GAM example
Calculating odds ratio for specific increment steps of a continuous variable
In this example we take predictor x2 (randomly chosen). We need to define start and stop values via argument values.
or_gam(data = data_gam, model = fit_gam, pred = "x2",
values = c(0.099, 0.198))
#> # A tibble: 1 x 6
#> predictor value1 value2 oddsratio `CI_low (2.5%)` `CI_high (97.5%)`
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 x2 0.099 0.198 23.3 23.3 23.3In the plot it turns out that the odds of response y happening are 22 times higher when predictor x2 increases from 0.099 to 0.198 while holding all other predictors constant.
What is going on behind the scenes? Usually, this calculation is done by
- setting all predictors to their mean value,
- predict the response,
- change the desired predictor to a new value and predict the response again. These steps result in two “log odds” values, which are transformed into “odds” afterwards. Finally, the odds ratio can be calculated from these two odds values.
Calculating odds ratio for a level change of a nominal variable
If the predictor is an indicator/nominal/factor variable (i.e. consists of fixed levels) you can use the function in the same way by just putting in the respective factor levels:
or_gam(data = data_gam, model = fit_gam,
pred = "x4", values = c("A", "B"))
#> # A tibble: 1 x 6
#> predictor value1 value2 oddsratio `CI_low (2.5%)` `CI_high (97.5%)`
#> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 x4 A B 1.38 1.33 1.42Here, the change in odds of y happening if predictor x4 is changing from level A to B is rather small. In detail, an increase in odds of 37.8% is reported.
Calculating odds ratio for percentage increments of a continuous predictor
To get an impression of odds ratio changes throughout the complete range of the smoothing function of the fitted GAM model for a specific predictor, you can calculate odds ratios based on percentage breaks of the predictors distribution.
Here we slice predictor x2 into 5 parts by taking the predictor values of every 20% increment step.
or_gam(data = data_gam, model = fit_gam, pred = "x2",
percentage = 20, slice = TRUE)
#> # A tibble: 5 x 8
#> predictor value1 value2 perc1 perc2 oddsratio `CI_low (2.5%)`
#> <chr> <dbl> <dbl> <chr> <chr> <dbl> <dbl>
#> 1 x2 0.001 0.2 0 20 2511. 1092.
#> 2 x2 0.2 0.4 20 40 0.03 0.03
#> 3 x2 0.4 0.599 40 60 0.580 0.56
#> 4 x2 0.599 0.799 60 80 0.06 0.06
#> 5 x2 0.799 0.998 80 100 0.41 0.75
#> # … with 1 more variable: `CI_high (97.5%)` <dbl>We can see that there is a high odds ratio reported when increasing predictor x2 from 0.008 to 0.206 while all further predictor increases decrease the odds of response y happening substantially.
Plot GAM(M) smoothing functions
Plotting smoother functions of GAM models is not very well supported in R. plot_gam() helps to simplify things:
You can further customize the look using other colors or line types. I highly recommend the themes from the cowplot in combination with oddsratio. However, you are of course free to go ahead with any other theme you prefer.
Add odds ratio information into smoothing function plot
So now, we computed the odds ratios and created a plot of a GAM smoothing function. Why not combine both? This is what insert_or() is for. Its main arguments are
ggplotplotting object containing the smooth function and- a data frame returned from
or_gam()containing information about the predictor and the respective values that should be inserted.
plot_object <- plot_gam(fit_gam, pred = "x2", title = "Predictor 'x2'")
or_object <- or_gam(data = data_gam, model = fit_gam,
pred = "x2", values = c(0.099, 0.198))
plot <- insert_or(plot_object, or_object, or_yloc = 3,
values_xloc = 0.05, arrow_length = 0.02,
arrow_col = "red")
plot +
theme_cowplot()
The odds ratio information is always centered between the two vertical lines. Hence it only looks nice if the gap between the two chosen values (here 0.099 and 0.198) is large enough. If the smoothing line crosses your inserted text, you can just correct it adjusting or_yloc. This argument sets the y-location of the inserted odds ratio information.
Depending on the digits of your chosen values (here 3), you might also need to adjust the x-axis location of the two values so that they do not interfere with the vertical line.
Let’s do all of this by inserting another odds ratio result into this plot! This time we simply take the already produced plot as an input to insert_or() and use a new odds ratio object:
or_object2 <- or_gam(data = data_gam, model = fit_gam,
pred = "x2", values = c(0.4, 0.6))
insert_or(plot, or_object2, or_yloc = 2.1, values_yloc = 2,
line_col = "green4", text_col = "black",
rect_col = "green4", rect_alpha = 0.2,
line_alpha = 1, line_type = "dashed",
arrow_xloc_r = 0.01, arrow_xloc_l = -0.01,
arrow_length = 0.02, rect = TRUE) +
theme_cowplot()
Using rect = TRUE, you can additionally highlight certain odds ratio intervals. Aesthetics like opacity or color are fully customizable.