| Title: | Implementation of BDAT Tree Taper Fortran Functions |
|---|---|
| Description: | Implementing the BDAT tree taper Fortran routines, which were developed for the German National Forest Inventory (NFI), to calculate diameters, volume, assortments, double bark thickness and biomass for different tree species based on tree characteristics and sorting information. See Kublin (2003) <doi:10.1046/j.1439-0337.2003.00183.x> for details. |
| Authors: | Christian Vonderach [aut, cre], Edgar Kublin [aut], Bernhard Bösch [aut], Gerald Kändler [aut], Dominik Cullmann [ctb] |
| Maintainer: | Christian Vonderach <[email protected]> |
| License: | BSD_2_clause + file LICENSE |
| Version: | 1.0.1.9000 |
| Built: | 2025-02-14 03:56:08 UTC |
| Source: | https://gitlab.com/vochr/rbdat |
Implementing the BDAT tree taper Fortran routines, which were developed for the German National Forest Inventory (NFI), to calculate diameters, volume, assortments, double bark thickness and biomass for different tree species based on tree characteristics and sorting information.
Kublin E. (2003): Einheitliche Beschreibung der Schaftform – Methoden und Programme – BDATPro. Forstw. Cbl. 122, 183–200, https://link.springer.com/article/10.1046/j.1439-0337.2003.00183.x
Kublin E., Scharnagl. G. (1988): Verfahrens- und Programmbeschreibung zum BWI-Unterprogramm BDAT: Abschlußbericht zum Forschungsauftrag: "Biometrische Lösungen für die Berechnung des Volumens, der Sortierung, der Rindenabzüge und der Ernteverluste im Rahmen der Bundeswaldinventur". ISSN: 0178-3165. Available at https://gitlab.com/vochr/rbdat/-/blob/master/bdatdocs/
Calculates volumes and assortments for given tree/s.
BDAT20( BDATArtNr, D1, H1 = 0, D2 = 0, H2 = 0, H, lX = 0, Hkz = 0, Skz = 0, Az = 0, Hsh = 0, Zsh = 0, Zab = 0, Sokz = 1, NMaxFixLng = 0, FixLngDef = matrix(rep(0, length(BDATArtNr) * 4), ncol = 4), result = "raw" )BDAT20( BDATArtNr, D1, H1 = 0, D2 = 0, H2 = 0, H, lX = 0, Hkz = 0, Skz = 0, Az = 0, Hsh = 0, Zsh = 0, Zab = 0, Sokz = 1, NMaxFixLng = 0, FixLngDef = matrix(rep(0, length(BDATArtNr) * 4), ncol = 4), result = "raw" )
BDATArtNr |
numeric, 1 <= spp <= 36, see |
D1 |
numeric, first measured diameter [cm], usually in 1.3m |
H1 |
numeric, height of first measured diameter [m] |
D2 |
numeric, second measured diameter [cm], or form parameter,
see |
H2 |
H2: numeric, height of second measured diameter [m], or form
parameter, see |
H |
numeric, tree height [m] |
lX |
length of unusable wood at stem foot [m], defaults to 0 |
Hkz |
indicator for tree top, 0 - normal (default), 1 - Wipfelbruch, 2 - Gipfelbruch |
Skz |
indicator for stem type, defaults to 0, see |
Az |
minimum cutting diameter over bark [cm], defaults to 0, using tabulated data depending on DBH (not documented) |
Hsh |
usable stem height, defaults to 0, i.e. 0.7*H |
Zsh |
minimum cutting diameter under bark for stem wood [cm], defaults to 0, using tabulated data depending on DBH (not documented) |
Zab |
minimum cutting diameter under bark for top segment [cm], defaults to 0, i.e. 14cm under bark. |
Sokz |
type assortment calculation, 0 - no assortment, 1 - mid diameter (Mittenstärke), 2 - Heilbronner Sortierung, defaults to 1 |
NMaxFixLng |
number of fixed length assortments at stem foot, defaults
to 0 (no fixed length assortments, irrespective of |
FixLngDef |
matrix of 4 * length(spp), having minimum cutting diameter, required assortment length, absolute and relative add-on |
result |
indicator about what information should be returned |
Using default value of result, which is 'raw', a list is
returned keeping information about the input value and produced assortments -
the unprocessed returns from the Fortran code.
See getAssortment for more details, as this function is
internally called.
getAssortment for a more flexible function with a
more convenient english name.
BDAT20(BDATArtNr = c(1, 1), D1 = c(30, 25), H = c(25, 20)) # returns long list BDAT20(BDATArtNr = c(1, 1), D1 = c(30, 25), H = c(25, 20), result = "Vol") # size class BDAT20(BDATArtNr = c(1, 1), D1 = c(30, 25), H = c(25, 20), result = "Skl") BDAT20( BDATArtNr = c(1, 1), D1 = c(30, 25), H = c(25, 20), NMaxFixLng = 1, result = "Fix" )BDAT20(BDATArtNr = c(1, 1), D1 = c(30, 25), H = c(25, 20)) # returns long list BDAT20(BDATArtNr = c(1, 1), D1 = c(30, 25), H = c(25, 20), result = "Vol") # size class BDAT20(BDATArtNr = c(1, 1), D1 = c(30, 25), H = c(25, 20), result = "Skl") BDAT20( BDATArtNr = c(1, 1), D1 = c(30, 25), H = c(25, 20), NMaxFixLng = 1, result = "Fix" )
BDAT-Function to get total aboveground biomass.
BDATBIOMASSE(BDATArtNr, D1, H1 = 0, D2 = 0, H2 = 0, H)BDATBIOMASSE(BDATArtNr, D1, H1 = 0, D2 = 0, H2 = 0, H)
BDATArtNr |
numeric vector of species code, see
|
D1 |
first measured diameter of tree [cm], e.g. diameter in breast height |
H1 |
measurement height of |
D2 |
second measured diameter of tree, see |
H2 |
measurement height of D2, see |
H |
total tree height [m] |
This function returns total aboveground biomass for given tree/s, based on the biomass functions developed for the german NFI 3. See the additional material for some german reference.
vector of biomass for given trees
getBiomass for a function with more convenient english
name
## simple call of function, with all parameters given BDATBIOMASSE(1, 30, 1.3, 0, 0, 25) ## same with variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 BDATBIOMASSE(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATBIOMASSE(getSpeciesCode(c("Fi", "Bu")), 30, H = 25) ## english abbreviated BDATBIOMASSE(getSpeciesCode(c("NS", "BE")), 30, H = 25)## simple call of function, with all parameters given BDATBIOMASSE(1, 30, 1.3, 0, 0, 25) ## same with variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 BDATBIOMASSE(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATBIOMASSE(getSpeciesCode(c("Fi", "Bu")), 30, H = 25) ## english abbreviated BDATBIOMASSE(getSpeciesCode(c("NS", "BE")), 30, H = 25)
Function to call BDAT Fortran subroutine to calculate diameter over bark in height Hx for specified tree/s.
BDATDMRHX(BDATArtNr, D1, H1, D2, H2, H, Hx)BDATDMRHX(BDATArtNr, D1, H1, D2, H2, H, Hx)
BDATArtNr |
numeric vector of species code; see
|
D1 |
first measured diameter of tree [cm], e.g. diameter in breast height. |
H1 |
measurement height of |
D2 |
second measured diameter of tree, see |
H2 |
measurement height of D2, see |
H |
total tree height [m] |
Hx |
height in tree for which diameter over bark is required |
conventional function interface for Fortran function BDATDMRHX. See
getDiameter for more details.
vector of diameters over bark
BDATDORHX for BDAT routine calculating diameter under
bark and getDiameter for a function with a more convenient
english name, more options and including a bark switch.
# simple call of function, with all parameters BDATDMRHX(1, 30, 1.3, 0, 0, 25, Hx = 1.3) # same with variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 Hx <- 1.3 BDATDMRHX(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, Hx = Hx) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATDMRHX(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, Hx = 1.3) ## english species names abbreviated BDATDMRHX(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, Hx = 1.3)# simple call of function, with all parameters BDATDMRHX(1, 30, 1.3, 0, 0, 25, Hx = 1.3) # same with variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 Hx <- 1.3 BDATDMRHX(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, Hx = Hx) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATDMRHX(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, Hx = 1.3) ## english species names abbreviated BDATDMRHX(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, Hx = 1.3)
Function to call BDAT Fortran subroutine to calculate diameter under bark in height Hx for specified tree/s.
BDATDORHX(BDATArtNr, D1, H1, D2, H2, H, Hx)BDATDORHX(BDATArtNr, D1, H1, D2, H2, H, Hx)
BDATArtNr |
numeric vector of species code; see
|
D1 |
first measured diameter of tree [cm], e.g. diameter in breast height |
H1 |
measurement height of |
D2 |
second measured diameter of tree, see |
H2 |
measurement height of D2, see |
H |
total tree height [m] |
Hx |
height in tree for which diameter under bark is required |
conventional function interface for BDATDORHX. See
getDiameter for more details.
vector of diameters under bark
BDATDMRHX for BDAT routine calculating diameter over
bark, getDiameter for a function with a more convenient english
name, more options and a bark switch.
# simple call of function, with all parameters BDATDORHX(1, 30, 1.3, 0, 0, 25, Hx = 1.3) # same with variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 Hx <- 1.3 BDATDORHX(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, Hx = Hx) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATDORHX(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, Hx = 1.3) ## english species names abbreviated BDATDORHX(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, Hx = 1.3)# simple call of function, with all parameters BDATDORHX(1, 30, 1.3, 0, 0, 25, Hx = 1.3) # same with variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 Hx <- 1.3 BDATDORHX(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, Hx = Hx) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATDORHX(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, Hx = 1.3) ## english species names abbreviated BDATDORHX(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, Hx = 1.3)
BDAT-Function to get double bark thickness at given height Hx
BDATRINDE2HX(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, Hx)BDATRINDE2HX(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, Hx)
BDATArtNr |
numeric vector of species code; see
|
D1 |
first measured diameter of tree [cm] e.g. diameter in breast height |
H1 |
measurement height of |
D2 |
second measured diameter of tree, see |
H2 |
measurement height of D2, see |
H |
total tree height [m] |
Hx |
height for which double bark thickness is required [m] |
This function returns double bark thickness in given height
Hx in stem
taper (hence, it depends on the diameter in given height). This can be added
onto a diameter under bark to receive diameter over bark.
vector of double bark thickness given height Hx inside stem
taper.
getBark for a function with a convenient english name
## simple call of function, with all parameters given BDATRINDE2HX(1, 30, 1.3, 0, 0, 25, Hx = 1.3) ## same with variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 Hx <- 1.3 BDATRINDE2HX(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, Hx = Hx) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATRINDE2HX(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, Hx = 1.3) ## english abbreviated BDATRINDE2HX(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, Hx = 1.3)## simple call of function, with all parameters given BDATRINDE2HX(1, 30, 1.3, 0, 0, 25, Hx = 1.3) ## same with variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 Hx <- 1.3 BDATRINDE2HX(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, Hx = Hx) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATRINDE2HX(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, Hx = 1.3) ## english abbreviated BDATRINDE2HX(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, Hx = 1.3)
BDAT-Function to get wood volume over bark of one or many trees of a section between height A and height B
BDATVOLABMR(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, A, B, SekLng = 2)BDATVOLABMR(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, A, B, SekLng = 2)
BDATArtNr |
numeric vector of species code; see
|
D1 |
first measured diameter of tree [cm], e.g. diameter in breast height. |
H1 |
measurement height of |
D2 |
second measured diameter of tree, see |
H2 |
measurement height of D2, see |
H |
total tree height [m] |
A |
lower height of section for which volume is required [m] |
B |
upper height of section for which volume is required [m] |
SekLng |
length of section over which the integral of taper form should be applied, defaults to 2.0m |
wood volume is calculated using BDAT Fortran routines.
vector of same length as input variables transformed into a data.frame, returning the required wood volume in cubic meter.
BDATVOLABOR for BDAT routine calculating volume under
bark, getVolume for a function with a convenient english name,
more options and a bark switch.
## simple call of function, with all parameters BDATVOLABMR(1, 30, 1.3, 0, 0, 25, .25, 5.25, 2.0) BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 A <- 1 B <- 10 ## same given variables BDATVOLABMR(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, A = A, B = B) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATVOLABMR(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, A = 0, B = 25) ## english abbreviated BDATVOLABMR(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, A = 0, B = 25)## simple call of function, with all parameters BDATVOLABMR(1, 30, 1.3, 0, 0, 25, .25, 5.25, 2.0) BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 A <- 1 B <- 10 ## same given variables BDATVOLABMR(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, A = A, B = B) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATVOLABMR(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, A = 0, B = 25) ## english abbreviated BDATVOLABMR(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, A = 0, B = 25)
BDAT-Function to get wood volume under bark of one or many trees of a section between height A and height B
BDATVOLABOR(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, A, B, SekLng = 2)BDATVOLABOR(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, A, B, SekLng = 2)
BDATArtNr |
numeric vector of species code; see |
D1 |
first measured diameter of tree [cm], e.g. diameter in breast height |
H1 |
measurement height of |
D2 |
second measured diameter of tree, see |
H2 |
measurement height of D2, see |
H |
total tree height [m] |
A |
lower height of section for which volume is required [m] |
B |
upper height of section for which volume is required [m] |
SekLng |
length of section over which the integral of taper form should be applied, defaults to 2.0m |
wood volume is calculated using BDAT Fortran routines.
vector of same length as input variables transformed into a data.frame, returning the required wood volume in cubic meter.
BDATVOLABMR for BDAT routine calculating volume over
bark, getVolume for a function with a convenient english name,
more options and including a bark switch.
## simple call of function, with all parameters BDATVOLABOR(1, 30, 1.3, 0, 0, 25, .25, 5.25, 2.0) BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 A <- 1 B <- 10 ## same with variables BDATVOLABOR(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, A = A, B = B) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATVOLABOR(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, A = 0, B = 25) ## english abbreviation BDATVOLABOR(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, A = 0, B = 25)## simple call of function, with all parameters BDATVOLABOR(1, 30, 1.3, 0, 0, 25, .25, 5.25, 2.0) BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 A <- 1 B <- 10 ## same with variables BDATVOLABOR(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, A = A, B = B) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATVOLABOR(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, A = 0, B = 25) ## english abbreviation BDATVOLABOR(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, A = 0, B = 25)
BDAT-Function to get (coarse) wood volume over bark up to a given diameter of one or many trees.
BDATVOLDHMR(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, DHGrz = 7, SekLng = 2)BDATVOLDHMR(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, DHGrz = 7, SekLng = 2)
BDATArtNr |
numeric vector of species code; see
|
D1 |
first measured diameter of tree [cm], e.g. diameter in breast height. |
H1 |
measurement height of |
D2 |
second measured diameter of tree, see |
H2 |
measurement height of D2, see |
H |
total tree height [m] |
DHGrz |
diameter over bark up to which volume should be calculated |
SekLng |
length of section over which the integral of taper form should be applied, defaults to 2.0m. |
Volume is calculated using BDAT Fortran routines. In particular,
BDATVOLDHMR internally calls BDATVOLABMR with parameter
A = 0, i.e. volume is calculated from forest floor up to given
diameter, which itself is transformed into height B.
vector of same length as input variables transformed into a data.frame, returning the required volume in cubic meter.
BDATVOLDHOR for BDAT routine calculating volume under
bark, getVolume for a function with a convenient english name,
more options and including a bark switch.
## simple call of function, with all parameters given BDATVOLDHMR(1, 30, 1.3, 0, 0, 25, 7, 2.0) BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 DHGrz <- 7 ## same using variables BDATVOLDHMR(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, DHGrz = DHGrz) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATVOLDHMR(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, DHGrz = 7) ## english abbreviation BDATVOLDHMR(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, DHGrz = 7)## simple call of function, with all parameters given BDATVOLDHMR(1, 30, 1.3, 0, 0, 25, 7, 2.0) BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 DHGrz <- 7 ## same using variables BDATVOLDHMR(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, DHGrz = DHGrz) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATVOLDHMR(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, DHGrz = 7) ## english abbreviation BDATVOLDHMR(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, DHGrz = 7)
BDAT-Function to get (coarse) wood volume under bark up to a given diameter of one or many trees.
BDATVOLDHOR(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, DHGrz = 7, SekLng = 2)BDATVOLDHOR(BDATArtNr, D1, H1 = 1.3, D2 = 0, H2 = 0, H, DHGrz = 7, SekLng = 2)
BDATArtNr |
numeric vector of species code; see
|
D1 |
first measured diameter of tree [cm], e.g. diameter in breast height. |
H1 |
measurement height of |
D2 |
second measured diameter of tree, see |
H2 |
measurement height of D2, see |
H |
total tree height [m] |
DHGrz |
diameter inside bark up to which volume should be calculated |
SekLng |
length of section over which the integral of taper form should be applied, defaults to 2.0m. |
Volume is calculated using BDAT Fortran routines. In particular,
BDATVOLDHOR internally calls BDATVOLABOR with parameter
A = 0, i.e. volume is calculated from forest floor up to given
diameter, which itself is transformed into height B.
vector of same length as input variables transformed into a data.frame, returning the required volume in cubic meter.
BDATVOLDHMR for BDAT routine calculating volume over
bark, getVolume for a function with a convenient english name,
more options and including a bark switch.
## simple call of function, with all parameters BDATVOLDHOR(1, 30, 1.3, 0, 0, 25, 7, 2.0) ## same using variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 DHGrz <- 7 BDATVOLDHOR(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, DHGrz = DHGrz) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATVOLDHOR(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, DHGrz = 7) ## english abbreviation BDATVOLDHOR(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, DHGrz = 7)## simple call of function, with all parameters BDATVOLDHOR(1, 30, 1.3, 0, 0, 25, 7, 2.0) ## same using variables BDATArtNr <- 1 D1 <- 30 H1 <- 1.3 D2 <- 0 H2 <- 0 H <- 25 DHGrz <- 7 BDATVOLDHOR(BDATArtNr = BDATArtNr, D1 = D1, H1 = H1, D2 = D2, H2 = H2, H = H, DHGrz = DHGrz) ## calling with a subset of tree characteristics ## german species names, abbreviated BDATVOLDHOR(getSpeciesCode(c("Fi", "Bu")), 30, 0, 0, 0, H = 25, DHGrz = 7) ## english abbreviation BDATVOLDHOR(getSpeciesCode(c("NS", "BE")), 30, 0, 0, 0, H = 25, DHGrz = 7)
this functions takes the data provided and builds a data.frame
to be used in other BDAT get*-functions. It discriminates between different
type of required output via the check-parameter. Checks are done on
the type and range of the variables given to make sure calls to the
Fortran routines do not suffer from type-mismatch (with potential freezing
of R).
buildTree(tree, check = NULL, vars = NULL, mapping = NULL)buildTree(tree, check = NULL, vars = NULL, mapping = NULL)
tree |
either a data.frame or a list containing the variables needed,
i.e. spp, D1, H and optionally H1, D2, H2. See details for more
information and parameter |
check |
character vector which indicates the type of required output and determines the checks to be done |
vars |
named list with additional variables for the specific
BDAT-functions; see |
mapping |
mapping of variable names in case a data.frame is given into
parameter |
Parameter tree is able to take either a data.frame with
correct variables names or arbitrary names if mapping is provided to
map the data.frame names to the required names by
c("df-colname" = "var-name") or to take a named list. If same-named
variables are present in both tree and vars, priority is put
on the ones in vars since explicitly given.
Possible variables are (*=required, depending on function):
spp*: numeric, 1 <= spp <= 36, see getSpeciesCode
D1*: numeric, first measured diameter [cm], usually at 1.3m
H1: numeric, height of first measured diameter [m], if zero, internally transformed to 1.3m
D2: numeric, second measured diameter [cm], or form parameter: latter
is defined in conjunction with H2:
D2=0 and H2=0 => taper form of volume tables according to Grundner & Schwappach (1906-1938), the default
D2=0 and 0 < H2 < 100 => german NFI1-taper form, with H2 given as
percentile of the NFI1--distribution; H2=50
corresponds to mean NFI1 taper form, H2<50 to slenderly and H2>50 to
thicker trees; see getForm for more information about
D2=0 and H2>100 => mean NFI1 taper form
D2>0 and H2=0 => D2 is a diameter and H2 is assumed to be 7m
D2>0 and H2>0 => D2 and H2 are given as diameter and height
-1<D2<0 => abs(D2) is interpreted as
-1>D2 => mean NFI1 taper form
H2: numeric, height of second measured diameter [m], or in
conjunction with D2, see there.
H*: numeric, tree height [m]
A*: numeric, lower diameter [cm] or height [m] of section for which
volume should be calculated, interpretation depends on iAB, see
getVolume
B*: numeric, upper diameter [cm] or height [m] of section for which
volume should be calculated, interpretation depends on iAB, see
getVolume
sl: numeric, length of section over which should be integrated, defaults to 2.0m
Dx*: diameter for which height or bark thickness is required
Hx*: height for which diameter is required
inv: inventory for which mean q03 is required, defaults to 1, see
getForm
For deriving assortments, the following variables are optional (if not given, default values are used):
lX: length of unusable wood at stem foot [m], defaults to 0 (X-Holz)
Hkz: indicator for tree top, 0 - normal (default), 1 - Wipfelbruch, 2 - Gipfelbruch
0 => H=H
1 => H=H+2
2 => DBH < 30 => H=DBH; dbh > 30 => H = 30 + (DBH-30) * 0.3
Skz: indicator for stem type, defaults to 0
0 => conifer trees => no restriction; deciduous trees => no assortments
1 => monopodial deciduous trees => Hsh = 0.7*H
2 => branching between dbh and 7m => Hsh = 5m
3 => crown base < 3m => Hsh=0.1
4 => dead or broken stem => Az = H*0.7
5 => dead tree => non-usable wood
Hsh: usable stem height, defaults to 0, i.e. 0.7*H
Az: minimum cutting diameter over bark [cm], defaults to 0, using an exponential function given DBH
Zsh: minimum cutting diameter under bark for stem wood [cm], defaults
to 0, using parameter Az if estimated length < maximum length (i.e. 20m)
Zab: minimum cutting diameter under bark for top segment [cm], defaults to 0, i.e. 14cm under bark
Sokz: type assortment calculation, 0 - no assortment, 1 - Mid diameter (Mittenstärke), 2 - Heilbronner Sortierung, defaults to 1
fixN: number of fixed length assortments at stem foot, defaults to 0 (no fixed length assortments, irrespective of other fix* parameters)
fixZ: mininum diameter under bark for fixed length assortment at stem foot, defaults to 0
fixL: length of fixed length assortment at stem foot, defaults to 0
fixA: fixed length assortement add-on in [cm], defaults to 0
fixR: fixed length assortement add-on in [%], defaults to 0
If parameter tree is used to hand over all tree data in form of
a data.frame, at least the parameter spp, D1, H must be provided, eventually
mapped via mapping.
Parameter Hx and Dx, which specify height and diameter for
which a diameter or height is requested, respectively, can either be included
to the definition of the tree data or alternatively given separately using
the vars parameter. In that case, vars is used in priority to a identically
named variable in tree. Additionally, tree and vars are
merged via a full outer join.
The add-on in fixed length assortments can be given in absolute and relative
units at the same time, but the higher value will be used.
a data.frame of class datBDAT.<check> having all variables needed in
specific functions. If check is NULL, only a basic tree-data.frame of
class "datBDAT" is returned.
## example for only tree data tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) res <- buildTree(tree = tree) head(res) class(res) tree <- list(species = c(1, 1), dbh = c(30, 25), h = c(25, 30)) mapping <- c("species" = "spp", "dbh" = "D1", "h" = "H") res <- buildTree(tree = tree, mapping = mapping) head(res) class(res) ## example for diameter calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- list(Hx = c(1.3, 1.3)) mapping <- NULL res <- buildTree(tree = tree, check = "diameter", vars = vars) head(res) class(res) tree <- list(Art = c(1, 1), Bhd = c(30, 25), H = c(25, 30)) vars <- list(X = c(1.3, 1.3)) mapping <- c("Art" = "spp", "Bhd" = "D1", "X" = "Hx") res <- buildTree(tree = tree, check = "diameter", vars = vars, mapping = mapping) head(res) class(res) ## example with many diameters for one tree tree <- list(spp = c(1), D1 = c(30), H = c(25)) vars <- list(Hx = seq(0, 25, 0.1)) mapping <- NULL res <- buildTree(tree = tree, check = "diameter", vars = vars) tree <- data.frame(s = 1, d = 30, h = 25, hx = 1.3) mapping <- c("s" = "spp", "d" = "D1", "h" = "H", "hx" = "Hx") res <- buildTree(tree, check = "diameter", mapping = mapping) head(res) class(res) ## example for height calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- list(Dx = c(30, 25)) res <- buildTree(tree = tree, check = "height", vars = vars) head(res) class(res) ## example for volume calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) check <- "volume" vars <- list(A = c(30, 25), B = c(7, 7), sl = 0.1) mapping <- NULL res <- buildTree(tree = tree, check = "volume", vars = vars) head(res) class(res) ## example for bark calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- list(Hx = c(1.3, 1.3)) res <- buildTree(tree = tree, check = "bark", vars = vars) head(res) class(res) ## example for assortment calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- list(fixN = 1, fixZ = 10, fixL = 5, fixA = 10, fixR = 0.1) res <- buildTree(tree = tree, check = "assortment", vars = vars) head(res) class(res) ## for cases where 'vars' could be a vector (i.e. getBark, getDiameter and ## getHeight), the following is also possible tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- c(1.3, 1.3) res <- buildTree(tree = tree, check = "bark", vars = vars) head(res) class(res) res <- buildTree(tree = tree, check = "height", vars = vars) head(res) class(res) ## but it is not possible in case of getVolume or getAssortment ## instead, use a named list to achieve a cross join / cartesian product vars <- list(A = rep(1, 3), B = 5:7) res <- buildTree(tree = tree, check = "volume", vars = vars) head(res) class(res) ## example for 'biomass' calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) res <- buildTree(tree = tree, check = "biomass") head(res) class(res) ## example with H1 != 1.3m tree <- list( spp = c(1, 1), D1 = c(30, 25), H1 = c(2, 2), H = c(25, 30) ) res <- buildTree(tree = tree, check = "biomass") head(res) class(res) getBiomass(res)## example for only tree data tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) res <- buildTree(tree = tree) head(res) class(res) tree <- list(species = c(1, 1), dbh = c(30, 25), h = c(25, 30)) mapping <- c("species" = "spp", "dbh" = "D1", "h" = "H") res <- buildTree(tree = tree, mapping = mapping) head(res) class(res) ## example for diameter calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- list(Hx = c(1.3, 1.3)) mapping <- NULL res <- buildTree(tree = tree, check = "diameter", vars = vars) head(res) class(res) tree <- list(Art = c(1, 1), Bhd = c(30, 25), H = c(25, 30)) vars <- list(X = c(1.3, 1.3)) mapping <- c("Art" = "spp", "Bhd" = "D1", "X" = "Hx") res <- buildTree(tree = tree, check = "diameter", vars = vars, mapping = mapping) head(res) class(res) ## example with many diameters for one tree tree <- list(spp = c(1), D1 = c(30), H = c(25)) vars <- list(Hx = seq(0, 25, 0.1)) mapping <- NULL res <- buildTree(tree = tree, check = "diameter", vars = vars) tree <- data.frame(s = 1, d = 30, h = 25, hx = 1.3) mapping <- c("s" = "spp", "d" = "D1", "h" = "H", "hx" = "Hx") res <- buildTree(tree, check = "diameter", mapping = mapping) head(res) class(res) ## example for height calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- list(Dx = c(30, 25)) res <- buildTree(tree = tree, check = "height", vars = vars) head(res) class(res) ## example for volume calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) check <- "volume" vars <- list(A = c(30, 25), B = c(7, 7), sl = 0.1) mapping <- NULL res <- buildTree(tree = tree, check = "volume", vars = vars) head(res) class(res) ## example for bark calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- list(Hx = c(1.3, 1.3)) res <- buildTree(tree = tree, check = "bark", vars = vars) head(res) class(res) ## example for assortment calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- list(fixN = 1, fixZ = 10, fixL = 5, fixA = 10, fixR = 0.1) res <- buildTree(tree = tree, check = "assortment", vars = vars) head(res) class(res) ## for cases where 'vars' could be a vector (i.e. getBark, getDiameter and ## getHeight), the following is also possible tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) vars <- c(1.3, 1.3) res <- buildTree(tree = tree, check = "bark", vars = vars) head(res) class(res) res <- buildTree(tree = tree, check = "height", vars = vars) head(res) class(res) ## but it is not possible in case of getVolume or getAssortment ## instead, use a named list to achieve a cross join / cartesian product vars <- list(A = rep(1, 3), B = 5:7) res <- buildTree(tree = tree, check = "volume", vars = vars) head(res) class(res) ## example for 'biomass' calculation tree <- list(spp = c(1, 1), D1 = c(30, 25), H = c(25, 30)) res <- buildTree(tree = tree, check = "biomass") head(res) class(res) ## example with H1 != 1.3m tree <- list( spp = c(1, 1), D1 = c(30, 25), H1 = c(2, 2), H = c(25, 30) ) res <- buildTree(tree = tree, check = "biomass") head(res) class(res) getBiomass(res)
Function to get assortments given harvest specifications for a tree of dimension D1, possible D2, and H. Assortments could be diameter or length constrained.
getAssortment(tree, ...) ## S3 method for class 'data.frame' getAssortment(tree, sort = NULL, mapping = NULL, value = "merge", ...) ## S3 method for class 'list' getAssortment(tree, sort = NULL, mapping = NULL, value = "merge", ...) ## S3 method for class 'datBDAT' getAssortment(tree, sort = NULL, mapping = NULL, value = "merge", ...)getAssortment(tree, ...) ## S3 method for class 'data.frame' getAssortment(tree, sort = NULL, mapping = NULL, value = "merge", ...) ## S3 method for class 'list' getAssortment(tree, sort = NULL, mapping = NULL, value = "merge", ...) ## S3 method for class 'datBDAT' getAssortment(tree, sort = NULL, mapping = NULL, value = "merge", ...)
tree |
either an object of class 'datBDAT.assortment' or a data.frame or
list containing the variables needed, i.e. spp, D1, H, and optionally
H1, D2, H2 for specifying the tree. See |
... |
passing arguments to methods. |
sort |
named list with variables specifying assortments, see
|
mapping |
mapping of variable names in case a data.frame is given into
parameter |
value |
character vector indicating return type: either "Vol", "Skl", "Fix", "LDSort", "merge" (default) or "raw". See section Value. |
Parameter 'tree' is able to take either a data.frame with correct
variables names or arbitrary names if mapping is provided to map the
data.frame names to the required names by c("df-colname" = "var-name")
or to take a named list.
Assortments are calculated using BDAT2.0 Fortran routines. Slightly extended, it now is possible to return length and diameter information also about standard assortments (which are held in "Vol"-element of return list, if value="raw" or value="Vol").
The standard assortment names are:
X = non-usable wood at stem foot (X-Holz)
Sth = stem wood
Ab = upper part of stem wood, second length after transport cut
Ind = industrial wood
nvDh = non-usable coarse wood
depending on value either information about 'Skl,' 'Vol' or
'Fix' (these are elements of standard output of Fortran BDAT20 subroutine)
and, additionally, information about the 'Vol' elements is retrieved by
value="LDSort" or
if value = 'merge' than a combined information of all produced
assortments with name, base position, assortment length, mid-diameter,
top-diameter and volume is produced. This is most likely what you want,
hence the default. Standard output of BDAT is provided by value="raw".
Since v0.4.0 a vectorized BDAT-fortran-function is implemented, so each
element of the returned list in case of value="raw" keeps information of all
trees given. Make sure to appropriately split and manipulate this data.
getAssortment(data.frame): transforming data.frame before calling
getAssortment using buildTree
getAssortment(list): transforming list before calling
getAssortment using buildTree
getAssortment(datBDAT): class method for class datBDAT
BDATVOLABMR and BDATVOLABOR for a
BDAT-type wrapper and function to keep back-compatability. To get coarse wood
volume over bark (>=7m diameter over bark) BDAT-type functions are
BDATVOLDHMR and BDATVOLDHOR.
tree <- data.frame(spp = 1, D1 = 30, H = 25) sort <- list(Az = 7, Sokz = 1) getAssortment(tree, sort, value = "Vol") getAssortment(tree, sort, value = "Skl") sort <- list(Az = 7, Sokz = 1, fixN = 1, fixZ = 10, fixL = 5, fixA = 10, fixR = 1) getAssortment(tree, sort, value = "Vol") getAssortment(tree, sort, value = "Skl") getAssortment(tree, sort, value = "Fix") getAssortment(tree, sort, value = "LDSort") getAssortment(tree, sort, value = "merge") ## prepare data for repeated sorting ## (get rid of preparating data handling) n <- 3 tree <- data.frame( spp = rep(1, n), D1 = seq(20, 50, length.out = n), H = seq(15, 40, length.out = n) ) sort <- list(lX = 0, Sokz = 1, Az = 7, fixN = 2, fixZ = 10, fixL = 5, fixA = 10, fixR = 1) tree <- buildTree(tree = tree, check = "assortment", vars = sort) getAssortment(tree, value = "Vol") getAssortment(tree, value = "Skl") getAssortment(tree, value = "Fix") getAssortment(tree, value = "LDSort") getAssortment(tree, value = "merge") ## to get bare BDAT-Output, use value='raw' # very long list, each element keeping all trees getAssortment(tree, value="raw") # bonus: it returns the calling parameters as welltree <- data.frame(spp = 1, D1 = 30, H = 25) sort <- list(Az = 7, Sokz = 1) getAssortment(tree, sort, value = "Vol") getAssortment(tree, sort, value = "Skl") sort <- list(Az = 7, Sokz = 1, fixN = 1, fixZ = 10, fixL = 5, fixA = 10, fixR = 1) getAssortment(tree, sort, value = "Vol") getAssortment(tree, sort, value = "Skl") getAssortment(tree, sort, value = "Fix") getAssortment(tree, sort, value = "LDSort") getAssortment(tree, sort, value = "merge") ## prepare data for repeated sorting ## (get rid of preparating data handling) n <- 3 tree <- data.frame( spp = rep(1, n), D1 = seq(20, 50, length.out = n), H = seq(15, 40, length.out = n) ) sort <- list(lX = 0, Sokz = 1, Az = 7, fixN = 2, fixZ = 10, fixL = 5, fixA = 10, fixR = 1) tree <- buildTree(tree = tree, check = "assortment", vars = sort) getAssortment(tree, value = "Vol") getAssortment(tree, value = "Skl") getAssortment(tree, value = "Fix") getAssortment(tree, value = "LDSort") getAssortment(tree, value = "merge") ## to get bare BDAT-Output, use value='raw' # very long list, each element keeping all trees getAssortment(tree, value="raw") # bonus: it returns the calling parameters as well
this function calculates double bark thickness in given height for a given tree
getBark(tree, ...) ## S3 method for class 'data.frame' getBark(tree, Hx = NULL, mapping = NULL, ...) ## S3 method for class 'list' getBark(tree, Hx = NULL, mapping = NULL, ...) ## S3 method for class 'datBDAT' getBark(tree, Hx = NULL, mapping = NULL, ...)getBark(tree, ...) ## S3 method for class 'data.frame' getBark(tree, Hx = NULL, mapping = NULL, ...) ## S3 method for class 'list' getBark(tree, Hx = NULL, mapping = NULL, ...) ## S3 method for class 'datBDAT' getBark(tree, Hx = NULL, mapping = NULL, ...)
tree |
either a data.frame or a list containing the variables needed to
decribe a tree, i.e. spp, D1, H, and optionally H1, D2, H2. Additionally,
parameter |
... |
passing arguments to methods. |
Hx |
height in tree for which double bark thickness is required |
mapping |
mapping of variable names in case a data.frame is given into
parameter |
This function returns double bark thickness in given height Hx in stem
taper (hence, it depends on the diameter in given height). This can be added
to an diameter under bark to get the diameter over bark.
Parameter tree is able to take either a data.frame with correct
variables names or arbitrary names if mapping is provided to map the
data.frame names to the required names by c("df-colname" = "var-name")
or to take a named list.
vector of double bark thickness given height Hx inside stem taper
getBark(data.frame): transforming data.frame before calling
getBark using buildTree
getBark(list): transforming list before calling
getBark using buildTree
getBark(datBDAT): class method for class datBDAT
tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 25), Hx = c(1.3, 22.248)) getBark(tree) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 25), Hx = c(1.3, 22.248)) getBark(tree, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 25)) Hx <- list(Hx = c(1.3, 22.248)) getBark(tree = tree, Hx = Hx, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H"))tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 25), Hx = c(1.3, 22.248)) getBark(tree) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 25), Hx = c(1.3, 22.248)) getBark(tree, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 25)) Hx <- list(Hx = c(1.3, 22.248)) getBark(tree = tree, Hx = Hx, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H"))
this function calculates total aboveground biomass for a given tree
getBiomass(tree, ...) ## S3 method for class 'data.frame' getBiomass(tree, mapping = NULL, ...) ## S3 method for class 'list' getBiomass(tree, mapping = NULL, ...) ## S3 method for class 'datBDAT' getBiomass(tree, mapping = NULL, ...)getBiomass(tree, ...) ## S3 method for class 'data.frame' getBiomass(tree, mapping = NULL, ...) ## S3 method for class 'list' getBiomass(tree, mapping = NULL, ...) ## S3 method for class 'datBDAT' getBiomass(tree, mapping = NULL, ...)
tree |
either a data.frame or a list containing the variables needed to
decribe a tree, i.e. spp, D1, H, and optionally H1, D2, H2. See
|
... |
passing arguments to methods. |
mapping |
mapping of variable names in case a data.frame is given into
parameter |
This function returns total aboveground biomass according to the biomass functions developed for the german NFI3 (BWI3) on the basis of a field survey covering whole Germany from 2007 to 2010. Hence, the base data differs from those used to fit the taper functions. Neverteless and although the original fortran code does not provide an interface to pass H2 or negative D2 values to the functions (they were fitted with abolute D03-values, i.e. diameter in 30 for reasons of consistency.
The functions themselves are fitted for four species (Norway spruce, Scots pine, European beech and Oak spp.) directly, and for another fourteen species by generating pseudo-observations and fitting the functions to these. See the enclosed report for details.
The biomass functions integrate four different ranges of validity: (i) tree height below 1.3m, (ii) dbh below 10cm, (iii) dbh between 10cm and the 99th-quantile of the data and (iv) dbh above.
vector of total aboveground biomass
getBiomass(data.frame): transforming data.frame before calling
getBiomass using buildTree
getBiomass(list): transforming list before calling
getBiomass using buildTree
getBiomass(datBDAT): class method for class datBDAT
Riedel, T. and G. Kaendler (2017). "Nationale Treibhausgasberichterstattung: Neue Funktionen zur Schätzung der oberirdischen Biomasse am Einzelbaum." Forstarchiv 88(2): 31-38.
tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 25)) getBiomass(tree) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 25)) getBiomass(tree, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 25)) getBiomass(tree = tree, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) ## this is standard usage of the fortran code ## now changing the taper form via second diameter D2 tree <- data.frame(spp = 1, D1 = 30, D2 = c(26, 24), H = 25) getBiomass(tree) ## the following usage of D2 and H2 w.r.t. the biomass functions are new ## and unique to R ## now changing the taper form via quantile of second diameter in H2 tree <- data.frame(spp = 1, D1 = 30, H2 = c(25, 50, 75), H = 25) getBiomass(tree) ## now changing the taper form via form quotient (i.e. negative D2) fq <- getForm(list(spp = 1, D1 = 30, H = 25), inv = 1:4) tree <- data.frame(spp = 1, D1 = 30, D2 = -fq, H = 25) getBiomass(tree) # biomass of an average tree according to different inventoriestree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 25)) getBiomass(tree) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 25)) getBiomass(tree, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 25)) getBiomass(tree = tree, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) ## this is standard usage of the fortran code ## now changing the taper form via second diameter D2 tree <- data.frame(spp = 1, D1 = 30, D2 = c(26, 24), H = 25) getBiomass(tree) ## the following usage of D2 and H2 w.r.t. the biomass functions are new ## and unique to R ## now changing the taper form via quantile of second diameter in H2 tree <- data.frame(spp = 1, D1 = 30, H2 = c(25, 50, 75), H = 25) getBiomass(tree) ## now changing the taper form via form quotient (i.e. negative D2) fq <- getForm(list(spp = 1, D1 = 30, H = 25), inv = 1:4) tree <- data.frame(spp = 1, D1 = 30, D2 = -fq, H = 25) getBiomass(tree) # biomass of an average tree according to different inventories
this function calculates the diameter inside or outside bark of in given height for a given tree
getDiameter(tree, ...) ## S3 method for class 'data.frame' getDiameter(tree, Hx = NULL, bark = TRUE, mapping = NULL, ...) ## S3 method for class 'list' getDiameter(tree, Hx = NULL, bark = TRUE, mapping = NULL, ...) ## S3 method for class 'datBDAT' getDiameter(tree, Hx = NULL, bark = TRUE, mapping = NULL, ...)getDiameter(tree, ...) ## S3 method for class 'data.frame' getDiameter(tree, Hx = NULL, bark = TRUE, mapping = NULL, ...) ## S3 method for class 'list' getDiameter(tree, Hx = NULL, bark = TRUE, mapping = NULL, ...) ## S3 method for class 'datBDAT' getDiameter(tree, Hx = NULL, bark = TRUE, mapping = NULL, ...)
tree |
either a data.frame, a list or an object of class |
... |
passing arguments to methods. |
Hx |
height in tree for which diameter over or under bark is required; defaults to NULL |
bark |
logical, if TRUE returned diameter |
mapping |
mapping of variable names in case a data.frame is given into
parameter |
if tree does not includes variable Hx, a full outer join is generated between both
a matrix with one row for each tree and one column for each Hx
given, holding the diameter over or under bark of provided height Hx
inside stem taper. The matrix is simplified by [,,drop=TRUE],
especially if Hx=NULL.
getDiameter(data.frame): transforming data.frame before calling
getDiameter using buildTree
getDiameter(list): transforming list before calling
getDiameter using buildTree
getDiameter(datBDAT): class method for class datBDAT
tree <- data.frame(spp = c(1, 1), D1 = c(30, 30), H = c(25, 25), Hx = c(1.3, 22.248)) getDiameter(tree, bark = TRUE) getDiameter(tree, bark = FALSE) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 30), h = c(25, 25), Hx = c(1.3, 22.248)) getDiameter(tree, bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 30), h = c(25, 25)) Hx <- c(1.3, 22.248) getDiameter(tree, Hx = Hx, bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H"))tree <- data.frame(spp = c(1, 1), D1 = c(30, 30), H = c(25, 25), Hx = c(1.3, 22.248)) getDiameter(tree, bark = TRUE) getDiameter(tree, bark = FALSE) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 30), h = c(25, 25), Hx = c(1.3, 22.248)) getDiameter(tree, bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 30), h = c(25, 25)) Hx <- c(1.3, 22.248) getDiameter(tree, Hx = Hx, bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H"))
this function returns for a given dbh-height-class and species the estimated mean of the q03-distribution, which can be considered as a form factor for different inventories (i.e. NFI 1, NSoG, IS08, NFI3).
getForm(tree, ...) ## S3 method for class 'data.frame' getForm(tree, inv = NULL, mapping = NULL, ...) ## S3 method for class 'list' getForm(tree, inv = NULL, mapping = NULL, ...) ## S3 method for class 'datBDAT' getForm(tree, inv = NULL, mapping = NULL, ...)getForm(tree, ...) ## S3 method for class 'data.frame' getForm(tree, inv = NULL, mapping = NULL, ...) ## S3 method for class 'list' getForm(tree, inv = NULL, mapping = NULL, ...) ## S3 method for class 'datBDAT' getForm(tree, inv = NULL, mapping = NULL, ...)
tree |
either a data.frame or a list containing the variables needed to
decribe a tree, i.e. spp, D1, H, and optionally H1, D2, H2. See
|
... |
passing arguments to methods. |
inv |
integer, indicator for which inventory the form factor should be
returned; defaults to 1 (0=volume tables of Grundner-Schwappach 1921,
1=NFI1, 2=NSoG, 3=IS08, 4=NFI3).
Any other value is silently set back to |
mapping |
mapping of variable names in case a data.frame is given into
parameter |
This function returns the estimated mean of the q03-distribution for a given dbh-height-class and species. The q03-distribution is the ratio between the diameter in 30% of tree height and 5% of tree height and describes the form of the taper curve. This value can be returned for different inventories, during which upper stem diameters have been sampled.
Only spp, D1 and H are used to estimate mean q03, if provided and H1 equals 1.3m, otherwise dbh is estimated using BDAT functions (i.e. getDiameter(tree, Hx=1.3)).
vector of form factor q03.
getForm(data.frame): transforming data.frame before calling
getForm using buildTree
getForm(list): transforming list before calling
getForm using buildTree
getForm(datBDAT): class method for class datBDAT
tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 25)) tree <- buildTree(tree, check = "form", vars = list(inv = 1)) str(tree) getForm(tree) # default is 'inv=1' getForm(tree, inv = 0) # taper form of BDAT from model fit getForm(tree, inv = 1) # NFI 1 (without NSoG) getForm(tree, inv = 2) # NSoG = New States of Germany getForm(tree, inv = 3) # carbon inventory 2008 getForm(tree, inv = 4) # NFI 3 (reunificated Germany)tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 25)) tree <- buildTree(tree, check = "form", vars = list(inv = 1)) str(tree) getForm(tree) # default is 'inv=1' getForm(tree, inv = 0) # taper form of BDAT from model fit getForm(tree, inv = 1) # NFI 1 (without NSoG) getForm(tree, inv = 2) # NSoG = New States of Germany getForm(tree, inv = 3) # carbon inventory 2008 getForm(tree, inv = 4) # NFI 3 (reunificated Germany)
this function calculates the height of a given diameter inside or outside bark for a given tree
getHeight(tree, ...) ## S3 method for class 'data.frame' getHeight(tree, Dx = NULL, bark = TRUE, mapping = NULL, ...) ## S3 method for class 'list' getHeight(tree, Dx = NULL, bark = TRUE, mapping = NULL, ...) ## S3 method for class 'datBDAT' getHeight(tree, Dx = NULL, bark = TRUE, mapping = NULL, ...)getHeight(tree, ...) ## S3 method for class 'data.frame' getHeight(tree, Dx = NULL, bark = TRUE, mapping = NULL, ...) ## S3 method for class 'list' getHeight(tree, Dx = NULL, bark = TRUE, mapping = NULL, ...) ## S3 method for class 'datBDAT' getHeight(tree, Dx = NULL, bark = TRUE, mapping = NULL, ...)
tree |
either a data.frame or a list containing the variables needed to
decribe a tree, i.e. spp, D1, H, and optionally H1, D2, H2. See
|
... |
passing arguments to methods. |
Dx |
diameter of tree for which height is required; defaults to NULL |
bark |
logical, if TRUE given diameter |
mapping |
mapping of variable names in case a data.frame is given into
parameter |
see buildTree for how to specify a tree object
a matrix with one row for each tree and one column for each Dx
given, holding the height of provided diameter Dx inside stem taper.
The matrix is simplified by [,,drop=TRUE], especially if
Dx=NULL.
getHeight(data.frame): transforming data.frame before calling
getHeight using buildTree
getHeight(list): transforming list before calling
getHeight using buildTree
getHeight(datBDAT): class method for class datBDAT
tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 20), Dx = c(7, 7)) getHeight(tree, bark = TRUE) getHeight(tree, bark = FALSE) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 20), Dx = c(7, 7)) getHeight(tree, bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 20)) Dx <- c(7, 5) getHeight(tree, Dx = Dx, bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 20), Dx = c(7, 7)) getHeight(tree, Dx = c(1:5), bark = TRUE)tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 20), Dx = c(7, 7)) getHeight(tree, bark = TRUE) getHeight(tree, bark = FALSE) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 20), Dx = c(7, 7)) getHeight(tree, bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(BDATCode = c(1, 1), dbh = c(30, 25), h = c(25, 20)) Dx <- c(7, 5) getHeight(tree, Dx = Dx, bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H")) tree <- data.frame(spp = c(1, 1), D1 = c(30, 25), H = c(25, 20), Dx = c(7, 7)) getHeight(tree, Dx = c(1:5), bark = TRUE)
Function to get BDAT species code, or transform it to a german or english name, possibly an abbreviated version or even a scientific name
getSpeciesCode(inSp = NULL, outSp = NULL)getSpeciesCode(inSp = NULL, outSp = NULL)
inSp |
species information given, either numeric or character |
outSp |
character vector of names, for which information should be returned |
The function matches inSp to outSp. Depending on inSp, being either a numeric vector of values between 1 and 36 or a character vector of species names. Possible names are those which could be return values. One can get all names and the respective species code by calling the function with inSP=NULL and outSP=NULL (the default).
English species names and codes are taken from https://www.forestry.gov.uk/pdf/PF2011_Tree_Species.pdf/$FILE/PF2011_Tree_Species.pdf while slightly adjusting the codes to be unique compared to the german codes (e.g. European larch is now ELA instead of EL).
Any given species code outside the interval [1, 36] is given the code 1 (i.e. Norway spruce), while throwing a warning. If any inSp - name is invalid, i.e. not in species list, this throws an error.
All elements of outSp, which are not colnames of the default returned data.frame, are silently dropped.
vector or data.frame, depending on length of 'outSp'.
getSpeciesCode(inSp = NULL, outSp = NULL) ## the default getSpeciesCode() ## the same getSpeciesCode(outSp = "scientific") getSpeciesCode(inSp = c(1, 2)) ## giving codes getSpeciesCode(inSp = c(1, 2, -1, 37)) ## values outside [1, 36] are given code 1 getSpeciesCode(inSp = c(1, 2), outSp = c("scientific")) ## output a vector getSpeciesCode(inSp = c("Bu", "Fi")) ## asking for codes of abbreviated german names getSpeciesCode(inSp = c("Bu", "Fi", "Bu")) ## order is preserved getSpeciesCode(inSp = c("Buche", "Fichte")) ## asking for codes of german names getSpeciesCode(inSp = c("BE", "NS")) ## ... abbreviated english names getSpeciesCode(inSp = c("beech", "Norway spruce")) ## ... english names getSpeciesCode(inSp = c("Fagus sylvatica", "Picea abies")) ### ... scientific namesgetSpeciesCode(inSp = NULL, outSp = NULL) ## the default getSpeciesCode() ## the same getSpeciesCode(outSp = "scientific") getSpeciesCode(inSp = c(1, 2)) ## giving codes getSpeciesCode(inSp = c(1, 2, -1, 37)) ## values outside [1, 36] are given code 1 getSpeciesCode(inSp = c(1, 2), outSp = c("scientific")) ## output a vector getSpeciesCode(inSp = c("Bu", "Fi")) ## asking for codes of abbreviated german names getSpeciesCode(inSp = c("Bu", "Fi", "Bu")) ## order is preserved getSpeciesCode(inSp = c("Buche", "Fichte")) ## asking for codes of german names getSpeciesCode(inSp = c("BE", "NS")) ## ... abbreviated english names getSpeciesCode(inSp = c("beech", "Norway spruce")) ## ... english names getSpeciesCode(inSp = c("Fagus sylvatica", "Picea abies")) ### ... scientific names
Function to get segment volume over or under bark for a tree of dimension D1, possible D2, and H. Volume is calculated for a given segment defined by A and B, which might be specified as heights or diameters.
getVolume(tree, ...) ## S3 method for class 'data.frame' getVolume(tree, AB = NULL, iAB = "H", bark = TRUE, mapping = NULL, ...) ## S3 method for class 'list' getVolume(tree, AB = NULL, iAB = "H", bark = TRUE, mapping = NULL, ...) ## S3 method for class 'datBDAT' getVolume(tree, AB = NULL, iAB = "H", bark = TRUE, mapping = NULL, ...)getVolume(tree, ...) ## S3 method for class 'data.frame' getVolume(tree, AB = NULL, iAB = "H", bark = TRUE, mapping = NULL, ...) ## S3 method for class 'list' getVolume(tree, AB = NULL, iAB = "H", bark = TRUE, mapping = NULL, ...) ## S3 method for class 'datBDAT' getVolume(tree, AB = NULL, iAB = "H", bark = TRUE, mapping = NULL, ...)
tree |
either a data.frame or a list containing the variables needed to
decribe a tree, i.e. spp, D1, H, and optionally H1, D2, H2. See
|
... |
passing arguments to methods. |
AB |
list with heights or diameters A and B of section for which volume
over or under bark should be calculated. Additionally, add in |
iAB |
character indicating how to interpret given A and B values. Either "H" (the default), "Dob" (diameter over bark) or "Dub" (diameter under bark). Could be of length one or two, depending on whether A and B are both height or diameter variables or not. See examples. |
bark |
boolean of length one indicator for whether required volume should
include bark volume or not. Defaults to TRUE. Coerced to logical by
|
mapping |
mapping of variable names in case a data.frame is given into
parameter |
iAB can be a vector of length two, indicating how to interpret
A and B. Hence, one can calculate volume between a given
height and a given diameter, either over or under bark. If of length one,
it is assumed the indicator applies to both A and B.
Internally, provided diameters in A or B are tranformed to
heights by BDATHXDX if iAB="dob" or by BDATHXDXOR if
iAB="dub".
vector of same length as tree, returning the required volume in cubic meter.
getVolume(data.frame): transforming data.frame before calling
getVolume using buildTree
getVolume(list): transforming data.frame before calling
getVolume using buildTree
getVolume(datBDAT): class method for class datBDAT
BDATVOLABMR and BDATVOLABOR for a
BDAT-type wrapper and function to keep back-compatability. To get total
coarse wood volume (>=7m diameter over bark) BDAT-type functions are
BDATVOLDHMR and BDATVOLDHOR.
## default return with just one or several trees given is total coarse wood ## volume over bark, i.e. stock volume (in german: Vfm m.R.) getVolume(list(spp = 1, D1 = 30, H = 25)) ## first using a data.frame and height information tree <- data.frame(spp = 1, D1 = 30, H = 25, A = 0.1, B = 10) getVolume(tree) # iAB = "H", bark = TRUE, mapping = NULL as default values getVolume(tree, iAB = "H", bark = FALSE, mapping = NULL) ## now, use diameter information tree <- data.frame(spp = 1, D1 = 30, H = 25, A = 30, B = 7) getVolume(tree, iAB = "Dob", bark = TRUE, mapping = NULL) ## now use both diameter and height information tree <- data.frame(spp = 1, D1 = 30, H = 25, A = 0, B = 7) getVolume(tree, iAB = c("H", "Dob"), bark = TRUE, mapping = NULL) ## is equivalent to the original BDAT-function: BDATVOLDHMR(1, 30, 0, 0, 0, H = 25) ## and getVolume(tree, iAB = c("H", "Dob"), bark = FALSE, mapping = NULL) ## is equivalent to: BDATVOLDHOR(1, 30, 0, 0, 0, H = 25) ## use a misnamed data.frame and mapping argument tree <- data.frame(BDATCode = 1, dbh = 30, h = 25, l = 30, u = 7) getVolume(tree, iAB = "Dob", bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H", "l" = "A", "u" = "B") ) ## using a list to provide the data tree <- list( spp = c(1, 1), D1 = c(30, 25), H = c(25, 30), A = c(30, 25), B = c(7, 7) ) getVolume(tree, iAB = "Dob") #' defaults: bark = TRUE, mapping = NULL getVolume(tree, iAB = "Dob", bark = FALSE) #' defaults: mapping = NULL ## using a misnamed list and mapping argument tree <- list( BDATCode = c(1, 1), dbh = c(30, 25), H = c(25, 30), A = c(0.1, 0.1), B = c(1, 1) ) getVolume(tree, mapping = c("BDATCode" = "spp", "dbh" = "D1")) ## using parameter AB to provide the segment data ## in this case a cross join between tree and AB is produced and evaluated tree <- list(BDATCode = c(1, 1), dbh = c(30, 25), H = c(25, 30)) AB <- list(A = c(0.1, 1), B = c(1, 2)) getVolume(tree, AB, iAB = "H", bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1")) ## effect of adjusting 'sl' tree <- list(spp = 1, D1 = 30, H = 25) getVolume(tree = tree, AB = list(A = 0.1, B = 5.1, sl = 2)) # default getVolume(tree = tree, AB = list(A = 0.1, B = 5.1, sl = 1)) getVolume(tree = tree, AB = list(A = 0.1, B = 5.1, sl = 0.1)) getVolume(tree = tree, AB = list(A = 0.1, B = 5.1, sl = 0.01)) ## compare Smalian formula to mid-diameter volume for sl=5 R1 <- getDiameter(tree, Hx = 1.3) / 100 / 2 # radius in m R2 <- getDiameter(tree, Hx = 6.3) / 100 / 2 # radius in m h <- 5 pi * ((R1 + R2) / 2)^2 * h # average of bottom and top diameter (h * pi) / 3 * (R1^2 + R1 * R2 + R2^2) # truncated-cone volume getVolume(tree, AB = list(A = 1.3, B = 6.3, sl = 5)) # mid-diameter volume getVolume(tree, AB = list(A = 1.3, B = 6.3, sl = 0.01)) # physical volume## default return with just one or several trees given is total coarse wood ## volume over bark, i.e. stock volume (in german: Vfm m.R.) getVolume(list(spp = 1, D1 = 30, H = 25)) ## first using a data.frame and height information tree <- data.frame(spp = 1, D1 = 30, H = 25, A = 0.1, B = 10) getVolume(tree) # iAB = "H", bark = TRUE, mapping = NULL as default values getVolume(tree, iAB = "H", bark = FALSE, mapping = NULL) ## now, use diameter information tree <- data.frame(spp = 1, D1 = 30, H = 25, A = 30, B = 7) getVolume(tree, iAB = "Dob", bark = TRUE, mapping = NULL) ## now use both diameter and height information tree <- data.frame(spp = 1, D1 = 30, H = 25, A = 0, B = 7) getVolume(tree, iAB = c("H", "Dob"), bark = TRUE, mapping = NULL) ## is equivalent to the original BDAT-function: BDATVOLDHMR(1, 30, 0, 0, 0, H = 25) ## and getVolume(tree, iAB = c("H", "Dob"), bark = FALSE, mapping = NULL) ## is equivalent to: BDATVOLDHOR(1, 30, 0, 0, 0, H = 25) ## use a misnamed data.frame and mapping argument tree <- data.frame(BDATCode = 1, dbh = 30, h = 25, l = 30, u = 7) getVolume(tree, iAB = "Dob", bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1", "h" = "H", "l" = "A", "u" = "B") ) ## using a list to provide the data tree <- list( spp = c(1, 1), D1 = c(30, 25), H = c(25, 30), A = c(30, 25), B = c(7, 7) ) getVolume(tree, iAB = "Dob") #' defaults: bark = TRUE, mapping = NULL getVolume(tree, iAB = "Dob", bark = FALSE) #' defaults: mapping = NULL ## using a misnamed list and mapping argument tree <- list( BDATCode = c(1, 1), dbh = c(30, 25), H = c(25, 30), A = c(0.1, 0.1), B = c(1, 1) ) getVolume(tree, mapping = c("BDATCode" = "spp", "dbh" = "D1")) ## using parameter AB to provide the segment data ## in this case a cross join between tree and AB is produced and evaluated tree <- list(BDATCode = c(1, 1), dbh = c(30, 25), H = c(25, 30)) AB <- list(A = c(0.1, 1), B = c(1, 2)) getVolume(tree, AB, iAB = "H", bark = TRUE, mapping = c("BDATCode" = "spp", "dbh" = "D1")) ## effect of adjusting 'sl' tree <- list(spp = 1, D1 = 30, H = 25) getVolume(tree = tree, AB = list(A = 0.1, B = 5.1, sl = 2)) # default getVolume(tree = tree, AB = list(A = 0.1, B = 5.1, sl = 1)) getVolume(tree = tree, AB = list(A = 0.1, B = 5.1, sl = 0.1)) getVolume(tree = tree, AB = list(A = 0.1, B = 5.1, sl = 0.01)) ## compare Smalian formula to mid-diameter volume for sl=5 R1 <- getDiameter(tree, Hx = 1.3) / 100 / 2 # radius in m R2 <- getDiameter(tree, Hx = 6.3) / 100 / 2 # radius in m h <- 5 pi * ((R1 + R2) / 2)^2 * h # average of bottom and top diameter (h * pi) / 3 * (R1^2 + R1 * R2 + R2^2) # truncated-cone volume getVolume(tree, AB = list(A = 1.3, B = 6.3, sl = 5)) # mid-diameter volume getVolume(tree, AB = list(A = 1.3, B = 6.3, sl = 0.01)) # physical volume
creating a plot of the taper curve of a tree, over or under bark
## S3 method for class 'datBDAT' plot(x, bark = NULL, col.bark = NULL, legend = FALSE, assort = NULL, ...)## S3 method for class 'datBDAT' plot(x, bark = NULL, col.bark = NULL, legend = FALSE, assort = NULL, ...)
x |
an object of class 'datBDAT' |
bark |
either NULL or logical; if TRUE taper curve over bark is plotted, if FALSE taper curve under bark is plotted; if NULL, both are plotted |
col.bark |
color to be used for plot of bark, if plot of taper curve over and under bark is requested |
legend |
logical, if legend should be added |
assort |
assortments produced by |
... |
further arguments for |
Creates graphics of the taper curve of trees. Either over bark or
under bark, or both. Elements design can partly be chosen. If assortments are
given, these are added to the plot. Doing that, the assortment bottom and top
position is indicated by a vertical line and mid-diameter is shown as a point
with vertical dashed line. N.B. the mid-diameter shown is under bark and
rounded downwards for 0.5 cm if mid-diameter < 20 and for 0.75 cm if bigger.
Assortment volume is calculated using this diameter according to the legal
rules for roundwood assortments (formerly german Forst-HKS and now RVR).
Additionally, assortment names are indicated.
One can provide assortment names in a column of assort named
'assortname', which will be used if available, otherwise the 'Sort'-column
will be used. See Examples.
No return value, called for side effects
## plotting the taper curve of a tree oldpar <- par(no.readonly = TRUE) par(mfrow = c(1, 1)) t <- data.frame(spp = 1, D1 = 40, H = 35) tree <- buildTree(tree = t) plot(tree, type = "l", las = 1, legend = TRUE) plot(tree, bark = TRUE, las = 1) plot(tree, bark = FALSE, las = 1) t <- data.frame(spp = c(1, 1), D1 = c(40, 35), H = c(35, 30)) tree <- buildTree(tree = t) plot(tree, bark = FALSE, las = 1, legend = TRUE) plot(tree, bark = TRUE, las = 1, legend = TRUE) t <- data.frame(spp = c(1, 8), D1 = 40, H = 35) tree <- buildTree(tree = t) plot(tree, bark = NULL, las = 1, col.bark = "blue", legend = TRUE) plot(tree[1, ], main = getSpeciesCode(tree[1, ]$spp, out = "long")) plot(tree[2, ], main = getSpeciesCode(tree[2, ]$spp, out = "scientific")) par(mfrow = c(2, 1)) plot(tree, bark = TRUE, las = 1) ## now add assortments into taper curve par(mfrow = c(1, 1)) ass <- getAssortment(tree, sort = list(lX = 1, fixN = 2, fixL = 4, fixA = 10)) plot(tree, assort = ass) plot(tree, bark = FALSE, assort = ass) plot(tree, bark = FALSE, assort = ass, legend = TRUE) plot(tree[1, ], assort = ass[ass$tree == 1, ], main = "first tree in subset") plot(tree[2, ], assort = ass[ass$tree == 2, ], main = "second tree in subset") ## adding own assortment labels using column 'assortname' ass$assortname <- ifelse(grepl("Fix", ass$Sort), paste0("Fix:", ass$length), ass$Sort) plot(tree, assort = ass) par(oldpar)## plotting the taper curve of a tree oldpar <- par(no.readonly = TRUE) par(mfrow = c(1, 1)) t <- data.frame(spp = 1, D1 = 40, H = 35) tree <- buildTree(tree = t) plot(tree, type = "l", las = 1, legend = TRUE) plot(tree, bark = TRUE, las = 1) plot(tree, bark = FALSE, las = 1) t <- data.frame(spp = c(1, 1), D1 = c(40, 35), H = c(35, 30)) tree <- buildTree(tree = t) plot(tree, bark = FALSE, las = 1, legend = TRUE) plot(tree, bark = TRUE, las = 1, legend = TRUE) t <- data.frame(spp = c(1, 8), D1 = 40, H = 35) tree <- buildTree(tree = t) plot(tree, bark = NULL, las = 1, col.bark = "blue", legend = TRUE) plot(tree[1, ], main = getSpeciesCode(tree[1, ]$spp, out = "long")) plot(tree[2, ], main = getSpeciesCode(tree[2, ]$spp, out = "scientific")) par(mfrow = c(2, 1)) plot(tree, bark = TRUE, las = 1) ## now add assortments into taper curve par(mfrow = c(1, 1)) ass <- getAssortment(tree, sort = list(lX = 1, fixN = 2, fixL = 4, fixA = 10)) plot(tree, assort = ass) plot(tree, bark = FALSE, assort = ass) plot(tree, bark = FALSE, assort = ass, legend = TRUE) plot(tree[1, ], assort = ass[ass$tree == 1, ], main = "first tree in subset") plot(tree[2, ], assort = ass[ass$tree == 2, ], main = "second tree in subset") ## adding own assortment labels using column 'assortname' ass$assortname <- ifelse(grepl("Fix", ass$Sort), paste0("Fix:", ass$length), ass$Sort) plot(tree, assort = ass) par(oldpar)
function replaces calls to package 'rBDATPRO' by calls to package 'rBDAT', simply by replacing the package name.
updateBdatNamespace(inpath = file.choose(), outpath = NULL)updateBdatNamespace(inpath = file.choose(), outpath = NULL)
inpath |
path of file to process |
outpath |
either a file name or a directory, both or NULL, see details. |
This function merely exists to account for the renaming of the
package from rBDATPRO (which was internally used for some period of
time) to rBDAT. Its sole purpose is to update R-scripts which use
rBDATPRO and now should be updated to use rBDAT. Internally,
gsub is used.
outpath can be (i) a filename, then the newly generated file
is stored under that name in the inpath directory, (ii) a directory,
then the inpath-filename is used with prefixed rbdat_, (iii) a
complete path (directory name and file name), then this is used to store the
file, (iv) NULL, then the inpath is used with prefixed rbdat_ to the
inpath filename.
a character holding path and filename of the updated file
## Not run: p <- tempdir() f <- "rbdatpro.r" tx <- c("require(rBDATPRO)", "library(rBDATPRO)", "rBDATPRO::getDiameter(list(spp=1, D1=30, H=27))") pf <- file.path(p, f) writeLines(tx, con=pf) file.exists(pf) list.files(p) # file.show(pf) ## define different output specs outpath1 <- file.path(tempdir(), "devel/rbdatScript.r") outpath2 <- p outpath3 <- "rbdatScript.r" (updated_file <- updateBdatNamespace(pf, outpath = NULL)) list.files(p) # file.show(updated_file) (updated_file <- updateBdatNamespace(pf, outpath1)) list.files(file.path(p, "devel")) # file.show(updated_file) (updated_file <- updateBdatNamespace(pf, outpath2)) list.files(p) # file.show(updated_file) (updated_file <- updateBdatNamespace(pf, outpath3)) list.files(p) # file.show(updated_file) ## End(Not run)## Not run: p <- tempdir() f <- "rbdatpro.r" tx <- c("require(rBDATPRO)", "library(rBDATPRO)", "rBDATPRO::getDiameter(list(spp=1, D1=30, H=27))") pf <- file.path(p, f) writeLines(tx, con=pf) file.exists(pf) list.files(p) # file.show(pf) ## define different output specs outpath1 <- file.path(tempdir(), "devel/rbdatScript.r") outpath2 <- p outpath3 <- "rbdatScript.r" (updated_file <- updateBdatNamespace(pf, outpath = NULL)) list.files(p) # file.show(updated_file) (updated_file <- updateBdatNamespace(pf, outpath1)) list.files(file.path(p, "devel")) # file.show(updated_file) (updated_file <- updateBdatNamespace(pf, outpath2)) list.files(p) # file.show(updated_file) (updated_file <- updateBdatNamespace(pf, outpath3)) list.files(p) # file.show(updated_file) ## End(Not run)