Analyze results with maps

Usage

anlzMWRmap(
  res = NULL,
  param,
  acc = NULL,
  sit = NULL,
  fset = NULL,
  site = NULL,
  resultatt = NULL,
  locgroup = NULL,
  dtrng = NULL,
  ptsize = 4,
  repel = TRUE,
  labsize = 3,
  palcol = "Greens",
  palcolrev = FALSE,
  sumfun = "auto",
  crs = 4326,
  zoom = 11,
  addwater = "medium",
  watercol = "lightblue",
  maptype = NULL,
  buffdist = 2,
  scaledist = "km",
  northloc = "tl",
  scaleloc = "br",
  latlon = TRUE,
  ttlsize = 1.2,
  bssize = 11,
  runchk = TRUE,
  warn = TRUE
)

Arguments

res: character string of path to the results file or data.frame for results returned by readMWRresults
param: character string of the parameter to plot, must conform to entries in the "Simple Parameter" column of paramsMWR
acc: character string of path to the data quality objectives file for accuracy or data.frame returned by readMWRacc
sit: character string of path to the site metadata file or data.frame of site metadata returned by readMWRsites
fset: optional list of inputs with elements named res, acc, frecom, sit, or wqx overrides the other arguments
site: character string of sites to include, default all
resultatt: character string of result attributes to plot, default all
locgroup: character string of location groups to plot from the "Location Group" column in the site metadata file, default all
dtrng: character string of length two for the date ranges as YYYY-MM-DD, default all
ptsize: numeric for size of the points, use a negative value to omit the points
repel: logical indicating if overlapping site labels are offset
labsize: numeric for size of the site labels
palcol: character string indicating the color palette to be used from RColorBrewer, see details
palcolrev: logical indicating if color palette in palcol is reversed
sumfun: character indicating one of "auto" (default), "mean", "geomean", "median", "min", or "max", see details
crs: numeric as a four-digit EPSG number for the coordinate reference system, see details
zoom: numeric indicating resolution of the base map, see details
addwater: character string as "low", "medium" (default), "high", or NULL (to suppress) to include water features with varying detail from the National Hydrography dataset, see details
watercol: character string of color for water objects if addwater is not NULL
maptype: character string indicating the basemap type, see details
buffdist: numeric for buffer around the bounding box for the selected sites in kilometers, see details
scaledist: character string indicating distance unit for the scale bar, "km" or "mi"
northloc: character string indicating location of the north arrow, see details
scaleloc: character string indicating location of the scale bar, see details
latlon: logical to include latitude and longitude labels on the plot, default TRUE
ttlsize: numeric value indicating font size of the title relative to other text in the plot
bssize: numeric for overall plot text scaling, passed to theme_gray
runchk: logical to run data checks with checkMWRresults, checkMWRacc, or checkMWRsites, applies only if res, acc, or sit are file paths
warn: logical to return warnings to the console (default)

Value

A ggplot object that can be further modified.

Details

This function creates a map of summarized results for a selected parameter at each monitoring site. By default, all dates for the parameter are averaged. Options to filter by site, date range, and result attribute are provided. Only sites with spatial information in the site metadata file are plotted and a warning is returned for those that do not have this information. The site labels are also plotted next to each point. The labels can be suppressed by setting labsize = NULL.

Any acceptable color palette from RColorBrewer can be used for palcol, which is passed to the palette argument in scale_fill_distiller. These could include any of the sequential color palettes, e.g., "Greens", "Blues", etc. The diverging and qualitative palettes will also work, but may return uninterpretable color scales. The palette can be reversed by setting palcolrev = TRUE.

The default value for crs is EPSG 4326 for the WGS 84 projection in decimal degrees. The crs argument is passed to st_as_sf and any acceptable CRS appropriate for the data can be used.

The results shown on the map represent the parameter summary for each site within the date range provided by dtrng. If sumfun = "auto" (default), the mean is used where the distribution is determined automatically from the data quality objective file for accuracy, i.e., parameters with "log" in any of the columns are summarized with the geometric mean, otherwise arithmetic. Any other valid summary function will be applied if passed to sumfun ("mean", "geomean", "median", "min", "max"), regardless of the information in the data quality objective file for accuracy.

Using addwater = "medium" (default) will include lines and polygons of natural water bodies defined using the National Hydrography Dataset (NHD). The level of detail can be changed to low or high using addwater = "low" or addwater = "high", respectively. Use addwater = NULL to not show any water features.

A base map can be plotted using the maptype argument. The zoom value specifies the resolution of the map. Use higher values to download map tiles with greater resolution, although this increases the download time. The maptype argument describes the type of base map to download. Acceptable options include "OpenStreetMap", "OpenStreetMap.DE", "OpenStreetMap.France", "OpenStreetMap.HOT", "OpenTopoMap", "Esri.WorldStreetMap", "Esri.DeLorme", "Esri.WorldTopoMap", "Esri.WorldImagery", "Esri.WorldTerrain", "Esri.WorldShadedRelief", "Esri.OceanBasemap", "Esri.NatGeoWorldMap", "Esri.WorldGrayCanvas", "CartoDB.Positron", "CartoDB.PositronNoLabels", "CartoDB.PositronOnlyLabels", "CartoDB.DarkMatter", "CartoDB.DarkMatterNoLabels", "CartoDB.DarkMatterOnlyLabels", "CartoDB.Voyager", "CartoDB.VoyagerNoLabels", or "CartoDB.VoyagerOnlyLabels". Use maptype = NULL to suppress the base map.

The area around the summarized points can be increased or decreased using the buffdist argument. This creates a buffered area around the bounding box for the points, where the units are kilometers.

A north arrow and scale bar are also placed on the map as defined by the northloc and scaleloc arguments. The placement for both can be chosen as "tl", "tr", "bl", or "br" for top-left, top-right, bottom-left, or bottom-right respectively. Setting either of the arguments to NULL will suppress the placement on the map.

Examples

# results data path
respth <- system.file('extdata/ExampleResults.xlsx', package = 'MassWateR')

# results data
resdat <- readMWRresults(respth)
#> Running checks on results data...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking valid Activity Types... OK
#> 	Checking Activity Start Date formats... OK
#> 	Checking depth data present... OK
#> 	Checking for non-numeric values in Activity Depth/Height Measure... OK
#> 	Checking Activity Depth/Height Unit... OK
#> 	Checking Activity Relative Depth Name formats... OK
#> 	Checking values in Activity Depth/Height Measure > 1 m / 3.3 ft... OK
#> 	Checking Characteristic Name formats... OK
#> 	Checking Result Values... OK
#> 	Checking for non-numeric values in Quantitation Limit... OK
#> 	Checking QC Reference Values... OK
#> 	Checking for missing entries for Result Unit... OK
#> 	Checking if more than one unit per Characteristic Name... OK
#> 	Checking acceptable units for each entry in Characteristic Name... OK
#> 
#> All checks passed!

# accuracy path
accpth <- system.file('extdata/ExampleDQOAccuracy.xlsx', package = 'MassWateR')

# accuracy data
accdat <- readMWRacc(accpth)
#> Running checks on data quality objectives for accuracy...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking column types... OK
#> 	Checking no "na" in Value Range... OK
#> 	Checking for text other than <=, ≤, <, >=, ≥, >, ±, %, AQL, BQL, log, or all... OK
#> 	Checking overlaps in Value Range... OK
#> 	Checking gaps in Value Range... OK
#> 	Checking Parameter formats... OK
#> 	Checking for missing entries for unit (uom)... OK
#> 	Checking if more than one unit (uom) per Parameter... OK
#> 	Checking acceptable units (uom) for each entry in Parameter... OK
#> 	Checking empty columns... OK
#> 
#> All checks passed!

# site data path
sitpth <- system.file('extdata/ExampleSites.xlsx', package = 'MassWateR')

# site data
sitdat <- readMWRsites(sitpth)
#> Running checks on site metadata...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking for missing latitude or longitude values... OK
#> 	Checking for non-numeric values in latitude... OK
#> 	Checking for non-numeric values in longitude... OK
#> 	Checking for positive values in longitude... OK
#> 	Checking for missing entries for Monitoring Location ID... OK
#> 
#> All checks passed!

# \donttest{
# map with NHD water bodies
anlzMWRmap(res = resdat, param = 'DO', acc = accdat, sit = sitdat, addwater = 'medium')

# }