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NBA index plot function

Source: R/graphs.R
nba_index_plot.Rd

Generates the Red List Index (RLI) plots for species and ecosystems, or the Ecosystem Protection Level Index (EPLI). Supports multiple index types: RLIs (species), RLIe (ecosystems), and EPLI (protection level).

Usage

nba_index_plot(
  TYPE = c("RLIs", "RLIe", "EPLI"),
  DF = NULL,
  YEAR = NULL,
  RLI = NULL,
  MIN = NULL,
  MAX = NULL,
  ASSESSMENT_YEAR = NULL,
  GROUP = NULL,
  RLIE = NULL,
  BIOME = NULL,
  EPLI_list = NULL,
  PALETTE = "taxon",
  AGGREGATE = TRUE,
  SAVE = NULL
)

Arguments

TYPE

Type of index to plot. Options: "RLIs", "RLIe", or "EPLI".

DF

Input dataset containing index data (depending on TYPE).

YEAR

Column name for year variable.

RLI

Column name for RLI (for TYPE = "RLIs").

MIN

Column name for lower bound (for TYPE = "RLIs").

MAX

Column name for upper bound (for TYPE = "RLIs").

ASSESSMENT_YEAR

Year to highlight assessment points (optional).

GROUP

Column name for taxon or biome grouping (for TYPE = "RLIs").

RLIE

Column name for ecosystem RLI (for TYPE = "RLIe").

BIOME

Column name for biome (for TYPE = "RLIe" or "EPLI").

EPLI_list

List of EPLI datasets keyed by year (for TYPE = "EPLI").

PALETTE

Choose color palette "taxon" or "biome".

AGGREGATE

Whether to include an aggregate line. Default = TRUE.

SAVE

Optional filename to save the plot PNG in outputs/.

Value

Returns a multiple line plot with points

Examples



# Example 1: RLIs grouped by Taxon
nba_index_plot(
  TYPE = "RLIs",
  DF = NBA_example_rlis_data,
  YEAR = Year,
  RLI = RLI,
  ASSESSMENT_YEAR = Assessment_Year,
  GROUP = Taxon,
  PALETTE = "taxon",
  AGGREGATE = TRUE,
  SAVE = NULL
)
#> Warning: There were 62 warnings in `summarise()`.
#> The first warning was:
#> ℹ In argument: `MIN = mean(NULL, na.rm = TRUE)`.
#> ℹ In group 1: `Taxon = "Amphibians"` `Year = 1990`.
#> Caused by warning in `mean.default()`:
#> ! argument is not numeric or logical: returning NA
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 61 remaining warnings.


# Example 2: RLIe
nba_index_plot(
  TYPE = "RLIe",
  DF = NBA_example_rlie_data,
  YEAR = "Year",
  RLIE = "RLIE",
  BIOME = "Biome",
  PALETTE = "biome",
  SAVE = NULL
)
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the nbaR package.
#>   Please report the issue at <https://github.com/TashBes/NBA.package/issues>.
#> Warning: Ignoring unknown aesthetics: shape


# Example 3: EPLI
nba_index_plot(
  TYPE = "EPLI",
  EPLI_list = list(
    "2018" = NBA_example_epli2018_data,
    "2024" = NBA_example_epli2024_data
  ),
  PALETTE = "biome",
  SAVE = NULL
)