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Using {densityarea}
To get started with using {densityarea}, we’ll need to
load some packages, and some data to work with.
{densityarea} is meant to play nicely with tidyverse-style
data processing, in addition to loading the package itself, we’ll also
load {dplyr}. We have the option of working with the
density polygons in the form of simple features from {sf},
so we’ll load that as well. Finally, we’ll load {ggplot2}
and {ggdensity} for the sake of data visualization.
# package depends
library(densityarea)
library(dplyr)
library(sf)
library(ggdensity)
The dataset s01 is a data frame of vowel formant
measurements.
data(s01, package = "densityarea")
head(s01)
#> # A tibble: 6 × 10
#> name age sex word vowel plt_vclass ipa_vclass F1 F2 dur
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 s01 y f OKAY EY eyF ejF 764. 2088. 0.2
#> 2 s01 y f UM AH uh ʌ 700. 1881. 0.19
#> 3 s01 y f I'M AY ay aj 889. 1934. 0.07
#> 4 s01 y f LIVED IH i ɪ 556. 1530. 0.05
#> 5 s01 y f IN IH i ɪ 612. 2323. 0.06
#> 6 s01 y f COLUMBUS AH @ ə 612. 1904. 0.07
Initial look at the data
Let’s plot the original, raw data from s01, with the
Highest Density Regions overlaid (thanks to the {ggdensity}
package).
ggplot(data = s01,
aes(x = F2,
y = F1)
)+
geom_point(alpha = 0.1)+
stat_hdr(probs = c(0.8, 0.5),
aes(fill = after_stat(probs)),
color = "black",
alpha = 0.8)+
scale_y_reverse()+
scale_x_reverse()+
scale_fill_brewer(type = "seq")+
coord_fixed()
The function ggdensity::get_hdr() is perfect for quickly
adding interpretable densities to your plots. To work with these
densities as polygons, we can use
densityarea::density_polygons().
Getting density areas
Per the name of the package, we can get the area within each of these
density polygons with density_area().
As a first data processing step, let’s log transform and flip our
F1 and F2 values.
s01 |>
mutate(
lF1 = -log(F1),
lF2 = -log(F2)
) ->
s01
To get the area within the 80% density polygon for the entire data
set, we’ll pass s01 through a dplyr::reframe()
function.
s01 |>
group_by(name) |>
reframe(
density_area(lF2, lF1, probs = 0.8)
)
#> # A tibble: 1 × 4
#> name level_id prob area
#> <chr> <int> <dbl> <dbl>
#> 1 s01 1 0.8 0.406
Or, if we wanted the areas associated with subsets of the data (say,
for each vowel) we’d just change our
dplyr::group_by() call.
s01 |>
group_by(name, vowel) |>
reframe(
density_area(lF2, lF1, probs = 0.8)
) ->
vowel_areas
Let’s rearrange the order of rows to see the largest areas first.
vowel_areas |>
arrange(desc(area))
#> # A tibble: 15 × 5
#> name vowel level_id prob area
#> <chr> <chr> <int> <dbl> <dbl>
#> 1 s01 AO 1 0.8 0.488
#> 2 s01 AA 1 0.8 0.278
#> 3 s01 AH 1 0.8 0.274
#> 4 s01 AE 1 0.8 0.258
#> 5 s01 UW 1 0.8 0.229
#> 6 s01 EH 1 0.8 0.226
#> 7 s01 IY 1 0.8 0.206
#> 8 s01 UH 1 0.8 0.203
#> 9 s01 OW 1 0.8 0.197
#> 10 s01 IH 1 0.8 0.186
#> 11 s01 AY 1 0.8 0.171
#> 12 s01 AW 1 0.8 0.170
#> 13 s01 ER 1 0.8 0.145
#> 14 s01 EY 1 0.8 0.101
#> 15 s01 OY 1 0.8 0.0904
Density Polygons
Polygon Data Frames
A single probability level
In the simplest approach, we can use density_polygons()
to return a data frame for just one probability level, 60%.
s01 |>
group_by(name) |>
reframe(
density_polygons(lF2, lF1, probs = 0.6)
)->
sixty_poly_df
head(sixty_poly_df)
#> # A tibble: 6 × 7
#> name level_id id prob lF2 lF1 order
#> <chr> <int> <int> <dbl> <dbl> <dbl> <int>
#> 1 s01 1 1 0.6 -7.44 -6.78 1
#> 2 s01 1 1 0.6 -7.42 -6.76 2
#> 3 s01 1 1 0.6 -7.41 -6.75 3
#> 4 s01 1 1 0.6 -7.40 -6.72 4
#> 5 s01 1 1 0.6 -7.40 -6.69 5
#> 6 s01 1 1 0.6 -7.40 -6.69 6
Now, it’s possible for the HDR polygon to actually come in
multiple pieces, but in this case, there’s just one polygon, so we can
plot it.
ggplot(sixty_poly_df,
aes(lF2, lF1))+
geom_polygon(
aes(color = prob,
group = prob),
fill = NA,
linewidth = 1
)+
coord_fixed()
Multiple probability levels
To get polygons associated with multiple probability levels, we
simply pass a vector of values to probs.
s01 |>
group_by(name) |>
reframe(
density_polygons(lF2,
lF1,
probs = c(0.6, 0.8))
)->
multi_poly_df
head(multi_poly_df)
#> # A tibble: 6 × 7
#> name level_id id prob lF2 lF1 order
#> <chr> <int> <int> <dbl> <dbl> <dbl> <int>
#> 1 s01 2 1 0.8 -7.78 -6.01 1
#> 2 s01 2 1 0.8 -7.80 -6.01 2
#> 3 s01 2 1 0.8 -7.82 -6.02 3
#> 4 s01 2 1 0.8 -7.85 -6.02 4
#> 5 s01 2 1 0.8 -7.87 -6.02 5
#> 6 s01 2 1 0.8 -7.90 -6.02 6
ggplot(multi_poly_df,
aes(lF2, lF1))+
geom_polygon(
aes(color = prob,
group = prob),
fill = NA,
linewidth = 1
)+
coord_fixed()
Polygon Simple Features
We can also get density_polygons() to return the
polygons as simple features, as defined in the {sf}
package, by passing it the argument as_sf = TRUE.
s01 |>
group_by(name) |>
reframe(
density_polygons(lF2,
lF1,
probs = c(0.8, 0.6),
as_sf = TRUE)
) |>
st_sf()->
multi_poly_sf
The final function there, sf::st_sf(), wasn’t strictly
necessary, but makes life a little easier for plotting. Here’s what the
result looks like:
multi_poly_sf
#> Simple feature collection with 2 features and 3 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: -7.93703 ymin: -6.913825 xmax: -7.208434 ymax: -6.009484
#> CRS: NA
#> # A tibble: 2 × 4
#> name level_id prob geometry
#> <chr> <int> <dbl> <POLYGON>
#> 1 s01 1 0.6 ((-7.636315 -6.19764, -7.645598 -6.201069, -7.65986 -6.2…
#> 2 s01 2 0.8 ((-7.777586 -6.009484, -7.801131 -6.010429, -7.824676 -6…
And here’s a plot.
ggplot(multi_poly_sf)+
geom_sf(aes(color = prob),
fill = NA)
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