metrics_plots: Pairwise metric plots

In phuais/multilandR: Landscape Analysis at Multiple Spatial Scales

Pairwise metric plots

Description

Plots pair of metric values in two-dimensional plots.

Usage

metrics_plots(
  x,
  raster = NULL,
  classes = NULL,
  radii = NULL,
  c_level = NULL,
  l_level = NULL,
  ext_raster = NULL,
  show_class_names = FALSE,
  upper = TRUE,
  diag = TRUE,
  smooth = TRUE,
  method = "loess",
  se = FALSE,
  st_points = list(shape = 21, size = 2, col = "black", fill = "white", alpha = 1),
  st_lines = list(lty = 1, lwd = 1, col = "black", alpha = 0.6),
  ...
)

Arguments

x	An object of class 'Multiland' generated with mland().
raster, ext_raster, classes, radii, l_level, c_level	Parameters to subset plots. See Details.
show_class_names	logical. Whether to show classes with its previously defined names (if defined) when generating the 'MultiLand' object (TRUE), or not (FALSE, default).
upper	logical. Whether to plot upper-diagonal plots or not. Default TRUE
diag	logical. Whether to plot diagonal density plots or not. Default TRUE.
smooth	logical. If TRUE (default) a pattern between the pair of metric values is plotted, with a smoothing method as defined in method.
method	Smoothing method (function) to use, as in ggplot2::geom_smooth(). It accepts "loess" (default), "lm", "gam", among others. See ?ggplot2::geom_smooth() for more details.
se	logical. Whether to show (TRUE) or not (FALSE) confidence intervals when smooth = TRUE.
st_points	List of aesthetic arguments for points plotting: shape for points shape, size for points size, col for points border color, fill for points fill color and alpha for point transparency.
st_lines	List of aesthetic arguments for lines plotting (if smooth = TRUE): lty for linetype, lwd for linewidth, col for line color and alpha for line transparency.
...	Other parameters to be passed to ggplot2::geom_smooth(), if smooth = TRUE.

Details

metrics_plots() mainly relies on GGally::ggpairs() to generate pair plots between metrics values. Arguments upper and diag are specific arguments of GGally::ggpairs(), here adapted to the context of continuous values only.

Argument raster, classes, radii, l_level and c_level can be defined to subset the plots. In each one of these, an all-positive or an all-negative vector can be passed, whether to include (all-positive) or exclude (all-negative) the elements to be taken into account for the subsetting:

• rasterlayers: a numeric vector with the number of the raster layers to be included/excluded. For example: c(1, 2, 4) to include raster layers 1, 2 and 4; c(-2, -3) to exclude raster layers 2 and 3.

• classes: must be a list with as many elements as defined raster layers in argument raster. Each element of the list must be a numeric vector (classes identities) with the classes to be included/excluded. If provided a character vector, metrics_corr() assumes that classes names are provided. For example, for the case with 2 raster layers: list(c(3, 20, 35), c("Forest", "Crops")) would include classes 3, 20 and 35 from raster layer 1 and classes "Forest" and "Crops" for raster layer 2. For the case of a unique raster layer, there is no need to input a list. For example, for the case of a unique raster layer and the exclusion of some classes: c(-5, -10, -15) to exclude classes 5, 10 and 15 of the unique raster layer; c("-Forest", "-Grassland") to exclude classes "Forest" and "Grassland". Note the "-" before each class name to indicate the exclusion of the classes.

• radii: a numeric vector to include/exclude particular radii. For example: c(1000, 2000) to include only radii of 1000 and 2000 m; c(-500, -1500) to exclude radii of 500 and 1500 m.

• c_level: character vector with the class-level metrics to be included/excluded from the analysis. For example: c("np", "pland") will include only the metrics "number of patches" ("np") and "percentage of the landscape" ("pland") in the analysis, whereas c("-np", "-pland") will exclude them. Note the "-" before each metric name to indicate the exclusion of the metrics.

• l_level: character vector with the landscape-level metrics to be included/excluded from the analysis. Other calculations for extra raster layers are considered as landscape-level metrics, and must be provided as "fun_" + the name of the function (e.g. "fun_mean").

Names of the available metrics of the 'MultiLandMetrics' object provided in x can be accessed with x@metrics and x@ext_calc.

Note that patch-level metrics, if exists in x metric's data.frame, are excluded from calculations, as this function works at a landscape scale.

Value

A panel with several plots returned by GGally::ggpairs() relating pair of metrics values. Metrics names are presented at the top and right of the panel (strips), with the following format: "level""metric_name""radius". For a landscape-level metric, a plausible metric name could be "l_np_1500" indicating a landscape-level metric, which is "np" ("number of patches") at a scale (radius) of 1500 m. For a class-level metric a plausible metric name could be "c4_pland_1000", indicating a class-level metric of class 4 (the value of the raster), which is "pland" ("percentage of landscape") at a scale (radius) of 1000 m. If more that one rasterlayer is being analyzed, the prefix "r1", "r2", "r3", ..., "rn" (referring to rasterlayer 1, 2, 3, ..., n) is added to the metric name.

See Also

mland_metrics(), metrics_corr()

Examples

# Pair plots between metrics "pland" of classes 1 to 4, for radius 3000 m
metrics_plots(ed_metrics, classes = 1:4, radii = 3000, show_class_names = TRUE,
              c_level = "pland")

# Without smooth pattern
metrics_plots(ed_metrics, classes = 1:4, radii = 3000, show_class_names = TRUE,
              c_level = "pland", smooth = FALSE)


# Changing aesthetics
metrics_plots(ed_metrics, classes = 1:4, radii = 3000, show_class_names = TRUE,
              c_level = "pland", smooth = FALSE, size = 1.5, shape = 21,
              fill = "red", alpha = 0.4)

# Assessing two radii values at the same time
metrics_plots(ed_metrics, classes = 1:4, radii = c(1000, 5000),
              show_class_names = TRUE, c_level = "pland", smooth = FALSE,
              size = 1.5, shape = 21, fill = "red", alpha = 0.4)

# An example with hundreds of points
metrics_plots(otf_metrics, classes = c("Forest", "Crops"))

# Plots can be combined with ggplot2::theme
metrics_plots(otf_metrics, classes = c("Forest", "Crops")) +
  ggplot2::theme_bw()

phuais/multilandR documentation built on Feb. 21, 2025, 7:52 a.m.