MapTaxaObs: Taxa Observation Maps

In leppott/BioMonTools: Tools for Biomonitoring and Bioassessment

Taxa Observation Maps

Description

Map taxonomic observations from a data frame. Input a dataframe with SampID, TaxaID, TaxaCount, Latitude, and Longitude. Other arguments are format (jpg vs. pdf), file name prefix, and output directory. Files are saved with the prefix "map.taxa." by default.

Usage

MapTaxaObs(
  df_obs,
  SampID,
  TaxaID,
  TaxaCount,
  Lat,
  Long,
  output_dir = NULL,
  output_prefix = "maps.taxa",
  output_type = "pdf",
  database,
  regions,
  map_grp = NULL,
  leg_loc = "right",
  ...
)

Arguments

df_obs	Observation data frame
SampID	df_obs column name, Unique Sample identifier
TaxaID	df_obs column name, Unique Taxa identifier
TaxaCount	df_obs column name, Number of individuals for TaxonID and SampID
Lat	df_obs column name, Latitude
Long	df_obs column name, Longitude
output_dir	Directory to save output. Default is working directory.
output_prefix	Prefix to TaxaID for each file. Default = "map.taxa."
output_type	File format for output; jpg or pdf.
database	maps::map function database; world, usa, state, county
regions	maps::map function regions. Names pertinent to map_db.
map_grp	Map grouping variable from df_obs. Will generate legend and color code the points on the map. Default = NULL
leg_loc	Legend location text. Default = "right" Other values may not work properly.
...	Optional arguments to be passed to methods.

Details

The user will pass arguments for maps::map function that is used for the map. For example, 'database' and 'regions'. Without these arguments no map will be created.

The map will have all points and colored points for each taxon. In addition the map will include the number of samples by taxon.

The example data is fish but can be used for benthic macroinvertebrates as well.

If use grouping variable colors are from grDevices::rainbow()

Jpg file names replace all non-alphanumeric characters with "_".

The R package maps is required for this function.

Value

Taxa maps to user defined directory as jpg or pdf.

Examples

df_obs <- data_Taxa_MA
SampID <- "estuary"
TaxaID <- "TaxaName"
TaxaCount <- "Count"
Lat <- "Latitude"
Long <- "Longitude"
output_dir <- tempdir()
output_prefix <- "maps.taxa."
output_type <- "pdf"

myDB <- "state"
myRegion <- "massachusetts"
myXlim     <- c(-(73+(30/60)), -(69+(56/60)))
myYlim     <- c((41+(14/60)),(42+(53/60)))

# Run function with extra arguments for map
## Not run: 
MapTaxaObs(df_obs
           , SampID
           , TaxaID
           , TaxaCount
           , Lat
           , Long
           , database="state"
           , regions="massachusetts"
           , xlim = myXlim
           , ylim = myYlim
           , map_grp = "estuary"
           , leg_loc = "bottomleft")

## End(Not run)

leppott/BioMonTools documentation built on March 1, 2025, 7:18 a.m.