazyLoad: | yes |
| ByteCompile: | yes |
| Packaged: | 2022-06-24 12:10:25 UTC; hornik |
| NeedsCompilation: | no |
| Repository: | CRAN |
| Date/Publication: | 2022-06-24 12:29:29 UTC |
| Depends: | R (≥ 2.10) |
Geological Time Scale Plotting
Description
Functions for plotting time-series and distributions data against the international geological time scale.
Details
| Package: | geoscale |
| Type: | Package |
| Version: | 2.0 |
| Date: | 2015-05-12 |
| License: | GPL (>=2) |
| LazyLoad: | no |
Author(s)
Mark A. Bell <mark.bell521@gmail.com>
References
Gradstein, F. M., Ogg, J. M., and Schmitz, M., 2012, A geologic time scale, Boston, USA, Elsevier.
Examples
data(traits)
attach(traits)
geoscalePlot(age,trait,boxes="Age",ts.col=TRUE,scale="Period",type="l")
Ammonite biozone ages for the Upper Cretaceous
Description
This dataset provides the lower and upper ages of ammonite biozones between the Turonian and the Maastrichtian.
Usage
data(biozones)Format
A matrix of 50 biozonal ages.
Source
Hardenbol, J., Thierry, J., Farley, M. B., Jacquin, T., Graciansky, P.-C., and Vail, P. R., 1998, Mesozoic and Cenozoic sequence chronostratigraphic framework of European basins, in Graciansky, P.-C., Hardenbol, J., Jacquin, T., and Vail, P. R., eds., Mesozoic and Cenozoic sequence stratigraphy of European basins, Volume 60: Tulisa, OK, Society of Economic Palaeontologists and Mineralogists (SEPM) Special Publications, p. 3-14.
Geological box plots.
Description
Plots a series of box plots against the geological time-scale.
Usage
geoscaleBox(data, ages, units = c("Age", "Epoch", "Period"),
tick.scale = "myr", boxes = "Age", abbrev, cex.age = 0.3, cex.ts = 0.4,
cex.pt = 1, age.lim= NULL, data.lim = NULL, box.width=1, user.scale,
ts.col = TRUE, ts.width = 0.3, label,vers="ICS2015",no.axis=FALSE,
notch=FALSE,log=FALSE, color,direction ="horizontal",erotate,arotate,urotate,...)Arguments
data |
The distributions to be plotted, either a matrix of columns or as a list (see examples below). |
ages |
The ages in millions of years for each box to be plotted. |
units |
The temporal unit(s) to be included in the timescale, options include: "Eon", "Era", "Period", "Epoch", "Age" and "User". The option "User" is required when including a user-defined timescale. This also requires an object to be assigned to user.scale. |
tick.scale |
The resolution of the tick marks at the base of the timescale, the default is the same as units. The resolution of the scale can also be chosen by specifiying a value or removed entirely by using "no". |
boxes |
Option to include grey boxes for individual time bins. Same options as for scale. |
abbrev |
Option to abbreviate names of geological units in the time scale, options are the same as for units. |
cex.age |
Size of the numbers on the scale bar. |
cex.ts |
Size of the text in the time scale. |
cex.pt |
Size of the individual points. |
age.lim |
The range of values for the x-axis. |
data.lim |
The range of values for the y-axis. |
box.width |
The width of the boxes in millions of years. |
user.scale |
The data object to be used when including a user-defined time scale, requires the option "User" to be included in units. See data(UKzones) as an example of the required data format. |
ts.col |
Whether to include colours in the timescale. |
ts.width |
Proportion of the plot used for the time scale, value must be between 0 and 1. |
label |
Label for the y-axis. |
vers |
The version of the time scale to use. Options include: "ICS2015","ICS2014","ICS2013","ICS2012","ICS2010","ICS2009" or "ICS2008". |
no.axis |
Option to remove the label on the y-axis. |
notch |
Option to draw notches in the individual boxes, see help(boxplot). |
log |
Option to plot the y-axis on a log scale, default is FALSE. |
color |
Option for the color of the boxes. |
direction |
The orientation of the plot, can be either "horizontal" or "vertical". |
erotate |
A numerical value for the rotation for the Epoch/Series temporal units, default values are 0 when direction = "upwards" and 90 when direction = "rightwards". |
arotate |
A numerical value for the rotation for the Age/Stage temporal units, default values are 0 when direction = "upwards" and 90 when direction = "rightwards". |
urotate |
A numerical value for the rotation for the User temporal units, default values are 0 when direction = "upwards" and 90 when direction = "rightwards". |
... |
All other options passed to points. |
Author(s)
Mark A. Bell mark.bell521@gmail.com
Examples
## Plotting data from a matrix
data1 <- matrix(ncol=10,nrow=30,data=runif(30,0,100))
ages <- seq(10,100,10)
geoscaleBox(data1,ages,boxes="Age",pch=19,box.width=2)
## Plotting data from a list
data2 <- vector("list",10)
for(d in 1:length(data2)){
data2[[d]] <- runif(30,0,100)
}
ages <- seq(10,100,10)
geoscaleBox(data2,ages,boxes="Age",pch=19,box.width=2)
## Example dataset
data(size)
ages <- as.numeric(colnames(size))
geoscaleBox(data=size,ages=ages,pch=19,boxes="Age")
# Plotting on a log scale
geoscaleBox(data=size,ages=ages,pch=19,boxes="Age",log=TRUE)
Geological time scale plotting.
Description
Plots two variables and includes the geological time-scale with a number of possible scales.
Usage
geoscalePlot(ages,data,units=c("Age","Epoch","Period"),
tick.scale="myr",boxes="Age",abbrev, cex.age=0.3,cex.ts=0.4,cex.pt=1,
age.lim=NULL,data.lim=NULL,user.scale,ts.col=TRUE,ts.width=0.3,label,
vers="ICS2015",no.axis=FALSE,direction="horizontal",erotate,arotate,
urotate,...)Arguments
ages |
The first dataset, should be the age variable. |
data |
The second dataset, should be the data variable. |
units |
The temporal unit(s) to be included in the timescale, options include: "Eon", "Era", "Period", "Epoch", "Age" and "User". The option "User" is required when including a user-defined timescale. This also requires an object to be assigned to user.scale. |
tick.scale |
The resolution of the tick marks at the base of the timescale, the default is the same as units. The resolution of the scale can also be chosen by specifiying a value or removed entirely by using "no". |
boxes |
Option to include grey boxes for individual time bins. Same options as for scale. |
abbrev |
Option to abbreviate names of geological units in the time scale, options are the same as for units. |
cex.age |
Size of the numbers on the scale bar. |
cex.ts |
Size of the text in the time scale. |
cex.pt |
Size of the individual points. |
age.lim |
The temporal range for the plot. |
data.lim |
The range of data to the plotted. |
user.scale |
The data object to be used when including a user-defined time scale, requires the option "User" to be included in units. See data(UKzones) as an example of the required data format. |
ts.col |
Whether to include colours in the timescale. |
ts.width |
Amount of space taken up by plotting the time scale, value must be between 0 and 1. |
label |
Label for the data axis. |
vers |
The version of the time scale to use. Options include: "ICS2015","ICS2014","ICS2013","ICS2012","ICS2010","ICS2009" or "ICS2008". |
no.axis |
Option to remove the label on the y-axis. |
direction |
The orientation of the plot, can be either "horizontal" or "vertical". |
erotate |
A numerical value for the rotation for the Epoch/Series temporal units, default values are 90 when direction='horizontal' and 0 when direction='vertical'. |
arotate |
A numerical value for the rotation for the Age/Stage temporal units, default values are 90 when direction='horizontal' and 0 when direction='vertical'. |
urotate |
A numerical value for the rotation for the User temporal units, default values are 90 when direction='horizontal' and 0 when direction='vertical'. |
... |
Other arguments passed to points. |
Author(s)
Mark A. Bell mark.bell521@gmail.com
Examples
### Basic plots
data(traits)
attach(traits)
## 1. A simple bivariant plot
geoscalePlot(age,trait)
## 2. Including the entire time scale
geoscalePlot(age,trait,units=c("Eon","Era","Age","Epoch","Period"),type="l")
## 3. Including abbreviations in the time scale
# (a) For one or more temporal units
geoscalePlot(age,trait,units=c("Eon","Era","Age","Epoch","Period"),type="l",
abbrev=c("Age","Epoch"))
# (b) For all temporal units
geoscalePlot(age,trait,units=c("Eon","Era","Age","Epoch","Period"),type="l",
abbrev=c("All"))
## 4. Rotating names in the time scale
geoscalePlot(age,trait,units=c("Eon","Era","Age","Epoch","Period"),type="l",
erotate=45)
### Including a user defined timescale
data(traits)
attach(traits)
data(biozones)
geoscalePlot(age,trait,boxes="User",user.scale=biozones,type="o",
units=c("Age","Period","User"),xlim=c(65,95),tick.scale="User")
Body-size data from trilobite specimens
Description
This dataset contains the measurements of trilobite specimens from the Cambrian and Ordovician. Each column represents a geological Stage.
Usage
data(timescales)Format
A matrix of geological stages for the Cambrian and Ordovician containing measurements of trilobite specimens.
Source
Bell, M, 2009, unpublished PhD Thesis, University of Bristol.
Geological time scale from Harland et al., (2012)
Description
This dataset provides the geological ages for the entire geological timescale from Gradstein (2012) along with the RGB colour values used in the current version.
Usage
data(timescales)Format
A matrix of first and last datums along with RBG values for each geological time period.
Source
Gradstein, F. M., Ogg, J. M., and Schmitz, M., 2012, A geologic time scale, Boston, USA, Elsevier.
A time-series for one trait.
Description
A set of randomly generated trait values along with their associated geological ages.
Usage
data(traits)Format
A matrix of 30 trait values and geological ages.