microbiome#601 and OMA issue #482 (microbiome#602)

Co-authored-by: Tuomas Borman <[email protected]>
Co-authored-by: Leo Lahti <[email protected]>

DESCRIPTION

@@ -28,7 +28,20 @@ Authors@R:
       person(given = "Giulio", family = "Benedetti", role=c("ctb")),
       person(given = c("Moritz", "Emanuel"), family = "Beber",
              email = "[email protected]", role = c("ctb"),
-             comment = c(ORCID = "0000-0003-2406-1978")))
+             comment = c(ORCID = "0000-0003-2406-1978")),
+      person(given = "Nitesh", family = "Turaga", role=c("ctb")),
+      person(given = "Chouaib", family = "Benchraka", role=c("ctb")),
+      person(given = "Akewak", family = "Jeba", role=c("ctb")),
+      person(given = "Himmi", family = "Lindgren", role=c("ctb")),
+      person(given = "Noah", family = "De Gunst", role=c("ctb")),
+      person(given = "Théotime", family = "Pralas", role=c("ctb")),
+      person(given = "Shadman", family = "Ishraq", role=c("ctb")),
+      person(given = "Eineje", family = "Ameh", role=c("ctb")),
+      person(given = "Artur", family = "Sannikov", role=c("ctb")),
+      person(given = "Hervé", family = "Pagès", role=c("ctb")),
+      person(given = "Rajesh", family = "Shigdel", role=c("ctb")),
+      person(given = "Katariina", family = "Pärnänen", role=c("ctb")),
+      person(given = "Pande", family = "Erawijantari", role=c("ctb")))
 Title: Microbiome analysis
 Description:
     mia implements tools for microbiome analysis based on the 

R/addAlpha.R

@@ -487,7 +487,8 @@ setMethod("addAlpha", signature = c(x = "SummarizedExperiment"),
         }
         # Check if index exists. For each index input, detect it and get
         # information (e.g. internal function) to calculate the index.
-        index <- .get_indices(index, name, x, ...)
+        index <- .get_indices(index, name, x, assay.type, ...)
+
         ############################ Input check end ###########################
         # Looping over the vector of indices to be estimated
         for( i in seq_len(nrow(index)) ){
@@ -512,7 +513,8 @@ setMethod("addAlpha", signature = c(x = "SummarizedExperiment"),
 ################################ HELP FUNCTIONS ################################
 
 # Search alpha diversity index that user wants to calculate.
-.get_indices <- function(index, name, x, tree = NULL, ...){
+
+.get_indices <- function(index, name, x, assay.type, tree = NULL,...){
     # Initialize list for supported indices
     supported <- list()
     # Supported diversity indices
@@ -523,6 +525,7 @@ setMethod("addAlpha", signature = c(x = "SummarizedExperiment"),
     temp[["measure"]] <- "diversity"
     temp[["index_long"]] <- paste0(temp[["index"]], "_", temp[["measure"]])
     temp[["FUN"]] <- ".estimate_diversity"
+    temp[["non_neg"]] <- c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE)
     supported[["diversity"]] <- temp
     # Supported dominance indices
     temp <- c(
@@ -532,6 +535,7 @@ setMethod("addAlpha", signature = c(x = "SummarizedExperiment"),
     temp[["measure"]] <- "dominance"
     temp[["index_long"]] <- paste0(temp[["index"]], "_", temp[["measure"]])
     temp[["FUN"]] <- ".estimate_dominance"
+    temp[["non_neg"]] <- c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)
     supported[["dominance"]] <- temp
     # Supported eveness indices
     temp <- c(
@@ -540,6 +544,7 @@ setMethod("addAlpha", signature = c(x = "SummarizedExperiment"),
     temp[["measure"]] <- "evenness"
     temp[["index_long"]] <- paste0(temp[["index"]], "_", temp[["measure"]])
     temp[["FUN"]] <- ".estimate_evenness"
+    temp[["non_neg"]] <- c(FALSE, FALSE, FALSE, FALSE, FALSE)
     supported[["eveness"]] <- temp
     # Supported richness indices
     temp <- c(
@@ -548,6 +553,7 @@ setMethod("addAlpha", signature = c(x = "SummarizedExperiment"),
     temp[["measure"]] <- "richness"
     temp[["index_long"]] <- paste0(temp[["index"]], "_", temp[["measure"]])
     temp[["FUN"]] <- ".estimate_richness"
+    temp[["non_neg"]] <- c(FALSE, FALSE, FALSE, FALSE)
     supported[["richness"]] <- temp
     # Combine
     supported <- do.call(rbind, supported)
@@ -583,7 +589,18 @@ setMethod("addAlpha", signature = c(x = "SummarizedExperiment"),
         FUN("'faith' index can be calculated only for TreeSE with rowTree(x) ",
             "populated or with 'tree' provided separately.", call. = FALSE)
     }
-    # Check if there are indices left
+    # Check for unsupported values (negative values)
+    if( any(assay(x, assay.type) < 0) ){
+        ind <- detected[["non_neg"]]
+        index_rm <- detected[!ind, "index"]
+        detected <- detected[ind, ]
+        if( length(index_rm) > 0 ){
+            FUN <- if (nrow(detected) == 0) stop else warning
+            FUN("The following indices cannot be calculated due to unsupported 
+                values (negative values): ", paste(index_rm, collapse = ", "), 
+                call. = FALSE)
+        }
+    }
     return(detected)
 }
 

R/runCCA.R

@@ -58,7 +58,9 @@
 #'   the significance test used to analyse \code{vegan::betadisper} results.
 #'   Options include 'permanova' (\code{vegan::permutest}), 'anova'
 #'   (\code{stats::anova}) and 'tukeyhsd' (\code{stats::TukeyHSD}).
-#'   (Default: \code{"permanova"})}
+#'   (By default: \code{homogeneity.test="permanova"})}
+#'   \item{\code{permutations} a numeric value specifying the number of permutations 
+#'   for significance testing in \code{vegan::anova.cca}. (By default: \code{permutations=999})}
 #' }
 #' 
 #' @details
@@ -120,6 +122,8 @@
 #' # can be returned.
 #'  tse <- addRDA(
 #'      tse, data ~ SampleType, homogeneity.test = "anova", full = TRUE)
+#' # Example showing how to pass extra parameters, such as 'permutations', to anova.cca
+#' tse <- addRDA(tse, data ~ SampleType, permutations = 500)
 #' 
 NULL