Calculates transition rates.

Share:

Description

Calculates transition rates from netcdf file output by MC2.

Usage

1
VegTypeChanges(tgtFile, baseCalibration, vtXpvt)

Arguments

tgtFile

String: Full path to the netcdf output file.

baseCalibration

String: currently 'CONUS', or 'WCR'.

vtXpvt

data frame, lookup table linking veg type indexes and PVT abbreviations.

Value

Returns a list object of length 6, containing:

tgtFile, years, vts2keep, vtFracsReduced, changeFracsReduced, and vt2pvtlut

Author(s)

Dave Conklin

Examples

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
## Please refer to the document "MakingThePATHmegamodel.pdf" in inst/doc.
## Step numbers given below refer to the step numbers in that document.	
	
## The function is currently defined as
function (tgtFile, tgtVarName, baseCalibration, dontskipVTs, 
    vt2pvtlut) 
{
    tgtP = open.nc(tgtFile)
    tgtLonInfo = dim.inq.nc(tgtP, "lon")
    tgtLonDimID = tgtLonInfo$id
    tgtLatInfo = dim.inq.nc(tgtP, "lat")
    tgtLatDimID = tgtLatInfo$id
    tgtYrInfo = dim.inq.nc(tgtP, "year")
    tgtYrDimID = tgtYrInfo$id
    years = var.get.nc(tgtP, "year")
    tgtVarInfo = var.inq.nc(tgtP, tgtVarName)
    tgtVarDimIds = tgtVarInfo$dimids
    stopifnot(length(tgtVarDimIds) == 3)
    stopifnot(tgtLonDimID == tgtVarDimIds[1])
    stopifnot(tgtLatDimID == tgtVarDimIds[2])
    stopifnot(tgtYrDimID == tgtVarDimIds[3])
    tgtVar = var.get.nc(tgtP, tgtVarName)
    tgtDim = dim(tgtVar)
    stopifnot(length(tgtDim) == 3)
    nCols = tgtDim[1]
    nRows = tgtDim[2]
    nYrs = tgtDim[3]
    stopifnot(nYrs >= 2)
    nCells = nCols * nRows
    dim(tgtVar) = c(nCells, nYrs)
    nVTall = length(VTnames(baseCalibration))
    vtCounts = array(0, c(nVTall, nYrs))
    for (yr in 1:nYrs) vtCounts[, yr] = tabulate(tgtVar[, yr], 
        nbins = nVTall)
    changePairs = array(FALSE, c(nVTall, nVTall))
    for (yr in 2:nYrs) {
        for (cell in 1:nCells) {
            vtPrev = tgtVar[cell, yr - 1]
            stopifnot((1 <= vtPrev && vtPrev <= nVTall) || is.na(vtPrev))
            vtCurr = tgtVar[cell, yr]
            stopifnot((1 <= vtCurr && vtCurr <= nVTall) || is.na(vtCurr))
            if (!is.na(vtPrev) && !is.na(vtCurr)) 
                changePairs[vtPrev, vtCurr] = changePairs[vtPrev, 
                  vtCurr] || (vtPrev != vtCurr)
        }
    }
    vts2omit = rep(TRUE, times = nVTall)
    for (vtPrev in 1:nVTall) {
        for (vtCurr in 1:nVTall) {
            if (changePairs[vtPrev, vtCurr]) 
                vts2omit[vtPrev] = FALSE
        }
    }
    rm(changePairs)
    if (length(dontskipVTs) > 0) {
        for (k in 1:length(dontskipVTs)) vts2omit[dontskipVTs[k]] = FALSE
    }
    changeCounts = array(0, c(nVTall, nVTall, nYrs - 1))
    changeFracs = array(0, c(nVTall, nVTall, nYrs - 1))
    for (yr in 2:nYrs) {
        for (cell in 1:nCells) {
            vtPrev = tgtVar[cell, yr - 1]
            vtCurr = tgtVar[cell, yr]
            if (!is.na(vtPrev) && 1 <= vtPrev && vtPrev <= nVTall && 
                !is.na(vtCurr) && 1 <= vtCurr && vtCurr <= nVTall) 
                changeCounts[vtPrev, vtCurr, yr - 1] = changeCounts[vtPrev, 
                  vtCurr, yr - 1] + 1
        }
        for (vtPrev in 1:nVTall) {
            for (vtCurr in 1:nVTall) {
                count = changeCounts[vtPrev, vtCurr, yr - 1]
                vtPrevTot = vtCounts[vtPrev, yr - 1]
                if (count > 0) {
                  stopifnot(vtPrevTot >= 1)
                  changeFracs[vtPrev, vtCurr, yr - 1] = count/vtPrevTot
                }
                else if (vtPrevTot == 0 && yr > 2) {
                  changeFracs[vtPrev, vtCurr, yr - 1] = changeFracs[vtPrev, 
                    vtCurr, yr - 2]
                }
            }
        }
    }
    nVTreduced = nVTall - sum(vts2omit)
    vtCountsReduced = array(0, c(nVTreduced, nYrs))
    k = 0
    for (vt in 1:nVTall) {
        if (!vts2omit[vt]) {
            k = k + 1
            vtCountsReduced[k, ] = vtCounts[vt, ]
        }
    }
    vtFracsReduced = array(0, c(nVTreduced, nYrs))
    for (yr in 1:nYrs) {
        totCounts = sum(vtCountsReduced[, yr])
        vtFracsReduced = vtCountsReduced/totCounts
    }
    changeFracsReducedByRows = array(0, c(nVTall, nVTreduced, 
        nYrs - 1))
    vts2keep = rep(0, times = nVTreduced)
    for (yr in 1:(nYrs - 1)) {
        k = 0
        for (vt in 1:nVTall) {
            if (!vts2omit[vt]) {
                k = k + 1
                vts2keep[k] = vt
                changeFracsReducedByRows[, k, yr] = changeFracs[, 
                  vt, yr]
            }
        }
    }
    changeFracsReduced = array(0, c(nVTreduced, nVTreduced, nYrs - 
        1))
    k = 0
    for (vt in 1:nVTall) {
        if (!vts2omit[vt]) {
            k = k + 1
            changeFracsReduced[k, , ] = changeFracsReducedByRows[vt, 
                , ]
        }
    }
    return(list(tgtFile = tgtFile, years = years, vts2keep = vts2keep, 
        vtFracsReduced = vtFracsReduced, changeFracsReduced = changeFracsReduced, 
        vt2pvtlut = vt2pvtlut))
  }

## Step 1
#ncdf.path = "MC2toPath/netcdf/WW2100_HadGEM2-ES85_year_sample.nc"
ncdf.path <- system.file("netcdf", "WW2100_HadGEM2-ES85_year_sample.nc", package = "MC2toPath")

## Step 2
base.calibration = "CONUS"

## Step 3
## This is what you would really do...
## vegChanges = VegTypeChanges(ncdf.th <- system.file("netcdf", "WW2100_HadGEM2-ES85_year_sample.nc", PACKAGE = "MC2toPath")path, base.calibration) 
## but we do this instead to save execution time for CRAN...
data(vegChanges_step3)
vegChanges = vegChanges_step3

## Step 7
VTs = c(6, 7, 8, 10, 11, 12, 16, 22, 36)
PVTs = c("fmh", "fwi", "fdd", "fvg", "fdw", "fuc", "fto", "ftm", "fsi")
Strata = c("OWC_fmh", "OWC_fwi", "OSW_fdd", "OWC_fvg", "OWC_fdw", "OSW_fuc", "OWC_fto", 
	"OSW_ftm", "OWC_fsi")
vt2pvtlut = data.frame(VT=VTs, PVT=PVTs, Stratum=Strata)

## Step 8
climateChangeTransitionTypes = paste(rep(PVTs, length(PVTs)), "2", rep(PVTs, 
	each = length(PVTs)), sep="")

## Step 11
## This is what you would really do...
# vegChanges = VegTypeChanges(ncdf.path, base.calibration, vt2pvtlut)
## but we do this instead to save execution time for CRAN...
data(vegChanges_step11)
vegChanges = vegChanges_step11

## Step 12
SaveVegChangeProbabilityMultipliers(vegChanges, base.calibration, 
	climateChangeTransitionTypes, vt2pvtlut)

## Step 13
SaveFireProbabilityMultipliers(ncdf.path, base.calibration, vt2pvtlut)