Merge pull request #79 from jasenfinch/devel

v0.14.2
jasenfinch · May 5, 2021 · 75bf394 · 75bf394
2 parents c2dac81 + ce77102
commit 75bf394
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
-Version: 0.14.1
+Version: 0.14.2
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
 URL:  https://jasenfinch.github.io/metabolyseR

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+# metabolyseR 0.14.2
+
+* Package version, creation date and verbose argument added to prototype of `Analysis` class.
+
+* All generics are now defined as standard generics.
+
+* Added `metrics` method for `Analysis` class.
+
+* `metrics` method for lists now ignores list elements that are not of class `RandomForest`.
+
 # metabolyseR 0.14.1
 
 * Changed the `RSDthresh` argument default to 50% instead of 0.5% in `QCrsdFilter` generic.

diff --git a/R/QC.R b/R/QC.R
@@ -58,9 +58,7 @@ setGeneric("QCimpute",
              occupancy = 2/3, 
              parallel = 'variables', 
              seed = 1234) 
-           {
-             standardGeneric("QCimpute")
-           })
+             standardGeneric("QCimpute"))
 
 #' @rdname QC
 #' @importFrom missForest missForest
@@ -99,9 +97,7 @@ setGeneric("QCoccupancy",
              cls = 'class', 
              QCidx = 'QC', 
              occupancy = 2/3) 
-           {
-             standardGeneric("QCoccupancy")
-           })
+             standardGeneric("QCoccupancy"))
 
 #' @rdname QC
 #' @export
@@ -122,9 +118,8 @@ setMethod('QCoccupancy',signature = 'AnalysisData',
 #' @rdname QC
 #' @export
 
-setGeneric("QCremove", function(d,cls = 'class', QCidx = 'QC') {
-  standardGeneric("QCremove")
-})
+setGeneric("QCremove", function(d,cls = 'class', QCidx = 'QC')
+  standardGeneric("QCremove"))
 
 #' @rdname QC
 #' @importFrom stats sd
@@ -146,9 +141,7 @@ setGeneric("QCrsdFilter",
              cls = 'class',
              QCidx = 'QC', 
              RSDthresh = 50) 
-           {
-             standardGeneric("QCrsdFilter")
-           })
+             standardGeneric("QCrsdFilter"))
 
 #' @rdname QC
 #' @importFrom stats sd

diff --git a/R/aggregate.R b/R/aggregate.R
@@ -40,9 +40,9 @@
 #'  plotPCA(cls = 'day',ellipses = FALSE)
 #' @export
 
-setGeneric("aggregateMean", function(d,cls = 'class') {
+setGeneric("aggregateMean", function(d,cls = 'class') 
   standardGeneric("aggregateMean")
-})
+)
 
 #' @rdname aggregate
 
@@ -72,9 +72,9 @@ setMethod('aggregateMean',signature = 'AnalysisData',
 #' @rdname aggregate
 #' @export
 
-setGeneric("aggregateMedian", function(d,cls = 'class') {
+setGeneric("aggregateMedian", function(d,cls = 'class') 
   standardGeneric("aggregateMedian")
-})
+)
 
 #' @rdname aggregate
 
@@ -104,9 +104,9 @@ setMethod('aggregateMedian',signature = 'AnalysisData',
 #' @rdname aggregate
 #' @export
 
-setGeneric("aggregateSum", function(d,cls = 'class') {
+setGeneric("aggregateSum", function(d,cls = 'class') 
   standardGeneric("aggregateSum")
-})
+)
 
 #' @rdname aggregate
 #' @importFrom dplyr arrange_all group_by_all

diff --git a/R/allClasses.R b/R/allClasses.R
@@ -64,6 +64,12 @@ setClass('Analysis',
            `pre-treated` = 'AnalysisData',
            modelling = 'list',
            correlations = 'tbl_df'
+         ),
+         prototype = list(
+           log = list(packageVersion =  packageVersion('metabolyseR') %>% 
+                        as.character(),
+                      analysis = date(),
+                      verbose = TRUE)
          )
 )
 

diff --git a/R/analysis-accessors.R b/R/analysis-accessors.R
@@ -46,9 +46,9 @@
 #' nFeatures(d)
 #' @export
 
-setGeneric("dat", function(x,...) {
+setGeneric("dat", function(x,...) 
   standardGeneric("dat")
-})
+)
 
 #' @rdname analysis-accessors
 
@@ -81,9 +81,9 @@ setMethod('dat',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("dat<-", function(x,...,value) {
+setGeneric("dat<-", function(x,...,value) 
   standardGeneric("dat<-")
-})
+)
 
 #' @rdname analysis-accessors
 
@@ -119,9 +119,9 @@ setMethod('dat<-',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("sinfo", function(x,...) {
+setGeneric("sinfo", function(x,...) 
   standardGeneric("sinfo")
-})
+)
 
 #' @rdname analysis-accessors
 
@@ -155,9 +155,9 @@ setMethod('sinfo',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("sinfo<-", function(x,...,value) {
+setGeneric("sinfo<-", function(x,...,value) 
   standardGeneric("sinfo<-")
-})
+)
 
 #' @rdname analysis-accessors
 
@@ -194,9 +194,9 @@ setMethod('sinfo<-',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("raw", function(x) {
+setGeneric("raw", function(x) 
   standardGeneric("raw")
-})
+)
 
 #' @rdname analysis-accessors
 
@@ -209,9 +209,8 @@ setMethod('raw',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("raw<-", function(x,value) {
-  standardGeneric("raw<-")
-})
+setGeneric("raw<-", function(x,value)
+  standardGeneric("raw<-"))
 
 #' @rdname analysis-accessors
 
@@ -225,9 +224,8 @@ setMethod('raw<-',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("preTreated", function(x) {
-  standardGeneric("preTreated")
-})
+setGeneric("preTreated", function(x)
+  standardGeneric("preTreated"))
 
 #' @rdname analysis-accessors
 
@@ -240,9 +238,8 @@ setMethod('preTreated',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("preTreated<-", function(x,value) {
-  standardGeneric("preTreated<-")
-})
+setGeneric("preTreated<-", function(x,value)
+  standardGeneric("preTreated<-"))
 
 #' @rdname analysis-accessors
 
@@ -256,9 +253,8 @@ setMethod('preTreated<-',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("features", function(x, ...) {
-  standardGeneric("features")
-})
+setGeneric("features", function(x, ...)
+  standardGeneric("features"))
 
 #' @rdname analysis-accessors
 
@@ -291,9 +287,8 @@ setMethod('features',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("nSamples", function(x, ...) {
-  standardGeneric("nSamples")
-})
+setGeneric("nSamples", function(x, ...)
+  standardGeneric("nSamples"))
 
 #' @rdname analysis-accessors
 
@@ -326,9 +321,8 @@ setMethod('nSamples',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric("nFeatures", function(x, ...) {
-  standardGeneric("nFeatures")
-})
+setGeneric("nFeatures", function(x, ...)
+  standardGeneric("nFeatures"))
 
 #' @rdname analysis-accessors
 
@@ -364,9 +358,8 @@ setMethod('nFeatures',signature = 'Analysis',
 #' @rdname analysis-accessors
 #' @export
 
-setGeneric('analysisResults',function(x,element){
-  standardGeneric('analysisResults')
-})
+setGeneric('analysisResults',function(x,element)
+  standardGeneric('analysisResults'))
 
 #' @rdname analysis-accessors
 

diff --git a/R/correction.R b/R/correction.R
@@ -34,9 +34,7 @@ setGeneric("correctionCenter",
              d, 
              block = 'block', 
              type = c('mean','median')) 
-           {
-             standardGeneric("correctionCenter")
-           })
+             standardGeneric("correctionCenter"))
 
 #' @rdname correction
 #' @importFrom furrr future_map 

diff --git a/R/correlations.R b/R/correlations.R
@@ -19,9 +19,8 @@
 #' correlations(d)
 #' @export
 
-setGeneric("correlations", function(d,...) {
-  standardGeneric("correlations")
-})
+setGeneric("correlations", function(d,...)
+  standardGeneric("correlations"))
 
 #' @rdname correlations
 

diff --git a/R/impute.R b/R/impute.R
@@ -44,9 +44,7 @@ setGeneric("imputeAll",
              occupancy = 2/3, 
              parallel = 'variables', 
              seed = 1234) 
-           {
-             standardGeneric("imputeAll")
-           })
+             standardGeneric("imputeAll"))
 
 #' @rdname impute
 #' @importFrom missForest missForest
@@ -114,9 +112,7 @@ setGeneric("imputeClass",
              cls = 'class', 
              occupancy = 2/3, 
              seed = 1234) 
-           {
-             standardGeneric("imputeClass")
-           })
+             standardGeneric("imputeClass"))
 
 #' @rdname impute
 #' @importFrom furrr furrr_options

diff --git a/R/info.R b/R/info.R
@@ -52,9 +52,8 @@
 #' clsExtract(d,'treatment')
 #' @export
 
-setGeneric("clsAdd", function(d,cls,value,...) {
-  standardGeneric("clsAdd")
-})
+setGeneric("clsAdd", function(d,cls,value,...)
+  standardGeneric("clsAdd"))
 
 #' @rdname cls
 #' @importFrom rlang :=
@@ -103,9 +102,8 @@ setMethod('clsAdd',
 #' @rdname cls
 #' @export
 
-setGeneric("clsArrange", function(d,cls = 'class', descending = FALSE, ...) {
-  standardGeneric("clsArrange")
-})
+setGeneric("clsArrange", function(d,cls = 'class', descending = FALSE, ...)
+  standardGeneric("clsArrange"))
 
 #' @rdname cls
 #' @importFrom dplyr desc
@@ -166,9 +164,8 @@ setMethod('clsArrange',
 #' @rdname cls
 #' @export
 
-setGeneric("clsAvailable", function(d,...) {
-  standardGeneric("clsAvailable")
-})
+setGeneric("clsAvailable", function(d,...)
+  standardGeneric("clsAvailable"))
 
 #' @rdname cls
 
@@ -199,9 +196,8 @@ setMethod('clsAvailable',signature = 'Analysis',function(d,type = c('raw','pre-t
 #' @rdname cls
 #' @export
 
-setGeneric("clsExtract", function(d,cls = 'class', ...) {
-  standardGeneric("clsExtract")
-})
+setGeneric("clsExtract", function(d,cls = 'class', ...)
+  standardGeneric("clsExtract"))
 
 #' @rdname cls
 
@@ -237,9 +233,8 @@ setMethod('clsExtract',
 #' @rdname cls
 #' @export
 
-setGeneric("clsRemove", function(d,cls,...) {
-  standardGeneric("clsRemove")
-})
+setGeneric("clsRemove", function(d,cls,...)
+  standardGeneric("clsRemove"))
 
 #' @rdname cls
 
@@ -283,9 +278,8 @@ setMethod('clsRemove',
 #' @rdname cls
 #' @export
 
-setGeneric("clsRename", function(d,cls,newName, ...) {
-  standardGeneric("clsRename")
-})
+setGeneric("clsRename", function(d,cls,newName, ...)
+  standardGeneric("clsRename"))
 
 #' @rdname cls
 
@@ -324,9 +318,8 @@ setMethod('clsRename',
 #' @rdname cls
 #' @export
 
-setGeneric("clsReplace", function(d,value,cls = 'class', ...) {
-  standardGeneric("clsReplace")
-})
+setGeneric("clsReplace", function(d,value,cls = 'class', ...)
+  standardGeneric("clsReplace"))
 
 #' @rdname cls
 #' @description Replace a given sample info column from an Analysis or