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Plots to explore environmental factors in environmental and geographic space

Source: R/explore_data_EG.R
explore_data_EG.Rd

Creates a four-panel plot with information of two environmental predictors (at a time) in the region of interest (or region reduced with mask, if used). The two top panels contain the information in geographic space (one predictor per panel). The two panels at the bottom contain information in a 2D environmental space for the two variables.

Usage

explore_data_EG(master, variable_1, variable_2, region_border = TRUE,
                mask_border = FALSE, col_variable1 = NULL,
                col_variable2 = NULL, col_points = NULL, col_density = NULL)

Arguments

master

master_matrix object derived from function prepare_master_matrix or master_selection object derived from functions uniformG_selection, uniformE_selection or EG_selection.

variable_1

(character or numeric) name or position of the first variable (x-axis) to be explored.

variable_2

(character or numeric) name or position of the second variable (y-axis) to be explored (must be different from the first one).

region_border

(logical) whether to add region border to the plot. Default = TRUE.

mask_border

(logical) whether to add mask border to the plot. Ignored if mask is not present in master_selection. Default = FALSE.

col_variable1

a color palette for variable_1 defined using functions like heat.colors, or one generated using functions like colorRampPalette. The default, NULL, uses a colorblind friendly palette similar to viridis.

col_variable2

a color palette for variable_2 defined using functions like heat.colors, or one generated using functions like colorRampPalette. The default, NULL, uses a colorblind friendly palette similar to viridis.

col_points

color for points in environmental space. The default, NULL, uses the 25th color of the default palette for col_variable1 with an alpha of 0.6.

col_density

color palette to represent representation density of points in environmental space. This palette can be defined using functions like heat.colors, or one generated using functions like colorRampPalette. The default, NULL, uses a colorblind friendly palette similar to magma, and changes the first color in the palette to NA.

Value

A multi-panel plot showing two of the environmental predictors in the region of interest in both spaces, geographic and environmental.

Examples

# Data
m_matrix <- read_master(system.file("extdata/m_matrix.rds",
                                    package = "biosurvey"))

colnames(m_matrix$data_matrix)
#>  [1] "Longitude"            "Latitude"             "Mean_temperature"    
#>  [4] "Max_temperature"      "Min_temperature"      "Annual_precipitation"
#>  [7] "Prec_wettest_month"   "Prec_driest_month"    "PC1"                 
#> [10] "PC2"                 

# Plot
# \donttest{
explore_data_EG(m_matrix, variable_1 = "Mean_temperature",
                variable_2 = "Annual_precipitation")

# }