Using HDF5/zlib Compression in NetCDF4

Not too long ago, I posted an entry on writing NetCDF files in C and loading them in R.  In that post, I mentioned that the latest and greatest version of NetCDF includes HDF5/zlib compression, but I didn’t say much more beyond that.  In this post, I’ll explain briefly how to use this compression feature in your NetCDF4 files.

Disclaimer: I’m not an expert in any sense on the details of compression algorithms.  For more details on how HDF5/zlib compression is integrated into NetCDF, check out the NetCDF Documentation.  Also, I’ll be assuming that the NetCDF4 library was compiled on your machine to enable HDF5/zlib compression.  Details on building and installing NetCDF from source code can be found in the documentation too.

I will be using code similar to what was in my previous post.  The code generates three variables (x, y, z) each with 3 dimensions.  I’ve increased the size of the dimensions by an order of magnitude to better accentuate the compression capabilities.

  // Loop control variables
  int i, j, k;
  
  // Define the dimension sizes for
  // the example data.
  int dim1_size = 100;
  int dim2_size = 50;
  int dim3_size = 200;
  
  // Define the number of dimensions
  int ndims = 3;
  
  // Allocate the 3D vectors of example data
  float x[dim1_size][dim2_size][dim3_size]; 
  float y[dim1_size][dim2_size][dim3_size];
  float z[dim1_size][dim2_size][dim3_size];
  
  // Generate some example data
  for(i = 0; i < dim1_size; i++) {
        for(j = 0; j < dim2_size; j++) {
                for(k = 0; k < dim3_size; k++) {
                        x[i][j][k] = (i+j+k) * 0.2;
                        y[i][j][k] = (i+j+k) * 1.7;
                        z[i][j][k] = (i+j+k) * 2.4;
                }
          }
        }

Next is to setup the various IDs, create the NetCDF file, and apply the dimensions to the NetCDF file.  This has not changed since the last post.

  // Allocate space for netCDF dimension ids
  int dim1id, dim2id, dim3id;
  
  // Allocate space for the netcdf file id
  int ncid;
  
  // Allocate space for the data variable ids
  int xid, yid, zid;
  
  // Setup the netcdf file
  int retval;
  if((retval = nc_create(ncfile, NC_NETCDF4, &ncid))) { ncError(retval); }
  
  // Define the dimensions in the netcdf file
  if((retval = nc_def_dim(ncid, "dim1_size", dim1_size, &dim1id))) { ncError(retval); }
  if((retval = nc_def_dim(ncid, "dim2_size", dim2_size, &dim2id))) { ncError(retval); }
  if((retval = nc_def_dim(ncid, "dim3_size", dim3_size, &dim3id))) { ncError(retval); }
  
  // Gather the dimids into an array for defining variables in the netcdf file
  int dimids[ndims];
  dimids[0] = dim1id;
  dimids[1] = dim2id;
  dimids[2] = dim3id;

Here’s where the magic happens.  The next step is to define the variables in the NetCDF file.  The variables must be defined in the file before you tag it for compression.

  // Define the netcdf variables
  if((retval = nc_def_var(ncid, "x", NC_FLOAT, ndims, dimids, &xid))) { ncError(retval); }
  if((retval = nc_def_var(ncid, "y", NC_FLOAT, ndims, dimids, &yid))) { ncError(retval); }
  if((retval = nc_def_var(ncid, "z", NC_FLOAT, ndims, dimids, &zid))) { ncError(retval); }

Now that we’ve defined the variables in the NetCDF file, let’s tag them for compression.

  // OPTIONAL: Compress the variables
  int shuffle = 1;
  int deflate = 1;
  int deflate_level = 4;
  if((retval = nc_def_var_deflate(ncid, xid, shuffle, deflate, deflate_level))) { ncError(retval); }
  if((retval = nc_def_var_deflate(ncid, yid, shuffle, deflate, deflate_level))) { ncError(retval); }
  if((retval = nc_def_var_deflate(ncid, zid, shuffle, deflate, deflate_level))) { ncError(retval); }

The function nc_def_var_deflate() performs this.  It takes the following parameters:

  • int ncid – The NetCDF file ID returned from the nc_create() function
  • int varid – The variable ID associated with the variable you would like to compress.  This is returned from the nc_def_var() function
  • int shuffle – Enables the shuffle filter before compression.  Any non-zero integer enables the filter.  Zero disables the filter.  The shuffle filter rearranges the byte order in the data stream to enable more efficient compression. See this performance evaluation from the HDF group on integrating a shuffle filter into the HDF5 algorithm.
  • int deflate – Enable compression at the compression level indicated in the deflate_level parameter.  Any non-zero integer enables compression.
  • int deflate_level – The level to which the data should be compressed.  Levels are integers in the range [0-9].  Zero results in no compression whereas nine results in maximum compression.

The rest of the code doesn’t change from the previous post.

  // OPTIONAL: Give these variables units
  if((retval = nc_put_att_text(ncid, xid, "units", 2, "cm"))) { ncError(retval); }
  if((retval = nc_put_att_text(ncid, yid, "units", 4, "degC"))) { ncError(retval); }
  if((retval = nc_put_att_text(ncid, zid, "units", 1, "s"))) { ncError(retval); }
  
  // End "Metadata" mode
  if((retval = nc_enddef(ncid))) { ncError(retval); }
  
  // Write the data to the file
  if((retval = nc_put_var(ncid, xid, &x[0][0][0]))) { ncError(retval); }
  if((retval = nc_put_var(ncid, yid, &y[0][0][0]))) { ncError(retval); }
  if((retval = nc_put_var(ncid, zid, &z[0][0][0]))) { ncError(retval); }
  
  // Close the netcdf file
  if((retval = nc_close(ncid))) { ncError(retval); }

So the question now is whether or not it’s worth compressing your data.  I performed a simple experiment with the code presented here and the resulting NetCDF files:

  1. Generate the example NetCDF file from the code above using each of the available compression levels.
  2. Time how long the code takes to generate the file.
  3. Note the final file size of the NetCDF.
  4. Time how long it takes to load and extract data from the compressed NetCDF file.

Below is a figure illustrating the results of the experiment (points 1-3).

compress_plot

Before I say anything about these results, note that individual results may vary.  I used a highly stylized data set to produce the NetCDF file which likely benefits greatly from the shuffle filtering and compression.  These results show a compression of 97% – 99% of the original file size.  While the run time did increase, it barely made a difference until hitting the highest compression levels (8,9).  As for point 4, there was only a small difference in load/read times (0.2 seconds) between the uncompressed and any of the compressed files (using ncdump and the ncdf4 package in R).  There’s no noticeable difference among the load/read times for any of the compressed NetCDF files.  Again, this could be a result of the highly stylized data set used as an example in this post.

For something more practical, I can only offer anecdotal evidence about the compression performance.  I recently included compression in my current project due to the large possible number of multiobjective solutions and states-of-the-world (SOW).  The uncompressed file my code produced was on the order of 17.5 GB (for 300 time steps, 1000 SOW, and about 3000 solutions).  I enabled compression of all variables (11 variables – 5 with three dimensions and 6 with two dimensions – compression level 4).  The next run produced just over 7000 solutions, but the compressed file size was 9.3 GB.  The down side is that it took nearly 45 minutes to produce the compressed file, as opposed to 10 minutes with the previous run.  There are many things that can factor into these differences that I did not control for, but the results are promising…if you’ve got the computer time.

I hope you found this post useful in some fashion.  I’ve been told that compression performance can be increased if you also “chunk” your data properly.  I’m not too familiar with chunking data for writing in NetCDF files…perhaps someone more clever than I can write about this?

Acknowledgement:  I would like to acknowledge Jared Oyler for his insight and helpful advice on some of the more intricate aspects of the NetCDF library.

From Writing NetCDF Files in C to Loading NetCDF Files in R

So much data from such little models…

It’s been my experience that even simple models can generate lots of data. If you’re a regular reader of this blog, I can imagine you’ve had similar experiences as well. My most recent experience with this is the work I’ve done with the Dynamic Integrated Climate-Economic model (DICE). I had inherited a port of the 2007 version of the model, which would print relevant output to the screen. During my initial runs with the model, I would simply redirect the output to ascii files for post-processing. I knew that eventually I would be adding all sorts of complexity to this model, ultimately leading to high-dimensional model output and rendering the use of ascii files as impractical. I knew that I would need a better way to handle all this data. So in updating the model to the 2013 version, I decided to incorporate support for netCDF file generation.

You can find details about the netCDF file format through Unidata (a University Cooperation for Atmospheric Research [UCAR] Community Program) and through some of our previous blog posts (here, here, and here). What’s important to note here is that netCDF is a self-describing file format designed to manage high-dimensional hierarchical data sets.

I had become accustomed to netCDF files in my previous life as a meteorologist. Output from complex numerical weather prediction models would often come in netCDF format. While I had never needed to generate my own netCDF output files, I found it incredibly easy and convenient to process them in R (my preferred post-processing and visualization software). Trying to incorporate netCDF output support in my simple model seemed daunting at first, but after a few examples I found online and a little persistence, I had netCDF support incorporated into the DICE model.

The goal of this post is to guide you through the steps to generate and process a netCDF file. Some of our earlier posts go through a similar process using the Python and Matlab interfaces to the netCDF library. While I use R for post-processing, I generally use C/C++ for the modeling; thus I’ll step through generating a netCDF file in C and processing the generated netCDF file in R on a Linux machine.

Edit:  I originally put a link to following code at the bottom of this post.  For convenience, here’s a link to the bitbucket repository that contains the code examples below.

Writing a netCDF file in C…

Confirm netCDF installation

First, be sure that netCDF is installed on your computing platform. Most scientific computing clusters will have the netCDF library already installed. If not, contact your system administrator to install the library as a module. If you would like to install it yourself, Unidata provides the source code and great documentation to step you through the process. The example I provide here isn’t all that complex, so any recent version (4.0+) should be able to handle this with no problem.

Setup and allocation

Include the header files

With the netCDF libraries installed, you can now begin to code netCDF support into your model. Again, I’ll be using C for this example. Begin by including the netCDF header file with your other include statements:

#include <stdlib.h>
#include <stdio.h>
#include <netcdf.h>

Setup an error handler

The netCDF library includes a nice way of handling possible errors from the various netCDF functions. I recommend writing a simple wrapper function that can take the returned values of the netCDF functions and produce the appropriate error message if necessary:

void ncError(int val)
{
  printf("Error: %s\n", nc_strerror(val));
  exit(2);
}

Generate some example data

Normally, your model will have generated important data at this point. For the sake of the example, let’s generate some data to put into a netCDF file:

  // Loop control variables
  int i, j, k;
  
  // Define the dimension sizes for
  // the example data.
  int dim1_size = 10;
  int dim2_size = 5;
  int dim3_size = 20;
  
  // Define the number of dimensions
  int ndims = 3;
  
  // Allocate the 3D vectors of example data
  float x[dim1_size][dim2_size][dim3_size]; 
  float y[dim1_size][dim2_size][dim3_size];
  float z[dim1_size][dim2_size][dim3_size];
  
  // Generate some example data
  for(i = 0; i < dim1_size; i++) {
      for(j = 0; j < dim2_size; j++) {
          for(k = 0; k < dim3_size; k++) {
              x[i][j][k] = (i+j+k) * 0.2;
              y[i][j][k] = (i+j+k) * 1.7;
              z[i][j][k] = (i+j+k) * 2.4;
          }
      }
    }

This generates three variables, each with three different size dimensions. Think of this, for example, as variables on a 3-D map with dimensions of [latitude, longitude, height]. In my modeling application, my dimensions were [uncertain state-of-the-world, BORG archive solution, time].

Allocate variables for IDs

Everything needed in creating a netCDF file depends on integer IDs, so the next step is to allocate variables for the netCDF file id, the dimension ids, and the variable ids:

// Allocate space for netCDF dimension ids
int dim1id, dim2id, dim3id;
  
// Allocate space for the netcdf file id
int ncid;
  
// Allocate space for the data variable ids
int xid, yid, zid;

Each one of these IDs will be returned through reference by the netCDF functions. While we’re at it, let’s make a variable to hold the return status of the netCDF function calls:

// Allocate return status variable
int retval;

Define the meta-data

Now we will start to build the netCDF file. This is a two-part process. The first part is defining the meta-data for the file and the second part is assigning the data.

Create an empty netCDF file

First, create the file:

// Setup the netcdf file
if((retval = nc_create("example.nc", NC_NETCDF4, &ncid))) { ncError(retval); }

Note that we store the return status of the function call in retval and test the return status for an error. If there’s an error, we pass retval to our error handler. The first parameter to the function call is the name of the netCDF file. The second parameter is a flag that determines the type of netCDF file. Here we use the latest-and-greatest type of NETCDF4, which includes the HDF5/zlib compression features. If you don’t need these features, or you need a version compatible with older versions of netCDF libraries, then use the default or 64-bit offset (NC_64BIT_OFFSET) versions. The third parameter is the netCDF integer ID used for assigning variables to this file.

 Add the dimensions

Now that we have a clean netCDF file to work with, let’s add the dimensions we’ll be using:

 // Define the dimensions in the netcdf file
 if((retval = nc_def_dim(ncid, "dim1_size", dim1_size, &dim1id))) { ncError(retval); }
 if((retval = nc_def_dim(ncid, "dim2_size", dim2_size, &dim2id))) { ncError(retval); }
 if((retval = nc_def_dim(ncid, "dim3_size", dim3_size, &dim3id))) { ncError(retval); }
  
 // Gather the dimids into an array for defining variables in the netcdf file
 int dimids[ndims];
 dimids[0] = dim1id;
 dimids[1] = dim2id;
 dimids[2] = dim3id;

Just as before, we catch and test the function return status for any errors. The function nc_def_dim() takes four parameters. First is the netCDF file ID returned when we created the file. The second parameter is the name of the dimension. Here we’re using “dimX_size” – you would want to use something descriptive of this dimension (i.e. latitude, time, solution, etc.). The third parameter is the size of this dimension (i.e. number of latitude, number of solutions, etc.). The last is the ID for this dimension, which will be used in the next step of assigning variables. Note that we create an array of the dimension IDs to use in the next step.

 Add the variables

The last step in defining the meta-data for the netCDF file is to add the variables:

// Define the netcdf variables
if((retval = nc_def_var(ncid, "x", NC_FLOAT, ndims, dimids, &xid))) { ncError(retval); }
if((retval = nc_def_var(ncid, "y", NC_FLOAT, ndims, dimids, &yid))) { ncError(retval); }
if((retval = nc_def_var(ncid, "z", NC_FLOAT, ndims, dimids, &zid))) { ncError(retval); }

The nc_def_var() function takes 6 parameters. These include (in order) the netCDF file ID, the variable name to be displayed in the file, the type of data the variable contains, the number of dimensions of the variable, the IDs for each of the dimensions, and the variable ID (which is returned through reference). The type of data in our example is NC_FLOAT, which is a 32-bit floating point. The netCDF documentation describes the full set of data types covered. The IDs for each dimension are passed as that combined array of dimension IDs we made earlier.

 Optional: Add variable attributes

This part is optional, but is incredibly useful and true to the spirit of making a netCDF file. When sharing a netCDF file, the person receiving the file should have all the information they need about the data within the file itself. This can be done by adding “attributes”. For example, let’s add a “units” attribute to each of the variables:

 // OPTIONAL: Give these variables units
 if((retval = nc_put_att_text(ncid, xid, "units", 2, "cm"))) { ncError(retval); }
 if((retval = nc_put_att_text(ncid, yid, "units", 4, "degC"))) { ncError(retval); }
 if((retval = nc_put_att_text(ncid, zid, "units", 1, "s"))) { ncError(retval); }

The function nc_put_att_text() puts a text-based attribute onto a variable. The function takes the netCDF ID, the variable ID, the name of the attribute, the length of the string of characters for the attribute, and the text associated with the attribute. In this case, we’re adding an attribute called “units”. Variable ‘x’ has units of “cm”, which has a length of 2. Variable ‘y’ has units of “degC”, which has a length of 4 (and so on). You can apply text-based attributes as shown here or numeric-based attributes using the appropriate nc_put_att_X() function (see documentation for the full list of numeric attribute functions). You can also apply attributes to dimensions by using the appropriate dimension ID or set a global attribute using the ID “0” (zero).

 End the meta-data definition portion

At this point, we’ve successfully created a netCDF file and defined the necessary meta-data. We can now end the meta-data portion:

 // End "Metadata" mode
  if((retval = nc_enddef(ncid))) { ncError(retval); }

…and move on to the part 2 of the netCDF file creation process.

Populate the file with data

Put your data into the netCDF file

Here, all we do is put data into the variables we defined in the file:

 // Write the data to the file
 if((retval = nc_put_var(ncid, xid, &x[0][0][0]))) { ncError(retval); }
 if((retval = nc_put_var(ncid, yid, &y[0][0][0]))) { ncError(retval); }
 if((retval = nc_put_var(ncid, zid, &z[0][0][0]))) { ncError(retval); }

The function nc_put_var() takes three parameters: the netCDF file ID, the variable ID, and the memory address of the start of the multi-dimensional data array. At this point, the data will be written to the variable in the netCDF file. There is a way to write to the netCDF file in data chunks, which can help with memory management, and a way to use parallel I/O for writing data in parallel to the file, but I have no experience with that (yet). I refer those interested in these features to the netCDF documentation.

Finalize the netCDF file

That’s it! We’re done writing to the netCDF file. Time to close it completely:

 // Close the netcdf file
 if((retval = nc_close(ncid))) { ncError(retval); }

Compile and run the code

Let’s compile and run the code to generate the example netCDF file:

gcc -o netcdf_example netcdf_write_example.c -lnetcdf

Some common problems people run into here are not including the netCDF library flag at the end of the compilation call, not having the header files in the include-path, and/or not having the netCDF library in the library-path. Check your user environment to make sure the netCDF paths are included in your C_INCLUDE_PATH and LIBRARY_PATH:

env | grep –i netcdf

Once the code compiles, run it to generate the example netCDF file:

./netcdf_example

If everything goes according to plan, there should be a file called “example.nc” in the same directory as your compiled code. Let’s load this up in R for some post-processing.

 Reading a netCDF file in R…

Install and load the “ncdf4” package

To start using netCDF files in R, be sure to install the netCDF package “ncdf4”:

install.packages("ncdf4")
library(ncdf4)

Note that there’s also an “ncdf” package. The “ncdf” package reads and writes the classic (default) and 64-bit offset versions of netCDF file. I recommend against using this package as the new package “ncdf4” can handle the old file versions as well as the new netCDF4 version.  Turns out the “ncdf” package has been removed from the CRAN repository.  It’s just as well since the new “ncdf4” package obsoletes the “ncdf” package.


Open the netCDF file

With the library installed and sourced, let’s open the example netCDF file we just created:

 nc <- nc_open("example.nc")

This stores an open file handle to the netCDF file.

View summary of netCDF file

Calling or printing the open file handle will produce a quick summary of the contents of the netCDF file:

 print(nc)

This summary produces the names of the available variables, the appropriate dimensions, and any global/dimension/variable attributes.

Extract variables from the netCDF file

To extract those variables, use the command:

x <- ncvar_get(nc, "x")
y <- ncvar_get(nc, "y")
z <- ncvar_get(nc, "z")

At this point, the data you extracted from the netCDF file are loaded into your R environment as 3-dimensional arrays. You can treat these the same as you would any multi-dimensional array of data (i.e. subsetting, plotting, etc.). Note that the dimensions are reported in reverse order from which you created the variables.

dim(x)

 Close the netCDF file

When you’re done, close the netCDF file:

nc_close(nc)

And there you have it! Hopefully this step-by-step tutorial has helped you incorporate netCDF support into your project. The code I described here is available through bitbucket.

Happy computing!

~Greg

Survival Function Plots in R

Survival Function Plots in R

A survival function (aka survivor function or reliability function) is a function often used in risk management for visualizing system failure points. For example, it can be used to show the frequency of a coastal defense structure failure (such as a breach in a levee) in a future state of the world.

The function itself is quite simple. For a distribution of events, the survival function (SF) is 1-CDF where CDF is the cumulative distribution function. If you’re deriving the distribution empirically, you can substitute the CDF with the cumulative frequency. It is often plotted on a semi-log scale which makes tail-area analysis easier.

I’ve written some R code that creates a primitive Survival Function plot from a vector of data.  Below is the function (Note: You can find the code and an example of its usage on bitbucket https://bitbucket.org/ggg121/r_survival_function.git)

plot.sf <- function(x, xlab=deparse(substitute(x)), left.tail=F,
  ylab=ifelse(left.tail, "SF [Cum. Freq.]", "SF  [1 - Cum. Freq.]"),
  make.plot=T, ...)
{
  num.x <- length(x)
  num.ytics <- floor(log10(num.x))
  sf <- seq(1,1/num.x,by=-1/num.x)
  
  if(left.tail){
    order.x <- order(x, decreasing=T)
    order.sf <- sf[order(order.x)]
    
  }  else {
    order.x <- order(x)
    order.sf <- sf[order(order.x)]
  }
  
  if(make.plot) {
    plot(x[order.x], sf, log="y", xlab=xlab, ylab=ylab, yaxt="n", ...)
    axis(2, at=10^(-num.ytics:0), 
         label=parse(text=paste("10^", -num.ytics:0, sep="")), las=1)
  }
  invisible(order.sf)
}

Download and source the code at the start of your R script and you’re good to go. The function, by default, creates a plot in the current plotting device and invisibly returns the survival function values corresponding to the vector of data provided. The parameter left.tail sets the focus on the left-tail of the distribution (or essentially plots the CDF on a semi-log scale). By default, the function puts the focus on the right tail (left.tail = FALSE). The make.plot parameter allows you to toggle plotting of the survival function (default is on or make.plot=TRUE. This is useful when you simply need the survival function values for further calculations or custom plots. Additional parameters are passed to the plot() function. Below is an example (which is also available in the repository).

# Source the function
source("plot_sf.r")

# Set the seed
set.seed(1234)

# Generate some data to use
my.norm <- rnorm(10000, 10, 2)
my.unif <- runif(10000)
my.weib <- rweibull(10000, 20, 5)
my.lnorm <- rlnorm(10000, 1, 0.5)


# Make the plots ----------------------
par(mfrow=c(2,2), mar=c(5,4,1,1)+0.1)

# Default plot settings
plot.sf(my.norm)

# Function wraps the standard "plot" function, so you can pass
# the standard "plot" parameters to the function
plot.sf(my.unif, type="l", lwd=2, col="blue", bty="l",
        ylab="Survival", xlab="Uniform Distribution")

# If the parameter "left.tail" is true, the plot turns into 
# a cumulative frequency plot (kind of like a CDF) that's plotted
# on a log scale.  This is good for when your data exhibits a left or
# negative skew.
plot.sf(my.weib, type="l", left.tail=T, xlab="Left-tailed Weibull Dist.")

# The function invisibly returns the survival function value.
lnorm.sf <- plot.sf(my.lnorm, type="l")
points(my.lnorm, lnorm.sf, col="red")
legend("topright", bty="n", 
       legend=c("Function Call", "Using returned values"), 
       lty=c(1,NA), pch=c(NA,1), col=c("black", "red") )

# The 'make.plot' parameter toggles plotting.
# Useful if you just want the survival function values.
norm.sf <- plot.sf(my.norm, make.plot=F)

And here’s the resulting figure from this example:

survival_function_plot_example

Now you can easily show, for example, tail-area frequency of events. For example, below is a survival function plot of a normal distribution:

survival_plot_norm_didactic

For this example, we can imagine this as a distribution of flood heights (x-axis would be flood height – note that a real distribution of flood heights would likely look drastically different from a normal distribution). With this visualization, we can easily depict the “1 in 10” or the “1 in 1,000” flood height by following the appropriate survival function value over to the corresponding flood height on the plot. Alternatively, you can determine the return period of a given flood height by following the flood height up to the plot and reading off the survival function value. Comparing multiple distributions together on a single plot (think deep uncertainty) can produce interesting decision-relevant discussion about changes in return periods for a given event or the range of possible events for a given return period.

I hope this post is useful. Survival function plots are incredibly versatile and informative…and I’ve only started to scratch the surface!

Easy labels for multi-panel plots in R

There are a number of ways to make multi-panel figures in R.  Probably the easiest and most commonly used method is to set par(mfrow=c(r,c)) to the  number of rows (r) and columns (c) you would like to use for your figure panels (Note: par(mfcol=c(r,c)) produces the same thing, only it renders the figures by column rather than by row).  Other methods include par(fig=c(x1,x2,y1,y2), new=T) and layout(mat), but these will be for another post.

What I found challenging was putting a label in a consistent location on each of the panels.  Using the text() function would be the go-to function for this, but the default coordinate system used in the text() is the plot’s coordinate system, and you’ll have to set an additional plotting option (par(xpd)) to plot outside of the figure region.

Since I regularly make multi-panel figures, I decided to write a wrapper function around text() that can easily and consistently place a label on a generated plot without having to worry about plotting coordinates.  Below is the function (Note: You can find the code and an example of its usage on bitbucket https://bitbucket.org/ggg121/r_figure_letter.git)

put.fig.letter <- function(label, location="topleft", x=NULL, y=NULL, 
                           offset=c(0, 0), ...) {
  if(length(label) > 1) {
    warning("length(label) > 1, using label[1]")
  }
  if(is.null(x) | is.null(y)) {
    coords <- switch(location,
                     topleft = c(0.015,0.98),
                     topcenter = c(0.5525,0.98),
                     topright = c(0.985, 0.98),
                     bottomleft = c(0.015, 0.02), 
                     bottomcenter = c(0.5525, 0.02), 
                     bottomright = c(0.985, 0.02),
                     c(0.015, 0.98) )
  } else {
    coords <- c(x,y)
  }
  this.x <- grconvertX(coords[1] + offset[1], from="nfc", to="user")
  this.y <- grconvertY(coords[2] + offset[2], from="nfc", to="user")
  text(labels=label[1], x=this.x, y=this.y, xpd=T, ...)
}

Simply source the code at the start of your R script and you’re good to go.  For convenience, the wrapper function allows you to use text-based locations for common figure-label locations akin to the keyword functionality in the legend() function.  Also, additional parameters can be passed to text() through this function.  Below is an example.

# Source the legend function file
source("put_fig_letter.r")

# Set the seed
set.seed(1234)

# Generate a data point to plot
x <- matrix(rnorm(60), ncol=6)
y <- matrix(rnorm(60), ncol=6)

# Apply a random scale to each column
x <- apply(x, 2, function(x) x*runif(1)*10)
y <- apply(y, 2, function(x) x*runif(1)*10)

# Setup multiple plot regions
par(mfrow=c(2,3), mar=c(5,4,1.5,1)+0.1)

# You can feed an (x,y) location to put the figure
# letter if you like, or you can use a predefined
# location by name kind of like legend()
my.locations <- c("topleft", "topcenter", "topright",
            "bottomleft", "bottomcenter", "bottomright")

# Make the plots and append a figure letter to each
# Note: put.fig.letter() sends additional parameters to
# the text() function.
for(i in 1:6) {
  plot(x[,i], y[,i], pch=16, xlab="x", ylab="y")
  my.label <- paste(letters[i], ".", sep="")
  put.fig.letter(label=my.label, location=my.locations[i], font=2)
}

And here’s the resulting figure: