[Dplr-commits] r1078 - in pkg/dplR: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jan 29 19:11:11 CET 2018
Author: mvkorpel
Date: 2018-01-29 19:11:10 +0100 (Mon, 29 Jan 2018)
New Revision: 1078
Modified:
pkg/dplR/R/plotRings.R
pkg/dplR/man/plotRings.Rd
Log:
Cleanup
Modified: pkg/dplR/R/plotRings.R
===================================================================
--- pkg/dplR/R/plotRings.R 2018-01-29 17:29:31 UTC (rev 1077)
+++ pkg/dplR/R/plotRings.R 2018-01-29 18:11:10 UTC (rev 1078)
@@ -1,11 +1,11 @@
plotRings <- function(year, trwN, trwS = NA, trwE = NA, trwW =NA,
- animation = FALSE, sys.sleep = 0.2,
- year.labels = TRUE,
- d2pith = NA,
- col.rings = "grey", col.outring = "black",
- x.rings = "none", col.x.rings = "red",
- species.name = NA,
- saveGIF=FALSE, fname="GIF_plotRings.gif") {
+ animation = FALSE, sys.sleep = 0.2,
+ year.labels = TRUE,
+ d2pith = NA,
+ col.rings = "grey", col.outring = "black",
+ x.rings = "none", col.x.rings = "red",
+ species.name = NA,
+ saveGIF=FALSE, fname="GIF_plotRings.gif") {
## Creating a data.frame
TRW <- data.frame(row.names = year, trwN = trwN,
Modified: pkg/dplR/man/plotRings.Rd
===================================================================
--- pkg/dplR/man/plotRings.Rd 2018-01-29 17:29:31 UTC (rev 1077)
+++ pkg/dplR/man/plotRings.Rd 2018-01-29 18:11:10 UTC (rev 1078)
@@ -6,7 +6,11 @@
Make a plot of a cross section based on up to four ring-width series.
}
\usage{
-plotRings(year, trwN, trwS = NA, trwE = NA, trwW = NA, animation = FALSE, sys.sleep = 0.2, year.labels = TRUE, d2pith = NA, col.rings = "grey", col.outring = "black", x.rings = "none", col.x.rings = "red", species.name = NA, saveGIF=FALSE, fname="GIF_plotRings.gif")
+plotRings(year, trwN, trwS = NA, trwE = NA, trwW = NA,
+ animation = FALSE, sys.sleep = 0.2, year.labels = TRUE,
+ d2pith = NA, col.rings = "grey", col.outring = "black",
+ x.rings = "none", col.x.rings = "red", species.name = NA,
+ saveGIF = FALSE, fname = "GIF_plotRings.gif")
}
\arguments{
@@ -18,20 +22,20 @@
\item{trwS}{ an optional \code{numeric} vector giving a tree-ring
series to make the plot. It will be arbitrarily defined as South
- or 180 degrees from \code{trwN}. }
+ or 180 degrees from \code{\var{trwN}}. }
\item{trwE}{ an optional \code{numeric} vector giving a tree-ring
series to make the plot. It will be arbitrarily defined as East or
- 90 degrees from \code{trwN}. }
+ 90 degrees from \code{\var{trwN}}. }
\item{trwW}{ an optional \code{numeric} vector giving a tree-ring
series to make the plot. It will be arbitrarily defined as West or
- 270 degrees from \code{trwN}. }
+ 270 degrees from \code{\var{trwN}}. }
\item{animation}{ \code{logical} flag. If \code{TRUE} then each
ring will be individually plotted as an animation within the
- R-GUI. A working copy of ``ImageMagick'' is required. See
- \code{Details}. }
+ R-GUI. A working copy of \dQuote{ImageMagick} is required. See
+ \sQuote{Details}. }
\item{sys.sleep}{ a \code{numeric} value defining the sleep pause
in between rings during animation. }
@@ -43,52 +47,54 @@
ring to the pith of the tree. }
\item{col.rings}{ The color to be used for the interior rings.
- See section `Color Specification' for suitable values. }
+ See section \sQuote{Color Specification} for suitable values. }
\item{col.outring}{ The color to be used for the outer ring.
- See section `Color Specification' for suitable values. }
+ See section \sQuote{Color Specification} for suitable values. }
\item{x.rings}{ a \code{character} string to color narrow and
- wider rings of the series. Possible values are ``none'',
- "narrow.rings" to highlight the rings <= quantile 25\%, and
- "wider.rings" to highlight the rings >= quantile 75\%. }
+ wider rings of the series. Possible values are \code{"none"},
+ \code{"narrow.rings"} to highlight the rings <= quantile 25\%, and
+ \code{"wider.rings"} to highlight the rings >= quantile 75\%. }
- \item{col.x.rings}{ The color to be used for the \code{x.rings}.
- See section `Color Specification' for suitable values. }
+ \item{col.x.rings}{ The color to be used for the \code{\var{x.rings}}.
+ See section \sQuote{Color Specification} for suitable values. }
- \item{species.name}{ a optional \code{character} string that
- definesthe species name in the plot. }
+ \item{species.name}{ an optional \code{character} string that
+ defines the species name in the plot. }
- \item{saveGIF}{ \code{logical}. If TRUE a GIF will be saved. }
+ \item{saveGIF}{ \code{logical}. If \code{TRUE} a \acronym{GIF} will be
+ saved. }
- \item{fname}{ \code{character}. Filename for GIF. }
+ \item{fname}{ \code{character}. Filename for \acronym{GIF}. }
}
\details{
This makes a simple plot, drawing all rings from tree-ring series on a
-cartesian plane of up to four cardinal directions (N, S, E, W)
+Cartesian plane of up to four cardinal directions (N, S, E, W)
defining the eccentricity of the stem. It can be plotted using
-only data from one ratio, or up to four diferent radii from same tree.
+only data from one ratio, or up to four different radii from same tree.
This function can plot each individual ring as an animation within
-the R-GUI, as an GIF-file, or it can plot all rings at once.
+the R-GUI, as a \acronym{GIF}-file, or it can plot all rings at once.
-Animations require a functional installation of of ImageMagick.
+Animations require a functional installation of ImageMagick.
See \code{\link{saveGIF}} for details.
}
\value{
A \code{data.frame} giving the original data of each tree-ring
- series (\code{var{trwN}}, \code{var{trwS}}, \code{var{trwE}},
- \code{var{trwW}}), a mean of all tree-ring series (\code{trw.means}),
- cummulative values from \code{trw.means} (\code{trw.acc}),
+ series (\code{"trwN"}, \code{"trwS"}, \code{"trwE"},
+ \code{"trwW"}), a mean of all tree-ring series (\code{"trw.means"}),
+ cumulative values from \code{"trw.means"} (\code{"trw.acc"}),
the difference of North - South and East - West tree-ring series
- (\code{N_S}, \code{E_W}), the basal area increment of \code{trw.acc}
- (\code{bai.acc}), and the bai for each individual tree ring
- (\code{bai.ind}).
+ (\code{"N_S"}, \code{"E_W"}), the basal area increment of \code{"trw.acc"}
+ (\code{"bai.acc"}), and the bai for each individual tree ring
+ (\code{"bai.ind"}).
}
-\author{ Code by Darwin Pucha-Cofrep and Jakob Wernicke. Patched and improved by Andy Bunn and Mikko Korpela. }
+\author{ Code by Darwin Pucha-Cofrep and Jakob Wernicke. Patched and
+improved by Andy Bunn and Mikko Korpela. }
\examples{
# with tree-ring series from Rothenburg data
@@ -96,37 +102,48 @@
yrs <- as.numeric(rownames(anos1))
# Plot rings with data of two radii from same individual tree
-res <- plotRings(yrs, anos1[,4], trwW = anos1[,5], sp="Cedrela odorata") # Playing with colors
-res <- plotRings(yrs, anos1[,4], trwW = anos1[,5], col.rings = "tan", col.outring = "blue")
+res <- plotRings(yrs, anos1[,4], trwW = anos1[,5],
+ species.name = "Cedrela odorata")
+# Playing with colors
+res <- plotRings(yrs, anos1[,4], trwW = anos1[,5],
+ col.rings = "tan", col.outring = "blue")
+res <- plotRings(yrs, anos1[,4], trwW = anos1[,5],
+ col.rings = terrain.colors(nrow(anos1)))
-res <- plotRings(yrs, anos1[,4], trwW = anos1[,5], col.rings = terrain.colors(nrow(anos1)))
+# Specifying x.rings highlighting only narrow rings
+res <- plotRings(yrs, anos1[,4], trwW = anos1[,5],
+ x.rings = "narrow.rings")
-# Specifying x.rings highlighting only narrow rings
-res <- plotRings(yrs, anos1[,4], trwW = anos1[,5], x.rings = 'narrow.rings')
# Highlighting and coloring only wider rings
-res <- plotRings(yrs, anos1[,4], trwW = anos1[,5], x.rings = 'wider.rings', col.x.rings = "green")
+res <- plotRings(yrs, anos1[,4], trwW = anos1[,5],
+ x.rings = "wider.rings", col.x.rings = "green")
-## Not run
+\dontrun{
# Plot Rings and animate (requires ImageMagick)
-res <- plotRings(yrs, anos1[,4], trwW = anos1[,5], animation=TRUE, sys.sleep=0.1)
+res <- plotRings(yrs, anos1[,4], trwW = anos1[,5],
+ animation = TRUE, sys.sleep = 0.1)
# Plot Rings and save as GIF (requires ImageMagick)
-res <- plotRings(yrs, anos1[,4], trwW = anos1[,5], saveGIF=TRUE, sys.sleep = 0.1)
+res <- plotRings(yrs, anos1[,4], trwW = anos1[,5],
+ saveGIF = TRUE, sys.sleep = 0.1)
+}
# with four fake tree-ring series
-trw <- data.frame (trw01.n = abs(rnorm(100, 10, 7.5)), # North direction
- trw01.s = abs(rnorm(100, 10, 7.5)), # South direction
- trw01.w = abs(rnorm(100, 10, 2.5)), # West direction
- trw01.e = abs(rnorm(100, 10, 2.5)), # East direction
- row.names = 1918:2017)
+trw <- data.frame(trw01.n = abs(rnorm(100, 10, 7.5)), # North direction
+ trw01.s = abs(rnorm(100, 10, 7.5)), # South direction
+ trw01.w = abs(rnorm(100, 10, 2.5)), # West direction
+ trw01.e = abs(rnorm(100, 10, 2.5)), # East direction
+ row.names = 1918:2017)
year <- as.numeric(rownames(trw))
# Default plot with 2, 3 and 4 radii
-res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4])
+res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4])
# with d2pith values (see the hole before the first rings in the plot)
-res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4], d2pith = 500)
-res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4], d2pith = c(200, NA, NA, 50))
+res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4],
+ d2pith = 500)
+res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4],
+ d2pith = c(200, NA, NA, 50))
}
\keyword{ hplot }
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