Category Archives: Uncategorized

Calculating the area of a convex hull

A reader recently posted a comment on my plotting convex hull post asking how to calculate the area of a convex hull. While this never occurred to me before, I decided to make a quick post on how to do it. To make this snippet of script work, you’ll need to install the package “sp” using the install.pacakages() function.

First I’ll create some dummy data, in this case, it will be a simple box (so we can make sure that the area is correct):

box.coords <- matrix(c(1, 1,
                       4, 1,
                       1, 4,
                       4, 4), nrow = 4, ncol = 2, byrow = T)
plot(box.coords[,1], box.coords[,2], pch = 20)

We have a square with sides of length 3. So, we know beforehand that we should get an area of 9. Next, we will use the chull() to extract the coordinates that make up the convex hull (in this case, all of the points, since we only have 4 points!). Also, we’ll need to close the convex hull by repeating the first row in the last row. The reason for this will be apparent in minute. Finally, we create a new matrix with the convex hull points, that includes the repeated coordinates to close off the convex hull:

box.hpts <- chull(x = box.coords[,1], y = box.coords[,2])
box.hpts <- c(box.hpts, box.hpts[1])
box.chull.coords <- box.coords[box.hpts,]

Finally, we load the “sp” package so we can use the function Polygon(). If you read the help files for Polygon(), you’ll see the first argument is the a two row matrix of coordinates (x, y), with the coordinates in the first repeated again in the last row (aha!) This will close off the polygon and allow Polygon() to calculate an area. To extract the area of the polygon, you need to access the attributes of a SpatialPolygon object, using the @area symbol:

chull.poly <- Polygon(box.chull.coords, hole=F)
chull.area <- chull.poly@area
> chull.area
[1] 9

Not too hard! You can do this with any polygon, as long as it is a valid SpatialPolygon object. Here is a quick examples using more realistic data:


x1 <- rnorm(100, 0.8, 0.3)
y1 <- rnorm(100, 0.8, 0.3)
hpts <- chull(x = x1, y = y1)
hpts <- c(hpts, hpts[1])
xy.coords <- cbind(x1, y1)
chull.coords <- xy.coords[hpts,]
chull.poly <- Polygon(chull.coords, hole=F)
chull.area <- chull.poly@area

Just remember, that calculating an area of a convex hull only makes sense if the units of the X and Y axes are the same. Hope this answers the question!


Happy New Year!

It’s been a few months (OK, 8 months according to the sidebar…). I’ve been busy wrapping up my PhD (woohoo!) but I’ve wanted to update the blog to introduce a really great update to the R Shiny family: It’s a free R web app hosting site that (once you’ve registered) will let you host apps in the cloud for public consumption. It’s nicely integrated with RStudio, so I was able to quickly post my 3000 hit app for all to try out.

There’s no downloading code, running it locally etc… Just click on this link to try it out.  I still haven’t figured out why it’s slow to load at certain time and fast other times. It seems to happen randomly but often enough that it’s annoying. It’s probably something with the code, but it could have to do with sending commands to the server; the server might be dealing with other people’s requests (it is a free service after all!) Anyway, try it out, I still recommend it. And happy new year!

Plotting DEMs in 3D using persp(): Part 2

Quick Note: In my last post, I introduced some of the basics of the persp() function, and how to shade the facets of a persp() plot using a desired color ramp. I’m going to build off this earlier post to show how you can take a 2D DEM, and plot it in 3 dimensions. I’m going to be using the output from the script from this post, so don’t forget to run that script first before you start running the script below.

First, I’m going to extract some summary information from our final DEM, “interpDEM_mask”, particularly the minimum elevation value, summary.elev[1]. I then create a simple function, setBaseElev, that sets all NA’s in our raster to the minimum elevation value. This allows us to plot a base surface around our DEM, and give our 3D plot some spatial context:

summary.elev <- summary(interpDEM_mask)
setBaseElev <- function(x) {
  x[] <- as.numeric(summary.elev[1])
elev3D <- calc(interpDEM_mask, setBaseElev)

Next, we convert our Raster object to a regular matrix, so that we can extract the nrow and ncol, and eventually use persp() to plot it. You’ll also notice that I’ve trimmed a few rows and columns from my matrix. This isn’t necessary, but I did this because I realized that my bounding box for the raster was waaay larger than the actual DEM:

zData <-round(as.matrix(elev3D),1)
zData <- zData[c(50:540), c(50:300)]

The next lines of code are required so that we can plot our DEM using the graphics package version of persp(). If you read the persp() help page, you’ll find that both the x and y vectors need to be INCREASING in values. Since we are only plotting for the visual effect, and not for analyzing data, we can simply create vectors that have the same length as the dimensions of zData. You’ll notice that the x and y vectors are multipled by 12; this is to match the resolution of the raster we created earlier:

x = (12 * (1:nrow(zData)))    
y = (12 * (1:ncol(zData)))

We want to color our DEM based on the elevation data of our DEM (duh!), so we create a matrix, containing elevation data derived from our DEM data, which will tell R how to color the facets. This matrix MUST BE one less that the number of rows and columns in the elevation matrix (zData). We use the same function we introduced in Part 1 to calculate the elevation values that go into the zfacet matrix:

zfacet <- (zData[-1, -1] + zData[-1, -ncz] + 
           zData[-nrz, -1] + zData[-nrz, -ncz])/4

We then create a vector of colors that we will use to color the DEM facets. Here I am creating a vector with 100 colors, the first being “grey”, and the rest in hexadecimal (hex) notation from the built-in terrain.colors() color ramp. We use the cut() function to divide up the zfacet elevation data in 100 equal ranges. Each of these ranges is then assigned the corresponding color from the color vector, starting with the lowest elevation being “grey”, and so on and so forth:

nbcol <- 99
color <- c("grey", terrain.colors(nbcol))
facetcol <- cut(zfacet, nbcol+1)

Finally, we are ready to plot! I’ve added a bunch of arguements to the persp() function to make the output look pretty, but you can play around with different values to see how they change the final product:

res = persp(x, y, z = zData*2, theta = 90, phi = 30,
            col = color[facetcol],
            scale = FALSE, expand = 0.75, 
            ltheta = 75, shade = 0.75, border = NA,
            box = F, ticktype = "detailed")
3d plot of our DEM using persp().

3d plot of our DEM using persp().

Pretty nice DEM! I’m working on few new posts, so hope to get them up soon. Ciao!

Plotting DEMs in 3D using persp()

A little background… I got the idea to plot DEMs in 3D from a great R website that seemed quite popular a few years ago, but appears to have been taken down. This site helped me tremendously when I was first learning R. Anyway, one script demonstrated how to plot a DEM in 3D using persp(), but I always felt the script was more complicated that it needed to be.

Fast forward a couple years, and with the creation of the great raster package, working with rasters seems to have gotten a lot easier. Raster has a function (also called persp()) that allows you to plot raster* objects in 3D, without having to convert any data. It works well, but seems rather limited. Coloring the cells (or facets as they are referred to the help page) according to the z value seemed particularly difficult.

So, I decided to go back and see if I could simplify plotting DEMs using the graphic package version of persp(). I’ll demonstrate how I’ve plotted DEMs using persp() in an upcoming post, but I thought it’d be good to go back and review how persp() works, since I’ve had some battles getting data to plot correctly in the past.

Here are some key points to remember when using persp() to plot raster (or any type of data). I’ll then demonstrate them using a simple data matrix.

Key Point 1) The z matrix represents the “wire frame” of the plot NOT the cell centers.
Key Point 2) the x and y vectors represent the (x,y) coordinates where each value in the z matrix is plotted. Also, the x and y vectors MUST be increasing. This means that the z matrix is rotated 90 degrees counterclockwise when plotted. The length of the x vector must be the same length as the nrow(z) and the length of the y vector must equal ncol(z).
Key Point 3) When a nr x nc z matrix is plotted, it creates a (nr-1) x (nc-1) matrix of facets (cells) that can be colored using the “col” argument. This matrix is also rotated 90 degrees counterclockwise when plotted.

To demostrate these points, I will create a simple 4×4 matrix, and x and y coordinate vectors that increase:

zmat <- matrix(seq(1,16,1), nc = 4)
x <- seq(1, 4, 1)
y <- seq(1, 4, 1)
     [,1] [,2] [,3] [,4]
[1,]    1    5    9   13
[2,]    2    6   10   14
[3,]    3    7   11   15
[4,]    4    8   12   16
persp(x, y, zmat, axes= T, nticks = 4,
      ticktype = "detailed", theta = 320)

persp() plot our our simple DEM.

persp() plot our our simple DEM.

See that zmat[1,1] of our persp() surface is plotted at the origin (1,1,1), which is the lower left corner (of the x-y plane). persp() converts the x and y vectors to (x,y) coordinates using something similar to:

n = 1
coords <- list()
for(i in 1:length(x)){
  for(j in 1:length(y)){
    coords[[n]] <- c(x[i], y[j])
    n <- n+1

You can see that zmat[1,1] get plotted at (1,1,zmat[1,1]), zmat[1,2] get plotted at (1,2,zmat[1,2]), …. You’ll also notice in the image above, the wireframe created a 3×3 matrix of facets (cells) that can be colored according to a 3×3 matrix of colors. To borrow some code from for the persp() help page:

# create 3x3 matrix which averages the value of
# the 4 points bounding each facet.
nrzmat <- nrow(zmat)
nczmat <- ncol(zmat)
facetValues <- (zmat[-1, -1] + zmat[-1, -nczmat] + 
          zmat[-nrzmat, -1] + zmat[-nrzmat, -nczmat])/4

#Color Ramp
jet.colors <- colorRampPalette( c("blue", "green") )
# Generate the desired number of colors from this palette
nbcol <- 100
color <- jet.colors(nbcol)
# Recode facetValues into color indices
facetcol <- cut(facetValues, nbcol)

persp(x, y, zmat, axes= T, nticks = 4, ticktype = "detailed",
      theta = 320, col = color[facetcol])
persp() plot of DEM colored according to facetValue matrix.

persp() plot of DEM colored according to facetValue matrix.

The cool trick I learned from the help page example is the equation used to calculate the facetValue matrix. This will come in handy when plotting our own DEM. The equation simply calculates the average value of the four points that make up each facet, and this is what determines the facet color!

I’ve decided to break this post up into two parts. I’ll have part 2 up shortly. Cheers!

Creating DEMs from contour lines using R

UPDATE: I made a slight change to the script, because I was getting an error when I ran the script on Windows, but not on Linux.  Previously, the script read:

# Create raster grid where we are going to interpolate our
# elevation data.
contourBBox <- bbox(contour3m)
contourRaster <- raster(xmn=contourBBox[1,1], 
                        crs = CRS("+init=epsg:26918"),
                        resolution = c(12,12))

But I found, that the resolution = c(12,12) argument was giving an error on my Windows computer.  Fortunately, there is an easy fix. Just remove the argument and add the line res(contourRaster) <- 12:

# Create raster grid where we are going to interpolate our
# elevation data.
contourBBox <- bbox(contour3m)
contourRaster <- raster(xmn=contourBBox[1,1], 
                        crs = CRS("+init=epsg:26918"))
res(contourRaster) <- 12

Everything should work smoothly now!

Quick Note: A few years ago I did a post on using R for spatial analyses. I recently thought I’d return to the topic, mainly to show how versatile R is and how many of the things you can do in dedicated GIS software (which can cost thousands of dollars to license!) can be re-created easily and quickly using R.

DEMs, or digitial elevation models, are one of the most common types of data used in spatial analysis. DEMs are raster files that contains elevation information for each cell in the raster. I recently was give a shapefile of contour lines for a particular area and needed to create a DEM from them. As such, I thought I’d demonstrate how I created a DEM from the contour lines that were in a vector shapefile (.shp), one of the most common GIS file types.

I won’t go into all the differences between rasters and vectors (ArcGIS has some good online resources in case you need to brush up) but the basic steps are:

1. Read in the files to R.
2. Create a raster “grid” to interpolate the elevation data onto.
3. Convert the contour lines to points so you can interpolate between elevation points.
4. Interpolate the elevation data onto the raster grid.
5. Crop the DEM raster to the boundary of the area of interest.

Before I begin, I obtained my data from the Mass GIS webportal, which is a really nice web-based GIS for querying all types of spatial data within the Commonwealth of Massachusetts. Since I’m interested in elevation data only, I looked for a sub-basin (ie. watershed) that had a nice topographic range and shape. I then downloaded the watershed boundaries, and the 3m contour lines that covered the watershed, as separate shapefiles.

Step 1. This is quite simple, since there are some really nice R packages for dealing with spatial data. To read in our data, we will use the maptools library. You’ll notice that the readShapeLines() and readShapePoly() has a proj4string argument. This is where you tell R what the projection and datum are for your data. MassGIS actually asks which projection you’d like your data in, so I knew ahead of time what EPSG I needed to input:


#Read in shape files
contour3m <- readShapeLines("GISDATA_CONTOURS5K_ARC",
                            proj4string = CRS("+init=epsg:26918"))

ws_bound <- readShapePoly("GISDATA_SUBBASINS_POLY",
                           proj4string = CRS("+init=epsg:26918"))

Lets plot up the files to see what we are working with. I’m interested in the watershed in the center, but you can see that the downloaded data included adjacent watersheds. Also, the contours extend beyond the watershed of interest. We’ll deal with this later when we crop and clean up our data:

# plot of ws_bound with watershed of interest highlighted
spplot(ws_bound, zcol = "SUB_ID", col = "black", colorkey = F,
       fill = "grey80", 
       panel = function(x, y, ...){
         panel.polygonsplot(x,y, ...)
         sp.polygons(ws_bound[as.character(ws_bound$SUB_ID) == 1007, ],
                    fill = "magenta")

# same plot as above, but include contour3m lines
spplot(ws_bound, zcol = "SUB_ID", col = "black", colorkey = F,
       fill = "grey80", 
       panel = function(x, y, ...){
         panel.polygonsplot(x,y, ...)
         sp.polygons(ws_bound[as.character(ws_bound$SUB_ID) == 1007, ],
                     fill = "magenta")
         sp.lines(HudsonWS_contourSub, col = "black")
watershed boundaries downloaded from MassGIS.  The watershed of interest is highlighted in magenta.

Watershed boundaries downloaded from MassGIS. The watershed of interest is highlighted in magenta.

Added 3m contour lines to plot to show extent of contour lines outside watershed of interest.

Added 3m contour lines to plot to show extent of contour lines outside watershed of interest.

Step 2. I need to create an empty raster grid that spans the range of my sub-basin. Since I’m using the contour lines to create the DEM, I used them as the basis for my raster grid. Notice that I manually set the resolution (size) of each cell in the raster to be square (12m x 12m). This is required if you ever want to import your data into ArcGIS (as far as I’m aware). I also set the resolution so that I didn’t have too many cells. The resolution should depend on your needs and computing power:

# Create raster grid where we are going to interpolate our
# elevation data.
contourBBox <- bbox(contour3m)
contourRaster <- raster(xmn=contourBBox[1,1], 
                        crs = CRS("+init=epsg:26918"),
                        resolution = c(12,12))

Step 3. Since interpolation methods were conceived to work with point data, we need to convert the elevation contour lines to elevation points. Fortunately, this is quite easy to do in R using as(). Essentially we are creating points along each contour line that has as its value the elevation of the associated contour line:

# Create points from contour lines so we can
# interpolate between points.
p <- as(contour3m, 'SpatialPointsDataFrame')

Step 4. Now we have points from which we can interpolate a elevation raster. There are probably many different intrpolation packages out there, but I’m going to use gstat, since it seems pretty robust for spatial statistics, and there are nice examples using the gstat and raster packages together for interpolating point data to rasters. We will use gstat() to create a model for interpolating our point elevation data using inverse distance weighting. Then, we use interpolate() to predict the elevation value at each cell in contourRaster. Note that this step can take some time depending on the computing power of your computer:

#interpolate between points using IDW into contourRaster
g <- gstat(id="ELEV_M", formula = ELEV_M~1, data=p,
           nmax=7, set=list(idp = .5))
interpDEM <- interpolate(contourRaster, g)

Step 5. Finally, we can clean up the data by clipping our DEM to the boundaries of the watershed. We can also clip our contour lines to the boundaries of our watershed:

# extract the watershed boundary of interest
HudsonWS_bound <- ws_bound[as.character(ws_bound$SUB_ID) == 1007, ]
# clip raster to watershed boundaries
interpDEM_mask <- mask(interpDEM, HudsonWS_bound)
# clip contours to watershed boundary
HudsonWS_contour <- crop(contour3m,HudsonWS_bound)

That wasn’t too bad. We can plot it up nicely using spplot() like I did in a previous post:

# subset 3m contours for nice plotting
HudsonWS_contourSub <- HudsonWS_contour[(HudsonWS_contour$ELEV_M) %in% 
                                          seq(354, 993, 30), ]
# Plot it up!
spplot(interpDEM_mask, col.regions = heat.colors(100),
       xlim=c(bbox(interpDEM_mask)[1,1] + 900,
              bbox(interpDEM_mask)[1,2] - 900),
       ylim=c(bbox(interpDEM_mask)[2,1] + 1150,
              bbox(interpDEM_mask)[2,2] - 900),
       colorkey = list(space = "top", width = 1), main = "Elev. (m)",
       panel = function(x, y, ...){
         panel.gridplot(x,y, ...)
         sp.lines(HudsonWS_contourSub, col = "black")
Final DEM with 30m contour lines.

Final DEM with 30m contour lines.

Not too shabby! Anyway, keep an eye on Chit Chat R for more spatial analysis in near future…

Fitting a (non-linear) curve to data points

Anyone who has taken a high school math class is probably familiar with fitting a straight line to data points:

1. graph the points
2. draw a best fit straight line through the points
3. calculate the slope, m = (y2 – y1)/(x2 – x1), where (x1, y1) and (x2, y2) are two different points on the best fit line
4. Continue the best fit line through the y-axis to determine b, the y-intercept.

Voila! You have a equation for a straight line in the form y = mx + b! If you’re like me and are lazy, you can use R to calculate the two parameters (m and b), using the lm() function along with the summary() function.

The above steps are all well and good if your data approximates a straight line, but what if your data are non-linear (ie. curved) and you want to fit a line to it?

Well, (not surprisingly) R has you covered. R has a nice built in function called nls(), that can fit a non-linear equation to your data. To use this function, all you need to do is decide on a model to fit to your data. This may seem simple, but choosing the correct model can be quite important. Typically in the natural sciences, we try and choose models that make sense physically (ie. the parameters of the model can be related back to real world phenomena) or a model that is well accepted in a particular area of research. Nonetheless, just keep in mind that model selection is a critical step.

With that out of the way, I’ve decided to demonstrate nls() using some real world data, namely daily maximum temperature data (TMAX) taken from a great of source free climate data, NOAA. They have a really nice user interface to search for all different types of climate data.

On the National Climate Data Center website, I was quickly able to locate daily MAX and MIN temperature data from Logan International Airport in Boston, MA. Within a few hours of submitting my data request, I received an email telling me my data was ready to be downloaded. Let us begin!

They email had a link to a .dat file to download the data from the web, so I used R to grab the data and load it into a data frame ((I don’t know how long NOAA data links are active, so I suggest requesting your own data if you are following my script…) We are just interested in the date and TMAX data columns so we extract those:

url <- paste("", sep="")
dat <- read.table(url, sep = "", skip = 2, header = F)
bostonTemp <- data.frame(dat[c("V11", "V13")])
headers <- read.table(url, colClasses = "character", sep = "",
                      nrow = 1, header = F)
names(bostonTemp) <- c(headers[c("V6", "V8")])

Now that we have the data in a usable form, we can do some cleaning up. First, the temperature is given in tenths of a degree Celcius (I have no idea why…) so we can easily convert that into more familiar values by dividing by 10. Next, to make plotting easier, we can convert the dates into a time format that R likes, using the chron() function in the “chron” package. Finally, we can plot the data to see what it looks like:

bostonTemp$TMAX <- bostonTemp$TMAX/10
bostonTemp$DATE <- as.chron(paste(substr(bostonTemp$DATE, 5,6),
                                  substr(bostonTemp$DATE, 7,8),
                         substr(bostonTemp$DATE, 1,4), sep="/"))

par(font=2, font.axis = 2, tck = 0.01)
plot(bostonTemp$DATE, bostonTemp$TMAX)
2000-2014 TMAX data from Logan International Airport.

2000-2014 TMAX data from Logan International Airport.

As you can see I downloaded data spanning 1/1/2000 through the present. Clearly the temperature flucuates in a repeating fashion, cold in the winter and hot in the summer (obviously). Let’s look at the most recent year where we have a full year of data, 2013:

bostonTemp2013 <- subset(bostonTemp, 
                         bostonTemp$DATE >= as.chron("01/01/2013") & 
                         bostonTemp$DATE <= as.chron("12/31/2013"))
plot(bostonTemp2013$DATE, bostonTemp2013$TMAX) 
2013 TMAX data from Logan International Airport.

2013 TMAX data from Logan International Airport.

It appears that the TMAX data have a convex upward shape, with the highest values of TMAX in the middle of the year and the lowest values at the beginning and the end. You could say that the data has the shape of a parabola! Hmm, let’s fit it.

Knowing the vertex form of the parabola equation: y = a*(x – h)^2 + k, we can use this as our model. We also need to supply nls() with a starting value for each of the unknown parameters that we are going to estimate (a, h and k). Knowing the physical meaning behind each of the model parameters (see this website for a quick refresher), we can guess that h is approximately the date where TMAX is the greatest, and k is the maximum TMAX, and we can assume a is a negative value (since we want the parabola to open downwards), let’s say -1. Finally, we need to convert bostonTemp2013$DATE to a numeric format using as.numeric() so that we can fit a equation to the data:

x <- as.numeric(bostonTemp2013$DATE)
y <- bostonTemp2013$TMAX
h1 <- mean(x)
k1 <- max(y)
a1 <- -1

yfit<- nls(y ~ a*(x-h)^2 + k, start = list(a = a1, h = h1, k = k1))
yfitParm <- summary(yfit)$para[,1]

If we look at the parameter estimates nls() gave us, they weren’t too far off from our initial guesses!

> cbind(h1, k1, a1)
        h1   k1 a1
[1,] 15888 37.2  -1
> yfitParm
            a             h             k 
-8.329497e-04  1.590282e+04  2.480478e+01 

Now lets see how nls() did when fitting our data with a parabola:

ymod <- yfitParm[1]*(x-yfitParm[2])^2 + yfitParm[3]

par(font=2, font.axis = 2, tck = 0.01)
plot(bostonTemp2013$DATE, bostonTemp2013$TMAX)
lines(x, ymod)
2013 TMAX data from Logan Internaltional Airport fitted with a parabola.

2013 TMAX data from Logan Internaltional Airport fitted with a parabola.

Not too bad! There may be more appropriate models out there for fitting temperature data, but this model seems to do the trick. Till next time…

Back to basics: Plotting two y-axes on the same plot

After another lengthy hiatus (PhD work isn’t all fun and games!), I’m back and decided to make a post about a particular problem that I keep coming across when I’m making my figures.  Many times, you want to plot two variables, say y1 and y2, on the same graph, against another variable (say x1), but the y variables have very different units/scales/etc.  This comes up a lot with time series data, when y1 and y2 span the same time but are measured on different days and/or represent different variables.

To overcome this issue, we can take advantage of a few built-in features of R, namely the par(new=T). This allows you to create a new plotting device (as R likes to call plots), without erasing the previous plot. Essentially what we are going to do is plot two figure on top of one another, but with a different y axis range specified in the second plot() function.

Let’s work through the code:

First we create or dummy data. For this example, both y1 and y2 are assumed to have the same x variable (“dates”):

### Create Dummy Data
dates <- seq.dates("1/1/2014", "3/1/2014", by = "days")
y1 <- seq(1, length(dates), 1) + rnorm (length(dates), mean =1, sd= 0.5)
y2 <- rev(seq(1+100, length(dates)+100, 1)) + rnorm (length(dates),
                                                     mean =1, sd= 0.5)

Next we calculate the range for our dates and y1 variable and plot it up. Note we are NOT actually plotting axes or points at this time (ie. plot(..., type = "n", ...)):

par(mar = c(5,4,3,4), mgp = c(1,0.3,0), font=2,
    font.axis = 2, tck = 0.01)
date.range = sort(dates)
y1.range <- c(min(floor(range(y1))), max(ceiling(range(y1))))
plot(dates, y1, ylim = c(y1.range), ann = F, axes = F, type = "n",
     xlim = c(date.range[1], date.range[length(date.range)]))

We then add the box around the plotting region, and both the x axis (which are dates) and the y axis. Wa also add the points (finally!):

### Add axes for dates and y1
axis.Date(1, at = seq(date.range[1], date.range[length(date.range)],
                      4), format="%m/%d/%y", labels = F, tck = 0.01)
label=seq(date.range[1], date.range[length(date.range)],4)
text(x=label[1:x.len],  par("usr")[3]-1.35, srt = 45, adj = 1,
     labels = label, xpd = T, cex.axis  = 1.5)
axis(2, at = round(seq(y1.range[1], y1.range[2], 5)), las = 2,
     cex.axis = 1.25)
mtext(side = 2, "Y variable 1", at = 35, line = 2.3, cex = 1.5,
      col = "black")
mtext(side = 1, "Date", cex = 1.5, line = 3.2)

### Add Y1 points
points(dates, y1, pch = 20, cex = 1.5, col = "black")

Finally, we can add the second variable. But first don’t forget to add par(new=T) BEFORE you add the second plot! Also note that the second plot uses the y2 variable, not y1, and the ylim is set to match the range of the y2 variable:

### Now we add second Y axis and points----------------------------------------#
y2.range <- c(min(floor(range(y2))), max(ceiling(range(y2))))
plot(dates, y2, ylim = c(y2.range), ann = F, axes = F, type = "n",
     xlim = c(date.range[1], date.range[length(date.range)]))
points(dates, y2, col="red", pch = 20)

### Add 2nd y axis
axis(4, at = round(seq(y2.range[1], y2.range[2], 5)), las = 2,
     cex.axis = 1.25,
     col = "red", col.axis = "red")
mtext(side = 4, "Y variable 2", at = 135, line = 2.3, cex = 1.5,
      col = "red")
Example of xy-plot with two y variables that span different ranges

Example of xy-plot with two y variables that span different ranges

The above case works when both y1 and y2 have the same x variable. But, it’s not hard to imagine that y1 and y2 were measured on different days. This is actually quite easy to handle. The only difference from the above code is that when we add the points for the second y variable (in the second points() function above), we would use a the correct x variable. To add a 3rd variable to the plot above, which was measured on different days:

### add third Y variable----------------------------------------#
y3 <- rep(mean(y2),20) + rnorm (20, mean =10, sd= 5)
y3.dates <- dates[seq(2, 40, 2)] + 13
y3.range <- c(min(floor(range(y3))), max(ceiling(range(y3))))
plot(dates, y3, ylim = c(y3.range), ann = F, axes = F, type = "n",
     xlim = c(date.range[1], date.range[length(date.range)]))
points(y3.dates, y3, col="magenta", pch = 20)
lines(y3.dates, y3, col="magenta", lwd=2, pch = 20)

Here the final product!

Added a 3rd y variable, but with a different length x variable.

Added a 3rd y variable, but with a different length x variable.