Package 'linkages'

LINKAGES birth function

Description

BIRTH CALCULATES SEEDLING AND SPROUT BIRTH BASED ON SPECIES FECUNDITY, SEEDBED CONDITIONS, SUSCEPTIBILITY TO BROWSING, AND THE DEGREE TO WHICH LIGHT, SOIL MOISTURE, AND DEGREE DAYS ARE LESS THAN OPTIMUM FOR GROWTH. SOIL MOISTURE AND DEGREE DAY MULTIPLIERS ARE SUPPLIED BY SUBROUTINE GMULT. A SPECIES CAN HAVE SPROUTS IF AT LEAST ONE TREE WITH DIAMETER BETWEEN SPRTMN AND SPRTMX DIED LAST YEAR (KSPRT INCREMENTED BY 1 IN KILL). RANDOM NUMBERS USED TO DETERMINE OCCURENCE OF BROWSING, NUMBERS OF SEEDLINGS AND SPROUTS, AND DBH SUPPLIED BY rand.

Usage

birth(nspec, ntrees, frt, iage, slta, sltb, dbh, fwt, switch.mat, degd, dmin,
  dmax, frost, rt, itol, mplant, nogro, ksprt, sprtnd, max.ind, smgf, degdgf)

Arguments

nspec	number of species
ntrees	number of trees of each species
frt	foliage retention time
iage	age of each individual
slta	parameter to calculate crown area from diameter
sltb	parameter to calculate crown area from diameter
dbh	diameter of each individual
fwt	leaf weight per unit crown area
switch.mat	TRUE/FALSE switches for each species
degd	growing degree days from tempe.R
dmin	degree day minimum for each species
dmax	degree day maximum for each species
frost	minimum January temperature tolerated
rt	current monthly temperatures
itol	shade tolerance code for each species
mplant	maximum seeding in rate per plot
nogro	flags individuals that aren't growing well
ksprt	flags individuals that could sprout
sprtnd	number of sprouts per stump
max.ind	maximum number of individuals in a plot
smgf	soil moisture growing factor from gmult.R
degdgf	growing degree day growing factor from gmult.R

Value

iage age of each individual

dbh diameter of each individual

nogro flags individuals growing slowly

ntrees number of trees of each species

newtr records species considered 'eligible'

ksprt flags individuals that could sprout

Author(s)

Ann Raiho

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LINKAGES decomp function

Description

DECOMP CALCULATES CARBON AND NITROGEN FLOWS THROUGH SOIL. AVAILABLE N (AVAILN) IS USED IN GMULT TO CALCULATE SOIL NITROGEN GROWTH MULTIPLIERS. AET IS FED IN FROM MOIST. THIS YEAR'S LEAF, TWIG, ROOT, AND WOOD LITTER IS FED IN FROM KILL (ARRAY TYL). THE SIMULATION STARTS ON BARE GROUND (ONLY HUMUS PRESENT. BASESC AND BASESN ARE STARTING HUMUS WEIGHT AND N CONTENTS READ IN INPUT). THREE TYPES OF SOIL ORGANIC MATTER ARE RECOGNIZED: COHORTS EITHER IMMOBILIZING OR RAPIDLY MINERALIZING NITROGEN AND A HOMOGENOUS HUMUS POOL SLOWLY MINERALIZING N.

Usage

decomp(fdat, aet, ncohrt, fc, dry, tyl, C.mat)

Arguments

fdat	current year
aet	average temperature by month for current year
ncohrt	average precipitation by month for current year
fc	field capacity
dry	wilting point
tyl	total yearly litter
C.mat	carbon matrix

Value

ff weights and n content of forest floor by litter type

availn available N

tyln leaf litter N content

hcn humus C:N ratio

sco2 total soil co2-c

ncohrt number of cohorts

C.mat matrix for data on litter cohorts

Author(s)

Ann Raiho

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LINKAGES gmult function

Description

GMULT CALCULATES DEGREE DAY, SOIL MOISTURE, AND SOIL NITROGEN MULTIPLIERS USED IN SUBROUTINES BIRTH AND GROW BASED ON ON DEGD (SUPPLIED BY TEMPE), FJ (SUPPLIED BY MOIST), AND AVAILN (SUPPLIED BY DECOMP), RESPECTIVELY.

Usage

gmult(egs, bgs, availn, degd, dmin, dmax, d3, fj, cm1, cm3, cm2, cm4, cm5,
  nspec)

Arguments

egs	end of growing season day of year
bgs	beginning of growing season day of year
availn	available nitrogen
degd	total growing degree days
dmin	degree day minimum for each species
dmax	degree day maximum for each species
d3	drought tolerance (fraction of the growing season)
fj	number of dry days
cm1	parameter for nitrogen growth multipliers
cm3	parameter for nitrogen growth multipliers
cm2	parameter for nitrogen growth multipliers
cm4	parameter for nitrogen growth multipliers
cm5	parameter for nitrogen growth multipliers
nspec	number of species

Value

smgf soil moisture growth factor

sngf soil nitrogen growth factor

degdgf growing degree day growth factor

availn available nitrogen

Author(s)

Ann Raiho

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LINKAGES growth function

Description

GROW CALCULATES DIAMETER GROWTH FOR EACH TREE BY DECREASING MAXIMAL GROWTH TO THE EXTENT THAT THE MOST LIMITING RESOURCE IS LESS THAN OPTIMAL.

Usage

grow(max.ind, nspec, ntrees, frt, slta, sltb, dbh, fwt, b2, b3, itol, g, degdgf,
  smgf, sngf, frost, rt, iage, nogro)

Arguments

max.ind	maximum number of individuals
nspec	number of species
ntrees	number of trees of each species
frt	foliage retention time
slta	parameter to calculate crown area from diameter
sltb	parameter to calculate crown area from diameter
dbh	diameter of each tree
fwt	leaf weight per unit crown area
b2	growth scaling parameter
b3	growth scaling parameter
itol	shade tolerance code for each species
g	scalar for species maximum diameter increment
degdgf	growing degree day growth factor from gmult.R
smgf	soil moisture growth factor from gmult.R
sngf	soil nitrogen growth factor from gmult.R
frost	minimum January temperature tolerated
rt	current monthly temperature
iage	age of each individual
nogro	flags slow growing individuals

Value

dbh diameter of each individual

ntrees number of trees of each species

awp aboveground woody production

Author(s)

Ann Raiho

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Hello, World!

Description

Prints 'Hello, world!'.

Usage

hello()

Examples

hello()

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LINKAGES kill function

Description

KILL KILLS TREES BY AGE DEPENDENT MORTALITY (ONLY 1 REACH MAXIMUM AGE) AND AGE INDEPENDENT MORTALITY (PROBABILITY OF SURVIVING 10 CONSECUTIVE YEARS OF SLOW GROWTH (SEE GROW) = 1 DECISIONS ON WHETHER OR NOT TO KILL A TREE ARE PARTLY BASED ON RANDOM NUMBERS SUPPLIED BY rand. KILL ALSO CALCULATES LITTER AMOUNTS, WHICH ARE DECAYED IN SUBROUTINE DECOMP.

Usage

kill(nspec, ntrees, slta, sltb, dbh, agemx, ksprt, sprtmn, sprtmx, iage, nogro,
  tl, rtst, fwt, max.ind, frt)

Arguments

nspec	number of species
ntrees	number of trees of each species
slta	parameter to calculate crown area from diameter
sltb	parameter to calculate crown area from diameter
dbh	diameter of each individual
agemx	max age
ksprt	flags if stump can sprout
sprtmn	minimum diameter for a stump to sprout
sprtmx	maximum diameter for a stump to sprout
iage	age of each individual
nogro	flags slow growing individuals
tl	leaf litter quality class
rtst	root-shoot ratio for each species
fwt	leaf weight per unit crown area
max.ind	maximum number of individuals
frt	foliage retention time
ncohrt	number of cohorts

Value

dbh diameter of each individual

ntrees number of trees of each species

iage age of each individual

nogro flags individuals growing slowly

ncohrt number of cohorts

tyl total yearly litter,

ksprt flags stumps that could sprout

Author(s)

Ann Raiho

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LINKAGES main function

Description

Main function for running all LINKAGES subroutines

Usage

linkages(linkages.input, outdir, restart = NULL, linkages.restart = NULL)

Arguments

iplot	PEcAn settings object
nyear	number of years
nspec	number of species
fc	field capacity
dry	wilting point
bgs	beginning of growing season
egs	end of growing season
max.ind	maximum number of indiviuals allowed to grow in a plot
plat	latitude
temp.mat	monthly temperature matrix (nyear x 12)
precip.mat	monthly precipitation matrix (nyear x 12)
spp.params	species parameter matrix
switch.mat	species switches matrix
fdat	underground parameter matrix
clat	climate correction factor matrix
basesc	initial humus weight
basesn	initial N in soil

Value

year vector of years

ag.biomass above ground biomass in kgC/m2

total.soil.carbon soil organic matter + leaf litter in kgC/m2

leaf.litter leaf litter in kgC/m2

ag.npp above ground net primary production in kgC/m2/second

hetero.resp heterotrophic respiration in kgC/m2/second

nee net ecosystem exchange in kgC/m2/second

et annual evapotransipiration kgC/m2/s

agb.pft = agb.pft above ground biomass by plant functional type (species in LINKAGES)

f.comp = f.comp fractional composition (sums to 1 each year)

ntrees.birth=ntrees.birth number of trees born of each species each year

ntrees.kill = ntrees.kill number of trees killed of each species each year

tstem=tstem stem density

tab=tab total aboveground biomass without unit conversion

fl=fl total leaf litter without unit conversion

totl=totl leaf litter nitrogen

tnap=tnap total net above ground production without unit conversion

avln=avln available nitrogen

cn=cn carbon to nitrogen ratio

sco2c=sco2c soil repiration without unit conversion

som=som soil organic matter

bar=bar biomass by species without unit conversion

aet.save=aet.save annual evapotranspiration without unit conversion

nogro.save=nogro.save matrix of trees not growing each year

dbh.save=dbh.save matrix of dbh increment of trees each year

iage.save=iage.save matrix of age of each tree each year

Author(s)

Ann Raiho

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LINKAGES moist function

Description

Calculates actual evapotranspiration (AET) for the current year

Usage

moist(kyr, temp.vec, precip.vec, fc, dry, bgs, egs, plat, clat)

Arguments

kyr	current year
temp.vec	average temperature by month for current year
precip.vec	average precipitation by month for current year
fc	field capacity
dry	wilting point
bgs	beginning growing season day of year
egs	end growing season day of year
plat	plot latititude
clat	climate adjustment matrix

Value

aet actual evapotranspiration (units:mm)

fj total number of dry days

Author(s)

Ann Raiho

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LINKAGES output function

Description

OUTPUT coverts model variables into ecosystem variables of interest

Usage

output(availn, tyln, nspec, frt, iage, slta, sltb, dbh, fwt, tyl, max.ind,
  ntrees, awp)

Arguments

availn	available nitrogen
tyln	leaf litter N content from "decomp.r"
nspec	number of species
frt, slta, sltb, fwt	species specific parameters
iage	age of each individual
dbh	diameter of each individual
tyl	total yearly litter
max.ind	maximum number of individual
ntrees	number of trees of each species
awp	aboveground woody production

Value

atot total number of trees per ha

tbar total aboveground biomass

tyln leaf litter N content

tynap total aboveground production

availn available N

bar specieis biomass t/ha

Author(s)

Ann Raiho

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LINKAGES plotin function

Description

Sets up initial conditions for LINAKGES

Usage

plotin(iplot, basesc, basesn, max.ind, nspec)

Arguments

iplot	number of plots
basesc	initial humus weight
basesn	initial humus nitrogen content
max.ind	maximum number of individuals
nspec	number of species in simulation

Value

ntrees matrix for number of trees for each species

dbh matrix for diameter at breast height for each tree

nogro used to flag slow growing trees

ksprt used to flag trees eligible to sprout

iage matrix for age of each tree

C.mat matrix for data on litter cohorts

ncohrt number of cohorts

tyl total yearly litter

Author(s)

Ann Raiho

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LINKAGES tempe function

Description

Calculates total growing degree days for each year, i

Usage

tempe(temp.vec)

Arguments

temp.vec

mean temperature for each month

Value

degd total growing degree days for each year

Author(s)

Ann Raiho

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