plot_var_compare: Plot matching heatmaps for modeled and observed temp

In USGS-R/glmtools: Tools for working with the General Lake Model (GLM)

Plot matching heatmaps for modeled and observed temp

Description

Plot matching heatmaps for modeled and observed temp

Usage

plot_var_compare(
  nc_file,
  field_file,
  var_name = "temp",
  fig_path = NULL,
  resample = TRUE,
  precision = "hours",
  conversion = NULL,
  legend.title = NULL,
  interval = 1,
  method = "match",
  text.size = 12,
  color.palette = "RdYlBu",
  color.direction = -1,
  obs.color = "white",
  obs.alpha = 0.6,
  obs.shape = 16,
  obs.size = 1,
  shiftPalette = NULL,
  zlim = NULL,
  ...
)

Arguments

nc_file	Netcdf model output file
field_file	CSV or TSV field data file (see resample_to_field for format)
var_name	a character vector of valid variable names (see sim_vars)
fig_path	Default is NULL (only plots to screen). Enter string path to save as output file. File type can be anything supported by ggplot2:ggsave. See examples.
resample	sample the model output to the same time points as the observations?
precision	the time interval of the output.nc file and the field file must match (options: 'secs', 'mins','hours', or 'days')
conversion	conversion multiplier to adjust model output to field data units
legend.title	Vector string; Default ('NULL') will use variable and units from netcdf file
interval	Positive number indicating the depth interval in meters to interpolate output data. Must be less than max depth of lake. Default = 0.5 m.
method	String; 'match' for exact match or 'interp' for temporal interpolation
text.size	Integer; Default is 12. Higher values will increase text size in plot.
color.palette	See: ggplot2:scale_color_distiller. If a string, will use that named palette. Default is 'RdYlBu'. If a number, will index into the list of palettes of appropriate. Palettes available include: Diverging: BrBG, PiYG, PRGn, PuOr, RdBu, RdGy, RdYlBu, RdYlGn. Spectral. Qualitative: Accent, Dark2, Paired, Pastel1, Pastel2, Set1, Set2, Set3. Sequential: Blues, BuGn, BuPu, GnBu, Greens, Greys, Oranges, OrRd, PuBu, PuBuGn, PuRd, Purples, RdPu, Reds, YlGn, YlGnBu, YlOrBr, YlOrRd.
color.direction	Sets the order of colors in the scale. If 1, colors are as output by brewer.pal. If -1, the order of colors is reversed (default).
obs.color	Color of observation points. For options see: vignette("ggplot2-specs")
obs.alpha	Alpha transparency of observation points. If set to 0, no points will appear. For options see: vignette("ggplot2-specs")
obs.shape	Shape of observation points. For options see: vignette("ggplot2-specs")
obs.size	Size of observation points. For options see: vignette("ggplot2-specs", package = 'ggplot2')
shiftPalette	See values argument in: ggplot2:scale_color_distiller. Default is c(0,1). To shift pallete lower. Use c(0,0.2,1).
zlim	Color palette limits for z-variable. Default is maximum range of variable. Set as c(value,value).
...	additional arguments passed to ggsave()

Author(s)

Jordan S. Read, Luke A. Winslow, Hilary A. Dugan

See Also

Internally uses get_var and resample_to_field

Examples

nc_file <- system.file("extdata", "output/output.nc", package = "glmtools")
field_file <- system.file("extdata", "LakeMendota_field_data_hours.csv", package = "glmtools")

plot_var_compare(nc_file, field_file, 'temp', resample = FALSE) ##makes a plot

## Not run: 
#Change color palette, custom legend title, save figure:
plot_var_compare(nc_file, field_file, var_name = 'temp', resample = TRUE, 
legend.title = 'Temp (*C)', color.palette = 'PuBuGn', color.direction = 1,
fig_path = './figtest.png', width = 6, height = 8, units = 'in')

## End(Not run)

USGS-R/glmtools documentation built on March 26, 2024, 5:43 p.m.