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Taxa Maps

2025-10-06

Purpose

To create taxa distribution maps.

Usage

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.

Uses the maps package map function.

For maps package map function need database (usa, state, county) and regions (e.g., maryland). Additional map function arguments can be passed through the MapTaxaObs function.

Example, Data

Data used should have Sample Identifier, Taxa Identifier, Taxa Count (can be 1 for all), Latitude/Longitude (decimal degrees).

estuary	CommonName	LifeStage	SalZone	Winter	Spring	Summer	Fall	All	TaxaName	State	Latitude	Longitude	Count	PctDensity
BOSTON HARBOR	ALEWIFE	ADULTS	0.5-25 ppt	0.0000000	2.333333	3.3333333	1.333333	1.7500000	ALEWIFE, ADULTS, 0.5-25 ppt	MA	42.335	-70.9815	1.7500000	0.0023913
BOSTON HARBOR	ALEWIFE	ADULTS	>25 ppt	0.0000000	2.333333	3.3333333	2.666667	2.0833333	ALEWIFE, ADULTS, >25 ppt	MA	42.335	-70.9815	2.0833333	0.0028467
BOSTON HARBOR	AMERICAN EEL	ADULTS	0.5-25 ppt	0.0000000	0.000000	0.6666667	2.666667	0.8333333	AMERICAN EEL, ADULTS, 0.5-25 ppt	MA	42.335	-70.9815	0.8333333	0.0011387
BOSTON HARBOR	AMERICAN EEL	ADULTS	>25 ppt	0.0000000	0.000000	0.6666667	2.666667	0.8333333	AMERICAN EEL, ADULTS, >25 ppt	MA	42.335	-70.9815	0.8333333	0.0011387
BOSTON HARBOR	AMERICAN LOBSTER	ADULTS	0.5-25 ppt	0.6666667	2.333333	4.0000000	3.333333	2.5833333	AMERICAN LOBSTER, ADULTS, 0.5-25 ppt	MA	42.335	-70.9815	2.5833333	0.0035299
BOSTON HARBOR	AMERICAN LOBSTER	ADULTS	>25 ppt	2.3333333	3.000000	4.0000000	3.333333	3.1666667	AMERICAN LOBSTER, ADULTS, >25 ppt	MA	42.335	-70.9815	3.1666667	0.0043270

Example, ggplot

The ggplot2 package can be used to create single maps that are returned to the console for further editing.

# Packages
#library(BioMonTools)
#library(ggplot2)
#library(knitr)

#
df_obs <- BioMonTools::data_Taxa_MA

TaxaID <- "TaxaName"
TaxaCount <- "Count"
Lat <- "Latitude"
Long <- "Longitude"

myTaxa <- "ALEWIFE, ADULTS, 0.5-25 ppt"

df_map <- subset(df_obs, df_obs[, TaxaID] == myTaxa)

myDB <- "state"
myRegion <- "massachusetts"

Lat <- "Latitude"
Long <- "Longitude"

# Base Map
m1 <- ggplot2::ggplot(data=subset(ggplot2::map_data(myDB)
                                  , region %in% c(myRegion))) + 
          ggplot2::geom_polygon(ggplot2::aes(x = long
                                    , y = lat
                                    , group = group)
                                , fill = "light gray",
                                color = "black") + 
          ggplot2::coord_fixed(1.3) + 
          ggplot2::theme_void()
# Add points (all)
m1 <- m1 + ggplot2::geom_point(data=df_obs
                               , ggplot2::aes(df_obs[, Long]
                                              , df_obs[, Lat])
                               , fill=NA
                               , color="gray")
# Add points (Taxa)
m1 <- m1 + ggplot2::geom_point(data=df_map
                               , ggplot2::aes(df_map[,Long]
                                              , df_map[,Lat])
                               , color="blue")
# Map Title (center)
m1 <- m1 + 
  ggplot2::labs(title = myTaxa) +
  ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))
# Caption (left justified)
m1 <- m1 + ggplot2::labs(caption = "caption1 \n caption2") + 
  ggplot2::theme(plot.caption = ggplot2::element_text(hjust = 0))

# Show Results
knitr::kable(head(df_obs))

estuary	CommonName	LifeStage	SalZone	Winter	Spring	Summer	Fall	All	TaxaName	State	Latitude	Longitude	Count	PctDensity
BOSTON HARBOR	ALEWIFE	ADULTS	0.5-25 ppt	0.0000000	2.333333	3.3333333	1.333333	1.7500000	ALEWIFE, ADULTS, 0.5-25 ppt	MA	42.335	-70.9815	1.7500000	0.0023913
BOSTON HARBOR	ALEWIFE	ADULTS	>25 ppt	0.0000000	2.333333	3.3333333	2.666667	2.0833333	ALEWIFE, ADULTS, >25 ppt	MA	42.335	-70.9815	2.0833333	0.0028467
BOSTON HARBOR	AMERICAN EEL	ADULTS	0.5-25 ppt	0.0000000	0.000000	0.6666667	2.666667	0.8333333	AMERICAN EEL, ADULTS, 0.5-25 ppt	MA	42.335	-70.9815	0.8333333	0.0011387
BOSTON HARBOR	AMERICAN EEL	ADULTS	>25 ppt	0.0000000	0.000000	0.6666667	2.666667	0.8333333	AMERICAN EEL, ADULTS, >25 ppt	MA	42.335	-70.9815	0.8333333	0.0011387
BOSTON HARBOR	AMERICAN LOBSTER	ADULTS	0.5-25 ppt	0.6666667	2.333333	4.0000000	3.333333	2.5833333	AMERICAN LOBSTER, ADULTS, 0.5-25 ppt	MA	42.335	-70.9815	2.5833333	0.0035299
BOSTON HARBOR	AMERICAN LOBSTER	ADULTS	>25 ppt	2.3333333	3.000000	4.0000000	3.333333	3.1666667	AMERICAN LOBSTER, ADULTS, >25 ppt	MA	42.335	-70.9815	3.1666667	0.0043270

m1

Example, PDF

The example below will create a PDF with one map per page.

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
BioMonTools::MapTaxaObs(df_obs, 
                        SampID, 
                        TaxaID, 
                        TaxaCount, 
                        Lat,
                        Long, 
                        output_dir, 
                        output_prefix, 
                        output_type,
                        database = "state", 
                        regions = "massachusetts",
                        xlim = myXlim, 
                        ylim = myYlim)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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