Settings for Charts, Maps and Output

This function sets, for the rest of the R session, how all functions of the package draw and save charts and maps. Call it without arguments to see the current settings, or with reset = TRUE to go back to the defaults. Each setting is stored as the R option faofishingreport.<name>, so it can also be set with options().

Usage

fao_settings(..., reset = FALSE)

Arguments

...

Settings to change, as name = value:

lang

Default language of charts: "en" (default), "zh" or "both". The lang argument of a function still takes precedence.

theme

Chart theme: "bw" (default), "classic", "minimal", "light", "linedraw", "gray" or "dark", or a ggplot2 theme object such as ggplot2::theme_bw(base_size = 14). Maps and pie charts keep a minimal theme.

base_size

Base font size of the chart theme. Default is 12.

font

Font family for chart text; see fao_font().

palette

Colours of categories (countries, species, groups): a palette of the ggsci package ("npg" (default), "lancet", "nejm", "jama", "aaas", "jco", "d3", ...), of RColorBrewer ("Set1", "Set2", "Dark2", "Paired", ...), of base R (grDevices::palette.pals(), e.g. "Okabe-Ito" or "Tableau 10"; or grDevices::hcl.pals(), e.g. "viridis" or "Dark 3"), or a vector of colours.

map_palette

Colours of map values: a Material Design palette of ggsci ("deep-orange" (default), "blue", "teal", "red", ...), an RColorBrewer palette ("YlOrRd", "Blues", ...), a viridis option ("viridis", "magma", "plasma", "inferno", "cividis", "mako", "rocket", "turbo"), a grDevices::hcl.pals() name, or a vector of colours.

map_center

Central longitude of maps: 0 (default) for longitudes -180 to 180 (Atlantic in the centre), or 180 for longitudes 0 to 360 (Pacific in the centre). The strings "-180-180" and "0-360" are also accepted.

map_projection

Map projection: "longlat" (default, plain longitude-latitude), "robinson", "mollweide", "equal_earth", "winkel_tripel" or "mercator", or any PROJ string or EPSG code (e.g. "EPSG:3857"; then map_center is not applied).

map_land

Fill colour of countries without data on maps. Default is "grey90".

map_ocean

Fill colour of the ocean on maps. Default is NA (no fill).

grid

Whether charts have background grid lines (and maps graticules). Default is FALSE.

dpi

Resolution of the PNG files. Default is 600.

pptx

Whether charts are also saved as editable PowerPoint files (needs the eoffice package). Default is FALSE.

data_dir

Folder where download_fao_data() saves FAO releases and where all functions look for them, e.g. a folder shared by a team. Default is NULL, the user data folder of R; see fao_data_dir().

online

Whether functions may connect to the internet to look for the newest FishBase release (see fishbase_table()). Default is TRUE; use FALSE to work offline with the downloaded copy, e.g. on a slow connection.

sst

The sea surface temperature (SST) data used by fao_area_sst() and mean_temperature_catch(): "ersst5" (default, NOAA ERSST v5, built into the package), a product downloaded with download_sst_data() (e.g. "hadisst1"), or the path of your own NetCDF file, or of a folder of NetCDF files (see fao_area_sst()).

silent

Whether the CMSY++ functions (cmsy_run(), cmsy_plot(), ...) work silently, without progress bars and messages. Default is FALSE. Their silent argument still takes precedence.

show_data

Whether an analysis function shows a short summary of its results in the console when it finishes: what was analysed, the first rows of its main table, the charts and tables it saved, and the parts of the result it returns. Default is TRUE. The results are returned invisibly: assign them to keep them, e.g. x <- stock_status(data).

plot_show

Whether charts are also drawn in the plot window (e.g. the Plots pane of RStudio) as they are saved. Default is FALSE. The plot_show argument of a function still takes precedence.

reset

A logical value. If TRUE, all settings go back to their defaults first.

Value

Invisibly, a list of the current settings.

See also

Other settings and language: fao_font(), fao_translate()

Examples

if (FALSE) { # \dontrun{
fao_settings()                                   # show the current settings
fao_settings(lang = "zh", palette = "lancet", theme = "classic")
fao_settings(map_center = 180, map_projection = "robinson", map_palette = "YlOrRd")
fao_settings(reset = TRUE)                       # back to the defaults
} # }