This note provides an brief background and overview introduction to the **R** package **loa**.

The **lattice**^{1} package that comes with **R** draws graphs.

**loa** is short for **L**attice **O**ptional extras and **A**dd-ins, and that pretty much describes **loa**.

This note assumes you already have R. If not but the note is of interest,

Ris open-source and free-to-distribute, and you can get it from >The R Project.

I originally packaged **loa** because I had a lot of plot code, most modifications of or extensions to existing **lattice** code, that I was using and replicating in several projects and I wanted to rationalise things.

The intention was also to automate and simplify some of the data handling needed when **lattice** plotting^{2}.

Installing **loa** from CRAN, the main R package archive:

```
#In R, type:
install.packages("loa")
```

Installing the developers version:

`install.packages("loa", repos="http://R-Forge.R-project.org")`

To load **loa** once it is installed:

`library(loa) #or require(loa)`

Note:

loaautomatically also loadslatticeso you, as well asloa, have access tolattice.

**loa** version 0.2.47.1^{3} contains:

- Several plot functions, e.g.
**loaPlot()**,**RgoogleMapsPlot()**and**trianglePlot()**; - Add-ins like
**panel**functions to change plot outputs; and - Some functions to automate handling of some of the more mundane plot parameters.

**loa** also contains one data set, **lat.lon.meuse**, and one map, **roadmap.meuse**, which are used in examples in the **loa** documentation.

**lat.lon.meuse** is a **data.set** containing metal concentrations measured in soil and sediment samples collected from a section of the Meuse floodplain in the Netherlands.

It is a modification of the **meuse** **data.set** in the **sp** package.^{4} It contains concentrations of four metals (**cadmium**, **copper**, **lead** and **zinc**), sampling location (**latitude**, **longitude**, **elevation**), and other related information (e.g. **soil** type) for 155 locations.

**roadmap.meuse** is a Google Map ‘roadmap’ for the meuse area used as a map layer in off-line **GoogleMap()** examples.

There are further details on both in the package documentation, see **?lat.lon.meuse** or **?roadmap.meuse**.

**loa** uses **lattice** plotting strategies^{5}.

Plot dimensions are set using a formula as the first argument of the plot command.

For those unfamiliar with the approach, it is probably easiest to think of a

latticeplot as a model likelm()but with a formula that maps one term onto a series of axes rather than a series of inputs.

For example, **loaPlot()** uses a formula structure **z ~ x * y | cond**, where:

**x**and**y**are the x and y axes,**z**is an optional term controlling the appearance (color and size) of points plotted at (x, y), and**cond**, also optional, is any additional term that can be used to subsample (x,y,z) data when plotting subsets separately.

The formula terms may be supplied directly or taken from a source identified using a second optional plot argument **data**. If supplied, **data** should be a **data.frame** or something that can be converted into one using **as.data.frame(data)**, e.g.:

`loaPlot(cadmium~longitude*latitude, data=lat.lon.meuse) `

Here, the **z** term, the cadmium data-series, is used to both color and size points plotted at **x** (**longitude**) and **y** (**latitude**) locations.

Additional arguments may be used to fine-tune the appearance of the plot, e.g. **groups** to group data within the plot:

```
loaPlot(cadmium~longitude*latitude, data=lat.lon.meuse,
groups=lat.lon.meuse$soil)
```

Here, the plot color-codes the points according to **soil** (soil type 1-3), also in **lat.lon.meuse**.

Note: By default,

groupssupersedeszas the coloring term when set but the points remain size scaled according toz.

By comparison, conditioning by **soil** type would produce:

```
loaPlot(cadmium~longitude*latitude|soil, data=lat.lon.meuse,
layout=c(3,1))
```

This plots data of different **soil** types in discrete plot panels, each, by default, plotted using the same **x**, **y**, **z** and **groups** plot settings. The standard **lattice** argument **layout** is also used to plot the **lattice** sub-plots (or panels) in a row.

Already introduced above, **loaPlot()** is a **z ~ x * y** bubble plot with default color (**col**) and size (**cex**) scaling linked to the **z** term unless **groups** are set, in which case **cex** is linked to **z** and **col** is linked to **groups**.

Many of the additional plot arguments are the same as in **lattice**, but some options have been enhanced or simplified, e.g.:

```
#fixed col (but automatic z size scale)
#key scale manually extended
loaPlot(cadmium~longitude*latitude, data=lat.lon.meuse,
col="darkred", key.z.at=c(3,6,9,12,15,18))
#replacing default blue scale with RColorBrewer palette
#adding transparency with alpha
#use color scale key like levelplot
loaPlot(cadmium~longitude*latitude, data=lat.lon.meuse,
col.regions="Spectral", alpha=0.5,
key.fun=draw.loaColorKey)
```

As in

**lattice**,**col**sets point color directly and**col.regions**sets the color palette colors are selected from. But**loa**also uses**RColorBrewer**^{6}to handle color ranges. So, the**loa**version of**col.regions**is a little more flexible than in**lattice**. For example,**loaPlot()**handles arguments like**col.regions = c(“green”, “red”)**.unlike

**xyplot()**in**lattice**,**loaPlot()**automatically generates a plot key if it thinks you need one, but (like in**lattice**),**key**and**key…**arguments can be used to modify the key, e.g.**key = FALSE**to remove the key.I have tried to simplify some common arguments that use list structures in

**lattice**. So, e.g. instead of using**key=list(z=list(at=c(…)))**you can use**key.z.at=c(…)**to manually set the points shown in the key. There are trade-offs in doing this, so it is currently only applied to selected cases in**loaPlot()**, but it does mean you can more easily change grid appearance with e.g.**grid.col=2**or**grid.lty=3**, etc.I also linked the

**loaPlot()**argument**zlab**to**key.z.main**so you could rename the z key like you would the x and y axes.

Note: The

loaPlot()key can includezandgroupselements. So, you need to specify which you want to change, hencekey.z.at=…(notkey.at=…).

Like **lattice** plots, **loaPlot()** also accepts other **panel** arguments to produce other plot types.

For example:

```
#panel.binPlot
loaPlot(cadmium~longitude*latitude, data=lat.lon.meuse,
panel=panel.binPlot, breaks=20, statistic=max)
#panel.surfaceSmooth
loaPlot(cadmium~longitude*latitude, data=lat.lon.meuse,
panel=panel.surfaceSmooth, too.far=0.1)
```

- The
**binPlot**panel expects**x**,**y**and**z**inputs and generates a heat map and color key similar to**levelplot()**but without the extra coding needed to get from**xyplot()**to**levelplot()**inputs. By default, it calculates means for each bin if**z**is supplied or generates a warning and counts bin sizes if not. You can also use arguments like**breaks**and**statistic**to change the number of bins and the way the binned data is handled. - The
**surfaceSmooth**panel also expects**x**,**y**and**z**and fits a color-surface to (**x**,**y**,**z**). By default, it extrapolates the surface to the**x**and**y**plot limits. However, the**too.far**argument (based on**too.far**in GAM visualizations in the**mgcv**package^{7}) can to used to limit the amount of extrapolation (0.1 = 10% of plot range from nearest point).

**loaPlot()** also allows you to supply multiple **z** values in form **z1 + z2 + … + zn ~ x + y**.

Note: This option is not intended to be used with

loaPlot()without additional option settings because it would just create over-plotting at each (x,y) point. However, it is useful when used with eitherzcase panelling or specialist panels designed for use with mulitplezinputs, e.g.:

```
#panel.zcases to condition by z1, z2, etc
loaPlot(cadmium*50+copper*10+lead*2+zinc~longitude*latitude,
data=lat.lon.meuse, zlab="Metals",
panel.zcases = TRUE)
#using the panel.zcasePiePlot and z1, z2, etc
loaPlot(cadmium*50+copper*10+lead*2+zinc~longitude*latitude,
data=lat.lon.meuse, zcaselab="Metals",
panel=panel.zcasePiePlot)
```

For further information on

loaPlot(), see in-package documentation?loaPlot.

Other plots in **loa** include **RgoogleMapsPlot()**, **trianglePlot()**, **stackPlot()** and **loaBarPlot()**:

```
#RgoogleMapsPlot
RgoogleMapsPlot(cadmium~latitude*longitude, data=lat.lon.meuse,
map=roadmap.meuse)
#trianglePlot
trianglePlot(cadmium~copper+lead+zinc, data=lat.lon.meuse)
#stackPlot
stackPlot(cadmium*40+copper*5+lead+zinc~dist.m, data=lat.lon.meuse)
#loaBarPlot
loaBarPlot(copper~soil, data=lat.lon.meuse, stat=mean)
```

**RgoogleMapsPlot()**is an extension of**loaPlot()**that adds a map layer to plots using the**RgoogleMaps**package^{8}. It uses a**z ~ latitude * longitude | cond**plot structure and accepts**loaPlot()**arguments to modify data layers as well as additional arguments to modify the map layer.**trianglePlot()**is a triangle (or ternary) plot that uses (a,b,c) axes and a**z ~ a + b + c | cond**plot structure.**stackPlot()**is a simple data-series stacking plot that uses a**y1 + y2 + … yn ~ x | cond**plot structure.**loaBarPlot()**is a simple bar plot that currently uses either a**y~x|cond**and**groups**plot structure or a more conventional**x, y, groups, cond**plot structure.

For further information on these, see in-package documentation.

Any thoughts, suggestions or problems, please let me know > Karl

Sarkar D (2008). Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5, <URL: http://lmdvr.r-forge.r-project.org>.↩︎

I presented earlier thoughts on this topic in e.g. Ropkins, K., Carslaw, D.C., Munir, S., Chen, H. R. (2012) lattice and RgoogleMaps: A practical framework for the development of new geovisualizations. ASA 2012 JSM. San Diego, US.↩︎

Code handling and outputs may vary with package version.↩︎

Pebesma EJ, Bivand RS (2005). “Classes and methods for spatial data in R.” R News,

*5*(2), 9-13. <URL: https://CRAN.R-project.org/doc/Rnews/>., Bivand RS, Pebesma E, Gomez-Rubio V (2013). Applied spatial data analysis with R, Second edition. Springer, NY. <URL: https://asdar-book.org/>.↩︎This is described in early chapters of Sarkar D (2008). Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5, <URL: http://lmdvr.r-forge.r-project.org>.↩︎

Neuwirth E (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1-2, <URL: https://CRAN.R-project.org/package=RColorBrewer>.↩︎

Wood SN (2011). “Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models.” Journal of the Royal Statistical Society (B),

*73*(1), 3-36., Wood S, N., Pya, S“afken B (2016).”Smoothing parameter and model selection for general smooth models (with discussion)." Journal of the American Statistical Association,*111*, 1548-1575., Wood SN (2004). “Stable and efficient multiple smoothing parameter estimation for generalized additive models.” Journal of the American Statistical Association,*99*(467), 673-686., Wood S (2017). Generalized Additive Models: An Introduction with R, 2 edition. Chapman and Hall/CRC., Wood SN (2003). “Thin-plate regression splines.” Journal of the Royal Statistical Society (B),*65*(1), 95-114.↩︎Loecher M, Ropkins K (2015). “RgoogleMaps and loa: Unleashing R Graphics Power on Map Tiles.” Journal of Statistical Software,

*63*(4), 1-18. <URL: http://www.jstatsoft.org/v63/i04/>.↩︎