map_taxa_age: Map pollen counts from a list of epd.entity.df objects
In dinilu/EPDr: Interact with the European Pollen Database (EPD)

Description Usage Arguments Value Examples

View source: R/EPDr-plotting_functions.R

This function uses information on multiple epd.entity.df-class objects to map counts for a particular taxa in a particular age (or time period). The function use ggplot function and allow for multiple parameters to further tune the resulting map. Each entity in the map is represented by a point, which size, border colour, and fill colour change according to the palynological count. When an entity is provided but it has no data for that particular age (or time period) the points are represented diferently to reflect NA, avoiding confusion with 0 (zero) values.

map_taxa_age(x, taxa, sample_label, pres_abse = FALSE, pollen_thres = NULL,
  zoom_coords = NULL, points_pch = 21, points_colour = NULL,
  points_fill = NULL, points_range_size = NULL, map_title = NULL,
  legend_range = NULL, legend_title = NULL, napoints_size = 0.75,
  napoints_colour = "grey45", napoints_fill = "grey45",
  countries_fill_colour = "grey80", countries_border_colour = "grey90")

`x`	List of `epd.entity.df-class` objects that are going to be included in the map.
`taxa`	Character string indicating the taxa that are going to be mapped.
`sample_label`	Character string indicating the age (or time period) to be mapped.
`pres_abse`	Logical value indicating whether the map will represent presence/absence or counts (absolute or percentages).
`pollen_thres`	Logical value indicating the pollen count threshold to plot an specific count as presence or absence.
`zoom_coords`	Numeric vector with 4 elements defining the bounding box of the map as geographical coordinates. It should have the following format `c(xmin, xmax, ymin, ymax)`. Where `x` represents longitude and `y` represents latitude. If not specified the function looks into the data and automatically selects an extent that encompases all entities.
`points_pch`	Any value accepted for `pch` by `geom_point`. This controls for the symbol to represent entities in the map.
`points_colour`	Two elements vector with any values accepted for `colour` by `geom_point`. You can use this to change border colours for points. The first element is used to select the border colour of the absence/minimum values, whereas the second value selects the border colour for presences/maximum values.
`points_fill`	Two elements vector with any values accepted for `fill` by `geom_point`. You can use this to change fill colours for points. The first element is used to select the fill colour of the absence/minimum values, whereas the second value selects the fill colour for presences/maximum values.
`points_range_size`	Two elements vector with any values accepted for `size` by `geom_point`. You can use this to change point sizes. The first element is used to select the size of the absence/minimum values, whereas the second value selects the size for presences/maximum values.
`map_title`	Character string with a title for the map.
`legend_range`	Two elements vector with numeric values to set different min and max limits of points representation. If you have a dataset where counts goes up to 98 but want the map to represent until 100, you can set `legend_range = c(0,100)`. By default the function uses the min and max values in the dataset.
`legend_title`	Character string with a title for the legend.
`napoints_size`	Any value accepted for `size` by `geom_point`. This control for the size of points representing `NA` values.
`napoints_colour`	Any value accepted for `colour` by `geom_point`. This control for the border colour of points representing `NA` values.
`napoints_fill`	Any value accepted for `fill` by `geom_point`. This control for the fill colour of points representing `NA` values.
`countries_fill_colour`	Any value accepted for `fill` by `borders`. This control for the fill colour of polygons representing countries.
`countries_border_colour`	Any value accepted for `colour` by `borders`. This control for the border colour of polygons representing countries.

The function displays a ggplot map with countries in the background and counts for particular taxa and age (or time periods) as points in the foreground.

## Not run: 
epd.connection <- connect_to_epd(host = "localhost", database = "epd",
                               user = "epdr", password = "epdrpw")
entity.list <- list_e(epd.connection, country = c("Spain","Portugal",
                                                  "France", "Switzerland",
                                                  "Austria", "Italy",
                                                  "Malta", "Algeria",
                                                  "Tunisia", "Morocco",
                                                  "Atlantic ocean",
                                                  "Mediterranean Sea"))
epd.all <- lapply(entity.list$e_, get_entity, epd.connection)
epd.all <- lapply(epd.all, filter_taxagroups, c("HERB", "TRSH", "DWAR",
                                                "LIAN", "HEMI", "UPHE"))
epd.all <- lapply(epd.all, giesecke_default_chron)
epd.all <- remove_restricted(epd.all)
epd.all <- remove_wo_ages(epd.all)

epd.int <- lapply(epd.all, interpolate_counts, seq(0, 22000, by = 1000))
epd.taxonomy <- get_taxonomy_epd(epd.connection)
epd.int <- lapply(epd.int, taxa_to_acceptedtaxa, epd.taxonomy)
epd.int <- unify_taxonomy(epd.int, epd.taxonomy)

epd.int.per <- lapply(epd.int, counts_to_percentage)

map_taxa_age(epd.int, "Cedrus", "21000", pres_abse = F)
map_taxa_age(epd.int, "Cedrus", "21000", pres_abse = T)
map_taxa_age(epd.int.per, "Cedrus", "21000", pres_abse = F)
map_taxa_age(epd.int.per, "Cedrus", "21000", pres_abse = T)

## End(Not run)