| Version: | 0.0-9 |
| Date: | 2025-03-17 |
| Title: | Sitree Extensions |
| Maintainer: | Ignacio Sevillano <ignacio.sevillano@nibio.no> |
| Depends: | R (≥ 3.1.0) |
| Imports: | data.table, sitree |
| Description: | Provides extensions for package 'sitree' for allometric variables, growth, mortality, recruitment, management, tree removal and external modifiers functions. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| LazyLoad: | yes |
| NeedsCompilation: | no |
| Packaged: | 2025-03-17 13:49:07 UTC; ign |
| Author: | Clara Anton Fernandez
 [aut],
Ignacio Sevillano
[cre] |
| Repository: | CRAN |
| Date/Publication: | 2025-03-18 08:30:06 UTC |
Climate-sensitive site index models for Norway
Description
Implementation of models for climate-sensitive site index models for Norway as described in Antón-Fernández et al. (2016).
Usage
AM2016ClimateSensitiveSINorway(soilquality, t.early.summer, waterbal, SI.spp)
Arguments
soilquality |
A factor with levels 1 to 5 indicating the soilquality category. 1 being the poorest soils and 5 the best soils |
t.early.summer |
A vector with sum temperatures (in C) in spring and early summer (april, june and july) |
waterbal |
A vector with the montly moisture surplus in June (difference between the 30-year mean precipitation in June and mean potential evapotranspiration in June.). |
SI.spp |
SI species, that is, the species for which SI should be calculated. 1 = spruce, 2 = pine, 3 = birch. |
Value
Returns a vector with the estimated SI.
Author(s)
Clara Anton-Fernandez
References
Anton-Fernandez, Clara, Blas Mola-Yudego, Lise Dalsgaard, and Rasmus Astrup. 2016. “Climate-Sensitive Site Index Models for Norway.” Canadian Journal of Forest Research 46 (6). doi: 10.1139/cjfr-2015-0155
Examples
AM2016ClimateSensitiveSINorway (soilquality = as.factor(c(1,2,3,4)),
t.early.summer = c(10,20,30,10),
waterbal = c(-40, 20,10,10),
SI.spp = c(1,2,2,3))
Basal area of larger trees
Description
It calculates the basal area of larger trees for a plot.
Usage
PBAL(BA)
Arguments
BA |
A vector of tree's basal area. |
Value
It returns a vector with the sum of the basal areas of larger trees. Trees with similar BA are not considered larger.
Examples
PBAL(c(1,2,3,4,4))
Basal area of larger trees which are at least X cm larger than the tree of interest
Description
Calculates the basal area (in cm2 if dbh is in mm) of trees that are at least X (in the same units as dbh) larger than the tree of interest for a list of trees.
Usage
PBAL.dbh.greater(dbh.mm, dbh.mm.diff)
Arguments
dbh.mm |
a vector of dbh in mm |
dbh.mm.diff |
minimum dbh difference between the tree and the tree of interest to be considered |
Details
It estimates the basal area (in cm2) of trees that are at least dbh.mm.diff mm larger than the tree of interest.
Value
It returns a list with the basal area of larger trees.
Author(s)
Cara Antón-Fernández (email: caf@nibio.no)
See Also
Examples
library(sitree)
PBAL.dbh.greater(c(100,89,51,74,4), 3)
aggregate(dbh ~ plot.id, data = tr, FUN = PBAL.dbh.greater, dbh.mm.diff = 2)
Convert Plot data to a data.frame/data.table format
Description
It attemps to convert the plot level information to a data.frame/data.list format. For example, if management is an element of the plot list (pd) it will melt it to a long format.
Usage
PlotDataToLong(pd)
Arguments
pd |
A list with plot information. It especifically looks for two elements 'stand.age.years' and 'management'. |
Value
It returns a data.table with all vector from pd as columns, and dataframes melted.
Examples
library(sitree)
result.sitree <- sitree (tree.df = tr,stand.df = fl,
functions = list(fn.growth ='grow.dbhinc.hgtinc',
fn.mort ='mort.B2007',
fn.recr ='recr.BBG2008',
fn.management ='management.prob',
fn.tree.removal ='mng.tree.removal',
fn.modif = NULL,
fn.prep.common.vars ='prep.common.vars.fun'),
n.periods = 5,
period.length = 5,mng.options = NA,
print.comments = FALSE,
fn.dbh.inc = "dbhi.BN2009",
fn.hgt.inc = "height.korf",
species.spruce = c(1, 2, 3),
species.pine = c(10, 11, 20, 21, 29),species.harw = c(30, 31),
fun.final.felling = "harv.prob",
fun.thinning = "thin.prob",per.vol.harv = 0.83)
PlotDataToLong(result.sitree$plot.data)
Marklund's biomass equations
Description
Implements Marklund's (1988) biomass equations for above-ground biomass and Petersson and Ståhl (2006) for below-ground biomass.
Usage
biomass.spruce.M1988(dbh.cm, H.m)
biomass.pine.M1988(dbh.cm, H.m)
biomass.birch.M1988(dbh.cm, H.m)
Arguments
dbh.cm |
A vector with the dbh (diameter at breast height) of the trees, in cm. |
H.m |
A vector with the heights of the trees, in meters. |
Value
It returns a data.frame with the following biomass components in kg: living.branches, dead.branches, stem.wood, stump.roots, bark, usoil, rot1, rot2, and foliage.
Author(s)
Clara Anton Fernandez caf@nibio.no
References
Marklund, L. G. 1988. “Biomassafunktioner för tall, gran och björk i Sverige [Biomass functions for pine, spruce and birch in Sweden].” Report 45. Umeå, Sweden: Swedish University of Agricultural Sciences. Department of Forest Survey. Petersson, Hans, and Göran Ståhl. 2006. “Functions for Below-Ground Biomass of Pinus Sylvestris, Picea Abies, Betula Pendula and Betula Pubescens in Sweden.” Scandinavian Journal of Forest Research 21 (S7): 84–93.
Examples
biomass.spruce.M1988(dbh.cm = c(10, 20), H.m = c(8, 12))
Implements biomass functions for birch for Norway from Smith et al (2014, 2016)
Description
Implements biomass functions for birch for Norway from Smith et al (2014, 2016). Total biomass aboveground does include stump calculated using biomass.birch.M1988. Total biomass belowground does not include stump.
Usage
biomass.birch.S2014(dbh.cm, H.m)
Arguments
dbh.cm |
dbh (diameter at breast height) in cm. |
H.m |
Tree height in meters. |
Details
It uses stump.roots from biomass.birch.M1988 to calculate aboveground biomass (in kg) and belowground biomass (in kg). Aboveground biomass is calculated as Smith's aboveground biomass (2014) + stump.roots. Belowground biomass is calcualted as Smith's belowground biomass (2016) - stump.roots.
Value
Returns a data.frame with the following biomass components: biomass.total.kg, biomass.aboveground.kg.S2014, biomass.belowground.kg.S2014, biomass.belowground.kg, biomass.aboveground.kg, living.branches, dead.branches, stem.wood, stump.roots, bark, usoil, rot1, rot2, foliage)
Author(s)
Clara Anton Fernandez (caf@nibio.no)
References
Smith, Aaron, Aksel Granhus, and Rasmus Astrup. 2016. “Functions for Estimating Belowground and Whole Tree Biomass of Birch in Norway.” Scandinavian Journal of Forest Research 31 (6): 568–82. https://doi.org/10.1080/02827581.2016.1141232 Smith, Aaron, Aksel Granhus, Rasmus Astrup, Ole Martin Bollandsås, and Hans Petersson. 2014. “Functions for Estimating Aboveground Biomass of Birch in Norway.” Scandinavian Journal of Forest Research 29 (6): 565–78. http://dx.doi.org/10.1080/02827581.2014.951389
See Also
Examples
biomass.birch.S2014(dbh.cm = c(10, 20), H.m = c(12, 16))
Calculates biomass for trees using the Norwegian biomass equations
Description
Calculates biomass for trees using the Norwegian biomass equations.
Usage
biomass.norway.sitree(dbh.mm, height.dm, tree.sp)
Arguments
dbh.mm |
Diameter at breast height in mm. |
height.dm |
Tree height in dm. |
tree.sp |
Tree species according to the Norwegian NFI. It will use
|
Value
Returns a data.table containing the 12 columns resulting from applying the biomass functions.
See Also
biomass.birch.S2014, biomass.pine.M1988, biomass.spruce.M1988
Examples
bio.nor <- biomass.norway.sitree (dbh.mm = c(50, 60, 100 ), height.dm = c(40, 60,
80),
tree.sp = c(1, 10, 30))
Biomass for live, dead, or removed trees using Norwegian biomass functions
Description
Calculates biomass for trees using the Norwegian biomass equations.
Usage
biomass.sitree(tr, plot.data)
Arguments
tr |
A trList or trListDead object. |
plot.data |
A data.frame or list with plot information. It should have at least plot.id and tree2ha. |
Value
Returns a data.table containing the 12 columns resulting from applying the biomass functions.
Author(s)
Clara Anton Fernandez caf@nibio.no
See Also
biomass.birch.S2014, biomass.birch.M1988,
biomass.pine.M1988, biomass.spruce.M1988, biomass.norway.sitree
Examples
library(sitree)
result.sitree <- sitree (tree.df = stand.west.tr,
stand.df = stand.west.st,
functions = list(
fn.growth = 'grow.dbhinc.hgtinc',
fn.mort = 'mort.B2007',
fn.recr = 'recr.BBG2008',
fn.management = NULL,
fn.tree.removal = NULL,
fn.modif = NULL,
fn.prep.common.vars = 'prep.common.vars.fun'
),
n.periods = 20,
period.length = 5,
mng.options = NA,
print.comments = FALSE,
fn.dbh.inc = "dbhi.BN2009",
fn.hgt.inc = "height.korf"
)
biom <- biomass.sitree(tr = result.sitree$live, plot.data = result.sitree$plot.data)
Mean height of X tallest trees
Description
It calculates the mean height of the X tallest trees by grouping variable (e.g. the plot ID)
Usage
height.of.X.tallest.trees(height, uplotID, num.trees)
Arguments
height |
A vector with heights |
uplotID |
A vector with the grouping variable, most often this would be the plot ID. |
num.trees |
Number of trees used to calculate the mean height. |
Value
It returns a data.frame with two columns containing the uplotID and the mean height of the X tallest trees.
Note
This function can be used to calculate the average of the X largest
values of any variable grouped by a grouping variable. It is mostly a
wrapper for aggregate.
Author(s)
Clara Antón Fernández (caf@nibio.no)
See Also
Examples
library(sitree)
height.of.X.tallest.trees(height = tr$height,
uplotID = tr$plot.id, 5)
Lorey's height
Description
Calculates Lorey's height (mean height weigted by basal area). If group.id is not NULL, it will calculate Lorey's height for each group.
Usage
lorey.height(BA, height, group.id = NULL)
Arguments
BA |
A vector with the basal areas of the trees |
height |
A vector with the height of the trees |
group.id |
An optional vector with a grouping variable. |
Value
If a grouping variable is provided it returns a data frame with two columns (group.id, and lorey.height). If a grouping variable is not provided it will return the Lorey's height.
Author(s)
Clara Anton Fernandez (caf@nibio.no)
See Also
Examples
library(sitree)
BA <- pi*(tr$dbh/2)^2
lorey.height(BA, tr$height)
lorey.height(BA, tr$height, tr$plot.id)
Top height of the n thickest trees
Description
Average height of the n thickest trees per ha
Usage
top.height(thickness, height, num.trees.per.ha, plot.id, plot.size.m2)
Arguments
thickness |
A vector with the thickness for every tree. Other variables can be used instead to thickness. This is only used to order the trees. |
height |
Height of the trees. |
num.trees.per.ha |
Number of trees per ha that the top height should correspond to. E.g. 100 trees per ha. |
plot.id |
Vector with the plot.id to which every tree corresponds to. |
plot.size.m2 |
Plot size in square meters. It can be either a single number if all plots have the same size of a vector of equal length as thickness, height, and plot.id with the corresponding plot size for each tree. |
Details
thickness, height, and plot.id should have the same length, that is, one value per tree.
Value
It returns a data.frame with two columns: top.heights in the same units as height, and plot.id.
Examples
top.height(thickness = runif(100, 10,40), height = runif(100, 12, 45),
num.trees.per.ha = 100, plot.id = 1, plot.size.m2 = 250)
EStimation of individual tree age
Description
Estimates individual tree age of trees within a plot based on basal area, site index, species, and development class.
Usage
tree.age(stand.age.years, plot.id, tree.BA.m2, dbh.mm,
SI.spp, SI.m, spp, dev.class, apply.correction = TRUE)
Arguments
stand.age.years |
The age of the stand in years. |
plot.id |
The unique ID of the stand |
tree.BA.m2 |
A vector with the basal areas of each tree in m2. |
dbh.mm |
A vector with the DBH in mm of each tree. |
SI.spp |
Species for which SI has been calculated (1, 2, 3). |
SI.m |
Site index (SI) in m. |
spp |
Species group classification. |
dev.class |
Development class. |
apply.correction |
TRUE/FALSE. If a correction to age should be applied |
Value
A vector with the estimated ages of trees
Author(s)
Clara Anton Fernandez caf@nibio.no
Examples
tree.age(stand.age.years = 40,
plot.id = c(1,1), tree.BA.m2 = c(0.05, 0.5),dbh.mm
= c(50,150), SI.spp = 2,
SI.m = 11, spp = c(1,1), dev.class = 3, apply.correction = TRUE)
Volume for sitree output for Norwegian conditions
Description
It calculates volume following the Norwegian national forest inventory equations for a trList or trListDead object
Usage
volume.sitree(tr, plot.data)
Arguments
tr |
a trListDead or trList object |
plot.data |
a list or data.frame containing at least a 'kom' and 'tree2ha' column/element. kom is the kommune (municipality) code, and tree2ha should be the expansion factor to go from tree to per ha basis. |
Details
It uses the volume.norway function to estimate the volume for all trees with dbh.mm greater than 0. It returns NA when dbh.mm is 0 or lower. tree2ha is included to facilitate the calculation of per ha values.
Value
It returns a data.table with columns for treeid, plot.id, dbh.mm, height.dm, kom, tree2ha, tree.sp, vol.w.tr.m3 (volume with bark in m3 per tree), and vol.wo.tr.m3 (volume without bark in m3 per tree)
Author(s)
Clara Antón-Fernández (email: caf@nibio.no)
Examples
library(sitree)
res <- sitree (tree.df = tr,
stand.df = fl,
functions = list(
fn.growth = 'grow.dbhinc.hgtinc',
fn.mort = 'mort.B2007',
fn.recr = 'recr.BBG2008',
fn.management = 'management.prob',
fn.tree.removal = 'mng.tree.removal',
fn.modif = NULL,
fn.prep.common.vars = 'prep.common.vars.fun'
),
n.periods = 5,
period.length = 5,
mng.options = NA,
print.comments = FALSE,
fn.dbh.inc = "dbhi.BN2009",
fn.hgt.inc = "height.korf",
species.spruce = c(1, 2, 3),
species.pine = c(10, 11, 20, 21, 29),
species.harw = c(30, 31),
fun.final.felling = "harv.prob",
fun.thinning = "thin.prob",
per.vol.harv = 0.83
)
volume.sitree(tr = res$live, plot.data = res$plot.data)