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Fix for issue #162: Replace is() with inherits when class2 is a vector #199

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Fix for issue #162: Replace is() with inherits when class2 is a vector #199

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2 changes: 1 addition & 1 deletion R/S3methods-print.R
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Original file line number Diff line number Diff line change
Expand Up @@ -614,7 +614,7 @@ print.summary <-
digits = x$digits

#--------------------- output pls/spls ---------------------#
if(is(x, c("pls", "spls"))){
if(inherits(x, c("pls", "spls"))){

if (is(x, "pls"))
{
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6 changes: 3 additions & 3 deletions R/plotIndiv.pls.R
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Expand Up @@ -52,11 +52,11 @@ plotIndiv.mixo_pls <-
size.axis = size.axis, size.legend = size.legend, size.legend.title = size.legend.title, legend.title = legend.title,
legend.title.pch = legend.title.pch, legend.position = legend.position, point.lwd = point.lwd)

if (is(object, c("mint.block.pls", "mint.block.spls", "mint.block.plsda", "mint.block.splsda")))
if (inherits(object, c("mint.block.pls", "mint.block.spls", "mint.block.plsda", "mint.block.splsda")))
stop("No plotIndiv for the following functions at this stage: mint.block.pls, mint.block.spls, mint.block.plsda, mint.block.splsda.")

#-- choose rep.space
if (is.null(rep.space) && is(object, "DA"))#"splsda", "plsda", "mlsplsda")))
if (is.null(rep.space) && inherits(object, "DA"))#"splsda", "plsda", "mlsplsda")))
{
rep.space = "X-variate"
} else if (is.null(rep.space)) {
Expand Down Expand Up @@ -182,4 +182,4 @@ plotIndiv.mixo_spls <- plotIndiv.mixo_pls

#' @method plotIndiv rcc
#' @export
plotIndiv.rcc <- plotIndiv.mixo_pls
plotIndiv.rcc <- plotIndiv.mixo_pls
10 changes: 5 additions & 5 deletions R/plotLoadings.R
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Expand Up @@ -956,7 +956,7 @@ check.input.plotLoadings <- function(object,
if (!is(object, "DA"))
{
block = object$names$blocks
} else if (is(object, c("mixo_plsda", "mixo_splsda"))) {
} else if (inherits(object, c("mixo_plsda", "mixo_splsda"))) {
block = "X"
} else {
if (!is.null(object$indY))
Expand All @@ -968,13 +968,13 @@ check.input.plotLoadings <- function(object,
}
}

if (is(object, c("mixo_plsda", "mixo_splsda")) & (!all(block %in% c(1,"X")) | length(block) > 1 ))
if (inherits(object, c("mixo_plsda", "mixo_splsda")) & (!all(block %in% c(1,"X")) | length(block) > 1 ))
stop("'block' can only be 'X' or '1' for plsda and splsda object")

if (is(object, c("mixo_plsda", "mixo_splsda","pca")))
if (inherits(object, c("mixo_plsda", "mixo_splsda","pca")))
{
object$indY = 2
} else if (is(object, c("mixo_pls", "mixo_spls"))) {
} else if (inherits(object, c("mixo_pls", "mixo_spls"))) {
object$indY = 3 # we don't want to remove anything in that case, and 3 is higher than the number of blocks which is 2
}

Expand Down Expand Up @@ -1189,7 +1189,7 @@ get.loadings.ndisplay <- function(object,

#comp
# ----
if (is(object, c("mixo_pls","mixo_spls", "rcc")))# cause pls methods just have 1 ncomp, block approaches have different ncomp per block
if (inherits(object, c("mixo_pls","mixo_spls", "rcc")))# cause pls methods just have 1 ncomp, block approaches have different ncomp per block
{
ncomp = object$ncomp
object$X = list(X = object$X, Y = object$Y) # so that the data is in object$X, either it's a pls or block approach
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6 changes: 3 additions & 3 deletions R/predict.R
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Expand Up @@ -185,7 +185,7 @@ predict.mixo_pls <-

# input parameter: noAveragePredict=> no averagePredict calculation, used in tune.block.splsda

if(is(object, c("rgcca","sparse.rgcca")))
if(inherits(object, c("rgcca","sparse.rgcca")))
stop("no prediction for RGCCA methods")

#check on dist
Expand Down Expand Up @@ -223,7 +223,7 @@ predict.mixo_pls <-
mint.object = c("mint.pls", "mint.spls", "mint.plsda", "mint.splsda")
block.object = c("block.pls", "block.spls", "block.plsda", "block.splsda")
### if the object is a block, the input newdata is different, we check newdata, make sure it's a list and check newdata/X
if(!is(object, block.object)) # not a block (pls/spls/plsda/splsda/mint...)
if(!inherits(object, block.object)) # not a block (pls/spls/plsda/splsda/mint...)
{
p=ncol(object$X)
if(is.list(object$X))
Expand Down Expand Up @@ -624,7 +624,7 @@ predict.mixo_pls <-
if(time) time4 = proc.time()

# basic prediction results
if(is(object, block.object) & length(object$X)>1 )
if(inherits(object, block.object) & length(object$X)>1 )
{
out=list(predict=Y.hat[which(!is.na(ind.match))],variates=t.pred[which(!is.na(ind.match))],B.hat=B.hat[which(!is.na(ind.match))])

Expand Down