Taxa Maps

2024-04-23

Source: vignettes/vignette_MapTaxaObs.Rmd

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 <- getwd()
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)