#' rcvirtual.conf: Configuration reference class
#'
#' @field daemon. Specifications for daemon
#' @field parameters. Specifications for parameters
#' @field strategy. Specifications for strategy
#' @field plotter. Specifications for plotter
#'
#' @importFrom methods new
#' @exportClass rcvirtual.conf
#'
setRefClass(
Class = "rcvirtual.conf",
contains = c("rcvirtual.basic", "VIRTUAL"),
fields = list(daemon = "ANY",
parameters = "ANY",
strategy = "ANY",
plotter = "ANY"
),
methods = list(
# ------------------------------------------------------
# Initializer methods ----------------------------------
# ------------------------------------------------------
construct = function(){
"Constructor of virtual conf"
callSuper()
conf.name <- (.self$getClass())@className[1]
conf.chunks <- strsplit(x = conf.name, split = '.', fixed = TRUE)[[1]]
.self$package.name <- conf.chunks[1]
x <- vector("list", length = 0)
.self$daemon <- x
.self$parameters <- x
.self$strategy <- x
.self$plotter <- x
},
# ------------------------------------------------------
# Set methods ------------------------------------------
# ------------------------------------------------------
set.trim = function() {
'Currently this only trims the parameters data frame'
.self$parameters <- .self$parameters[.self$parameters$in.model, ]
},
# ------------------------------------------------------
# Get methods ------------------------------------------
# ------------------------------------------------------
get.conf.template = function(){
name.vec <- c(
"alpha", "beta", "gamma", "delta", "epsilon",
"zeta", "eta", "theta", "iota", "kappa", "lambda",
"mu", "nu", "xi", "omicron", "pi", "rho", "sigma",
"tau", "upsilon", "phi", "chi", "psi", "omega",
"varphi", "varpi", "varrho", "vartheta", "varsigma",
"varepsilon", "ALPHA", "BETA", "GAMMA", "DELTA",
"EPSILON", "ZETA", "ETA", "THETA", "IOTA", "KAPPA",
"LAMBDA", "MU", "NU","XI","OMICRON", "PI", "RHO",
"SIGMA", "TAU", "UPSILON", "PHI", "CHI", "PSI",
"OMEGA", letters, LETTERS)
ll <- length(name.vec)
na.ini <- rep(NA, ll)
d.ini <- rep("-", ll)
o.ini <- rep(1, ll)
f.ini <- rep(FALSE, ll)
t.ini <- rep(TRUE, ll)
tpl <- data.frame(
name = d.ini, #variable name, or 1-letter codename
long.name = d.ini, #long variable name
in.model = f.ini, #is model?
type = d.ini, #fixed, unknown, derived
lbound = na.ini, #lower bound
ubound = na.ini, #upper bound
units = d.ini, #units of parameter
prior.distr = d.ini, #prior distribution codename
prior.mean = na.ini, #prior mean
prior.var = na.ini, #prior variance
sampler.type = d.ini, #type of sampler used
proposal.distr = d.ini, #prop. distribution codename
proposal.var = na.ini, #proposal variance
accept.rate = na.ini, #acceptance rate in M-H algor.
initial = na.ini, #initial value
is.spatial.avg = f.ini, #is this a spatial average?
size = o.ini, #size of vector parameter
input.file = d.ini, #input file
output.file = d.ini, #output file
store.in.ram = f.ini, #store object in memory?
stringsAsFactors = FALSE)
tpl$name <- name.vec
return(tpl)
}
# ------------------------------------------------------
# Is methods -------------------------------------------
# ------------------------------------------------------
)
)
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