runwithNMR: Runs microclimate model in hourly timesteps with NicheMapR
In ilyamaclean/microclimc: Below or above canopy microclimate modelling with R
View source: R/NicheMapRcode.R
runwithNMR R Documentation
Runs microclimate model in hourly timesteps with NicheMapR
Description
This function is a wrapper function for runNMR() and runmodelS() enabling
full microclimate model at any height above or below ground rapidly. NicheMapR is to
compute snowdepths, soil moistures and below-ground soil temperatures. The function
runmodelS is used to compute below or above canopy air temperatures.
Usage
runwithNMR(
climdata,
prec,
vegp,
soilp,
reqhgt,
lat,
long,
altt = 0,
slope = 0,
aspect = 0,
metopen = TRUE,
windhgt = 2,
surfwet = 1,
groundem = 0.95,
ERR = 1.5,
cap = 1,
hori = rep(0, 36),
maxpool = 1000,
rainmult = 1,
SoilMoist_Init = c(0.1, 0.12, 0.15, 0.2, 0.25, 0.3, 0.3, 0.3, 0.3, 0.3),
animal = FALSE
)
Arguments
climdata
data.frame of climate variables needed to run the run the model. The dataset should follow format
of weather()). Times must be in UTC.
prec
vector of hourly or daily precipitation (mm) (see details).
vegp
a list of vegetation parameters as returned by microctools::habitatvars().
soilp
a list of soil parameters as returned by soilinit().
reqhgt
height (m) for which microclimate is needed.
lat
latitude of location (decimal degrees).
long
longitude of location (decimal degrees).
altt
elevation of location (m).
slope
slope of ground surface (decimal degrees).
aspect
aspect of ground surface (decimal degrees, 0 = north).
metopen
optional logical indicating whether the wind measurement used as an input to
the model is from a nearby weather station located in open ground (TRUE) or above the canopy
for which temperatures are modelled (FALSE - see details)
windhgt
height above ground of wind measurement. If metopen is FALSE, must be above
canopy.
surfwet
proportion of leaf surface acting as free water surface.
groundem
thermal emissivity of ground layer.
ERR
Integrator error tolerance for soil temperature calculations.
cap
Is organic cap present on soil surface? (1 = Yes, 0 = No).
hori
Horizon angles (degrees), from 0 degrees azimuth (north) clockwise in 10 degree intervals.
maxpool
Max depth for water pooling on the surface (mm), to account for runoff.
rainmult
Rain multiplier for surface soil moisture (used to induce runon).
SoilMoist_Init
Initial volumetric soil water content at each soil node (m^3/m^3)
Details
This is a wrapper function for runmodelS() and runNMR() that allows fairly rapid
calaulation of microclimatic conditions below ground and/or above canopy. It uses the NicheMapR package
to calculate soil moisture-dependent soil temperatures, treating the vegetation canopy as a
single layer and then calculates air and leaf temperatures,air humidity and radiation using
runmodelS. Precipitation values are needed for computation of soil moisture and can either be
supplied as a vector of hourly values (must have identical number of values as in climdata) or
daily values (climdata must contain climate for entire days). It compares the length of the vector
to climdata to determine whether values are daily or hourly. In this function constant soil
poperties are are assumed throughout the soil profile. For more flexible implementation, runNMR()
and runmodelS() can be run seperately.
Value
a list of two objects:
a data.frame of microclimate variables for height reqhgt as returned by runmodelS()
a list of NicheMapR outputs as returned by runNMR()
See Also
runmodelS(), runNMR()
Examples
require(NicheMapR)
# ====================================================================== #
# ~~~~~~~~~~~~~~~ Run model using inbuilt weather datasets ~~~~~~~~~~~~~ #
# ====================================================================== #
tme<-as.POSIXlt(weather$obs_time,tz="UTC")
vegp <- habitatvars(4, 50.2178, -5.32656, tme, m = 10) # Decidious broadleaf forest
soilp<- soilinit("Loam")
climrun <- runwithNMR(weather,dailyprecip,vegp,soilp,1,50.2178,-5.32656)
# ====================================================================== #
# ~~~~~~~~~~~~~~~ Extract and view data from outputs ~~~~~~~~~~~~~~~~~~~ #
# ====================================================================== #
metout<-climrun$metout
nmrout<-climrun$nmrout
soiltemps<-as.data.frame(nmrout$soil)
head(metout)
head(soiltemps)
head(nmrout$soilmoist)
head(nmrout$sunsnow)
head(nmrout$plant)
# ====================================================================== #
# ~~~~~~~~~~~~~~~ Plot soil and air temperatures ~~~~~~~~~~~~~~~~~~~~~~~ #
# ====================================================================== #
tsoil1<-soiltemps$D2.5cm
tsoil2<-soiltemps$D50cm
tair<-metout$Tloc
tref<-metout$Tref
tleaf<-metout$tleaf
Month<-as.POSIXct(metout$obs_time,tz="UTC")
tmn<-min(tsoil1,tsoil2,tair,tref,tleaf)
tmx<-max(tsoil1,tsoil2,tair,tref,tleaf)
par(mfrow=c(2,1))
# Air
plot(tref~Month,type="l",col=rgb(0,0,0,0.3),ylab="Temperature",ylim=c(tmn,tmx))
par(new=T)
plot(tleaf~Month,type="l",col=rgb(0,1,0,0.3),xlab="",ylab="",ylim=c(tmn,tmx))
par(new=T)
plot(tair~Month,type="l",col=rgb(1,0,0,0.3),xlab="",ylab="",ylim=c(tmn,tmx))
# Soil
plot(tref~Month,type="l",col=rgb(0,0,0,0.5),ylab="Temperature",ylim=c(tmn,tmx))
par(new=T)
plot(tsoil1~Month,type="l",col="red",xlab="",ylab="",ylim=c(tmn,tmx))
par(new=T)
plot(tsoil2~Month,type="l",col="blue",lwd=2,xlab="",ylab="",ylim=c(tmn,tmx))
# ====================================================================== #
# ~~~~~~~~~~~~~~~ Plot data by monthly mean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# ====================================================================== #
tme<-as.POSIXlt(metout$obs_time,tz="UTC")
tsoil1m<-aggregate(tsoil1,by=list(tme$mon),mean)$x
tsoil2m<-aggregate(tsoil2,by=list(tme$mon),mean)$x
tairm<-aggregate(tair,by=list(tme$mon),mean)$x
trefm<-aggregate(tref,by=list(tme$mon),mean)$x
tleafm<-aggregate(tleaf,by=list(tme$mon),mean)$x
tmn<-min(tsoil1m,tsoil2m,tairm,trefm,tleafm)
tmx<-max(tsoil1m,tsoil2m,tairm,trefm,tleafm)
Month<-c(1:12)
# Air
par(mfrow=c(2,1))
plot(trefm~Month,type="l",lwd=2,col="darkgray",ylab="Temperature",ylim=c(tmn,tmx))
par(new=T)
plot(tleafm~Month,type="l",lwd=2,col="darkgreen",xlab="",ylab="",ylim=c(tmn,tmx))
par(new=T)
plot(tairm~Month,type="l",lwd=2,col="red",xlab="",ylab="",ylim=c(tmn,tmx))
plot(trefm~Month,type="l",lwd=2,col="darkgray",ylab="Temperature",ylim=c(tmn,tmx))
par(new=T)
plot(tsoil1m~Month,type="l",lwd=2,col="red",xlab="",ylab="",ylim=c(tmn,tmx))
par(new=T)
plot(tsoil2m~Month,type="l",lwd=2,col="blue",xlab="",ylab="",ylim=c(tmn,tmx))
# ====================================================================== #
ilyamaclean/microclimc documentation built on July 28, 2023, 1:40 a.m.
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View source: R/NicheMapRcode.R
| runwithNMR | R Documentation |
Runs microclimate model in hourly timesteps with NicheMapR
Description
This function is a wrapper function for runNMR() and runmodelS() enabling
full microclimate model at any height above or below ground rapidly. NicheMapR is to
compute snowdepths, soil moistures and below-ground soil temperatures. The function
runmodelS is used to compute below or above canopy air temperatures.
Usage
runwithNMR(
climdata,
prec,
vegp,
soilp,
reqhgt,
lat,
long,
altt = 0,
slope = 0,
aspect = 0,
metopen = TRUE,
windhgt = 2,
surfwet = 1,
groundem = 0.95,
ERR = 1.5,
cap = 1,
hori = rep(0, 36),
maxpool = 1000,
rainmult = 1,
SoilMoist_Init = c(0.1, 0.12, 0.15, 0.2, 0.25, 0.3, 0.3, 0.3, 0.3, 0.3),
animal = FALSE
)
Arguments
climdata |
data.frame of climate variables needed to run the run the model. The dataset should follow format
of |
prec |
vector of hourly or daily precipitation (mm) (see details). |
vegp |
a list of vegetation parameters as returned by |
soilp |
a list of soil parameters as returned by |
reqhgt |
height (m) for which microclimate is needed. |
lat |
latitude of location (decimal degrees). |
long |
longitude of location (decimal degrees). |
altt |
elevation of location (m). |
slope |
slope of ground surface (decimal degrees). |
aspect |
aspect of ground surface (decimal degrees, 0 = north). |
metopen |
optional logical indicating whether the wind measurement used as an input to the model is from a nearby weather station located in open ground (TRUE) or above the canopy for which temperatures are modelled (FALSE - see details) |
windhgt |
height above ground of wind measurement. If |
surfwet |
proportion of leaf surface acting as free water surface. |
groundem |
thermal emissivity of ground layer. |
ERR |
Integrator error tolerance for soil temperature calculations. |
cap |
Is organic cap present on soil surface? (1 = Yes, 0 = No). |
hori |
Horizon angles (degrees), from 0 degrees azimuth (north) clockwise in 10 degree intervals. |
maxpool |
Max depth for water pooling on the surface (mm), to account for runoff. |
rainmult |
Rain multiplier for surface soil moisture (used to induce runon). |
SoilMoist_Init |
Initial volumetric soil water content at each soil node (m^3/m^3) |
Details
This is a wrapper function for runmodelS() and runNMR() that allows fairly rapid
calaulation of microclimatic conditions below ground and/or above canopy. It uses the NicheMapR package
to calculate soil moisture-dependent soil temperatures, treating the vegetation canopy as a
single layer and then calculates air and leaf temperatures,air humidity and radiation using
runmodelS. Precipitation values are needed for computation of soil moisture and can either be
supplied as a vector of hourly values (must have identical number of values as in climdata) or
daily values (climdata must contain climate for entire days). It compares the length of the vector
to climdata to determine whether values are daily or hourly. In this function constant soil
poperties are are assumed throughout the soil profile. For more flexible implementation, runNMR()
and runmodelS() can be run seperately.
Value
a list of two objects:
a data.frame of microclimate variables for height reqhgt as returned by runmodelS()
a list of NicheMapR outputs as returned by runNMR()
See Also
runmodelS(), runNMR()
Examples
require(NicheMapR)
# ====================================================================== #
# ~~~~~~~~~~~~~~~ Run model using inbuilt weather datasets ~~~~~~~~~~~~~ #
# ====================================================================== #
tme<-as.POSIXlt(weather$obs_time,tz="UTC")
vegp <- habitatvars(4, 50.2178, -5.32656, tme, m = 10) # Decidious broadleaf forest
soilp<- soilinit("Loam")
climrun <- runwithNMR(weather,dailyprecip,vegp,soilp,1,50.2178,-5.32656)
# ====================================================================== #
# ~~~~~~~~~~~~~~~ Extract and view data from outputs ~~~~~~~~~~~~~~~~~~~ #
# ====================================================================== #
metout<-climrun$metout
nmrout<-climrun$nmrout
soiltemps<-as.data.frame(nmrout$soil)
head(metout)
head(soiltemps)
head(nmrout$soilmoist)
head(nmrout$sunsnow)
head(nmrout$plant)
# ====================================================================== #
# ~~~~~~~~~~~~~~~ Plot soil and air temperatures ~~~~~~~~~~~~~~~~~~~~~~~ #
# ====================================================================== #
tsoil1<-soiltemps$D2.5cm
tsoil2<-soiltemps$D50cm
tair<-metout$Tloc
tref<-metout$Tref
tleaf<-metout$tleaf
Month<-as.POSIXct(metout$obs_time,tz="UTC")
tmn<-min(tsoil1,tsoil2,tair,tref,tleaf)
tmx<-max(tsoil1,tsoil2,tair,tref,tleaf)
par(mfrow=c(2,1))
# Air
plot(tref~Month,type="l",col=rgb(0,0,0,0.3),ylab="Temperature",ylim=c(tmn,tmx))
par(new=T)
plot(tleaf~Month,type="l",col=rgb(0,1,0,0.3),xlab="",ylab="",ylim=c(tmn,tmx))
par(new=T)
plot(tair~Month,type="l",col=rgb(1,0,0,0.3),xlab="",ylab="",ylim=c(tmn,tmx))
# Soil
plot(tref~Month,type="l",col=rgb(0,0,0,0.5),ylab="Temperature",ylim=c(tmn,tmx))
par(new=T)
plot(tsoil1~Month,type="l",col="red",xlab="",ylab="",ylim=c(tmn,tmx))
par(new=T)
plot(tsoil2~Month,type="l",col="blue",lwd=2,xlab="",ylab="",ylim=c(tmn,tmx))
# ====================================================================== #
# ~~~~~~~~~~~~~~~ Plot data by monthly mean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# ====================================================================== #
tme<-as.POSIXlt(metout$obs_time,tz="UTC")
tsoil1m<-aggregate(tsoil1,by=list(tme$mon),mean)$x
tsoil2m<-aggregate(tsoil2,by=list(tme$mon),mean)$x
tairm<-aggregate(tair,by=list(tme$mon),mean)$x
trefm<-aggregate(tref,by=list(tme$mon),mean)$x
tleafm<-aggregate(tleaf,by=list(tme$mon),mean)$x
tmn<-min(tsoil1m,tsoil2m,tairm,trefm,tleafm)
tmx<-max(tsoil1m,tsoil2m,tairm,trefm,tleafm)
Month<-c(1:12)
# Air
par(mfrow=c(2,1))
plot(trefm~Month,type="l",lwd=2,col="darkgray",ylab="Temperature",ylim=c(tmn,tmx))
par(new=T)
plot(tleafm~Month,type="l",lwd=2,col="darkgreen",xlab="",ylab="",ylim=c(tmn,tmx))
par(new=T)
plot(tairm~Month,type="l",lwd=2,col="red",xlab="",ylab="",ylim=c(tmn,tmx))
plot(trefm~Month,type="l",lwd=2,col="darkgray",ylab="Temperature",ylim=c(tmn,tmx))
par(new=T)
plot(tsoil1m~Month,type="l",lwd=2,col="red",xlab="",ylab="",ylim=c(tmn,tmx))
par(new=T)
plot(tsoil2m~Month,type="l",lwd=2,col="blue",xlab="",ylab="",ylim=c(tmn,tmx))
# ====================================================================== #
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