R/operator.R
In heibl/ips: Interfaces to Phylogenetic Software in R
Defines functions
operator
Documented in
operator
#' @export
operator <- function(ops, x){
i <- 1
## ID differs for linked or unlinked trees!
## ----------------------------------------
# id <- ifelse(x$link.trees, "trees", x$id[i])
id <- x$partition[i]
## Library of possible BEAST parameters (not exhaustive!)
## ------------------------------------------------------
z <- list(
## Relaxed Clock Exponential
## -------------------------
ExpCategoriesRandomWalk.c = list(attrs = c(id = paste0("ExpCategoriesRandomWalk.c:", id),
parameter = paste0("@expRateCategories.c:", id),
spec = "IntRandomWalkOperator",
weight = "10.0",
windowSize = "1")),
ExpCategoriesSwapOperator.c = list(attrs = c(id = paste0("ExpCategoriesSwapOperator.c:", id),
intparameter = paste0("@expRateCategories.c:", id),
spec = "SwapOperator",
weight = "10.0")),
ExpCategoriesUniform.c = list(attrs = c(id = paste0("ExpCategoriesUniform.c:", id),
parameter = paste0("@expRateCategories.c:", id),
spec = "UniformOperator",
weight = "10.0")),
## Relaxed Clock Exponential (and Fossilized Birth Death)
## ------------------------------------------------------
ucedMeanScaler.c = list(attrs = c(id = paste0("ucedMeanScaler.c:", id),
spec = "ScaleOperator",
parameter = paste0("@ucedMean.c:", id),
scaleFactor = "0.5",
weight = "1.0")),
relaxedUpDownOperatorExp.c = list(attrs = c(id = paste0("relaxedUpDownOperatorExp.c:", id),
spec = "UpDownOperator",
scaleFactor = "0.75",
weight = "3.0"),
value = list(xmlNode("up", attrs = c(idref = paste0("ucedMean.c:", id))),
xmlNode("down", attrs = c(idref = paste0("Tree.t:", id))))),
## Relaxed Clock Log Normal
## -------------------------
ucldMeanScaler.c = list(attrs = c(id = paste0("ucldMeanScaler.c:", id),
parameter = paste0("@ucldMean.c:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "1.0")),
ucldStdevScaler.c = list(attrs = c(id = paste0("ucldStdevScaler.c:", id),
parameter = paste0("@ucldStdev.c:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "3.0")),
CategoriesRandomWalk.c = list(attrs = c(id = paste0("CategoriesRandomWalk.c:", id),
parameter = paste0("@rateCategories.c:", id),
spec = "IntRandomWalkOperator",
weight = "10.0",
windowSize = "1")),
CategoriesSwapOperator.c = list(attrs = c(id = paste0("CategoriesSwapOperator.c:", id),
intparameter = paste0("@rateCategories.c:", id),
spec = "SwapOperator",
weight = "10.0")),
CategoriesUniform.c = list(attrs = c(id = paste0("CategoriesUniform.c:", id),
parameter = paste0("@rateCategories.c:", id),
spec = "UniformOperator",
weight = "10.0")),
relaxedUpDownOperator.c = list(attrs = c(id = paste0("relaxedUpDownOperator.c:", id),
scaleFactor = "0.75",
spec = "UpDownOperator",
weight = "3.0"),
value = list(xmlNode("up", attrs = c(idref = paste0("ucldMean.c:", id))),
xmlNode("down", attrs = c(idref = paste0("Tree.t:", id))))),
## Random Local Clock
## -------------------------
randomClockScaler.c = list(attrs = c(id = paste0("randomClockScaler.c:", id),
parameter = paste0("@meanClockRate.c:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "1.0")),
randomClockUpDownOperator.c = list(attrs = c(id = paste0("randomClockUpDownOperator.c:", id),
scaleFactor = "0.75",
spec = "UpDownOperator",
weight = "3.0"),
value = list(xmlNode("up", attrs = c(idref = paste0("meanClockRate.c:", id))),
xmlNode("down", attrs = c(idref = paste0("Tree.t:", id))))),
IndicatorsBitFlip.c = list(attrs = c(id = paste0("IndicatorsBitFlip.c:", id),
parameter = paste0("@Indicators.c:", id),
spec = "BitFlipOperator",
weight = "15.0")),
ClockRateScaler.c = list(attrs = c(id = paste0("ClockRateScaler.c:", id),
parameter = paste0("@clockrates.c:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "15.0")),
## Yule
## ----
YuleBirthRateScaler.t = list(attrs = c(id = paste0("YuleBirthRateScaler.t:", id),
parameter = paste0("@birthRate.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "3.0")),
YuleModelTreeScaler.t = list(attrs = c(id = paste0("YuleModelTreeScaler.t:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
YuleModelTreeRootScaler.t = list(attrs = c(id = paste0("YuleModelTreeRootScaler.t:", id),
rootOnly = "true",
scaleFactor = "0.5",
spec = "ScaleOperator",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
YuleModelUniformOperator.t = list(attrs = c(id = paste0("YuleModelUniformOperator.t:", id),
spec = "Uniform",
tree = paste0("@Tree.t:", id),
weight = "30.0")),
YuleModelSubtreeSlide.t = list(attrs = c(id = paste0("YuleModelSubtreeSlide.t:", id),
spec = "SubtreeSlide",
tree = paste0("@Tree.t:", id),
weight = "15.0")),
YuleModelNarrow.t = list(attrs = c(id = paste0("YuleModelNarrow.t:", id),
spec = "Exchange",
tree = paste0("@Tree.t:", id),
weight = "15.0")),
YuleModelWide.t = list(attrs = c(id = paste0("YuleModelWide.t:", id),
isNarrow = "false",
spec = "Exchange",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
YuleModelWilsonBalding.t = list(attrs = c(id = paste0("YuleModelWilsonBalding.t:", id),
spec = "WilsonBalding",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
## Birth Death
## -----------
BirthDeathTreeScaler.t = list(attrs = c(id = paste0("BirthDeathTreeScaler.t:", id),
spec = "ScaleOperator",
scaleFactor = "0.5",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
BirthDeathTreeRootScaler.t = list(attrs = c(id = paste0("BirthDeathTreeRootScaler.t:", id),
spec = "ScaleOperator",
rootOnly = "true",
scaleFactor = "0.5",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
BirthDeathUniformOperator.t = list(attrs = c(id = paste0("BirthDeathUniformOperator.t:", id),
spec = "Uniform",
tree = paste0("@Tree.t:", id),
weight = "30.0")),
BirthDeathSubtreeSlide.t = list(attrs = c(id = paste0("BirthDeathSubtreeSlide.t:", id),
spec = "SubtreeSlide",
tree = paste0("@Tree.t:", id),
weight = "15.0")),
BirthDeathNarrow.t = list(attrs = c(id = paste0("BirthDeathNarrow.t:", id),
spec = "Exchange",
tree = paste0("@Tree.t:", id),
weight = "15.0")),
BirthDeathWide.t = list(attrs = c(id = paste0("BirthDeathWide.t:", id),
spec = "Exchange",
isNarrow = "false",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
BirthDeathWilsonBalding.t = list(attrs = c(id = paste0("BirthDeathWilsonBalding.t:", id),
spec = "WilsonBalding",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
BirthRateScaler.t = list(attrs = c(id = paste0("BirthRateScaler.t:", id),
spec = "ScaleOperator",
parameter = paste0("@BDBirthRate.t:", id),
scaleFactor = "0.75",
weight = "3.0")),
DeathRateScaler.t = list(attrs = c(id = paste0("DeathRateScaler.t:", id),
spec = "ScaleOperator",
parameter = paste0("@BDDeathRate.t:", id),
scaleFactor = "0.75",
weight = "3.0")),
## Strict Clock & Fossilized Birth Death
## -------------------------------------
originScalerFBD.t = list(attrs = c(id = paste0("originScalerFBD.t:", id),
parameter = paste0("@originFBD.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "3.0")),
divRateScalerFBD.t = list(attrs = c(id = paste0("divRateScalerFBD.t:", id),
parameter = paste0("@diversificationRateFBD.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "10.0")),
turnoverScalerFBD.t = list(attrs = c(id = paste0("turnoverScalerFBD.t:", id),
parameter = paste0("@turnoverFBD.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "10.0")),
samplingPScalerFBD.t = list(attrs = c(id = paste0("samplingPScalerFBD.t:", id),
parameter = paste0("@samplingProportionFBD.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "10.0")),
LeafToSAFBD.t = list(attrs = c(id = paste0("LeafToSAFBD.t:", id),
spec = "LeafToSampledAncestorJump",
tree = paste0("@Tree.t:", id),
weight = "10.0")),
SAWilsonBaldingFBD.t = list(attrs = c(id = paste0("SAWilsonBaldingFBD.t:", id),
spec = "SAWilsonBalding",
tree = paste0("@Tree.t:", id),
weight = "10.0")),
SAWideFBD.t = list(attrs = c(id = paste0("SAWideFBD.t:", id),
isNarrow = "false",
spec = "SAExchange",
tree = paste0("@Tree.t:", id),
weight = "10.0")),
SANarrowFBD.t = list(attrs = c(id = paste0("SANarrowFBD.t:", id),
spec = "SAExchange",
tree = paste0("@Tree.t:", id),
weight = "10.0")),
SAUniformOperatorFBD.t = list(attrs = c(id = paste0("SAUniformOperatorFBD.t:", id),
spec = "SAUniform",
tree = paste0("@Tree.t:", id),
weight = "20.0")),
SATreeRootScalerFBD.t = list(attrs = c(id = paste0("SATreeRootScalerFBD.t:", id),
rootOnly = "true",
scaleFactor = "0.95",
spec = "SAScaleOperator",
tree = paste0("@Tree.t:", id),
weight = "1.0")),
SATreeScalerFBD.t = list(attrs = c(id = paste0("SATreeScalerFBD.t:", id),
# rootOnly = "true", ## not in UCL + FBD
scaleFactor = "0.95",
spec = "SAScaleOperator",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
StrictClockRateScaler.c = list(attrs = c(id = paste0("StrictClockRateScaler.c:", id),
parameter = paste0("@clockRate.c:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "3.0")),
strictClockUpDownOperator.c = list(attrs = c(id = paste0("strictClockUpDownOperator.c:", id),
scaleFactor = "0.75",
spec = "UpDownOperator",
weight = "3.0"),
value = list(xmlNode("up", attrs = c(idref = paste0("clockRate.c:", id))),
xmlNode("down", attrs = c(idref = paste0("Tree.t:", id))))),
## Substitution models
KappaScaler.s = list(attrs = c(id = paste0("KappaScaler.s:", id),
parameter = paste0("@kappa.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
kappa1Scaler.s = list(attrs = c(id = paste0("kappa1Scaler.s:", id),
parameter = paste0("@kappa1.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
kappa2Scaler.s = list(attrs = c(id = paste0("kappa2Scaler.s:", id),
parameter = paste0("@kappa2.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateACScaler.s = list(attrs = c(id = paste0("RateACScaler.s:", id),
parameter = paste0("@rateAC.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateAGScaler.s = list(attrs = c(id = paste0("RateAGScaler.s:", id),
parameter = paste0("@rateAG.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateATScaler.s = list(attrs = c(id = paste0("RateATScaler.s:", id),
parameter = paste0("@rateAT.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateCGScaler.s = list(attrs = c(id = paste0("RateCGScaler.s:", id),
parameter = paste0("@rateCG.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateGTScaler.s = list(attrs = c(id = paste0("RateGTScaler.s:", id),
parameter = paste0("@rateGT.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
FrequenciesExchanger.s = list(attrs = c(delta = "0.01",
id = paste0("FrequenciesExchanger.s:", id),
spec = "DeltaExchangeOperator",
weight = "0.1"),
value = list(xmlNode("parameter",
attrs = c(idref = paste0("freqParameter.s:", id)))))
# + <operator delta='0.01' id='FrequenciesExchanger.s:bears' spec='DeltaExchangeOperator' weight='0.1'>
# + <parameter idref='freqParameter.s:bears' />
# + </operator>
)
ops <- match.arg(ops, names(z))
z <- z[[ops]]
if (is.null(z$value)){
xmlNode("operator", attrs = z$attrs)
} else {
xmlNode("operator", attrs = z$attrs, .children = z$value)
}
}
# operator_list <- read.csv("data/operator_list.csv", stringsAsFactors = FALSE)
# save(operator_list, file = "data/operator_list.rda")
heibl/ips documentation built on April 24, 2024, 3:19 a.m.
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Defines functions operator
Documented in operator
#' @export
operator <- function(ops, x){
i <- 1
## ID differs for linked or unlinked trees!
## ----------------------------------------
# id <- ifelse(x$link.trees, "trees", x$id[i])
id <- x$partition[i]
## Library of possible BEAST parameters (not exhaustive!)
## ------------------------------------------------------
z <- list(
## Relaxed Clock Exponential
## -------------------------
ExpCategoriesRandomWalk.c = list(attrs = c(id = paste0("ExpCategoriesRandomWalk.c:", id),
parameter = paste0("@expRateCategories.c:", id),
spec = "IntRandomWalkOperator",
weight = "10.0",
windowSize = "1")),
ExpCategoriesSwapOperator.c = list(attrs = c(id = paste0("ExpCategoriesSwapOperator.c:", id),
intparameter = paste0("@expRateCategories.c:", id),
spec = "SwapOperator",
weight = "10.0")),
ExpCategoriesUniform.c = list(attrs = c(id = paste0("ExpCategoriesUniform.c:", id),
parameter = paste0("@expRateCategories.c:", id),
spec = "UniformOperator",
weight = "10.0")),
## Relaxed Clock Exponential (and Fossilized Birth Death)
## ------------------------------------------------------
ucedMeanScaler.c = list(attrs = c(id = paste0("ucedMeanScaler.c:", id),
spec = "ScaleOperator",
parameter = paste0("@ucedMean.c:", id),
scaleFactor = "0.5",
weight = "1.0")),
relaxedUpDownOperatorExp.c = list(attrs = c(id = paste0("relaxedUpDownOperatorExp.c:", id),
spec = "UpDownOperator",
scaleFactor = "0.75",
weight = "3.0"),
value = list(xmlNode("up", attrs = c(idref = paste0("ucedMean.c:", id))),
xmlNode("down", attrs = c(idref = paste0("Tree.t:", id))))),
## Relaxed Clock Log Normal
## -------------------------
ucldMeanScaler.c = list(attrs = c(id = paste0("ucldMeanScaler.c:", id),
parameter = paste0("@ucldMean.c:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "1.0")),
ucldStdevScaler.c = list(attrs = c(id = paste0("ucldStdevScaler.c:", id),
parameter = paste0("@ucldStdev.c:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "3.0")),
CategoriesRandomWalk.c = list(attrs = c(id = paste0("CategoriesRandomWalk.c:", id),
parameter = paste0("@rateCategories.c:", id),
spec = "IntRandomWalkOperator",
weight = "10.0",
windowSize = "1")),
CategoriesSwapOperator.c = list(attrs = c(id = paste0("CategoriesSwapOperator.c:", id),
intparameter = paste0("@rateCategories.c:", id),
spec = "SwapOperator",
weight = "10.0")),
CategoriesUniform.c = list(attrs = c(id = paste0("CategoriesUniform.c:", id),
parameter = paste0("@rateCategories.c:", id),
spec = "UniformOperator",
weight = "10.0")),
relaxedUpDownOperator.c = list(attrs = c(id = paste0("relaxedUpDownOperator.c:", id),
scaleFactor = "0.75",
spec = "UpDownOperator",
weight = "3.0"),
value = list(xmlNode("up", attrs = c(idref = paste0("ucldMean.c:", id))),
xmlNode("down", attrs = c(idref = paste0("Tree.t:", id))))),
## Random Local Clock
## -------------------------
randomClockScaler.c = list(attrs = c(id = paste0("randomClockScaler.c:", id),
parameter = paste0("@meanClockRate.c:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "1.0")),
randomClockUpDownOperator.c = list(attrs = c(id = paste0("randomClockUpDownOperator.c:", id),
scaleFactor = "0.75",
spec = "UpDownOperator",
weight = "3.0"),
value = list(xmlNode("up", attrs = c(idref = paste0("meanClockRate.c:", id))),
xmlNode("down", attrs = c(idref = paste0("Tree.t:", id))))),
IndicatorsBitFlip.c = list(attrs = c(id = paste0("IndicatorsBitFlip.c:", id),
parameter = paste0("@Indicators.c:", id),
spec = "BitFlipOperator",
weight = "15.0")),
ClockRateScaler.c = list(attrs = c(id = paste0("ClockRateScaler.c:", id),
parameter = paste0("@clockrates.c:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "15.0")),
## Yule
## ----
YuleBirthRateScaler.t = list(attrs = c(id = paste0("YuleBirthRateScaler.t:", id),
parameter = paste0("@birthRate.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "3.0")),
YuleModelTreeScaler.t = list(attrs = c(id = paste0("YuleModelTreeScaler.t:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
YuleModelTreeRootScaler.t = list(attrs = c(id = paste0("YuleModelTreeRootScaler.t:", id),
rootOnly = "true",
scaleFactor = "0.5",
spec = "ScaleOperator",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
YuleModelUniformOperator.t = list(attrs = c(id = paste0("YuleModelUniformOperator.t:", id),
spec = "Uniform",
tree = paste0("@Tree.t:", id),
weight = "30.0")),
YuleModelSubtreeSlide.t = list(attrs = c(id = paste0("YuleModelSubtreeSlide.t:", id),
spec = "SubtreeSlide",
tree = paste0("@Tree.t:", id),
weight = "15.0")),
YuleModelNarrow.t = list(attrs = c(id = paste0("YuleModelNarrow.t:", id),
spec = "Exchange",
tree = paste0("@Tree.t:", id),
weight = "15.0")),
YuleModelWide.t = list(attrs = c(id = paste0("YuleModelWide.t:", id),
isNarrow = "false",
spec = "Exchange",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
YuleModelWilsonBalding.t = list(attrs = c(id = paste0("YuleModelWilsonBalding.t:", id),
spec = "WilsonBalding",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
## Birth Death
## -----------
BirthDeathTreeScaler.t = list(attrs = c(id = paste0("BirthDeathTreeScaler.t:", id),
spec = "ScaleOperator",
scaleFactor = "0.5",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
BirthDeathTreeRootScaler.t = list(attrs = c(id = paste0("BirthDeathTreeRootScaler.t:", id),
spec = "ScaleOperator",
rootOnly = "true",
scaleFactor = "0.5",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
BirthDeathUniformOperator.t = list(attrs = c(id = paste0("BirthDeathUniformOperator.t:", id),
spec = "Uniform",
tree = paste0("@Tree.t:", id),
weight = "30.0")),
BirthDeathSubtreeSlide.t = list(attrs = c(id = paste0("BirthDeathSubtreeSlide.t:", id),
spec = "SubtreeSlide",
tree = paste0("@Tree.t:", id),
weight = "15.0")),
BirthDeathNarrow.t = list(attrs = c(id = paste0("BirthDeathNarrow.t:", id),
spec = "Exchange",
tree = paste0("@Tree.t:", id),
weight = "15.0")),
BirthDeathWide.t = list(attrs = c(id = paste0("BirthDeathWide.t:", id),
spec = "Exchange",
isNarrow = "false",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
BirthDeathWilsonBalding.t = list(attrs = c(id = paste0("BirthDeathWilsonBalding.t:", id),
spec = "WilsonBalding",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
BirthRateScaler.t = list(attrs = c(id = paste0("BirthRateScaler.t:", id),
spec = "ScaleOperator",
parameter = paste0("@BDBirthRate.t:", id),
scaleFactor = "0.75",
weight = "3.0")),
DeathRateScaler.t = list(attrs = c(id = paste0("DeathRateScaler.t:", id),
spec = "ScaleOperator",
parameter = paste0("@BDDeathRate.t:", id),
scaleFactor = "0.75",
weight = "3.0")),
## Strict Clock & Fossilized Birth Death
## -------------------------------------
originScalerFBD.t = list(attrs = c(id = paste0("originScalerFBD.t:", id),
parameter = paste0("@originFBD.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "3.0")),
divRateScalerFBD.t = list(attrs = c(id = paste0("divRateScalerFBD.t:", id),
parameter = paste0("@diversificationRateFBD.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "10.0")),
turnoverScalerFBD.t = list(attrs = c(id = paste0("turnoverScalerFBD.t:", id),
parameter = paste0("@turnoverFBD.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "10.0")),
samplingPScalerFBD.t = list(attrs = c(id = paste0("samplingPScalerFBD.t:", id),
parameter = paste0("@samplingProportionFBD.t:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "10.0")),
LeafToSAFBD.t = list(attrs = c(id = paste0("LeafToSAFBD.t:", id),
spec = "LeafToSampledAncestorJump",
tree = paste0("@Tree.t:", id),
weight = "10.0")),
SAWilsonBaldingFBD.t = list(attrs = c(id = paste0("SAWilsonBaldingFBD.t:", id),
spec = "SAWilsonBalding",
tree = paste0("@Tree.t:", id),
weight = "10.0")),
SAWideFBD.t = list(attrs = c(id = paste0("SAWideFBD.t:", id),
isNarrow = "false",
spec = "SAExchange",
tree = paste0("@Tree.t:", id),
weight = "10.0")),
SANarrowFBD.t = list(attrs = c(id = paste0("SANarrowFBD.t:", id),
spec = "SAExchange",
tree = paste0("@Tree.t:", id),
weight = "10.0")),
SAUniformOperatorFBD.t = list(attrs = c(id = paste0("SAUniformOperatorFBD.t:", id),
spec = "SAUniform",
tree = paste0("@Tree.t:", id),
weight = "20.0")),
SATreeRootScalerFBD.t = list(attrs = c(id = paste0("SATreeRootScalerFBD.t:", id),
rootOnly = "true",
scaleFactor = "0.95",
spec = "SAScaleOperator",
tree = paste0("@Tree.t:", id),
weight = "1.0")),
SATreeScalerFBD.t = list(attrs = c(id = paste0("SATreeScalerFBD.t:", id),
# rootOnly = "true", ## not in UCL + FBD
scaleFactor = "0.95",
spec = "SAScaleOperator",
tree = paste0("@Tree.t:", id),
weight = "3.0")),
StrictClockRateScaler.c = list(attrs = c(id = paste0("StrictClockRateScaler.c:", id),
parameter = paste0("@clockRate.c:", id),
scaleFactor = "0.75",
spec = "ScaleOperator",
weight = "3.0")),
strictClockUpDownOperator.c = list(attrs = c(id = paste0("strictClockUpDownOperator.c:", id),
scaleFactor = "0.75",
spec = "UpDownOperator",
weight = "3.0"),
value = list(xmlNode("up", attrs = c(idref = paste0("clockRate.c:", id))),
xmlNode("down", attrs = c(idref = paste0("Tree.t:", id))))),
## Substitution models
KappaScaler.s = list(attrs = c(id = paste0("KappaScaler.s:", id),
parameter = paste0("@kappa.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
kappa1Scaler.s = list(attrs = c(id = paste0("kappa1Scaler.s:", id),
parameter = paste0("@kappa1.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
kappa2Scaler.s = list(attrs = c(id = paste0("kappa2Scaler.s:", id),
parameter = paste0("@kappa2.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateACScaler.s = list(attrs = c(id = paste0("RateACScaler.s:", id),
parameter = paste0("@rateAC.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateAGScaler.s = list(attrs = c(id = paste0("RateAGScaler.s:", id),
parameter = paste0("@rateAG.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateATScaler.s = list(attrs = c(id = paste0("RateATScaler.s:", id),
parameter = paste0("@rateAT.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateCGScaler.s = list(attrs = c(id = paste0("RateCGScaler.s:", id),
parameter = paste0("@rateCG.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
RateGTScaler.s = list(attrs = c(id = paste0("RateGTScaler.s:", id),
parameter = paste0("@rateGT.s:", id),
scaleFactor = "0.5",
spec = "ScaleOperator",
weight = "0.1")),
FrequenciesExchanger.s = list(attrs = c(delta = "0.01",
id = paste0("FrequenciesExchanger.s:", id),
spec = "DeltaExchangeOperator",
weight = "0.1"),
value = list(xmlNode("parameter",
attrs = c(idref = paste0("freqParameter.s:", id)))))
# + <operator delta='0.01' id='FrequenciesExchanger.s:bears' spec='DeltaExchangeOperator' weight='0.1'>
# + <parameter idref='freqParameter.s:bears' />
# + </operator>
)
ops <- match.arg(ops, names(z))
z <- z[[ops]]
if (is.null(z$value)){
xmlNode("operator", attrs = z$attrs)
} else {
xmlNode("operator", attrs = z$attrs, .children = z$value)
}
}
# operator_list <- read.csv("data/operator_list.csv", stringsAsFactors = FALSE)
# save(operator_list, file = "data/operator_list.rda")
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