dmd.view: Density Mangement Diagram generator

In mwritchie/standview: R Package for Stand Density Management Diagrams

Density Mangement Diagram generator

Description

This package provides function(s) to generate customizable stand density management diagrams in translated Reineke space, with log of qmd on the y-axis and log of tpa on the x-axis.

Usage

dmd.view(ineq = 3,
    inul = TRUE,
    insdi = TRUE,
    inply = TRUE,
    insdr = FALSE,
    insdl = FALSE,
    max.sdi=NA,
    dmd.title=" ",
    sdi.lines=NA,
    mgt.zone=c(0.35,0.60),
    reineke.term=1.605,
    bsi=90,
    mzcol="grey",
    sdicol="red",
    invol=FALSE,
    vcol="blue",
    use.metric=FALSE)

Arguments

ineq	Selects the values from a published DMD source (ineq=1-10) or a generic DMD with user-specified thresholds as well as published DMD volume and dominant height equations if available. This must be an integer value from 1 to 10. Default value is 3. Value of 1 generates a generic DMD space, no published volumes. Value is 2 for Long and Shaw (2005) ponderosa pine equations, Value of 3 for Jang et al. (2021) ponderosa pine equations. Value of 4 for Edminster (1988) ponderosa pine. Value of 5 for Cochran and Barrett (1992) ponderosa pine. Value of 6 for Long and Shaw (2012) California mixed-conifer. Value of 7 for Long et al. (1988) Douglas-fir. Value of 8 for Zhang et al. (2007) white fir. Value of 9 for McCarter and Long (1986) lodgepole pine. Value of 10 for Weiskittel and Woodall (2023) spruce-fir. Value of 11 for Weiskittel and Woodall (2023) red spruce. Value of 12 for Weiskittel and Woodall (2023) balsam fir. Value of 13 for Ritchie and Berrill (2022) redwood/Douglas-fir. Value of 14 for Ritchie and Berrill (2022) Douglas-fir/redwood. Value of 15 for Williams (1994) loblolly pine. Default=3.
inul	Selects to add Annotation for Upper limit, Reineke value and the upper limit to the sdi line. Default=TRUE.
insdi	Selects intermediate sdi lines to be drawn. The placement of these lines is determined by the values in sdi.lines and mgt.zone, Default=TRUE.
inply	Selects for presentation of a management zone polygon. Boundaries for the management zone are determined by the values in sdi.lines and mgt.zone. Default=TRUE.
insdr	Selects for annotation of sdi lines on right of graph. Default=FALSE. Note that selecting true for this variable is useless unless insdi=TRUE.
insdl	Selects for annotation of sdi lines on left of graph. Default=FALSE. Note that selecting true for this variable is useless unless insdi=TRUE. Note that if the sdi.lines settings place lines too close together, these annotations may overlap. Use of insdl may be preferred over inslr if invol=T. This will avoid overlap of annotations.
max.sdi	Defines upper limit of stand density index (maximum sdi). There is no default limit to SDI. This value is set by the selection of ineq. If ineq=1, 6, 10, 11 or 12 the user must specify a value. If use.metric=TRUE this value must be in metric units. Currently ineq=1 (generic DMD), ineq=6 (Long and Shaw 2012), ineq=10 or 11 (Weiskittel and Woodall 2023), ineq=13 or 14 (Ritchie and Berrill 2022) are the only DMD options where the user must actually specify this value. For most published DMDs the upper limit is fixed by the author and cannot be changed by user over-ride; in such cases, any user-specified upper limit will be ignored and the published value will be used to render the DMD. A value of ineq=1, requires English-unit max.sdi to be from 300-1000 (inclusive). A value of ineq=6, requires English-unit max.sdi to be from 450-600 (inclusive). A value of ineq=10 requires English-unit max.sdi to be from 527-564 (inclusive). A value of ineq=11 requires English-unit max.sdi to be from 547-608 (inclusive). A value of ineq=12 requires English-unit max.sdi to be from 502-669 (inclusive). A value of ineq=13 requires English-unit max.sdi to be from 700-1000 (inclusive). A value of ineq=14 requires English-unit max.sdi to be from 550-700 (inclusive).
dmd.title	Character string for title to be displayed. As an example could take the form of dmd.title="Ponderosa Pine".
sdi.lines	An array of values for plotting sdi iso-lines in the density management diagram. There is no default array for ineq=1 and the user must supply this array. For ineq>1, sdi.lines has default values. If the user selects to input an array for sdi.lines, thus replacing the default values, then care must be taken to select the proper units and provide well-spaced values. The default length of sdi.lines is six. Although not recommended, The user can provide a vector of values for sdi.lines that exceeds length of six but only the first six will be labeled.
mgt.zone	Explicitly sets the upper and lower limits of the management zone by proportion of the max.sdi. This will overwrite the 3rd and 5th elements in the sdi.lines array. If the User wishes to use fixed values for the management zone using the argument sdi.lines, then set mgt.zone=c(NA, NA). Acceptable Values for mgt.zone are 0.2 to 0.4 for lower limit (mgt.zone[1]), and 0.5 to 0.7 for upper limit (mgt.zone[2]).
reineke.term	This is the inverse of the slope of sdi lines in sdi space. The value presented by Reineke (1933) is 1.605. Limits are 1.3 and 2.0.
bsi	This is Barrett's site index (Barrett 1978) for use in the Cochran (1992) pine DMD (ineq=5). The default units for this argument is feet. If use.metric=TRUE is selected then the value for bsi should be reset by the user to meters. Value in English units must be between 70 and 100 feet. Value in metric must be between 21 and 34 m.
mzcol	Specifies color for management zone. Default="grey".
sdicol	Specifies color for stand density index lines. Default="red".
invol	Draws iso-volume lines. Default=FALSE.
vcol	Specifies color for volume iso-lines. Default="blue".
use.metric	Specifies use of metric, logical. Default=FALSE.

Value

Returns no value.

Note

It is important to note that the dmd.view function is designed to render a 6wx8h canvas. Any other aspect may produce annotations and axis labels that are misplaced. For this reason, it is suggested that one open a pdf device with the function call: pdf("myfile.pdf", width=6, height=8) prior to invoking the dmd.view function. When the figure is completely rendered, one should always close the device with dev.off(). See Examples below for how this can be done; to use this in examples, remove the comment on the pdf() call and the dev.off(). Also, the reineke.term for Coastal Douglas-fir was derived as 1.605, but from Drew and Flewelling there should be a 6 percent adjustment at lower densities. If one wishes to account for this a reineke.term of 1.71 is a compromise slope to remove some of this apparent error. See Drew and Flewelling (1979), page 521. Also, some default values will depend on the ineq value selected. Defaults shown here are for ineq=1 and may change according to selection of ineq to match published data. The user should be aware that annotations can sometimes be in conflict, causing overwriting. In this case it is best to try turning experimenting with the logical inputs that control the presence of these annotations to the figure.

Author(s)

Martin W. Ritchie, Research Forester, US Forest Service, Pacific Southwest Research Station. Email: [e-mail]

References

Barrett, J.W. (1978) Height growth and site index curves for managed even-aged stands of ponderosa pine in the Pacific Northwest. Res. Pap. PNW-232. USDA For. Serv. Pac. Northwest For. and Range Exp. Stn. 14p.

Drew, T.J. and J.W. Flewelling (1979). Stand density management: an alternative approach and its application to Douglas-fir plantations. For. Sci. 25(3):518-532

Cochran, P.H. and J.W. Barrett (1992) Stocking levels and underlying assumptions for uneven-aged ponderosa pine stands. Res. Note PNW-509. USDA For. Serv. Pac. Northwest For. and Range Exp. Stn. 10p.

Jang, W.S., M.W. Ritchie, and J. Zhang (2021) Improved equations for the density management diagram isolines of ponderosa pine stands. For. Sci. 67(1):93-102.

Long, J.N., J.B. McCarter, and S.B. Jack (1988) A modified density management diagram for coastal Douglas-fir. West. J. Appl. For. 3(3):88-89.

Long, J.N. and J.D. Shaw (2005) A density management diagram for even-aged ponderosa pine stands. West. J. Appl. For. 20(4):205-215.

Long, J.N. and J.D. Shaw (2012) A Density Management Diagram for Even-Aged Sierra Nevada Mixed-Conifer Stands. West. J. Appl. For. 27(4):187-195

McCarter, J.B. and J.N. Long (1986) A lodgepole pine density management diagram. West. J. Appl. For. 1(1)6-11.

Reineke, L.H. (1933) Perfecting a stand density index for even-aged forests. J. Ag. Res. 46:627-638.

Ritchie, M.W. and J.-P. Berrill (2022) Precommercial thinning in California Forests. In: Stewart, W. (editor) Reforestation practices for conifers in California. Davis CA: University of California, Agriculture and Natural Resources.

Weiskittel, A. & Woodall, C. (2023) Stand density index and relative density calculator for the United States. figshare. Software. https://doi.org/10.6084/m9.figshare.24412246.v1

Williams, R.A. (1994) Stand density management diagram for loblolly pine plantations in north Louisiana. South. J. Appl. For. 18(1):40-45.

Zhang, J., W.W. Oliver and M.W. Ritchie (2007) Effect of stand densities on stand dynamics in white fir (Abies concolor) forests in northeast California, USA. For. Ecol. and Manage. 244:50-59.

Examples

# 1. This example will produce a generic density mgt space in a file called myplot1.pdf:

#setwd("c:/mydir") # optional, to specify location (directory) for file input and output

#pdf("myplotr1.pdf", width=6, height=8) # recommended, open a 6x8 pdf file
opar <- par(mar = c(3.0,2.0,2.5,2.5)) # set some reasonable margins

dmd.view(ineq=1, use.metric=FALSE,
         sdi.lines=c(50, 100, 150, 200, 300, 400),
         max.sdi=420,
         insdr=TRUE,
         dmd.title="DMD with limit at 420")

par(opar)  # reset margins to default settings
#dev.off()  # close the recommended pdf file

# 2. This example will produce density mgt diagram myplot2.pdf :

#setwd("c:/mydir") # optional to select location for read and write

#pdf("myplotr2.pdf", width=6, height=8) # recommended, open a 6x8 pdf file
opar <- par(mar = c(3.0,2.0,2.5,2.5))

dmd.view(ineq=3, invol=TRUE ) # call dmd.view and request volume iso lines.

par(opar)
#dev.off() # close the recommended pdf file

# 3. This example shows a plot of data separating controls from treatments

#pdf("myplotr3.pdf", width=6, height=8) # recommended, open a 6x8 pdf file
opar <- par(mar = c(3.0,2.0,2.5,2.5))

dmd.view(ineq=2 ) # call dmd.view to generate DMD.

gama05$ppch<-21  # create a default character for plot
gama05[gama05$treatment=="Control",]$ppch<-2 # set plotting character for Control
points(x=gama05$tpa,
       y=gama05$qmd,
       cex=0.75, pch=gama05$ppch, col="black") # overlay data points

par(opar)
#dev.off()  # close optional pdf

# 4. Example calculating volumes for prescription, potting and annotations
DF<-dmd.volume(ineq=2, qmd=c(2, 2.5, 14, 15.5, 19), tpa=c(300, 150, 140, 80, 80))
DF

#pdf("myplotv1.pdf", width=6, height=8) # recommended, open a 6x8 pdf file
opar <- par(mar = c(3.0,2.0,2.5,2.5))

dmd.view(ineq=2 ) # call dmd.view.

points(x=DF$tpa, y=DF$qmd, cex=0.75, pch=21, col="black")
segments(300, 1, DF[1,]$tpa, DF[1,]$qmd, lwd=2)
for(i in 1:4){
  segments(DF$tpa[i], DF$qmd[i], DF$tpa[i+1], DF$qmd[i+1], lwd=2)
}
arrows(280, 19, 120, 14.8, length=0.10 )
text(300, 22, "Commercial thin")
text(300, 20, paste(round(DF$vol[3]-DF$vol[4]), "c.f. removed"))

par(opar)
#dev.off()  # close optional pdf

# 5. Example using spruce/fir option

#pdf("myplotsf.pdf", width=6, height=8) # recommended, open a 6x8 pdf file
opar <- par(mar = c(3.0,2.0,2.5,2.5))

dmd.view(ineq=10, max.sdi=590, insdr=TRUE ) # call dmd.view.
points(x=c(700,700,600,400,200),
       y=c(2.5,5.5,6.8,9.0,13.8), pch=21, cex=1, bg="black", col="black")
lines(x=c(700,700,600,400,200),
      y=c(2.5,5.5,6.8,9.0,13.8), lwd=2, col="black")
par(opar)
#dev.off()  # close optional pdf

mwritchie/standview documentation built on June 29, 2024, 11:56 a.m.