with()

A brief introduction to the with() function

Problem

Making graphics with base R is annoying for many reasons, but a big one is having to type the name of the data frame over and over again to reference different columns.

Context

Back to our Mississippi River fish data. I’ve aggregated my sampling points into polygons, and now I want to explore some of their characteristics. To do that, I’d like to make some tables and plots, and because these are just quick, exploratory plots, I don’t feel like dealing with ggplot.

Load in the data (accessible on GitHub).

# Load data from GitHub
polygon <- read.csv("https://tinyurl.com/rta6hkbo") 

# Look at what we're dealing with
dim(polygon) # How big is the data set? 

[1] 527  21

head(polygon, 3) # Look at the first few rows

     poly_id propsnag n_points habitat_code pool      Area Perimeter
1 P04_CFL_13   0.8000        5          CFL    4 105288.80  2067.890
2 P04_CFL_14   0.2000        5          CFL    4  42668.28  1770.465
3 P04_CFL_15   0.4375       16          CFL    4 678390.21  5226.963
  max_depth avg_depth tot_vol shoreline_density_index pct_aqveg
1      1.30 0.3625869   33955                1.797759 19.133960
2      0.74 0.3291391    5953                2.417852 41.252704
3      2.68 0.6159651  356757                1.790213  9.256465
  pct_terr pct_prm_wetf med_dist_to_land med_dist_to_forest
1 93.87983     79.67522         34.13379           34.13379
2 94.76871     42.44244         18.90166           32.64112
3 86.17161     41.27248         21.40210           39.27576
  med_current wingdam revetment tributary pct_shallow_area
1        0.02       0         1         0        0.9278354
2        0.02       0         0         0        1.0000000
3        0.01       1         1         1        0.9194788

First, I’d like to see how total volume tot_vol of the aquatic area scales with its Area.

In base R:

# Formula notation
plot(polygon$tot_vol ~ polygon$Area)
# OR: 

# Comma notation
plot(polygon$Area, polygon$tot_vol)

Either way, we get this:

Or a more informative plot, with both variables on a log scale:

plot(log(polygon$tot_vol) ~ log(polygon$Area))

This isn’t too too clunky, but if the data frame name or column names are long, it can get a little annoying.

Solution

The with() function allows you to specify the data frame your variables are coming from and then reference the variables with respect to the data frame, similar to the ggplot argument data =. Handy.

# Plot using the with() function 
with(polygon, plot(tot_vol ~ Area))

You can add any other arguments inside of the function, as normal, it’s just now wrapped in with().

# Log-transform variables and make the points blue dots, because why not?
with(polygon, plot(log(tot_vol) ~ log(Area), # log-transform 
                   pch = 20, # dots instead of circles 
                   col = "blue", # make the dots blue 
                   main = "Polygon volume by area, log-transformed") # title 
     )

It’s worth noting that this works for other functions besides plot(), too. Here’s an example with table(): let’s look at how many sampling polygons include revetment, broken down by navigation pool (area of the river). The data set contains three navigation pools: 4, 8, and 13.

# Two-way table by pool and revetment
with(polygon, table(revetment, pool))

         pool
revetment   4   8  13
        0  71 199 103
        1  57  53  44

Outcome

Quick plots and data manipulation made even quicker!

Resources

Discussion of when to use with(): https://stackoverflow.com/questions/42283479/when-to-use-with-function-and-why-is-it-good