This is a tidyverse-tidyverse-compatible version of the stats::mahalanobis function. It just
makes it easier to include it as part of a dplyr::mutate.
tidy_mahalanobis(...)A vector that contains the Mahalanobis distances for each observation.
Typically you'll want to group your data (using dplyr::group_by) by speaker and vowel
class so that you get the distance from vowel centroids.
I won't tell you what to do with those distances, but if you might consider looking at tokens where the square root of the Mahalanobis distance is greater than around 2. However, to be clear, the exact cutoff will vary depending on the size and variability of your data. You can see how you might isolate these points visually in the example code below.
One small modification that this function does that stats::mahalanobis does not do is that
if there are fewer than 5 measurements in a group, tidy_mahalanobis returns them all
as having a distance of zero. I found that this prevents some fatal errors from crashing the script
when running this function on smaller datasets.
Note that this function requires the MASS package to be installed to work, but you
don't need to load it.
suppressPackageStartupMessages(library(tidyverse))
df <- joeysvowels::midpoints
#> Error in loadNamespace(x): there is no package called ‘joeysvowels’
# Calculate the distances
m_dists <- df %>%
group_by(vowel) %>%
mutate(mahal_dist = tidy_mahalanobis(F1, F2))
#> Error in UseMethod("group_by"): no applicable method for 'group_by' applied to an object of class "function"
# Take a peek at the resulting dataset
m_dists %>%
select(vowel, F1, F2, mahal_dist) %>%
head()
#> Error: object 'm_dists' not found
# Plot potential outliers
ggplot(m_dists, aes(F2, F1, color = sqrt(mahal_dist) > 2)) +
geom_point() +
scale_x_reverse() +
scale_y_reverse()
#> Error: object 'm_dists' not found
# You can include whatever numeric variables you want, like duration
df %>%
group_by(vowel) %>%
mutate(dur = end - start) %>%
mutate(mahal_dist = tidy_mahalanobis(F1, F2, dur)) %>%
ggplot(aes(F2, F1, color = sqrt(mahal_dist) > 2.5)) +
geom_point() +
scale_x_reverse() +
scale_y_reverse()
#> Error in UseMethod("group_by"): no applicable method for 'group_by' applied to an object of class "function"
# Data cannot contain NAs. Remove them before running.
df[1,]$F1 <- NA
#> Error in `*tmp*`[1, ]: object of type 'closure' is not subsettable
df %>%
group_by(vowel) %>%
mutate(mahal_dist = tidy_mahalanobis(F1, F2))
#> Error in UseMethod("group_by"): no applicable method for 'group_by' applied to an object of class "function"
df %>%
group_by(vowel) %>%
filter(!is.na(F1)) %>%
mutate(mahal_dist = tidy_mahalanobis(F1, F2)) %>%
select(vowel_id, vowel, mahal_dist, F1, F2) %>%
head()
#> Error in UseMethod("group_by"): no applicable method for 'group_by' applied to an object of class "function"