Description Usage Arguments Details Author(s) Examples
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
)).
1 2 3 4 5 6 7 8 | 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)
|
data |
dataframe, |
y |
variable contained in |
grp |
variable contained in |
x |
variable contained in |
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 |
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 |
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 |
transform |
character; transformations to apply to plotted variable |
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. |
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).
Hunter Stanke and Andrew Finley
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | ## 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)
|
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