plotFIA: Static and animated plots of FIA summaries

In rFIA: Estimation of Forest Variables using the FIA Database

Description

Default behavior for non-spatial summaries produces time-series plots, and for spatial summaries (class sf) produces choropleth maps. For non-spatial summaries, the user may specify the grp parameter to produce plots with multiple lines, colored by a grouping variable. Additionally, users may specify an x-axis to produce plots other than time series (e.g. BAA (y) by size class (x) colored by species (grp)).

Usage

plotFIA(data, y = NULL, grp = NULL, x = NULL, animate = FALSE, facet = FALSE,
        se = FALSE,n.max = NULL, plot.title = NULL, y.lab = NULL, x.lab = NULL,
        legend.title = NULL, legend.labs = waiver(), limits = c(NA, NA),
        color.option = 'viridis', line.color = "gray30", line.width =1,
        min.year = 2005, direction = 1, alpha = .9, transform = "identity",
        text.size = 1, text.font = '', lab.width = 1, legend.height = 1,
        legend.width = 1, device = "png", savePath = NULL, fileName = NULL)
           

Arguments

data	dataframe, sf object, or FIA.Database object; FIA summary produced from other rFIA functions (e.g. tpa, biomass, etc.). Also accepts FIA.Database, will return map of plot locations.
y	variable contained in data which will be used as y-axis or to fill polygons (spatial). NOT quoted.
grp	variable contained in data which will be used as a grouping variable. Not meaningful for spatial summaries. NOT quoted.
x	variable contained in data which will be used as a x-axis in place of time. If NULL, time-series plot will be produced. Not meaningful for spatial summaries. NOT quoted.
animate	logical; if TRUE, produces temporally animated plots.
facet	logical; if TRUE, produces temporally grouped plots (stationary).
se	logical; if TRUE, plots error bars along with estimates. All error bars represent 68% confidence.
n.max	numeric; maximum number of groups to plot. If positive, will plot the top n groups with respect to y, and if negative, will plot the bottom n. Not meaningful for spatial summaries.
plot.title	character; plot title.
y.lab	character; y-axis label. Not meaningful for spatial summaries.
x.lab	character; x-axis label. Not meaningful for spatial summaries.
legend.title	character; title for legend.
legend.labs	character; labels for legend values.
limits	numeric vector of length 2; minumum and maximum of continuous scale for legend.
color.option	character; one of: "viridis" (default), "magma", "inferno", "plasma", or "cividis".
line.color	character; color of plotted line (non-spatial) or polygon outline color (spatial).
line.width	numeric; scalar for plotted line width (non-spatial) polygon outline width (spatial). Specify lineWidth = 0 for no outline.
min.year	numeric; earliest year to be included in animation. FIA data is sparse in years prior to 2005 and estimates are unlikely to be available.
direction	numeric; sets the order of colors in the scale. If 1, the default, colors are ordered from darkest to lightest. If -1, the order of colors is reversed.
alpha	numeric; alpha transparency, a number in [0,1], see argument alpha in hsv.
transform	character; transformations to apply to plotted variable y. Options include: "asn", "atanh", "boxcox", "exp", "identity", "log", "log10", "log1p", "log2", "logit", "reciprocal", "reverse", "sqrt".
text.size	numeric; scalar for text size (e.g. text.size = 2 would be twice the default size).
text.font	character; font family. Choose from: 'Short', 'Canonical', 'mono', 'Courier', 'sans', 'Helvetica', 'serif', 'Times', 'AvantGarde', 'Bookman', 'Helvetica-Narrow', 'NewCenturySchoolbook', 'Palatino', 'URWGothic', 'URWBookman', 'NimbusMon', 'URWHelvetica', 'NimbusSan', 'NimbusSanCond', 'CenturySch', 'URWPalladio', 'URWTimes', or 'NimbusRom'.
lab.width	numeric; scalar for legend title width. This value controls text wrapping in title.
legend.height	numeric; scalar for legend height.
legend.width	numeric; scalar for legend width.
device	character; device to use for image save. Can either be a device function (e.g. png()), or one of "eps", "ps", "tex" (pictex), "pdf", "jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only).
savePath	character; path to save plot to (combined with fileName).
fileName	character; file name to create on disk.

Details

To produce spatial plots, summaries must be returned as spatial objects (e.g. specify returnSpatial = TRUE when computing summaries using tpa). For animated plots, also requires that multiple reporting years be present in the summary data (animations iterate through time). For a map of plot locations contained in your FIA.Database, specify the object as the data argument.

For objects produced with byPlot = TRUE and returnSpatial = TRUE (spatial point patterns), a categorical grouping variable can be specified to grp. Point radii will reflect magnitude of y and color will reflect categorical groups (grp).

If animate = FALSE and multiple reporting years are present in the summary, produces plots of the most recent subset.

Specify savePath and fileName to save plots (animations saved as .gif files).

Author(s)

Hunter Stanke and Andrew Finley

Examples

## Load data from the rFIA package
data(fiaRI)
data(countiesRI)

## Not run: \donttest{

################### SPATIAL PLOTTING #############################
## Compute abundance estimates for live stems in Rhode Island
## for all available inventory years, summarized by counties and
## return a spatial object
tpaRI <- tpa(fiaRI, polys = countiesRI, returnSpatial = TRUE)

## Produce animated plot
plotFIA(tpaRI, y = TPA, animate = TRUE, legend.title = 'Abundance (TPA)')
## With a square root transform
plotFIA(tpaRI, y = TPA, animate = TRUE, legend.title = 'Abundance (TPA)', transform = 'sqrt')

## Same as above, but for static plots (most recent subset from RI)
tpaMR <- tpa(clipFIA(fiaRI), polys = countiesRI, returnSpatial = TRUE)
## Produce animated plot
plotFIA(tpaMR, y = TPA, animate = FALSE, plot.title = 'Abundance (TPA)')


################# NON-SPATIAL PLOTTING #########################
## Same as above, but return a non-spatial object (no spatial grouping)
tpaRI <- tpa(fiaRI)

## Plot TPA over time
plotFIA(tpaRI, TPA)

## BAA over time, grouped by ownership group
tpaRI_own <- tpa(fiaRI, grpBy = OWNGRPCD)
plotFIA(tpaRI_own, y = BAA, grp = OWNGRPCD)

## BAA by size class (not a time series) grouped by species
tpaRI_sc <- tpa(clipFIA(fiaRI), bySpecies = TRUE, bySizeClass = TRUE)
plotFIA(tpaRI_sc, y = BAA, grp = COMMON_NAME, x = sizeClass, n.max = 4)# Only the top 4

}

## End(Not run)

rFIA documentation built on Dec. 16, 2021, 1:07 a.m.