Rutils/globdims.r
In manfredo89/ED2io: Manages Input/Output for Ecosystem Demography 2 Model
#----- Some dimensions based on ED-2.2 default. -------------------------------------------#
npft <<- 17 # Number of plant functional types
nlu <<- 6 # Number of land use types.
nstyp <<- 17 # Number of default soil types
#------------------------------------------------------------------------------------------#
#----- Radiation thresholds. --------------------------------------------------------------#
cosz.min <<- 0.03 # cos(89*pi/180) # Minimum cosine of zenith angle
cosz.highsun <<- cos(84*pi/180) # Zenith angle to not be called sunrise or sunset
cosz.twilight <<- cos(96*pi/180) # Cosine of the end of civil twilight
fvis.beam.def <<- 0.43
fnir.beam.def <<- 1.0 - fvis.beam.def
fvis.diff.def <<- 0.52
fnir.diff.def <<- 1.0 - fvis.diff.def
phap.min <<- 25 # Minimum incoming radiation to be considered
# daytime
#------------------------------------------------------------------------------------------#
#----- Minimum R2 that we consider meaningful. --------------------------------------------#
r2.min <<- 0.36
#----- Typical p-value below which we reject the NULL hypothesis. -------------------------#
pval.max <<- 0.05
#----- p-value below which we reject the NULL hypothesis for u* filters. ------------------#
pval.ustar <<- 0.05
#------------------------------------------------------------------------------------------#
#----- Minimum pixel resolution which would allow MacArthur-Horn corrections. -------------#
min.mh.pixres <<- 5 # metres
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Tolerance for root-finding methods. #
#------------------------------------------------------------------------------------------#
toler <<- 1.e-6 # Tolerance for the root-finder algorithms
maxfpo <<- 60 # Maximum number of Regula-Falsi iterations
maxit <<- 150 # Maximum number of iterations in general
#------------------------------------------------------------------------------------------#
#----- Colours for months. ----------------------------------------------------------------#
month.at <<- (sequence(12) - 0.5 ) / 12
month.off <<- -1.5/12
month.cols <<- hsv( h = month.at
, s = 0.75 + 0.25 * cos((month.at - month.off) * 2 * pi)
, v = 0.75 + 0.25 * sin((month.at - month.off) * 2 * pi)
)#end hsv
#------------------------------------------------------------------------------------------#
#------ Define the colours and labels for IGBP land use maps. -----------------------------#
igbp.col <<- c( H2O = RGB( 0, 20, 82)
, ENF = RGB( 0, 100, 164)
, EBF = RGB( 0, 63, 0)
, DNF = RGB( 85, 192, 255)
, DBF = RGB( 97, 255, 96)
, MXF = RGB( 0, 156, 76)
, CSH = RGB( 255, 105, 0)
, OSH = RGB( 207, 151, 114)
, WSV = RGB( 72, 144, 0)
, SAV = RGB( 150, 255, 40)
, GSL = RGB( 233, 198, 9)
, PWL = RGB( 69, 35, 232)
, CRL = RGB( 166, 131, 0)
, URB = RGB( 96, 96, 96)
, CNV = RGB( 115, 158, 80)
, ICE = RGB( 0, 222, 255)
, BRN = RGB( 144, 3, 2)
, UND = RGB( 222, 222, 222)
)#end igbp.col
igbp.leg <<- names(igbp.col)
igbp.val <<- seq_along(igbp.col)-1
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Colours, labels, and conversion to simplified TerraClass categories. #
#------------------------------------------------------------------------------------------#
tc2012.col <<- c( H2O = RGB( 12, 84, 170) # 0 - Water
, FOR = RGB( 0, 79, 0) # 1 - Forest
, SCD = RGB( 0, 177, 0) # 2 - Secondary growth
, RFR = RGB( 58, 204, 0) # 3 - Reforestation
, MXL = RGB( 155, 155, 255) # 4 - Mixed landscape
, NFR = RGB( 255, 175, 0) # 5 - Non-forest
, PST = RGB( 243, 240, 96) # 6 - Pasture
, CRL = RGB( 176, 147, 81) # 7 - Cropland
, D12 = RGB( 205, 85, 0) # 8 - Deforestation 2012
, MIN = RGB( 148, 33, 147) # 9 - Mining
, URB = RGB( 113, 40, 197) # 10 - Urban
, UND = RGB( 222, 222, 222) # 11 - Undefined
)#end tc2012.col
tc2012.leg <<- names(tc2012.col)
tc2012.desc <<- c("Water","Forest","Secondary Growth","Reforestation"
,"Mixed Landscape","Non-forest","Pasture","Cropland"
,"Deforestation 2012","Mining","Urban","Unclassified")
tc2012.val <<- seq_along(tc2012.col)-1
tc2012.t2c <<- c(7,11,10,8,1,0,9,4,5,5,6,6,6,3,2,2)
#------------------------------------------------------------------------------------------#
#------ Define the colours and labels for ASPRS (LAS/LiDAR) classes. ----------------------#
asprs.col <<- c( CNC = RGB( 222, 222, 222)
, UND = RGB( 202, 202, 202)
, GND = RGB( 144, 3, 2)
, LVG = RGB( 166, 131, 0)
, MVG = RGB( 0, 100, 164)
, HVG = RGB( 0, 63, 0)
, BLD = RGB( 96, 96, 96)
, MKP = RGB( 233, 198, 9)
, H2O = RGB( 0, 20, 82)
, RSV = RGB( 192, 192, 192)
, R11 = RGB( 192, 192, 192)
, OLP = RGB( 0, 222, 255)
)#end asprs.col
asprs.leg <<- names(asprs.col)
asprs.val <<- seq_along(asprs.col)-1
#------------------------------------------------------------------------------------------#
#----- Define some default legend colours and names. --------------------------------------#
lunames <<- c("Agricultural","Plantation","Tree fall"
,"Burnt","Abandoned","Logged","Total")
lucols <<- c("#E65C17","#2996CC","#306614","#990F0F","#2996CC","#A3CC52",all.colour)
distnames <<- c("AGR->AGR" ,"FPL->AGR" ,"TFL->AGR","BRN->AGR","ABN->AGR","LOG->AGR"
,"AGR->FPL" ,"FPL->FPL" ,"TFL->FPL","BRN->FPL","ABN->FPL","LOG->FPL"
,"AGR->TFL" ,"FPL->TFL" ,"TFL->TFL","BRN->TFL","ABN->TFL","LOG->TFL"
,"AGR->BRN" ,"FPL->BRN" ,"TFL->BRN","BRN->BRN","ABN->BRN","LOG->BRN"
,"AGR->ABN" ,"FPL->ABN" ,"TFL->ABN","BRN->ABN","ABN->ABN","LOG->ABN"
,"AGR->LOG" ,"FPL->LOG" ,"TFL->LOG","BRN->LOG","ABN->LOG","LOG->LOG")
distcols <<- c("#66005A","#A80095","#E500CB","#FF4CEA","#FF998F","#FFCCF9"
,"#005A66","#00889A","#00B3CB","#00D3EF","#96F3FF","#CBF9FF"
,"#DEDEDE","#DEDEDE","#596500","#A0B310","#D1ED00","#F2FF91"
,"#DEDEDE","#DEDEDE","#983A2E","#D64F3D","#F29C91","#FFD1CB"
,"#007F0F","#00BE16","#DEDEDE","#DEDEDE","#DEDEDE","#DEDEDE"
,"#DEDEDE","#DEDEDE","#4C3FB2","#6E5AFF","#B0A6FF","#DED9FF")
#------------------------------------------------------------------------------------------#
#----- Growth respiration factor (to estimate when the actual variable is not there). -----#
growth.resp.fac <<- c(rep(0.333,times=5),rep(0.4503,times=3),rep(0,times=3)
,rep(0.333,times=4))
#------------------------------------------------------------------------------------------#
#----- fswh is the FSW that plants experience and they are happy (wilting point = 0). -----#
fswh <<- 0.99
#------------------------------------------------------------------------------------------#
#----- Years for which we have eddy flux tower. -------------------------------------------#
eft.year <<- c( 1998, 1999, 2000, 2001, 2002, 2003, 2004
, 2005, 2006, 2007, 2008, 2009, 2010, 2011
, 2012, 2013)
eft.pch <<- c( 0, 1, 6, 3, 4, 5, 13
, 15, 16, 17, 18, 9, 8, 7
, 14, 2)
eft.col <<- c("#7D6E93","#B49ED2","#39025D","#520485","#042E88","#0742C3","#00480E"
,"#006715","#31B223","#46FF32","#AB8C3D","#F5C858","#B23C00","#FF5700"
,"#70000E","#A00014")
#------------------------------------------------------------------------------------------#
#----- Standard colours and names for soil classes. ---------------------------------------#
stext.cols <<- c("gold","chartreuse","limegreen","darkgreen","purple3"
,"deepskyblue","aquamarine","slateblue2","darkorange3","sienna"
,"firebrick","grey61","grey29","orchid","olivedrab","goldenrod"
,"steelblue")
stext.names <<- c("Sand","Loamy Sand","Sandy loam","Silt loam","Loam","Sandy clay loam"
,"Silty clay loam","Clayey loam","Sandy clay","Silty clay","Clay","Peat"
,"Bedrock","Silt","Heavy clay","Clayey sand","Clayey silt")
stext.acron <<- c("Sa","LSa","SaL","SiL","L","SaCL","SiCL","CL"
,"SaC","SiC","C","Pe","BR","Si","CC","CSa","CSi")
#------------------------------------------------------------------------------------------#
#==========================================================================================#
#==========================================================================================#
# Patch information for POV-Ray. #
#------------------------------------------------------------------------------------------#
pov.dbh.min <<- 5 # Minimum DBH to be plotted
pov.patch.xmax <<- 16 # Size of each sub-plot in the x direction [m]
pov.patch.ymax <<- 16 # Size of each sub-plot in the y direction [m]
pov.nx.patch <<- 25 # Number of sub-plots in each x transect
pov.ny.patch <<- 25 # Number of sub-plots in each y transect
pov.nxy.patch <<- pov.nx.patch * pov.ny.patch
pov.total.area <<- pov.nxy.patch * pov.patch.xmax * pov.patch.ymax
pov.x0 <<- rep( x = -200 + seq(from=0,to=pov.nx.patch-1) * pov.patch.xmax
, times = pov.ny.patch
)#end rep
pov.y0 <<- rep( x = -200 + seq(from=0,to=pov.ny.patch-1) * pov.patch.ymax
, each = pov.nx.patch
)#end rep
#------------------------------------------------------------------------------------------#
#==========================================================================================#
#==========================================================================================#
# Census-related thresholds. If the script has different values, ignore these and #
# use whatever the main script says. #
#------------------------------------------------------------------------------------------#
#----- Minimum height to be considered for "ground-based observations". -------------------#
if ( "census.height.min" %in% ls()){
census.height.min <<- census.height.min
}else{
census.height.min <<- 1.5
}#end if
#----- Minimum DBH to be considered for "ground-based observations". ----------------------#
if ( "census.dbh.min" %in% ls()){
census.dbh.min <<- census.dbh.min
}else{
census.dbh.min <<- 10.
}#end if
#----- Minimum DBH to be considered for "ground-based observations". ----------------------#
if ( "recruit.dbh.min" %in% ls()){
recruit.dbh.min <<- recruit.dbh.min
}else{
recruit.dbh.min <<- 0.16
}#end if
#------------------------------------------------------------------------------------------#
#==========================================================================================#
#==========================================================================================#
# Define which DBH classes to use based on the DBH flag. #
#------------------------------------------------------------------------------------------#
if ("idbh.type" %in% ls()){
idbh.type <<- idbh.type
}else{
idbh.type <<- 1
}#end if
if (idbh.type == 1){
ndbh <<- 11
ddbh <<- 10
classdbh <<- seq(from=0,to=(ndbh-1)*ddbh,by=ddbh)
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhlabel <<- "11_szclss"
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "purple3", "mediumpurple1", "royalblue4"
, "steelblue3", "deepskyblue", "#004E00"
, "chartreuse3", "olivedrab3", "lightgoldenrod3"
, "yellow3", "darkorange1", "firebrick"
, all.colour
)#end c
}else if (idbh.type == 2){
ndbh <<- 5
classdbh <<- c(0,10,20,35,55)
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhlabel <<- "05_szclss"
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "royalblue3", "chartreuse3" , "yellow3"
, "darkorange1", "firebrick" , all.colour
)#end c
}else if (idbh.type == 3){
ndbh <<- 4
classdbh <<- c(0,10,35,55)
dbhlabel <<- "04_szclss"
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "#3B24B3", "#2996CC"
, "#FF9466", "#990F0F", all.colour
)#end c
}else if (idbh.type == 4){
ndbh <<- 6
classdbh <<- c(0,2,10,20,45,70)
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhlabel <<- "06_szclss"
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "purple3", "royalblue3", "chartreuse3"
, "yellow3", "darkorange1", "firebrick"
, all.colour
)#end c
}else if (idbh.type == 5){
ndbh <<- 17
classdbh <<- c(0,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,20)
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhlabel <<- "07_szclss"
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "purple3", "royalblue3", "chartreuse3"
, "yellow3", "darkorange1", "firebrick"
, all.colour
)#end c
}else{
cat(" In globdims.r:","\n")
cat(" IDBH.TYPE = ",idbh.type,"\n")
stop(" Invalid IDBH.TYPE, it must be between 1 and 5 (feel free to add more options.")
}#end if
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
# Define which height classes to use based on the DBH flag. #
#------------------------------------------------------------------------------------------#
if ("ihgt.type" %in% ls()){
ihgt.type <<- ihgt.type
}else{
ihgt.type <<- 1
}#end if
if (ihgt.type == 1){
nhgt <<- 8
classhgt <<- c(0,5,10,15,20,25,30,35)-0.001
roundhgt <<- round(classhgt,0)
breakhgt <<- c(-Inf,classhgt[-1],Inf)
hgtlabel <<- "08_htclss"
hgtkeys <<- paste(classhgt,"-",c(roundhgt[-1],Inf),sep="")
hgtnames <<- paste( c("<",paste(roundhgt[-c(1,nhgt)],"-",sep=""),">")
, c(roundhgt[-1],roundhgt[nhgt]),"m"
, sep=""
)#end paste
hgtcols <<- c( "slateblue4", "steelblue3", "deepskyblue"
, "#004E00", "chartreuse3", "lightgoldenrod3"
, "darkorange1", "firebrick", all.colour
)#end c
}else if (ihgt.type == 2){
nhgt <<- 13
classhgt <<- c(0,1,4,7,10,13,16,19,22,25,28,31,34)
hgtlabel <<- "13_szclss"
breakhgt <<- c(-Inf,classhgt[-1],Inf)
hgtkeys <<- paste(classhgt,"-",c(classhgt[-1],Inf),sep="")
hgtnames <<- paste( c("<",paste(classhgt[-c(1,nhgt)],"-",sep=""),">")
, c(classhgt[-1],classhgt[nhgt]),"cm"
, sep=""
)#end paste
hgtcols <<- c( "purple3", "mediumpurple1", "royalblue4"
, "steelblue3", "deepskyblue", "#004E00"
, "chartreuse3", "olivedrab3", "lightgoldenrod3"
, "yellow3", "darkorange1", "red3"
, "firebrick4", all.colour
)#end c
}else{
cat(" In globdims.r:","\n")
cat(" IHGT.TYPE = ",ihgt.type,"\n")
stop(" Invalid IHGT.TYPE, it must be between 1 and 2 (feel free to add more options.")
}#end if
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
# Define which height classes to use based on the DBH flag. #
#------------------------------------------------------------------------------------------#
if ("isld.type" %in% ls()){
isld.type <<- isld.type
}else{
isld.type <<- 1
}#end if
if (isld.type == 1){
nsld <<- 12
belowsld <<- c(-6.0,-5.5,-5.0,-4.5,-4.0,-3.5,-3.0,-2.5,-2.0,-1.5,-1.0,-0.5)
abovesld <<- c(belowsld[-1],0)
thicksld <<- diff(c(belowsld,0))
roundsld <<- round(belowsld,2)
breaksld <<- c(-Inf,belowsld[-1],Inf)
sldlabel <<- "cc_sdclss"
sldkeys <<- paste(roundsld,"-",c(roundsld[-1],0),sep="")
sldnames <<- paste( c("<",paste(roundsld[-c(1,nsld)],"-",sep=""),">")
, c(roundsld[-1],roundsld[nhgt]),"m"
, sep=""
)#end paste
sldcols <<- c( "purple3", "mediumpurple1", "royalblue4"
, "steelblue3", "deepskyblue", "#004E00"
, "chartreuse3", "olivedrab3", "lightgoldenrod3"
, "yellow3", "darkorange1", "red3"
, "firebrick4", all.colour
)#end c
}else{
cat(" In globdims.r:","\n")
cat(" ISLD.TYPE = ",isld.type,"\n")
stop(" Invalid ISLD.TYPE, it must be C or H (feel free to add more options.")
}#end if
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
# Define default weighting factor for carbon balance. #
#------------------------------------------------------------------------------------------#
if ("klight" %in% ls()){
klight <<- klight
}else{
klight <<- 0.8
}#end if
#==========================================================================================#
#==========================================================================================#
manfredo89/ED2io documentation built on May 21, 2019, 11:24 a.m.
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#----- Some dimensions based on ED-2.2 default. -------------------------------------------#
npft <<- 17 # Number of plant functional types
nlu <<- 6 # Number of land use types.
nstyp <<- 17 # Number of default soil types
#------------------------------------------------------------------------------------------#
#----- Radiation thresholds. --------------------------------------------------------------#
cosz.min <<- 0.03 # cos(89*pi/180) # Minimum cosine of zenith angle
cosz.highsun <<- cos(84*pi/180) # Zenith angle to not be called sunrise or sunset
cosz.twilight <<- cos(96*pi/180) # Cosine of the end of civil twilight
fvis.beam.def <<- 0.43
fnir.beam.def <<- 1.0 - fvis.beam.def
fvis.diff.def <<- 0.52
fnir.diff.def <<- 1.0 - fvis.diff.def
phap.min <<- 25 # Minimum incoming radiation to be considered
# daytime
#------------------------------------------------------------------------------------------#
#----- Minimum R2 that we consider meaningful. --------------------------------------------#
r2.min <<- 0.36
#----- Typical p-value below which we reject the NULL hypothesis. -------------------------#
pval.max <<- 0.05
#----- p-value below which we reject the NULL hypothesis for u* filters. ------------------#
pval.ustar <<- 0.05
#------------------------------------------------------------------------------------------#
#----- Minimum pixel resolution which would allow MacArthur-Horn corrections. -------------#
min.mh.pixres <<- 5 # metres
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Tolerance for root-finding methods. #
#------------------------------------------------------------------------------------------#
toler <<- 1.e-6 # Tolerance for the root-finder algorithms
maxfpo <<- 60 # Maximum number of Regula-Falsi iterations
maxit <<- 150 # Maximum number of iterations in general
#------------------------------------------------------------------------------------------#
#----- Colours for months. ----------------------------------------------------------------#
month.at <<- (sequence(12) - 0.5 ) / 12
month.off <<- -1.5/12
month.cols <<- hsv( h = month.at
, s = 0.75 + 0.25 * cos((month.at - month.off) * 2 * pi)
, v = 0.75 + 0.25 * sin((month.at - month.off) * 2 * pi)
)#end hsv
#------------------------------------------------------------------------------------------#
#------ Define the colours and labels for IGBP land use maps. -----------------------------#
igbp.col <<- c( H2O = RGB( 0, 20, 82)
, ENF = RGB( 0, 100, 164)
, EBF = RGB( 0, 63, 0)
, DNF = RGB( 85, 192, 255)
, DBF = RGB( 97, 255, 96)
, MXF = RGB( 0, 156, 76)
, CSH = RGB( 255, 105, 0)
, OSH = RGB( 207, 151, 114)
, WSV = RGB( 72, 144, 0)
, SAV = RGB( 150, 255, 40)
, GSL = RGB( 233, 198, 9)
, PWL = RGB( 69, 35, 232)
, CRL = RGB( 166, 131, 0)
, URB = RGB( 96, 96, 96)
, CNV = RGB( 115, 158, 80)
, ICE = RGB( 0, 222, 255)
, BRN = RGB( 144, 3, 2)
, UND = RGB( 222, 222, 222)
)#end igbp.col
igbp.leg <<- names(igbp.col)
igbp.val <<- seq_along(igbp.col)-1
#------------------------------------------------------------------------------------------#
#------------------------------------------------------------------------------------------#
# Colours, labels, and conversion to simplified TerraClass categories. #
#------------------------------------------------------------------------------------------#
tc2012.col <<- c( H2O = RGB( 12, 84, 170) # 0 - Water
, FOR = RGB( 0, 79, 0) # 1 - Forest
, SCD = RGB( 0, 177, 0) # 2 - Secondary growth
, RFR = RGB( 58, 204, 0) # 3 - Reforestation
, MXL = RGB( 155, 155, 255) # 4 - Mixed landscape
, NFR = RGB( 255, 175, 0) # 5 - Non-forest
, PST = RGB( 243, 240, 96) # 6 - Pasture
, CRL = RGB( 176, 147, 81) # 7 - Cropland
, D12 = RGB( 205, 85, 0) # 8 - Deforestation 2012
, MIN = RGB( 148, 33, 147) # 9 - Mining
, URB = RGB( 113, 40, 197) # 10 - Urban
, UND = RGB( 222, 222, 222) # 11 - Undefined
)#end tc2012.col
tc2012.leg <<- names(tc2012.col)
tc2012.desc <<- c("Water","Forest","Secondary Growth","Reforestation"
,"Mixed Landscape","Non-forest","Pasture","Cropland"
,"Deforestation 2012","Mining","Urban","Unclassified")
tc2012.val <<- seq_along(tc2012.col)-1
tc2012.t2c <<- c(7,11,10,8,1,0,9,4,5,5,6,6,6,3,2,2)
#------------------------------------------------------------------------------------------#
#------ Define the colours and labels for ASPRS (LAS/LiDAR) classes. ----------------------#
asprs.col <<- c( CNC = RGB( 222, 222, 222)
, UND = RGB( 202, 202, 202)
, GND = RGB( 144, 3, 2)
, LVG = RGB( 166, 131, 0)
, MVG = RGB( 0, 100, 164)
, HVG = RGB( 0, 63, 0)
, BLD = RGB( 96, 96, 96)
, MKP = RGB( 233, 198, 9)
, H2O = RGB( 0, 20, 82)
, RSV = RGB( 192, 192, 192)
, R11 = RGB( 192, 192, 192)
, OLP = RGB( 0, 222, 255)
)#end asprs.col
asprs.leg <<- names(asprs.col)
asprs.val <<- seq_along(asprs.col)-1
#------------------------------------------------------------------------------------------#
#----- Define some default legend colours and names. --------------------------------------#
lunames <<- c("Agricultural","Plantation","Tree fall"
,"Burnt","Abandoned","Logged","Total")
lucols <<- c("#E65C17","#2996CC","#306614","#990F0F","#2996CC","#A3CC52",all.colour)
distnames <<- c("AGR->AGR" ,"FPL->AGR" ,"TFL->AGR","BRN->AGR","ABN->AGR","LOG->AGR"
,"AGR->FPL" ,"FPL->FPL" ,"TFL->FPL","BRN->FPL","ABN->FPL","LOG->FPL"
,"AGR->TFL" ,"FPL->TFL" ,"TFL->TFL","BRN->TFL","ABN->TFL","LOG->TFL"
,"AGR->BRN" ,"FPL->BRN" ,"TFL->BRN","BRN->BRN","ABN->BRN","LOG->BRN"
,"AGR->ABN" ,"FPL->ABN" ,"TFL->ABN","BRN->ABN","ABN->ABN","LOG->ABN"
,"AGR->LOG" ,"FPL->LOG" ,"TFL->LOG","BRN->LOG","ABN->LOG","LOG->LOG")
distcols <<- c("#66005A","#A80095","#E500CB","#FF4CEA","#FF998F","#FFCCF9"
,"#005A66","#00889A","#00B3CB","#00D3EF","#96F3FF","#CBF9FF"
,"#DEDEDE","#DEDEDE","#596500","#A0B310","#D1ED00","#F2FF91"
,"#DEDEDE","#DEDEDE","#983A2E","#D64F3D","#F29C91","#FFD1CB"
,"#007F0F","#00BE16","#DEDEDE","#DEDEDE","#DEDEDE","#DEDEDE"
,"#DEDEDE","#DEDEDE","#4C3FB2","#6E5AFF","#B0A6FF","#DED9FF")
#------------------------------------------------------------------------------------------#
#----- Growth respiration factor (to estimate when the actual variable is not there). -----#
growth.resp.fac <<- c(rep(0.333,times=5),rep(0.4503,times=3),rep(0,times=3)
,rep(0.333,times=4))
#------------------------------------------------------------------------------------------#
#----- fswh is the FSW that plants experience and they are happy (wilting point = 0). -----#
fswh <<- 0.99
#------------------------------------------------------------------------------------------#
#----- Years for which we have eddy flux tower. -------------------------------------------#
eft.year <<- c( 1998, 1999, 2000, 2001, 2002, 2003, 2004
, 2005, 2006, 2007, 2008, 2009, 2010, 2011
, 2012, 2013)
eft.pch <<- c( 0, 1, 6, 3, 4, 5, 13
, 15, 16, 17, 18, 9, 8, 7
, 14, 2)
eft.col <<- c("#7D6E93","#B49ED2","#39025D","#520485","#042E88","#0742C3","#00480E"
,"#006715","#31B223","#46FF32","#AB8C3D","#F5C858","#B23C00","#FF5700"
,"#70000E","#A00014")
#------------------------------------------------------------------------------------------#
#----- Standard colours and names for soil classes. ---------------------------------------#
stext.cols <<- c("gold","chartreuse","limegreen","darkgreen","purple3"
,"deepskyblue","aquamarine","slateblue2","darkorange3","sienna"
,"firebrick","grey61","grey29","orchid","olivedrab","goldenrod"
,"steelblue")
stext.names <<- c("Sand","Loamy Sand","Sandy loam","Silt loam","Loam","Sandy clay loam"
,"Silty clay loam","Clayey loam","Sandy clay","Silty clay","Clay","Peat"
,"Bedrock","Silt","Heavy clay","Clayey sand","Clayey silt")
stext.acron <<- c("Sa","LSa","SaL","SiL","L","SaCL","SiCL","CL"
,"SaC","SiC","C","Pe","BR","Si","CC","CSa","CSi")
#------------------------------------------------------------------------------------------#
#==========================================================================================#
#==========================================================================================#
# Patch information for POV-Ray. #
#------------------------------------------------------------------------------------------#
pov.dbh.min <<- 5 # Minimum DBH to be plotted
pov.patch.xmax <<- 16 # Size of each sub-plot in the x direction [m]
pov.patch.ymax <<- 16 # Size of each sub-plot in the y direction [m]
pov.nx.patch <<- 25 # Number of sub-plots in each x transect
pov.ny.patch <<- 25 # Number of sub-plots in each y transect
pov.nxy.patch <<- pov.nx.patch * pov.ny.patch
pov.total.area <<- pov.nxy.patch * pov.patch.xmax * pov.patch.ymax
pov.x0 <<- rep( x = -200 + seq(from=0,to=pov.nx.patch-1) * pov.patch.xmax
, times = pov.ny.patch
)#end rep
pov.y0 <<- rep( x = -200 + seq(from=0,to=pov.ny.patch-1) * pov.patch.ymax
, each = pov.nx.patch
)#end rep
#------------------------------------------------------------------------------------------#
#==========================================================================================#
#==========================================================================================#
# Census-related thresholds. If the script has different values, ignore these and #
# use whatever the main script says. #
#------------------------------------------------------------------------------------------#
#----- Minimum height to be considered for "ground-based observations". -------------------#
if ( "census.height.min" %in% ls()){
census.height.min <<- census.height.min
}else{
census.height.min <<- 1.5
}#end if
#----- Minimum DBH to be considered for "ground-based observations". ----------------------#
if ( "census.dbh.min" %in% ls()){
census.dbh.min <<- census.dbh.min
}else{
census.dbh.min <<- 10.
}#end if
#----- Minimum DBH to be considered for "ground-based observations". ----------------------#
if ( "recruit.dbh.min" %in% ls()){
recruit.dbh.min <<- recruit.dbh.min
}else{
recruit.dbh.min <<- 0.16
}#end if
#------------------------------------------------------------------------------------------#
#==========================================================================================#
#==========================================================================================#
# Define which DBH classes to use based on the DBH flag. #
#------------------------------------------------------------------------------------------#
if ("idbh.type" %in% ls()){
idbh.type <<- idbh.type
}else{
idbh.type <<- 1
}#end if
if (idbh.type == 1){
ndbh <<- 11
ddbh <<- 10
classdbh <<- seq(from=0,to=(ndbh-1)*ddbh,by=ddbh)
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhlabel <<- "11_szclss"
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "purple3", "mediumpurple1", "royalblue4"
, "steelblue3", "deepskyblue", "#004E00"
, "chartreuse3", "olivedrab3", "lightgoldenrod3"
, "yellow3", "darkorange1", "firebrick"
, all.colour
)#end c
}else if (idbh.type == 2){
ndbh <<- 5
classdbh <<- c(0,10,20,35,55)
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhlabel <<- "05_szclss"
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "royalblue3", "chartreuse3" , "yellow3"
, "darkorange1", "firebrick" , all.colour
)#end c
}else if (idbh.type == 3){
ndbh <<- 4
classdbh <<- c(0,10,35,55)
dbhlabel <<- "04_szclss"
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "#3B24B3", "#2996CC"
, "#FF9466", "#990F0F", all.colour
)#end c
}else if (idbh.type == 4){
ndbh <<- 6
classdbh <<- c(0,2,10,20,45,70)
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhlabel <<- "06_szclss"
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "purple3", "royalblue3", "chartreuse3"
, "yellow3", "darkorange1", "firebrick"
, all.colour
)#end c
}else if (idbh.type == 5){
ndbh <<- 17
classdbh <<- c(0,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,20)
breakdbh <<- c(-Inf,classdbh[-1],Inf)
dbhlabel <<- "07_szclss"
dbhkeys <<- paste(classdbh,"-",c(classdbh[-1],Inf),sep="")
dbhnames <<- paste( c("<",paste(classdbh[-c(1,ndbh)],"-",sep=""),">")
, c(classdbh[-1],classdbh[ndbh]),"cm"
, sep=""
)#end paste
dbhcols <<- c( "purple3", "royalblue3", "chartreuse3"
, "yellow3", "darkorange1", "firebrick"
, all.colour
)#end c
}else{
cat(" In globdims.r:","\n")
cat(" IDBH.TYPE = ",idbh.type,"\n")
stop(" Invalid IDBH.TYPE, it must be between 1 and 5 (feel free to add more options.")
}#end if
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
# Define which height classes to use based on the DBH flag. #
#------------------------------------------------------------------------------------------#
if ("ihgt.type" %in% ls()){
ihgt.type <<- ihgt.type
}else{
ihgt.type <<- 1
}#end if
if (ihgt.type == 1){
nhgt <<- 8
classhgt <<- c(0,5,10,15,20,25,30,35)-0.001
roundhgt <<- round(classhgt,0)
breakhgt <<- c(-Inf,classhgt[-1],Inf)
hgtlabel <<- "08_htclss"
hgtkeys <<- paste(classhgt,"-",c(roundhgt[-1],Inf),sep="")
hgtnames <<- paste( c("<",paste(roundhgt[-c(1,nhgt)],"-",sep=""),">")
, c(roundhgt[-1],roundhgt[nhgt]),"m"
, sep=""
)#end paste
hgtcols <<- c( "slateblue4", "steelblue3", "deepskyblue"
, "#004E00", "chartreuse3", "lightgoldenrod3"
, "darkorange1", "firebrick", all.colour
)#end c
}else if (ihgt.type == 2){
nhgt <<- 13
classhgt <<- c(0,1,4,7,10,13,16,19,22,25,28,31,34)
hgtlabel <<- "13_szclss"
breakhgt <<- c(-Inf,classhgt[-1],Inf)
hgtkeys <<- paste(classhgt,"-",c(classhgt[-1],Inf),sep="")
hgtnames <<- paste( c("<",paste(classhgt[-c(1,nhgt)],"-",sep=""),">")
, c(classhgt[-1],classhgt[nhgt]),"cm"
, sep=""
)#end paste
hgtcols <<- c( "purple3", "mediumpurple1", "royalblue4"
, "steelblue3", "deepskyblue", "#004E00"
, "chartreuse3", "olivedrab3", "lightgoldenrod3"
, "yellow3", "darkorange1", "red3"
, "firebrick4", all.colour
)#end c
}else{
cat(" In globdims.r:","\n")
cat(" IHGT.TYPE = ",ihgt.type,"\n")
stop(" Invalid IHGT.TYPE, it must be between 1 and 2 (feel free to add more options.")
}#end if
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
# Define which height classes to use based on the DBH flag. #
#------------------------------------------------------------------------------------------#
if ("isld.type" %in% ls()){
isld.type <<- isld.type
}else{
isld.type <<- 1
}#end if
if (isld.type == 1){
nsld <<- 12
belowsld <<- c(-6.0,-5.5,-5.0,-4.5,-4.0,-3.5,-3.0,-2.5,-2.0,-1.5,-1.0,-0.5)
abovesld <<- c(belowsld[-1],0)
thicksld <<- diff(c(belowsld,0))
roundsld <<- round(belowsld,2)
breaksld <<- c(-Inf,belowsld[-1],Inf)
sldlabel <<- "cc_sdclss"
sldkeys <<- paste(roundsld,"-",c(roundsld[-1],0),sep="")
sldnames <<- paste( c("<",paste(roundsld[-c(1,nsld)],"-",sep=""),">")
, c(roundsld[-1],roundsld[nhgt]),"m"
, sep=""
)#end paste
sldcols <<- c( "purple3", "mediumpurple1", "royalblue4"
, "steelblue3", "deepskyblue", "#004E00"
, "chartreuse3", "olivedrab3", "lightgoldenrod3"
, "yellow3", "darkorange1", "red3"
, "firebrick4", all.colour
)#end c
}else{
cat(" In globdims.r:","\n")
cat(" ISLD.TYPE = ",isld.type,"\n")
stop(" Invalid ISLD.TYPE, it must be C or H (feel free to add more options.")
}#end if
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
#==========================================================================================#
# Define default weighting factor for carbon balance. #
#------------------------------------------------------------------------------------------#
if ("klight" %in% ls()){
klight <<- klight
}else{
klight <<- 0.8
}#end if
#==========================================================================================#
#==========================================================================================#
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