R/accessors.R

Defines functions ecoslot.W ecoslot.UPPR ecoslot.TREES ecoslot.TEST ecoslot.SUMMARY.MLM ecoslot.SP ecoslot.SELF ecoslot.ROW.SD ecoslot.RES ecoslot.PVAL ecoslot.PREDICTIONS ecoslot.POP ecoslot.POLY.DEG ecoslot.PAR.VAL ecoslot.PAR ecoslot.PADJUST ecoslot.OBS.RES ecoslot.OBS ecoslot.NSIM ecoslot.NONZEROIND ecoslot.NONZERO ecoslot.NAMES ecoslot.MULTI ecoslot.MODEL ecoslot.MLM ecoslot.METHOD ecoslot.MEAN ecoslot.LWR ecoslot.LOGMEAN ecoslot.IN ecoslot.GF ecoslot.FREQUENCIES ecoslot.EXP ecoslot.DISTMETHOD ecoslot.DF2 ecoslot.DF1 ecoslot.CONNECTED ecoslot.COND ecoslot.CARDINAL ecoslot.BREAKS ecoslot.AVERAGE ecoslot.ANOVA.MLM ecoslot.ANALYSIS ecoslot.ALTER

Documented in ecoslot.ALTER ecoslot.ANALYSIS ecoslot.ANOVA.MLM ecoslot.AVERAGE ecoslot.BREAKS ecoslot.CARDINAL ecoslot.COND ecoslot.CONNECTED ecoslot.DF1 ecoslot.DF2 ecoslot.DISTMETHOD ecoslot.EXP ecoslot.FREQUENCIES ecoslot.GF ecoslot.IN ecoslot.LOGMEAN ecoslot.LWR ecoslot.MEAN ecoslot.METHOD ecoslot.MLM ecoslot.MODEL ecoslot.MULTI ecoslot.NAMES ecoslot.NONZERO ecoslot.NONZEROIND ecoslot.NSIM ecoslot.OBS ecoslot.OBS.RES ecoslot.PADJUST ecoslot.PAR ecoslot.PAR.VAL ecoslot.POLY.DEG ecoslot.POP ecoslot.PREDICTIONS ecoslot.PVAL ecoslot.RES ecoslot.ROW.SD ecoslot.SELF ecoslot.SP ecoslot.SUMMARY.MLM ecoslot.TEST ecoslot.TREES ecoslot.UPPR ecoslot.W

#' Generic accessors for EcoGenetics objects
#' 
#' @name EcoGenetics accessors
#' 
#' @description These functions provide basic access to the slots of any object
#' of the formal classes defined in EcoGenetics. In addition, 
#' for ecogen objects a replace method is defined for the accessor, which enables
#' basic processing of individual slots. 
#' 
#' @param X Any S4 object of the formal classes defined in EcoGenetics.
#'
#' @format <\strong{ecoslot.}> + <\strong{name of the slot}> + <\strong{(name of the object)}>
#' 
#' @details The accessor notation in EcoGenetics consists of the prefix 
#' "ecoslot." followed by the name of the slot of interest. E.g., 
#' to access the slot "IN" of the object "X", type ecoslot.IN(X).
#' 
#' For example, the class eco.correlog of the function \code{\link{eco.correlog}}
#' has the slots OUT, IN, BREAKS CARDINAL, etc. 
#' An object X of class eco.correlog, generated with this function, 
#' has access to these slots using:
#' ecoslot.OUT(X), ecoslot.IN(X), ecoslot.BREAKS(X) and ecoslot.CARDINAL(X), 
#' respectively. 
#' 
#' 
#'    -----------------------------------------------------------------------
#' 
#' \strong{FOR ECOGEN CLASS ONLY}:
#' 
#' - The accessors in objects of class \code{\link{ecogen}} 
#' have a double usage. First, the extraction of data included in a slot (\strong{get mode}).  
#' Second, the assignment of data (\strong{set mode}). The data assigned 
#' to ecogen objects using this method is properly pre-processed. 
#' 
#' - The get mode is defined for ecoslot.XY, ecoslot.P, ecoslot.G, 
#' ecoslot.A, ecoslot.E, ecoslot.S and ecoslot.OUT. For any ecogen object X, 
#' type ecoslot.SLOT(X), where SLOT is the slot of interest: ecoslot.XY(X), 
#' ecoslot.P(X), ecoslot.G(X), ecoslot.A(X), ecoslot.E(X), ecoslot.S(X) 
#' and ecoslot.OUT(X, ...). In the latter, the three dots (...) are
#' objects in the slot OUT. 
#' 
#' - The set mode is a replacement method, i.e.,  
#' the assignation ecoslot.SLOT(X) <- VALUE is defined for the ecogen class. 
#' 
#' For a generic ecogen object "eco", the defined replacement methods are:
#' 
#' 1. ecoslot.P(eco) <- P data frame
#' 
#' 2. ecoslot.G(eco, ...) <- G data frame
#' 
#' #' In this case the three dots (...) consist of the following 
#' variables that can be passed to the function:
#' 
#' - G.processed
#' 
#' - order.G
#' 
#' - type
#' 
#' - ploidy
#' 
#' - sep
#' 
#' - ncod
#' 
#' - missing
#' 
#' - NA.char
#' 
#' - poly.level
#' 
#' - rm.empty.ind
#' 
#' See the arguments of \code{\link{ecogen}} for details about these values, and the
#' Examples section for details about usage.
#' 
#' 
#' \strong{IMPORTANT}: The assignation of data in the slot G, creates automatically the slot A.
#' An accessor is defined for the slot A only in get mode (to get the data frame in this slot, 
#' but not for replacement purposes). The slot A cannot be replaced with accessors 
#' and is generated when a genetic data frame is assigned to the slot G. 
#' 
#' 3. ecoslot.E(eco) <- E data frame
#' 
#' 4. ecoslot.S(eco) <- S data frame
#' 
#' 5. ecoslot.C(eco) <- C data frame
#' 
#' 6. ecoslot.OUT(eco, value) <- results to store in the slot OUT.
#' Here, value means any object(s). 
#' Several objects can be passed as a list. 
#' See the section Examples.
#' 
#' @rdname EcoGenetics-accessors
#' @author Leandro Roser \email{[email protected]@gmail.com} 
#' 
#' @examples
#' 
#' \dontrun{
#' 
#' #--------------
#' # GENERAL USE
#' #--------------
#' 
#' # Example 1
#' 
#' data(eco.test)
#' 
#' ## Test with phenotypic traits (example of ?eco.correlog)
#' moran <- eco.correlog(Z=eco[["P"]][,1], XY = eco[["XY"]], method = "I", smax=10, size=1000)
#  
#' # the slots are accesed with the generic format:
#' # ecoslot. + name of the slot + (name of the object)
#' 
#' ecoslot.OUT(moran)      # slot OUT
#' ecoslot.BREAKS(moran)   # slot BREAKS
#' 
#' 
#' #----------------------------------------------
#' # SPECIFIC USE OF ACCESSORS WITH ECOGEN OBJECTS
#' #----------------------------------------------
#' 
#' #1) GET MODE
#' 
#' # Example 2
#' 
#' # Example with G data of class "data.frame", corresponding to
#' # microsatellites of a diploid organism.
#' 
#' eco <- ecogen(XY = coordinates, P = phenotype, G = genotype,
#'               E = environment, S = structure, order.G = TRUE)
#' eco              
#' 
#' 
#' # Access to the slots   
#'
#' ecoslot.XY(eco) 
#' ecoslot.P(eco)
#' ecoslot.G(eco)
#' ecoslot.A(eco)
#' ecoslot.E(eco)
#' ecoslot.S(eco)
#' ecoslot.C(eco)
#' ecoslot.OUT(eco)         
#' 
#' # For ecogen objects, the double square brackets ("[[")
#' # are symbolic abbreviations of the accessors:
#' 
#' ecoslot.XY(eco) 
#' # is identical to:
#' eco[["XY"]]
#' 
#' #2) SET MODE (REPLACEMENT OF SLOTS)
#' 
#' # Example 3
#' 
#' eco <- ecogen(XY = coordinates, P = phenotype)
#' eco
#' 
#' ecoslot.G(eco, order.G = TRUE) <- genotype
#' 
#' # this is identical to
#' eco[["G", order.G=TRUE]] <- genotype
#' 
#' ecoslot.E(eco) <- environment
#' ecoslot.S(eco) <- structure
#' 
#' # Storing the data of Example 1 in the slot OUT
#' 
#' ecoslot.OUT(eco) <- moran
#'  
#' # Storing several data
#' singers <- c("carlos_gardel", "billie_holiday")
#' golden.number <- (sqrt(5) + 1) / 2
#' ecoslot.OUT(eco) <- list(singers, golden.number)    # several objects must be passed as a list
#'
#' # In get mode, ecoslot.OUT has a double behavior:
#' # when only the name of the ecogen object is passed to
#' # the accessor, it has an overview method, 
#' # returning a data frame with the objects
#' # stored and their classes
#' 
#' ecoslot.OUT(eco)
#' 
#' # ecoslot.OUT in get mode, has two arguments:
#' # ecoslot.OUT(object, ...)
#' # here, the three dots (...) means any object(s) stored in the slot OUT.
#' 
#' ecoslot.OUT(eco, "moran", "singers")
#' 
#' # In double square brackets notation, this is equivalent to
#' eco[["OUT"]][c("moran", "singers")]
#' # This is, it works as a list and have no overview method
#' eco[["OUT"]]
#' eco[["OUT"]]["moran"]
#' 
#' # ecoslot.OUT in set mode, has two arguments:
#' # ecoslot.OUT(object, value)
#' # here value means object(s) to store in the slot OUT. Several objects
#' # must be passed as a list.
#' # The names of the input data is recoded in case of
#' # duplicates
#' 
#' ecoslot.OUT(eco) <- singers
#' ecoslot.OUT(eco)
#' ecoslot.OUT(eco) <- list(singers, singers, singers)
#' ecoslot.OUT(eco)
#' 
#' # The set operation is equivalent with double square brackets
#' eco[["OUT"]] <- list(singers, c(1,2,3))
#' ecoslot.OUT(eco)
#' 
#' }
#' 
#' 
#' @export 
#' 
#' 

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.ALTER <- function(X) X@ALTER


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.ANALYSIS <- function(X) X@ANALYSIS

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.ANOVA.MLM <- function(X)  X@ANOVA.MLM


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.AVERAGE <- function(X) X@AVERAGE

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.BREAKS <- function(X) X@BREAKS

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.CARDINAL <- function(X) X@CARDINAL

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.COND <- function(X) X@COND


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.CONNECTED <- function(X) X@CONNECTED


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.DF1 <- function(X) X@DF1


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.DF2 <- function(X) X@DF2


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.DISTMETHOD <- function(X) X@DISTMETHOD

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.EXP <- function(X) X@EXP


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.FREQUENCIES <- function(X) X@FREQUENCIES

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.GF <- function(X) X@GF


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.IN <- function(X) X@IN

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.LOGMEAN <- function(X) X@LOGMEAN

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.LWR <- function(X) X@LWR

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.MEAN <- function(X) X@MEAN

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.METHOD <- function(X) X@METHOD


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.MLM <- function(X) X@MLM


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.MODEL <- function(X) X@MODEL


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.MULTI <- function(X) X@MULTI

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.NAMES <- function(X) X@NAMES

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.NONZERO <- function(X) X@NONZERO

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.NONZEROIND <- function(X) X@NONZEROIND

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.NSIM <- function(X) X@NSIM

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.OBS<- function(X) X@OBS

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.OBS.RES<- function(X) X@OBS.RES


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.PADJUST <- function(X) X@PADJUST

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.PAR <- function(X) X@PAR


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.PAR.VAL <- function(X) X@PAR.VAL


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.POLY.DEG <- function(X) X@POLY.DEG

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.POP <- function(X) X@POP

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.PREDICTIONS <- function(X) X@PREDICTIONS

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.PVAL <- function(X) X@PVAL

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.RES <- function(X) X@RES

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.ROW.SD <- function(X)  X@ROW.SD


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.SELF <- function(X) X@SELF

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.SP <- function(X) X@SP


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.SUMMARY.MLM <- function(X) X@SUMMARY.MLM

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.TEST <- function(X) X@TEST


#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.TREES <- function(X) X@TREES

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.UPPR <- function(X) X@UPPR

#' @rdname EcoGenetics-accessors
#' @export 

ecoslot.W <- function(X)  X@W

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EcoGenetics documentation built on June 24, 2018, 5:02 p.m.