Reexport pca() from dimensio

tesselle · Nov 17, 2023 · 3f2e39c · 3f2e39c
1 parent 5763dea
commit 3f2e39c
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Showing 8 changed files with 34 additions and 13 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -12,6 +12,7 @@ S3method(mean,CompositionMatrix)
 S3method(plot,CompositionMatrix)
 S3method(plot,LogRatio)
 S3method(plot,OutlierIndex)
+export(pca)
 export(remove_NA)
 export(remove_zero)
 export(replace_NA)
@@ -67,6 +68,7 @@ importFrom(arkhe,remove_NA)
 importFrom(arkhe,remove_zero)
 importFrom(arkhe,replace_NA)
 importFrom(arkhe,replace_zero)
+importFrom(dimensio,pca)
 importFrom(grDevices,hcl.colors)
 importFrom(methods,"as<-")
 importFrom(methods,"slot<-")

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -928,7 +928,7 @@ setGeneric(
 #' @author N. Frerebeau
 #' @docType methods
 #' @family multivariate analysis
-#' @name pca
+#' @name pca_coda
 #' @rdname pca
 NULL
 

diff --git a/R/pca.R b/R/pca.R
@@ -8,7 +8,7 @@ NULL
 setMethod(
   f = "pca",
   signature = c("CompositionMatrix"),
-  definition = function(object, center = TRUE, scale = TRUE, rank = NULL,
+  definition = function(object, center = TRUE, scale = FALSE, rank = NULL,
                         sup_row = NULL, sup_col = NULL,
                         weight_row = NULL, weight_col = NULL) {
     stop("You should not do that! Transform your data first.", call. = FALSE)
@@ -21,7 +21,7 @@ setMethod(
 setMethod(
   f = "pca",
   signature = c("LogRatio"),
-  definition = function(object, center = TRUE, scale = TRUE, rank = NULL,
+  definition = function(object, center = TRUE, scale = FALSE, rank = NULL,
                         sup_row = NULL, sup_col = NULL,
                         weight_row = NULL, weight_col = NULL) {
     z <- methods::callNextMethod()

diff --git a/R/reexport.R b/R/reexport.R
@@ -15,3 +15,7 @@ arkhe::remove_NA
 #' @importFrom arkhe remove_zero
 #' @export
 arkhe::remove_zero
+
+#' @importFrom dimensio pca
+#' @export
+dimensio::pca
diff --git a/man/pca.Rd b/man/pca.Rd
diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/man/subset.Rd b/man/subset.Rd
diff --git a/vignettes/nexus.Rmd b/vignettes/nexus.Rmd
@@ -184,12 +184,12 @@ barplot(coda, order = "Ca")
 ## Principle Component Analysis
 
 ```{r ceramics-pca, fig.width=7, fig.height=7, out.width='50%', fig.show='hold'}
-library(dimensio)
-
 ## CLR
 clr <- transform_clr(coda)
 
 ## PCA
+library(dimensio)
+
 clr_pca <- pca(clr, scale = FALSE)
 
 viz_individuals(clr_pca, highlight = get_groups(coda), pch = 16, 
@@ -200,15 +200,25 @@ viz_variables(clr_pca)
 ## MANOVA
 
 ```{r ceramics-manova}
-fit <- manova(transform_ilr(coda) ~ get_groups(coda))
+## ILR
+ilr <- transform_ilr(coda)
+
+## MANOVA
+fit <- manova(ilr ~ get_groups(ilr))
 summary(fit)
 ```
 
 The MANOVA results suggest that there are statistically significant differences between groups.
 
+## Discriminant Analysis
+
 ```{r ceramics-lda, fig.width=7, fig.height=7, out.width='100%'}
-discr <- MASS::lda(transform_ilr(coda), grouping = get_groups(coda))
+## LDA
+discr <- MASS::lda(ilr, grouping = get_groups(ilr))
 plot(discr)
+
+## Back transform results
+transform_inverse(discr$means, origin = ilr)
 ```
 
 # References