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R/InclusionZoneClass.R
In sampSurf: Sampling Surface Simulation for Areal Sampling Methods
#---------------------------------------------------------------------------
#
# This file holds the S4 class definitions for the Inclusion Zone method
# related classes. Inclusion zones are properties of the particular
# 'Stem' subclass, and 'ArealSampling' subclass.
#
# The following section holds all of the definitions for down logs, those
# for standing trees are after these in the file.
#
# Classes...
# 1. InclusionZone: virtual for all 'ArealSampling' methods and Stem
# classes
# 2. downLogIZ: virtual for all 'ArealSampling' methods and 'downLog'
# subclasses
# 3. standUpIZ: the standup method of sampling down cwd
# 4. chainSawIZ; the chain saw method for sampling down cwd
# 5. sausageIZ: the sausage method of sampling down cwd
# 6. fullChainSawIZ: the FCS has sausage IZ
# 7. pointRelascopeIZ: the point relascope method for sampling down cwd
# 8. perpendicularDistanceIZ: normal PDS
# 9. omnibusPDSIZ: for omnibus estimation under normal PDS
# 10. distanceLimitedIZ: for canonical distance limited sampling (dls)
# 11. distanceLimitedMCIZ: DLMC
# 12. distanceLimitedPDSIZ: for canonical DLPDS
# 13. omnibusDLPDSIZ: combines omnibus PDS component with DLMC component
# 14. hybridDLPDSIZ: DLMC & canonical PDS
#
# Search for "standingTreeIZ" to find the definitions for standing trees at
# the end of this file.
#
#Author... Date: 20-Aug-2010
# Jeffrey H. Gove
# USDA Forest Service
# Northern Research Station
# 271 Mast Road
# Durham, NH 03824
# jhgove@unh.edu
# phone: 603-868-7667 fax: 603-868-7604
#---------------------------------------------------------------------------
#
#=================================================================================================
#
# 1. define the virtual InclusionZone class...
#
setClass('InclusionZone',
#
# slots for the class and its subclasses...
#
representation(description = 'character',
units = 'character', #English or metric units
bbox = 'matrix', #overall bounding box
spUnits = 'CRS', #spatial units
puaBlowup = 'numeric', #per unit area expansion factor
puaEstimates = 'list', #per unit area estimates
userExtra = 'ANY' #anything else the user wants to include--no checks
),
prototype = list(description = 'Areal sampling inclusion zone', #some defaults for validity checking
units = .StemEnv$msrUnits$metric,
bbox = matrix(rep(0,4), nrow=2, dimnames=list(c('x','y'), c('min','max'))),
spUnits = CRS(projargs=as.character(NA)),
puaBlowup = 1, #does no harm
puaEstimates = list(), #empty list
userExtra = NULL
),
contains = 'VIRTUAL',
validity = function(object) {
if(!(object@units %in% .StemEnv$msrUnits))
return('units of measure must be "English" or "metric"')
if(length(object@puaBlowup) > 1)
return('puaBlowup must be a scalar!')
if(!is.na(object@puaBlowup) && object@puaBlowup < 0) #it can be NA for DLPDS total
return('puaBlowup factor must be non-negative!')
if(length(object@puaEstimates > 0)) {
estNames = match(names(object@puaEstimates), unlist(.StemEnv$puaEstimates))
if(any(is.na(estNames)))
return('invalid slots in puaEstimates list object!')
}
#essentially the same checks as in bboxCheck()...
#matrix inherits from array (3-Feb-2020)...
#if(!class(object@bbox) == 'matrix') #bad practice!
if(!is(object@bbox, 'matrix'))
return('bbox slot must be a 2x2 matrix')
bboxNames = match(rownames(object@bbox), c('x','y'))
if(any(is.na(bboxNames)))
return('slot bbox rownames must be "x", "y"!')
bboxNames = match(colnames(object@bbox), c('min','max'))
if(any(is.na(bboxNames)))
return('slot bbox colnames must be "min", "max"!')
if(any( apply(object@bbox,1,function(x) if(x['min'] >= x['max']) TRUE else FALSE) ))
return('in slot bbox, "min" must be less than "max" for x and y!')
if(!is.na(object@spUnits@projargs) && object@spUnits@projargs == '+proj=longlat')
return(paste('spUnits must be commensurate with units,',
'please convert to non-geographic coordinate system!')
)
return(TRUE)
} #validity check
) #class InclusionZone
#=================================================================================================
#
# 2. the down log inclusion zone class is just a direct descendant of 'InclusionZone'...
#
#
setClass('downLogIZ',
representation(downLog = 'downLog' #downLog object
),
#prototype = list(#downLog = new('downLog'), #some defaults for validity checking
# units = .StemEnv$msrUnits$metric
# ),
contains = c('InclusionZone', 'VIRTUAL'), #a subclass of the virtual 'InclusionZone' class
validity = function(object) {
if(!validObject(object@downLog))
return('object in downLog slot is an invalid object!')
if(!identical(object@downLog@units, object@units))
return('measurement units do not match between downLog and IZ objects!')
if(!identical(object@downLog@spUnits, object@spUnits))
return('Spatial units do not match between downLog and IZ objects!')
return(TRUE)
} #validity check
) #class downLogIZ
#=================================================================================================
#
# 3. the standup class is just a direct descendant of 'downLogIZ'...
#
#
setClass('standUpIZ',
representation(circularPlot = 'circularPlot' #circularPlot object
),
#prototype = list(#downLog = new('downLog'), #some defaults for validity checking
# ),
contains = 'downLogIZ', #a subclass of the virtual 'downLogIZ' class
validity = function(object) {
if(!validObject(object@circularPlot))
return('object in circularPlot slot is an invalid object!')
if(!identical(object@downLog@units, object@circularPlot@units))
return('measurement units do not match between downLog and circularPlot objects!')
if(!identical(object@downLog@spUnits, object@circularPlot@spUnits))
return('Spatial units do not match between downLog and circularPlot objects!')
return(TRUE)
} #validity check
) #class standUpIZ
#=================================================================================================
#
# 4. the 'chainSawIZ' class is just a direct descendant of 'downLogIZ'...
#
#
setClass('chainSawIZ',
representation(circularPlot = 'circularPlot', #circularPlot object
sliver = 'SpatialPolygons', #the intersection sliver w/in the log
bolt = 'list' #the bolt/sliver information
),
#prototype = list(
# ),
contains = 'downLogIZ', #a subclass of virtual 'downLogIZ' class
validity = function(object) {
if(!validObject(object@circularPlot))
return('object in circularPlot slot is an invalid object!')
if(!identical(object@downLog@units, object@circularPlot@units))
return('measurement units do not match between downLog and circularPlot objects!')
if(!identical(object@downLog@spUnits, object@circularPlot@spUnits))
return('Spatial units do not match between downLog and circularPlot objects!')
return(TRUE)
} #validity check
) #class chainSawIZ
#=================================================================================================
#
# 5. the sausage class is a direct descendant of 'downLogIZ'...
#
#
setClass('sausageIZ',
representation(sausage = 'matrix', #holds the sausage incl zone in matrix form
radius = 'numeric', #plot radius for sausage
area = 'numeric', #exact area of the inclusion zone
perimeter = 'SpatialPolygons', #sausage perimeter in 'SpatialPolygons' form
pgSausageArea = 'numeric' #polygon sausage area approximation
),
#prototype = list(#downLog = new('downLog'), #some defaults for validity checking
# ),
contains = 'downLogIZ', #a subclass of the 'downLogIZ' class
validity = function(object) {
if(object@radius <= 0 || is.na(object@radius))
return('plot radius must be positive non-missing!')
if(object@area < 0 || is.na(object@area))
return('object has negative or missing inlusion zone area!')
if(object@pgSausageArea < 0 || is.na(object@pgSausageArea))
return('object has negative or missing polygon area!')
return(TRUE)
} #validity check
) #class sausageIZ
#=================================================================================================
#
# 6. the fullChainSaw class is a direct descendant of 'sausageIZ'...
#
# This class was formalized with associated changes in the constructors, izGrid constructors,
# and sampSurf 30-Sept-2013. This was done to get rid of the special code (since it just uses
# a sausage IZ) and make the package totally OOP in this regard.
#
setClass('fullChainSawIZ',
contains = 'sausageIZ', #a subclass of the 'sausageIZ' class
) #class fullChainSawIZ
#=================================================================================================
#
# 7. the pointRelascope class is a direct descendant of 'downLogIZ'...
#
# I'll call the "mastercard" double/dual circle (blob) just "dual"...
#
# below: hc = homogeneous coordinates
#
# added: 13-Jan-2011
#
setClass('pointRelascopeIZ',
representation(prs = 'pointRelascope', #point relascope sampling object
dualCircle = 'matrix', #holds the blob perimeter in matrix form w/ hc
radius = 'numeric', #radius for each of the half blobs
area = 'numeric', #exact area of the inclusion zone
perimeter = 'SpatialPolygons', #blob perimeter in 'SpatialPolygons' form
pgDualArea = 'numeric', #polygon blob area approximation
dualCenters = 'matrix' #centers of each dual circle, w/o hc
),
contains = 'downLogIZ', #a subclass of the 'downLogIZ' class
validity = function(object) {
if(object@radius <= 0 || is.na(object@radius))
return('plot radius must be positive non-missing!')
if(object@area < 0 || is.na(object@area))
return('object has negative or missing inclusion zone area!')
if(object@pgDualArea < 0 || is.na(object@pgDualArea))
return('object has negative or missing polygon area!')
if(!identical(object@prs@units, object@units))
return('object units do not match the pointRelascope object units')
return(TRUE)
} #validity check
) #class pointRelascopeIZ
#=================================================================================================
#
# 8. the perpendicularDistanceIZ class is a direct descendant of 'downLogIZ'...
#
#
# below: hc = homogeneous coordinates
#
# added: 26-Jan-2011
#
setClass('perpendicularDistanceIZ',
representation(pds = 'perpendicularDistance', #perpendicular distance sampling object
izPerim = 'matrix', #holds the iz perimeter in matrix form w/ hc
area = 'numeric', #exact area of the inclusion zone
perimeter = 'SpatialPolygons', #izone perimeter in 'SpatialPolygons' form
pgArea = 'numeric', #polygon izone area approximation
pdsType = 'character' #protocol method: see validity below
),
contains = 'downLogIZ', #a subclass of the 'downLogIZ' class
validity = function(object) {
if(object@area < 0 || is.na(object@area))
return('object has negative or missing inclusion zone area!')
if(object@pgArea < 0 || is.na(object@pgArea))
return('object has negative or missing polygon area!')
if(!identical(object@pds@units, object@units))
return('object units do not match the perpendicularDistance object units')
if(!object@pdsType %in% .StemEnv$pdsTypes)
return('illegal pdsType requested!')
if(object@pds@units != object@downLog@units)
return('units for pds and downLog components incompatible!')
return(TRUE)
} #validity check
) #class perpendicularDistanceIZ
#=================================================================================================
#
# 9. the omnibusPDSIZ class is a direct descendant of 'perpendicularDistanceIZ'...
#
#
# added: 4-Feb-2011
#
setClass('omnibusPDSIZ',
contains = 'perpendicularDistanceIZ'
) #class omnibusPDSIZ
#=================================================================================================
#
# 10. the distanceLimitedIZ class is a direct descendant of 'downLogIZ'...
#
#
# below: hc = homogeneous coordinates
#
# added: 25-May-2011
#
setClass('distanceLimitedIZ',
representation(dls = 'distanceLimited', #the distanceLimited sampling object
izPerim = 'matrix', #holds the iz perimeter in matrix form w/ hc
area = 'numeric', #exact area of the inclusion zone
perimeter = 'SpatialPolygons', #izone perimeter in 'SpatialPolygons' form
pgArea = 'numeric' #polygon izone area approximation
),
contains = 'downLogIZ', #a subclass of the 'downLogIZ' class
validity = function(object) {
if(object@area < 0 || is.na(object@area))
return('object has negative or missing inclusion zone area!')
if(object@pgArea < 0 || is.na(object@pgArea))
return('object has negative or missing polygon area!')
return(TRUE)
} #validity check
) #class distanceLimitedIZ
#=================================================================================================
#
# 11. the distanceLimitedMCIZ class is a direct descendant of 'distanceLimitedIZ'; the dates
# below are off compared with the parent because I actually developed the MC version first,
# then added the distanceLimtedIZ class, this necessitated switching the defintion so
# that the parent was the base for this class of objects
#
# added: 22&23-Mar-2011
#
setClass('distanceLimitedMCIZ',
contains = 'distanceLimitedIZ'
) #class distanceLimitedMCIZ
#=================================================================================================
#
# 12. the distanceLimitedPDSIZ class is a direct descendant of 'perpendicularDistanceIZ'...
#
# Two class unions are defined below to allow the slots to be either filled with something
# of the correct class, or be empty with NULL
#
# added: 8&10-Mar-2011
#
setClassUnion('pdsIZNull', c('perpendicularDistanceIZ', 'omnibusPDSIZ', 'NULL')) #allow for omnibus
setClassUnion('dlsIZNull', c('distanceLimitedIZ', 'NULL'))
setClass('distanceLimitedPDSIZ',
representation(dls = 'distanceLimited', #the distanceLimited ArealSampling object
dlsDiameter = 'numeric', #limiting diameter
pdsPart = 'pdsIZNull', #pds object for pds section of the log
dlsPart = 'dlsIZNull', #distance limited component of the log
pdsFull = 'pdsIZNull' #as if this were a full PDS object (never NULL?)
),
contains = 'perpendicularDistanceIZ',
validity = function(object) {
if(object@dlsDiameter <= 0)
return('distance limit diameter must be positive')
return(TRUE)
} #validity check
) #class distanceLimitedPDSIZ
#=================================================================================================
#
# 13. the omnibusDLPDSIZ class is a direct descendant of 'distanceLimitedPDSIZ'...
#
# combines DL with omnibus PDS
#
# added: 15-Mar-2011
#
setClass('omnibusDLPDSIZ',
contains = 'distanceLimitedPDSIZ'
) #class omnibusDLPDSIZ
#=================================================================================================
#
# 14. the hybridDLPDSIZ class is a direct descendant of 'distanceLimitedPDSIZ'...
#
# combines DL with canonical PDS
#
# added: 26-July-2011
#
setClass('hybridDLPDSIZ',
contains = 'distanceLimitedPDSIZ'
) #class hybridDLPDSIZ
#---------------------------------------------------------------------------
#
# This section contains the InclusionZone class definitions for standing
# trees...
#
# Classes...
#
# 1. standingTreeIZ: virtual parent
# 2. circularPlotIZ: fixed-area circular plots
# 3. horizontalPointIZ: horizontal point sampling (6-Dec-2011)
#
#Author... Date: 1-Dec-2011
# Jeffrey H. Gove
# USDA Forest Service
# Northern Research Station
# 271 Mast Road
# Durham, NH 03824
# jhgove@unh.edu
# phone: 603-868-7667 fax: 603-868-7604
#---------------------------------------------------------------------------
#
#=================================================================================================
#
# 1. the standing tree inclusion zone class is just a direct descendant of 'InclusionZone'...
#
#
setClass('standingTreeIZ',
representation(standingTree = 'standingTree' #standingTree object
),
contains = c('InclusionZone', 'VIRTUAL'), #a subclass of the virtual 'InclusionZone' class
validity = function(object) {
if(!validObject(object@standingTree))
return('object in standingTree slot is an invalid object!')
if(!identical(object@standingTree@units, object@units))
return('measurement units do not match between standingTree and IZ objects!')
if(!identical(object@standingTree@spUnits, object@spUnits))
return('Spatial units do not match between standingTree and IZ objects!')
return(TRUE)
} #validity check
) #class standingTreeIZ
#=================================================================================================
#
# 2. the circularPlotIZ class is just a direct descendant of 'standingTreeIZ'...
#
#
setClass('circularPlotIZ',
representation(circularPlot = 'circularPlot' #circularPlot object
),
contains = 'standingTreeIZ', #a subclass of the virtual 'standingTreeIZ' class
validity = function(object) {
if(!validObject(object@circularPlot))
return('object in circularPlot slot is an invalid object!')
if(!identical(object@standingTree@units, object@circularPlot@units))
return('measurement units do not match between standingTree and circularPlot objects!')
if(!identical(object@standingTree@spUnits, object@circularPlot@spUnits))
return('Spatial units do not match between standingTree and circularPlot objects!')
return(TRUE)
} #validity check
) #class circularPlotIZ
#=================================================================================================
#
# 3. the horizontalPointIZ class is a direct descendant of 'circularPlotIZ'...
#
# what that means is that it saves coding further down the line as, for example, it will use
# the methods for InclusionZoneGrid, Plot, etc. generics.
#
#
setClass('horizontalPointIZ',
representation(angleGauge = 'angleGauge' #angleGauge object
),
contains = 'circularPlotIZ', #a subclass of the 'circularPlotIZ' class
validity = function(object) {
if(!validObject(object@angleGauge))
return('object in angleGauge slot is an invalid object!')
if(!identical(object@standingTree@units, object@angleGauge@units))
return('measurement units do not match between standingTree and angleGauge objects!')
return(TRUE)
} #validity check
) #class horizontalPointIZ
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#---------------------------------------------------------------------------
#
# This file holds the S4 class definitions for the Inclusion Zone method
# related classes. Inclusion zones are properties of the particular
# 'Stem' subclass, and 'ArealSampling' subclass.
#
# The following section holds all of the definitions for down logs, those
# for standing trees are after these in the file.
#
# Classes...
# 1. InclusionZone: virtual for all 'ArealSampling' methods and Stem
# classes
# 2. downLogIZ: virtual for all 'ArealSampling' methods and 'downLog'
# subclasses
# 3. standUpIZ: the standup method of sampling down cwd
# 4. chainSawIZ; the chain saw method for sampling down cwd
# 5. sausageIZ: the sausage method of sampling down cwd
# 6. fullChainSawIZ: the FCS has sausage IZ
# 7. pointRelascopeIZ: the point relascope method for sampling down cwd
# 8. perpendicularDistanceIZ: normal PDS
# 9. omnibusPDSIZ: for omnibus estimation under normal PDS
# 10. distanceLimitedIZ: for canonical distance limited sampling (dls)
# 11. distanceLimitedMCIZ: DLMC
# 12. distanceLimitedPDSIZ: for canonical DLPDS
# 13. omnibusDLPDSIZ: combines omnibus PDS component with DLMC component
# 14. hybridDLPDSIZ: DLMC & canonical PDS
#
# Search for "standingTreeIZ" to find the definitions for standing trees at
# the end of this file.
#
#Author... Date: 20-Aug-2010
# Jeffrey H. Gove
# USDA Forest Service
# Northern Research Station
# 271 Mast Road
# Durham, NH 03824
# jhgove@unh.edu
# phone: 603-868-7667 fax: 603-868-7604
#---------------------------------------------------------------------------
#
#=================================================================================================
#
# 1. define the virtual InclusionZone class...
#
setClass('InclusionZone',
#
# slots for the class and its subclasses...
#
representation(description = 'character',
units = 'character', #English or metric units
bbox = 'matrix', #overall bounding box
spUnits = 'CRS', #spatial units
puaBlowup = 'numeric', #per unit area expansion factor
puaEstimates = 'list', #per unit area estimates
userExtra = 'ANY' #anything else the user wants to include--no checks
),
prototype = list(description = 'Areal sampling inclusion zone', #some defaults for validity checking
units = .StemEnv$msrUnits$metric,
bbox = matrix(rep(0,4), nrow=2, dimnames=list(c('x','y'), c('min','max'))),
spUnits = CRS(projargs=as.character(NA)),
puaBlowup = 1, #does no harm
puaEstimates = list(), #empty list
userExtra = NULL
),
contains = 'VIRTUAL',
validity = function(object) {
if(!(object@units %in% .StemEnv$msrUnits))
return('units of measure must be "English" or "metric"')
if(length(object@puaBlowup) > 1)
return('puaBlowup must be a scalar!')
if(!is.na(object@puaBlowup) && object@puaBlowup < 0) #it can be NA for DLPDS total
return('puaBlowup factor must be non-negative!')
if(length(object@puaEstimates > 0)) {
estNames = match(names(object@puaEstimates), unlist(.StemEnv$puaEstimates))
if(any(is.na(estNames)))
return('invalid slots in puaEstimates list object!')
}
#essentially the same checks as in bboxCheck()...
#matrix inherits from array (3-Feb-2020)...
#if(!class(object@bbox) == 'matrix') #bad practice!
if(!is(object@bbox, 'matrix'))
return('bbox slot must be a 2x2 matrix')
bboxNames = match(rownames(object@bbox), c('x','y'))
if(any(is.na(bboxNames)))
return('slot bbox rownames must be "x", "y"!')
bboxNames = match(colnames(object@bbox), c('min','max'))
if(any(is.na(bboxNames)))
return('slot bbox colnames must be "min", "max"!')
if(any( apply(object@bbox,1,function(x) if(x['min'] >= x['max']) TRUE else FALSE) ))
return('in slot bbox, "min" must be less than "max" for x and y!')
if(!is.na(object@spUnits@projargs) && object@spUnits@projargs == '+proj=longlat')
return(paste('spUnits must be commensurate with units,',
'please convert to non-geographic coordinate system!')
)
return(TRUE)
} #validity check
) #class InclusionZone
#=================================================================================================
#
# 2. the down log inclusion zone class is just a direct descendant of 'InclusionZone'...
#
#
setClass('downLogIZ',
representation(downLog = 'downLog' #downLog object
),
#prototype = list(#downLog = new('downLog'), #some defaults for validity checking
# units = .StemEnv$msrUnits$metric
# ),
contains = c('InclusionZone', 'VIRTUAL'), #a subclass of the virtual 'InclusionZone' class
validity = function(object) {
if(!validObject(object@downLog))
return('object in downLog slot is an invalid object!')
if(!identical(object@downLog@units, object@units))
return('measurement units do not match between downLog and IZ objects!')
if(!identical(object@downLog@spUnits, object@spUnits))
return('Spatial units do not match between downLog and IZ objects!')
return(TRUE)
} #validity check
) #class downLogIZ
#=================================================================================================
#
# 3. the standup class is just a direct descendant of 'downLogIZ'...
#
#
setClass('standUpIZ',
representation(circularPlot = 'circularPlot' #circularPlot object
),
#prototype = list(#downLog = new('downLog'), #some defaults for validity checking
# ),
contains = 'downLogIZ', #a subclass of the virtual 'downLogIZ' class
validity = function(object) {
if(!validObject(object@circularPlot))
return('object in circularPlot slot is an invalid object!')
if(!identical(object@downLog@units, object@circularPlot@units))
return('measurement units do not match between downLog and circularPlot objects!')
if(!identical(object@downLog@spUnits, object@circularPlot@spUnits))
return('Spatial units do not match between downLog and circularPlot objects!')
return(TRUE)
} #validity check
) #class standUpIZ
#=================================================================================================
#
# 4. the 'chainSawIZ' class is just a direct descendant of 'downLogIZ'...
#
#
setClass('chainSawIZ',
representation(circularPlot = 'circularPlot', #circularPlot object
sliver = 'SpatialPolygons', #the intersection sliver w/in the log
bolt = 'list' #the bolt/sliver information
),
#prototype = list(
# ),
contains = 'downLogIZ', #a subclass of virtual 'downLogIZ' class
validity = function(object) {
if(!validObject(object@circularPlot))
return('object in circularPlot slot is an invalid object!')
if(!identical(object@downLog@units, object@circularPlot@units))
return('measurement units do not match between downLog and circularPlot objects!')
if(!identical(object@downLog@spUnits, object@circularPlot@spUnits))
return('Spatial units do not match between downLog and circularPlot objects!')
return(TRUE)
} #validity check
) #class chainSawIZ
#=================================================================================================
#
# 5. the sausage class is a direct descendant of 'downLogIZ'...
#
#
setClass('sausageIZ',
representation(sausage = 'matrix', #holds the sausage incl zone in matrix form
radius = 'numeric', #plot radius for sausage
area = 'numeric', #exact area of the inclusion zone
perimeter = 'SpatialPolygons', #sausage perimeter in 'SpatialPolygons' form
pgSausageArea = 'numeric' #polygon sausage area approximation
),
#prototype = list(#downLog = new('downLog'), #some defaults for validity checking
# ),
contains = 'downLogIZ', #a subclass of the 'downLogIZ' class
validity = function(object) {
if(object@radius <= 0 || is.na(object@radius))
return('plot radius must be positive non-missing!')
if(object@area < 0 || is.na(object@area))
return('object has negative or missing inlusion zone area!')
if(object@pgSausageArea < 0 || is.na(object@pgSausageArea))
return('object has negative or missing polygon area!')
return(TRUE)
} #validity check
) #class sausageIZ
#=================================================================================================
#
# 6. the fullChainSaw class is a direct descendant of 'sausageIZ'...
#
# This class was formalized with associated changes in the constructors, izGrid constructors,
# and sampSurf 30-Sept-2013. This was done to get rid of the special code (since it just uses
# a sausage IZ) and make the package totally OOP in this regard.
#
setClass('fullChainSawIZ',
contains = 'sausageIZ', #a subclass of the 'sausageIZ' class
) #class fullChainSawIZ
#=================================================================================================
#
# 7. the pointRelascope class is a direct descendant of 'downLogIZ'...
#
# I'll call the "mastercard" double/dual circle (blob) just "dual"...
#
# below: hc = homogeneous coordinates
#
# added: 13-Jan-2011
#
setClass('pointRelascopeIZ',
representation(prs = 'pointRelascope', #point relascope sampling object
dualCircle = 'matrix', #holds the blob perimeter in matrix form w/ hc
radius = 'numeric', #radius for each of the half blobs
area = 'numeric', #exact area of the inclusion zone
perimeter = 'SpatialPolygons', #blob perimeter in 'SpatialPolygons' form
pgDualArea = 'numeric', #polygon blob area approximation
dualCenters = 'matrix' #centers of each dual circle, w/o hc
),
contains = 'downLogIZ', #a subclass of the 'downLogIZ' class
validity = function(object) {
if(object@radius <= 0 || is.na(object@radius))
return('plot radius must be positive non-missing!')
if(object@area < 0 || is.na(object@area))
return('object has negative or missing inclusion zone area!')
if(object@pgDualArea < 0 || is.na(object@pgDualArea))
return('object has negative or missing polygon area!')
if(!identical(object@prs@units, object@units))
return('object units do not match the pointRelascope object units')
return(TRUE)
} #validity check
) #class pointRelascopeIZ
#=================================================================================================
#
# 8. the perpendicularDistanceIZ class is a direct descendant of 'downLogIZ'...
#
#
# below: hc = homogeneous coordinates
#
# added: 26-Jan-2011
#
setClass('perpendicularDistanceIZ',
representation(pds = 'perpendicularDistance', #perpendicular distance sampling object
izPerim = 'matrix', #holds the iz perimeter in matrix form w/ hc
area = 'numeric', #exact area of the inclusion zone
perimeter = 'SpatialPolygons', #izone perimeter in 'SpatialPolygons' form
pgArea = 'numeric', #polygon izone area approximation
pdsType = 'character' #protocol method: see validity below
),
contains = 'downLogIZ', #a subclass of the 'downLogIZ' class
validity = function(object) {
if(object@area < 0 || is.na(object@area))
return('object has negative or missing inclusion zone area!')
if(object@pgArea < 0 || is.na(object@pgArea))
return('object has negative or missing polygon area!')
if(!identical(object@pds@units, object@units))
return('object units do not match the perpendicularDistance object units')
if(!object@pdsType %in% .StemEnv$pdsTypes)
return('illegal pdsType requested!')
if(object@pds@units != object@downLog@units)
return('units for pds and downLog components incompatible!')
return(TRUE)
} #validity check
) #class perpendicularDistanceIZ
#=================================================================================================
#
# 9. the omnibusPDSIZ class is a direct descendant of 'perpendicularDistanceIZ'...
#
#
# added: 4-Feb-2011
#
setClass('omnibusPDSIZ',
contains = 'perpendicularDistanceIZ'
) #class omnibusPDSIZ
#=================================================================================================
#
# 10. the distanceLimitedIZ class is a direct descendant of 'downLogIZ'...
#
#
# below: hc = homogeneous coordinates
#
# added: 25-May-2011
#
setClass('distanceLimitedIZ',
representation(dls = 'distanceLimited', #the distanceLimited sampling object
izPerim = 'matrix', #holds the iz perimeter in matrix form w/ hc
area = 'numeric', #exact area of the inclusion zone
perimeter = 'SpatialPolygons', #izone perimeter in 'SpatialPolygons' form
pgArea = 'numeric' #polygon izone area approximation
),
contains = 'downLogIZ', #a subclass of the 'downLogIZ' class
validity = function(object) {
if(object@area < 0 || is.na(object@area))
return('object has negative or missing inclusion zone area!')
if(object@pgArea < 0 || is.na(object@pgArea))
return('object has negative or missing polygon area!')
return(TRUE)
} #validity check
) #class distanceLimitedIZ
#=================================================================================================
#
# 11. the distanceLimitedMCIZ class is a direct descendant of 'distanceLimitedIZ'; the dates
# below are off compared with the parent because I actually developed the MC version first,
# then added the distanceLimtedIZ class, this necessitated switching the defintion so
# that the parent was the base for this class of objects
#
# added: 22&23-Mar-2011
#
setClass('distanceLimitedMCIZ',
contains = 'distanceLimitedIZ'
) #class distanceLimitedMCIZ
#=================================================================================================
#
# 12. the distanceLimitedPDSIZ class is a direct descendant of 'perpendicularDistanceIZ'...
#
# Two class unions are defined below to allow the slots to be either filled with something
# of the correct class, or be empty with NULL
#
# added: 8&10-Mar-2011
#
setClassUnion('pdsIZNull', c('perpendicularDistanceIZ', 'omnibusPDSIZ', 'NULL')) #allow for omnibus
setClassUnion('dlsIZNull', c('distanceLimitedIZ', 'NULL'))
setClass('distanceLimitedPDSIZ',
representation(dls = 'distanceLimited', #the distanceLimited ArealSampling object
dlsDiameter = 'numeric', #limiting diameter
pdsPart = 'pdsIZNull', #pds object for pds section of the log
dlsPart = 'dlsIZNull', #distance limited component of the log
pdsFull = 'pdsIZNull' #as if this were a full PDS object (never NULL?)
),
contains = 'perpendicularDistanceIZ',
validity = function(object) {
if(object@dlsDiameter <= 0)
return('distance limit diameter must be positive')
return(TRUE)
} #validity check
) #class distanceLimitedPDSIZ
#=================================================================================================
#
# 13. the omnibusDLPDSIZ class is a direct descendant of 'distanceLimitedPDSIZ'...
#
# combines DL with omnibus PDS
#
# added: 15-Mar-2011
#
setClass('omnibusDLPDSIZ',
contains = 'distanceLimitedPDSIZ'
) #class omnibusDLPDSIZ
#=================================================================================================
#
# 14. the hybridDLPDSIZ class is a direct descendant of 'distanceLimitedPDSIZ'...
#
# combines DL with canonical PDS
#
# added: 26-July-2011
#
setClass('hybridDLPDSIZ',
contains = 'distanceLimitedPDSIZ'
) #class hybridDLPDSIZ
#---------------------------------------------------------------------------
#
# This section contains the InclusionZone class definitions for standing
# trees...
#
# Classes...
#
# 1. standingTreeIZ: virtual parent
# 2. circularPlotIZ: fixed-area circular plots
# 3. horizontalPointIZ: horizontal point sampling (6-Dec-2011)
#
#Author... Date: 1-Dec-2011
# Jeffrey H. Gove
# USDA Forest Service
# Northern Research Station
# 271 Mast Road
# Durham, NH 03824
# jhgove@unh.edu
# phone: 603-868-7667 fax: 603-868-7604
#---------------------------------------------------------------------------
#
#=================================================================================================
#
# 1. the standing tree inclusion zone class is just a direct descendant of 'InclusionZone'...
#
#
setClass('standingTreeIZ',
representation(standingTree = 'standingTree' #standingTree object
),
contains = c('InclusionZone', 'VIRTUAL'), #a subclass of the virtual 'InclusionZone' class
validity = function(object) {
if(!validObject(object@standingTree))
return('object in standingTree slot is an invalid object!')
if(!identical(object@standingTree@units, object@units))
return('measurement units do not match between standingTree and IZ objects!')
if(!identical(object@standingTree@spUnits, object@spUnits))
return('Spatial units do not match between standingTree and IZ objects!')
return(TRUE)
} #validity check
) #class standingTreeIZ
#=================================================================================================
#
# 2. the circularPlotIZ class is just a direct descendant of 'standingTreeIZ'...
#
#
setClass('circularPlotIZ',
representation(circularPlot = 'circularPlot' #circularPlot object
),
contains = 'standingTreeIZ', #a subclass of the virtual 'standingTreeIZ' class
validity = function(object) {
if(!validObject(object@circularPlot))
return('object in circularPlot slot is an invalid object!')
if(!identical(object@standingTree@units, object@circularPlot@units))
return('measurement units do not match between standingTree and circularPlot objects!')
if(!identical(object@standingTree@spUnits, object@circularPlot@spUnits))
return('Spatial units do not match between standingTree and circularPlot objects!')
return(TRUE)
} #validity check
) #class circularPlotIZ
#=================================================================================================
#
# 3. the horizontalPointIZ class is a direct descendant of 'circularPlotIZ'...
#
# what that means is that it saves coding further down the line as, for example, it will use
# the methods for InclusionZoneGrid, Plot, etc. generics.
#
#
setClass('horizontalPointIZ',
representation(angleGauge = 'angleGauge' #angleGauge object
),
contains = 'circularPlotIZ', #a subclass of the 'circularPlotIZ' class
validity = function(object) {
if(!validObject(object@angleGauge))
return('object in angleGauge slot is an invalid object!')
if(!identical(object@standingTree@units, object@angleGauge@units))
return('measurement units do not match between standingTree and angleGauge objects!')
return(TRUE)
} #validity check
) #class horizontalPointIZ
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