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minor code reformatting
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@venelin
venelin committed Feb 7, 2019
1 parent 26fd6da commit 5bdfab0
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Showing 5 changed files with 198 additions and 181 deletions.
38 changes: 19 additions & 19 deletions R/BM.R
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ PCMDescribe.BM <- function(model, ...) {

#' @export
PCMCond.BM <- function(
tree, model, r=1, metaI = PCMInfo(NULL, tree, model, verbose = verbose),
tree, model, r = 1, metaI = PCMInfo(NULL, tree, model, verbose = verbose),
verbose=FALSE) {

Sigma_x <- if(is.Global(model$Sigma_x)) as.matrix(model$Sigma_x) else as.matrix(model$Sigma_x[,, r])
Expand Down Expand Up @@ -60,23 +60,24 @@ PCMDescribeParameters.BM <- function(model, ...) {
#' @export
PCMListParameterizations.BM <- function(model, ...) {
list(
X0 = list(c("VectorParameter", "_Global"),
c("VectorParameter", "_Fixed", "_Global"),
c("VectorParameter", "_AllEqual", "_Global"),
c("VectorParameter", "_Omitted")),
Sigma_x =
list(c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal")),
X0 = list(
c("VectorParameter", "_Global"),
c("VectorParameter", "_Fixed", "_Global"),
c("VectorParameter", "_AllEqual", "_Global"),
c("VectorParameter", "_Omitted")),
Sigma_x = list(
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal")),

Sigmae_x =
list(c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Omitted"))
Sigmae_x = list(
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Omitted"))
)
}

Expand All @@ -87,8 +88,7 @@ PCMListDefaultParameterizations.BM <- function(model, ...) {
c("VectorParameter", "_Global"),
c("VectorParameter", "_Omitted")
),
Sigma_x =
list(
Sigma_x = list(
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal")
Expand Down
128 changes: 67 additions & 61 deletions R/DOU.R
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Original file line number Diff line number Diff line change
Expand Up @@ -79,70 +79,76 @@ PCMDescribeParameters.DOU <- function(model, ...) {
#' @export
PCMListParameterizations.DOU <- function(model, ...) {
list(
X0 = list(c("VectorParameter", "_Global"),
c("VectorParameter", "_Fixed", "_Global"),
c("VectorParameter", "_AllEqual", "_Global"),
c("VectorParameter", "_Omitted")),
H1 = list(c("MatrixParameter"),
c("MatrixParameter", "_Fixed"),
c("MatrixParameter", "_Symmetric"),
c("MatrixParameter", "_Diagonal"),
c("MatrixParameter", "_ScalarDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Schur", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_Diagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Global"),
c("MatrixParameter", "_Fixed", "_Global"),
c("MatrixParameter", "_Symmetric", "_Global"),
c("MatrixParameter", "_Diagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_Global"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Schur", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_Diagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global")),
H2 = list(c("MatrixParameter"),
c("MatrixParameter", "_Fixed"),
c("MatrixParameter", "_Symmetric"),
c("MatrixParameter", "_Diagonal"),
c("MatrixParameter", "_ScalarDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Schur", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_Diagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Global"),
c("MatrixParameter", "_Fixed", "_Global"),
c("MatrixParameter", "_Symmetric", "_Global"),
c("MatrixParameter", "_Diagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_Global"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Schur", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_Diagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global")),
X0 = list(
c("VectorParameter", "_Global"),
c("VectorParameter", "_Fixed", "_Global"),
c("VectorParameter", "_AllEqual", "_Global"),
c("VectorParameter", "_Omitted")),
H1 = list(
c("MatrixParameter"),
c("MatrixParameter", "_Fixed"),
c("MatrixParameter", "_Symmetric"),
c("MatrixParameter", "_Diagonal"),
c("MatrixParameter", "_ScalarDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Schur", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_Diagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Global"),
c("MatrixParameter", "_Fixed", "_Global"),
c("MatrixParameter", "_Symmetric", "_Global"),
c("MatrixParameter", "_Diagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_Global"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Schur", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_Diagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global")),
H2 = list(
c("MatrixParameter"),
c("MatrixParameter", "_Fixed"),
c("MatrixParameter", "_Symmetric"),
c("MatrixParameter", "_Diagonal"),
c("MatrixParameter", "_ScalarDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Schur", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_Diagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Schur", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Transformable"),
c("MatrixParameter", "_Global"),
c("MatrixParameter", "_Fixed", "_Global"),
c("MatrixParameter", "_Symmetric", "_Global"),
c("MatrixParameter", "_Diagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_Global"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Schur", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_Diagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global"),
c("MatrixParameter", "_Schur", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Transformable", "_Global")),

Theta = list(c("VectorParameter"),
c("VectorParameter", "_Fixed"),
c("VectorParameter", "_AllEqual")),
Theta = list(
c("VectorParameter"),
c("VectorParameter", "_Fixed"),
c("VectorParameter", "_AllEqual")),

Sigma_x = list(c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal")),
Sigma_x = list(
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal")),

Sigmae_x = list(c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Omitted"))
Sigmae_x = list(
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal"),
c("MatrixParameter", "_UpperTriangularWithDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Diagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_ScalarDiagonal", "_WithNonNegativeDiagonal", "_Global"),
c("MatrixParameter", "_Omitted"))
)
}

Expand Down
12 changes: 8 additions & 4 deletions R/GaussianPCM.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,11 @@ PCMParentClasses.GaussianPCM <- function(model) {
#' @export
PCMCond.GaussianPCM <- function(
tree, model, r=1,
metaI=PCMInfo(NULL, tree, model, verbose = verbose), verbose = FALSE) {
stop(paste('ERR:02111:PCMBase:GaussianPCM.R:PCMCond.GaussianPCM:: This is an abstract function which only defines an interface but should not be called explicitly. Possibly you forgot implementing PCMCond for a daughter class.'))
metaI = PCMInfo(NULL, tree, model, verbose = verbose), verbose = FALSE) {
stop(paste(
'ERR:02111:PCMBase:GaussianPCM.R:PCMCond.GaussianPCM:: This is an abstract', 'function which only defines an interface but should not be called ',
'explicitly. Possibly you forgot implementing PCMCond for a daughter class.'
))
}

#' @export
Expand All @@ -56,8 +59,9 @@ PCMMean.GaussianPCM <- function(
preord <- metaI$preorder

# create a list of random generator functions for each regime
PCMCondObjects <- lapply(1:metaI$RModel, function(r) {
PCMCond(tree, model = model, r = r, metaI = metaI, verbose = verbose)
PCMCondObjects <- lapply(seq_len(metaI$RModel), function(r) {

PCMCond(tree, model = model, r = r, metaI = metaI, verbose = verbose)
})

Mu <- matrix(as.double(NA), k, M)
Expand Down

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