inst/doc/microclimate_inputs.R
In mrke/NicheMapR: R implementation of Niche Mapper software for biophysical modelling
## ---- echo = FALSE------------------------------------------------------------
knitr::opts_chunk$set(
eval = TRUE
)
## ----table1, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
writecsv | - | 0 (off) or 1 (on) | make Fortran program write output as csv files
microdaily | - | 0 (off) or 1 (on) | run in daily mode (initial conditions from previous day)
runshade | - | 0 (off) or 1 (on) | run the model twice, once for each shade level
runmoist | - | 0 (off) or 1 (on) | run soil moisture model
snowmodel | - | 0 (off) or 1 (on) | run the snow model
hourly | - | 0 (off) or 1 (on) | run the model from hourly weather inputs
IR | - | 0 or 1 | longwave radiation algorithm
message | - | 0 or 1 | integrator messages
fail | - | integer | integrator failure count before quitting
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table2, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
doynum | days | positive integer | number of days to run the model
doy | day-of-year | 1-365 | vector of days of year (length must equal doynum)
idayst | - | 1-doynum | start day (usually 1)
ida | - | 1-doynum | end day (usually value of doynum)
HEMIS | - | 1 (N) or 2 (S) | hemisphere to run
ALAT | degrees | 0-90 | latitude (degrees)
AMINUT | dec. minutes | 0-60 | latitude (minutes)
ALONG | degrees | 0-180 | longitude (degrees)
ALMINT | dec. minutes | 0-60 | longitude (minutes)
ALREF | degrees | 0-180 | reference longitude (degrees) for time zone
EC | - | 0.0034 to 0.058 | eccenricity of the earth's orbit (presently 0.0167238)
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table3, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
RUF | m | 0.01-200 | roughness height
Refhyt | m | 0.50-10 | reference height for air temp, wind speed and humidity input data
Usrhyt | m | > 0.005, < Refhyt | local height at which to compute air temp, wind speed and humidity
ZH | m | > 0 (or else not used) | heat transfer roughness height (m)
D0 | m | > 0 | zero plane displacement correction factor (m) used with ZH
Z01 | m | 0 or (> Z02, < ZH2) | 1st segment, roughness height$^1$
Z02 | m | 0 or (> RUF, < Z01) | 2nd segment, roughness height$^1$
ZH1 | m | 0 or (> ZH2, < Refhyt)| 1st segment, height above surface$^1$
ZH2 | m | 0 or (> RUF, < ZH1) | 2nd segment, height above surface$^1$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table4, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
SLES | - | 0-1 | substrate longwave IR emissivity$^1$
REFLS | - | 0-1 | substrate solar reflectivity$^1$
CMH2O | cm | 0.1-2 | precipitable cm H$_2$O in air column
TAI | - | 1-doynum | aerosol optical extinction coefficients$^{1,2}$
solonly | - | 0-1 | flag to do only solar calcs
lamb | - | 0-1 | flag to return wavelength-specific solar radiation output
IUV | - | 0-1 | flag to use gamma function for scattered solar radiation$^{3}$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table5, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
ALTT | m | 0-10,000 | elevation
slope | decimal degrees | 0-90 | slope
azmuth | decimal degrees | 0-360 | aspect (0 is north)
hori | decimal degrees | 0-90 | horizon angles$^1$
VIEWF | - | 0-1 | view factor to sky$^2$
MINSHADES | % | 0-100 | minimum shade$^3$
MAXSHADES | % | 0-100 | maximum shade$^{3,4}$
PCTWETS | % | 0-100 | percentage of substrate unit area that is wet$^{3,5}$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table6, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
DEP | cm | 0-1000 | vector of 10 depths$^1$
ERR | - | >0 | integrator error (typically 1.5-2)
tannul | °C | -80 - +60 | annual mean temperature
spinup | - | 0 or 1 | repeate first day's simulation for steady state?
soilinit | °C | -80 - +60 | initial substrate temperature profile$^1$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table7, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
TIMINS | h | 0-23 | time of minima for air temp, wind, humidity and cloud cover$^1$
TIMAXS | h | 0-23 | time of maxima for air temp, wind, humidity and cloud cover$^2$
TMINN | °C | -80 - +60 | minimum air temperature (at reference height, Refhyt)$^3$
TMAXX | °C | -80 - +60 | maximum air temperature (at reference height, Refhyt)$^3$
RHMINN | % | 0-100 | minimum relative humidity (at reference height, Refhyt)$^3$
RHMAXX | % | 0-100 | maximum relative humidity (at reference height, Refhyt)$^3$
WNMINN | m s$^{-1}$ | 0-100 | minimum wind speed (at reference height, Refhyt)$^3$
WNMAXX | m s$^{-1}$ | 0-100 | maximum wind speed (at reference height, Refhyt)$^3$
CCMINN | % | 0-100 | minimum cloud cover; vector of length = doynum
CCMAXX | % | 0-100 | maximum cloud cover; vector of length = doynum
RAINFALL | mm | 0-2000 | daily total rainfall; vector of length = doynum
tannulrun | °C | -80 - +60 | daily deep soil temperature; vector of length = doynum
moists | decimal % | 0-1 | predefined soil daily moisture profile through time$^4$
TAIRhr | °C | -80 - +60 | hourly air temperature (at reference height, Refhyt)$^5$
RHhr | % | 0-100 | hourly relative humidity (at reference height, Refhyt)$^5$
WNhr | m s$^{-1}$ | 0-100 | hourly wind speed (at reference height, Refhyt)$^5$
CLDhr | % | 0-100 | hourly cloud cover$^5$
SOLRhr | W m$^{2}$ | 0-1367 | hourly solar radiation$^5$
RAINhr | mm | 0-2000 | hourly rainfall$^5$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table8, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | -------------------- | ------------------ | --------------
Numtyps | - | 1-10 | number of substrate types
Nodes$^{1,2}$ | - | 1-10 | nodes where substrate type transitions occur
soilprops[,1]$^{3}$ | Mg m$^{-3}$ | >0 | bulk density (must not exceed mineral density)
soilprops[,2]$^{3}$ | m$^{3}$ m$^{-3}$ | >0 | volumetric water content at saturation$^{4}$
soilprops[,3]$^{3}$ | W m$^{-1}$ K$^{-1}$ | >0 | thermal conductivity
soilprops[,4]$^{3}$ | J kg$^{-1}$ K$^{-1}$ | >0 | specific heat capacity
soilprops[,5]$^{3}$ | Mg m$^{-3}$ | >0 | mineral density
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table9, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | -------------------- | ----------------- | --------------
PE | J kg$^{-1}$ | 0.7-3.7 | air entry water potential; vector of 19 values$^{1}$
KS | kg s m$^{-3}$ | 1 x $10^{-5}$ | saturated conductivity; vector of 19 values$^{1}$
BB | - | 1.7-7.6 | Campbell's 'b' parameter; vector of 19 values$^{1}$
BD | Mg m$^{-3}$ | >0 | bulk density (should be matched to same variable in the soilprops matrix)
DD | Mg m$^{-3}$ | >0 | soil mineral density (should be matched to same variable in the soilprops matrix)
L | m$^{3}$ m$^{-3}$ | 0-90 | root density; vector of 19 values$^{1}$
R1 | m | 0-90 | root radius
RW | m$^{3}$ kg$^{-1}$ s$^{-1}$ | 0-90 | resistance per unit length of root
RL | m$^{3}$ kg$^{-1}$ s$^{-1}$ | 0-90 | resistance per unit length of leaf
PC | J kg$^{-1}$ | 0-90 | critical leaf water potential for stomatal closure
SP | - | >0 | stability parameter for stomatal closure equation
IM | kg | >0 | maximum allowable mass balance error
MAXCOUNT | - | >0 | maximum iterations for mass balance
LAI | - | 0-90 | leaf area index, used to partition traspiration/evaporation from PET
rainmult | - | >0 | rainfall multiplier to impose a catchment
maxpool | mm | >0 | max depth for surface water pooling$^{2}$
evenrain | - | 1 or 2 | even rainfall over 24hrs (1) or one event at midnight (2)
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table10, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'-------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | -------------------- | ------------------ | --------------
snowtemp | °C | -80 - 80 | temperature at which precipitation falls as snow
snowdens | Mg m$^{-3}$ | 0.05-1 | snow density
densfun | - | - | parameters of snow density function$^{1}$
snowmelt | decimal % | 0-1 | proportion of calculated snowmelt that doesn't refreeze
undercatch | - | >=1 | undercatch multipier for converting rainfall to snow
rainmelt | - | 0-2 | parameter for rain melting snow$^{2}$
snowcond | - | >0 | effective thermal conductivity of snow $W/mK$
intercept | - | 0-1 | proportion of snow intercepted by vegetation under shaded conditions
grasshade | - | 0 or 1 | if 1, shade is not present when snow is present (because shade is cast by grass/low veg)
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table11, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'-------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | -------------------- | ------------------ | --------------
tides[1:doynum,1] | - | 0 or 1 | tide in (1) or out(0); vector of length doynum
tides[1:doynum,2] | °C | -80 - 80 | sea water temperature; vector of length doynum
tides[1:doynum,3] | % | - | % surface wetness from wave splash; vector of length doynum
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
mrke/NicheMapR documentation built on April 3, 2024, 10:05 a.m.
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## ---- echo = FALSE------------------------------------------------------------
knitr::opts_chunk$set(
eval = TRUE
)
## ----table1, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
writecsv | - | 0 (off) or 1 (on) | make Fortran program write output as csv files
microdaily | - | 0 (off) or 1 (on) | run in daily mode (initial conditions from previous day)
runshade | - | 0 (off) or 1 (on) | run the model twice, once for each shade level
runmoist | - | 0 (off) or 1 (on) | run soil moisture model
snowmodel | - | 0 (off) or 1 (on) | run the snow model
hourly | - | 0 (off) or 1 (on) | run the model from hourly weather inputs
IR | - | 0 or 1 | longwave radiation algorithm
message | - | 0 or 1 | integrator messages
fail | - | integer | integrator failure count before quitting
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table2, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
doynum | days | positive integer | number of days to run the model
doy | day-of-year | 1-365 | vector of days of year (length must equal doynum)
idayst | - | 1-doynum | start day (usually 1)
ida | - | 1-doynum | end day (usually value of doynum)
HEMIS | - | 1 (N) or 2 (S) | hemisphere to run
ALAT | degrees | 0-90 | latitude (degrees)
AMINUT | dec. minutes | 0-60 | latitude (minutes)
ALONG | degrees | 0-180 | longitude (degrees)
ALMINT | dec. minutes | 0-60 | longitude (minutes)
ALREF | degrees | 0-180 | reference longitude (degrees) for time zone
EC | - | 0.0034 to 0.058 | eccenricity of the earth's orbit (presently 0.0167238)
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table3, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
RUF | m | 0.01-200 | roughness height
Refhyt | m | 0.50-10 | reference height for air temp, wind speed and humidity input data
Usrhyt | m | > 0.005, < Refhyt | local height at which to compute air temp, wind speed and humidity
ZH | m | > 0 (or else not used) | heat transfer roughness height (m)
D0 | m | > 0 | zero plane displacement correction factor (m) used with ZH
Z01 | m | 0 or (> Z02, < ZH2) | 1st segment, roughness height$^1$
Z02 | m | 0 or (> RUF, < Z01) | 2nd segment, roughness height$^1$
ZH1 | m | 0 or (> ZH2, < Refhyt)| 1st segment, height above surface$^1$
ZH2 | m | 0 or (> RUF, < ZH1) | 2nd segment, height above surface$^1$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table4, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
SLES | - | 0-1 | substrate longwave IR emissivity$^1$
REFLS | - | 0-1 | substrate solar reflectivity$^1$
CMH2O | cm | 0.1-2 | precipitable cm H$_2$O in air column
TAI | - | 1-doynum | aerosol optical extinction coefficients$^{1,2}$
solonly | - | 0-1 | flag to do only solar calcs
lamb | - | 0-1 | flag to return wavelength-specific solar radiation output
IUV | - | 0-1 | flag to use gamma function for scattered solar radiation$^{3}$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table5, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
ALTT | m | 0-10,000 | elevation
slope | decimal degrees | 0-90 | slope
azmuth | decimal degrees | 0-360 | aspect (0 is north)
hori | decimal degrees | 0-90 | horizon angles$^1$
VIEWF | - | 0-1 | view factor to sky$^2$
MINSHADES | % | 0-100 | minimum shade$^3$
MAXSHADES | % | 0-100 | maximum shade$^{3,4}$
PCTWETS | % | 0-100 | percentage of substrate unit area that is wet$^{3,5}$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table6, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
DEP | cm | 0-1000 | vector of 10 depths$^1$
ERR | - | >0 | integrator error (typically 1.5-2)
tannul | °C | -80 - +60 | annual mean temperature
spinup | - | 0 or 1 | repeate first day's simulation for steady state?
soilinit | °C | -80 - +60 | initial substrate temperature profile$^1$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table7, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | ----------------- | ----------------- | --------------
TIMINS | h | 0-23 | time of minima for air temp, wind, humidity and cloud cover$^1$
TIMAXS | h | 0-23 | time of maxima for air temp, wind, humidity and cloud cover$^2$
TMINN | °C | -80 - +60 | minimum air temperature (at reference height, Refhyt)$^3$
TMAXX | °C | -80 - +60 | maximum air temperature (at reference height, Refhyt)$^3$
RHMINN | % | 0-100 | minimum relative humidity (at reference height, Refhyt)$^3$
RHMAXX | % | 0-100 | maximum relative humidity (at reference height, Refhyt)$^3$
WNMINN | m s$^{-1}$ | 0-100 | minimum wind speed (at reference height, Refhyt)$^3$
WNMAXX | m s$^{-1}$ | 0-100 | maximum wind speed (at reference height, Refhyt)$^3$
CCMINN | % | 0-100 | minimum cloud cover; vector of length = doynum
CCMAXX | % | 0-100 | maximum cloud cover; vector of length = doynum
RAINFALL | mm | 0-2000 | daily total rainfall; vector of length = doynum
tannulrun | °C | -80 - +60 | daily deep soil temperature; vector of length = doynum
moists | decimal % | 0-1 | predefined soil daily moisture profile through time$^4$
TAIRhr | °C | -80 - +60 | hourly air temperature (at reference height, Refhyt)$^5$
RHhr | % | 0-100 | hourly relative humidity (at reference height, Refhyt)$^5$
WNhr | m s$^{-1}$ | 0-100 | hourly wind speed (at reference height, Refhyt)$^5$
CLDhr | % | 0-100 | hourly cloud cover$^5$
SOLRhr | W m$^{2}$ | 0-1367 | hourly solar radiation$^5$
RAINhr | mm | 0-2000 | hourly rainfall$^5$
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table8, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | -------------------- | ------------------ | --------------
Numtyps | - | 1-10 | number of substrate types
Nodes$^{1,2}$ | - | 1-10 | nodes where substrate type transitions occur
soilprops[,1]$^{3}$ | Mg m$^{-3}$ | >0 | bulk density (must not exceed mineral density)
soilprops[,2]$^{3}$ | m$^{3}$ m$^{-3}$ | >0 | volumetric water content at saturation$^{4}$
soilprops[,3]$^{3}$ | W m$^{-1}$ K$^{-1}$ | >0 | thermal conductivity
soilprops[,4]$^{3}$ | J kg$^{-1}$ K$^{-1}$ | >0 | specific heat capacity
soilprops[,5]$^{3}$ | Mg m$^{-3}$ | >0 | mineral density
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table9, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'--------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | -------------------- | ----------------- | --------------
PE | J kg$^{-1}$ | 0.7-3.7 | air entry water potential; vector of 19 values$^{1}$
KS | kg s m$^{-3}$ | 1 x $10^{-5}$ | saturated conductivity; vector of 19 values$^{1}$
BB | - | 1.7-7.6 | Campbell's 'b' parameter; vector of 19 values$^{1}$
BD | Mg m$^{-3}$ | >0 | bulk density (should be matched to same variable in the soilprops matrix)
DD | Mg m$^{-3}$ | >0 | soil mineral density (should be matched to same variable in the soilprops matrix)
L | m$^{3}$ m$^{-3}$ | 0-90 | root density; vector of 19 values$^{1}$
R1 | m | 0-90 | root radius
RW | m$^{3}$ kg$^{-1}$ s$^{-1}$ | 0-90 | resistance per unit length of root
RL | m$^{3}$ kg$^{-1}$ s$^{-1}$ | 0-90 | resistance per unit length of leaf
PC | J kg$^{-1}$ | 0-90 | critical leaf water potential for stomatal closure
SP | - | >0 | stability parameter for stomatal closure equation
IM | kg | >0 | maximum allowable mass balance error
MAXCOUNT | - | >0 | maximum iterations for mass balance
LAI | - | 0-90 | leaf area index, used to partition traspiration/evaporation from PET
rainmult | - | >0 | rainfall multiplier to impose a catchment
maxpool | mm | >0 | max depth for surface water pooling$^{2}$
evenrain | - | 1 or 2 | even rainfall over 24hrs (1) or one event at midnight (2)
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table10, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'-------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | -------------------- | ------------------ | --------------
snowtemp | °C | -80 - 80 | temperature at which precipitation falls as snow
snowdens | Mg m$^{-3}$ | 0.05-1 | snow density
densfun | - | - | parameters of snow density function$^{1}$
snowmelt | decimal % | 0-1 | proportion of calculated snowmelt that doesn't refreeze
undercatch | - | >=1 | undercatch multipier for converting rainfall to snow
rainmelt | - | 0-2 | parameter for rain melting snow$^{2}$
snowcond | - | >0 | effective thermal conductivity of snow $W/mK$
intercept | - | 0-1 | proportion of snow intercepted by vegetation under shaded conditions
grasshade | - | 0 or 1 | if 1, shade is not present when snow is present (because shade is cast by grass/low veg)
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
## ----table11, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'-------
tabl <- "
*Name* | *Units * | *Allowed Range* | *Description*
------------------------- | -------------------- | ------------------ | --------------
tides[1:doynum,1] | - | 0 or 1 | tide in (1) or out(0); vector of length doynum
tides[1:doynum,2] | °C | -80 - 80 | sea water temperature; vector of length doynum
tides[1:doynum,3] | % | - | % surface wetness from wave splash; vector of length doynum
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
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