diff --git a/DESCRIPTION b/DESCRIPTION
index b75873d4..334a9174 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
-Version: 0.14.8
+Version: 0.14.9
 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
@@ -57,6 +57,7 @@ Collate: allClasses.R
     info.R
     join.R
     keep.R
+    mds.R
     metabolyse.R
     metabolyseR.R
     modelling.R
@@ -80,6 +81,7 @@ Collate: allClasses.R
     remove.R
     randomForest.R
     rsd.R
+    roc.R
     show-method.R
     split.R
     transform.R
diff --git a/NAMESPACE b/NAMESPACE
index 4a9d6df1..40a9c352 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -43,6 +43,7 @@ export(keepClasses)
 export(keepFeatures)
 export(keepSamples)
 export(linearRegression)
+export(mds)
 export(metabolyse)
 export(metrics)
 export(modellingMethods)
@@ -72,6 +73,7 @@ export(preTreated)
 export(preTreatmentElements)
 export(preTreatmentMethods)
 export(preTreatmentParameters)
+export(proximity)
 export(randomForest)
 export(raw)
 export(reAnalyse)
@@ -79,6 +81,7 @@ export(removeClasses)
 export(removeFeatures)
 export(removeSamples)
 export(response)
+export(roc)
 export(rsd)
 export(sinfo)
 export(split)
@@ -113,6 +116,7 @@ importFrom(crayon,green)
 importFrom(crayon,red)
 importFrom(crayon,yellow)
 importFrom(doFuture,registerDoFuture)
+importFrom(dplyr,across)
 importFrom(dplyr,arrange)
 importFrom(dplyr,arrange_all)
 importFrom(dplyr,bind_cols)
@@ -124,14 +128,18 @@ importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_by_all)
 importFrom(dplyr,group_by_at)
+importFrom(dplyr,group_map)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_all)
 importFrom(dplyr,mutate_at)
+importFrom(dplyr,mutate_if)
 importFrom(dplyr,n)
+importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
+importFrom(dplyr,select_if)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_all)
 importFrom(dplyr,ungroup)
diff --git a/NEWS.md b/NEWS.md
index 793fd853..badde6a8 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,13 @@
+# metabolyseR 0.14.9
+
+* Suppressed name repair console message encountered during random forest permutation testing.
+
+* Added the [`proximity()`](https://jasenfinch.github.io/metabolyseR/reference/modelling-accessors.html) method for extracting sample proximities from the [`RandomForest`](https://jasenfinch.github.io/metabolyseR/reference/RandomForest-class.html) S4 class.
+
+* Added the [`mds()`](https://jasenfinch.github.io/metabolyseR/reference/mds.html) method to perform multidimensional scaling on sample proximities from the [`RandomForest`](https://jasenfinch.github.io/metabolyseR/reference/RandomForest-class.html) S4 class.
+
+* Added the [`roc()`](https://jasenfinch.github.io/metabolyseR/reference/roc.html) method to calculate receiver-operator characteristic curves from the [`RandomForest`](https://jasenfinch.github.io/metabolyseR/reference/RandomForest-class.html) S4 class.
+
 # metabolyseR 0.14.8
 
 * An error is now thrown during random forest classification when less than two classes are specified.
diff --git a/R/mds.R b/R/mds.R
new file mode 100644
index 00000000..e9c514cc
--- /dev/null
+++ b/R/mds.R
@@ -0,0 +1,103 @@
+#' Multidimensional scaling (MDS)
+#' @rdname mds
+#' @description Multidimensional scaling of random forest proximities.
+#' @param x S4 object of class `RandomForest`, `Analysis` or a list
+#' @param dimensions The number of dimensions by which the data are to be represented.
+#' @param idx sample information column to use for sample names. If `NULL`, the sample row number will be used. Sample names should be unique for each row of data.
+#' @return 
+#' A tibble containing the scaled dimensions.
+#' @examples
+#' library(metaboData)
+#' 
+#' x <- analysisData(abr1$neg[,200:300],abr1$fact) %>%
+#'        occupancyMaximum(cls = 'day') %>%
+#'        transformTICnorm()
+#'        
+#' rf <- randomForest(x,cls = 'day')
+#' 
+#' mds(rf)
+#' @export
+
+setGeneric("mds", function(x,dimensions = 2,idx = NULL) 
+  standardGeneric("mds")
+)
+
+#' @rdname mds
+#' @importFrom dplyr mutate_if group_map select_if across
+
+setMethod('mds',signature = 'RandomForest',
+          function(x,dimensions = 2,idx = NULL){
+            
+            group_vars <- switch(type(x),
+                                 classification = c('Response','Comparison'),
+                                 regression = 'Response',
+                                 unsupervised = NULL)
+            
+            dissimilarities <- x %>% 
+              proximity(idx = idx) %>% 
+              mutate(across(Sample1:Sample2,as.character)) %>% 
+              spread(Sample2,Proximity) %>% 
+              mutate_if(is.numeric,~ 1 - .x)
+            
+            mds_dimensions <- dissimilarities %>% 
+              group_by_at(group_vars) %>% 
+              group_map(~ .x %>% 
+                          select_if(is.numeric) %>% 
+                          cmdscale(k = dimensions) %>% 
+                          set_colnames(str_c('Dimension ',
+                                             seq_len(dimensions))) %>% 
+                          as_tibble() %>% 
+                          bind_cols(select_if(.x %>% 
+                                                ungroup(),
+                                              is.character)) %>%
+                          relocate(contains('Dimension'),
+                                   .after = last_col()),
+                        .keep = TRUE
+              ) %>% 
+              bind_rows() %>% 
+              rename(Sample = Sample1)
+            
+            if (is.null(idx)){
+              mds_dimensions <- mds_dimensions %>% 
+                mutate(Sample = as.numeric(Sample)) %>% 
+                arrange(across(c(group_vars,'Sample')))
+            }
+            
+            return(mds_dimensions)
+          }
+)
+
+#' @rdname mds
+
+setMethod('mds',signature = 'list',
+          function(x,dimensions = 2,idx = NULL){
+            object_classes <- x %>%
+              map_chr(class)
+            
+            if (FALSE %in% (object_classes == 'RandomForest')) {
+              message(
+                str_c('All objects contained within supplied list ',
+                      'that are not of class RandomForest will be ignored.'))
+            }
+            
+            x <- x[object_classes == 'RandomForest']
+            
+            if (length(x) > 0) {
+              x %>%
+                map(mds,dimensions = dimensions,idx = idx) %>%
+                bind_rows()  
+            } else {
+              tibble()
+            }
+            
+          })
+
+#' @rdname mds
+
+setMethod('mds',signature = 'Analysis',
+          function(x,dimensions = 2,idx = NULL){
+            x %>% 
+              analysisResults('modelling') %>% 
+              mds(dimensions = dimensions,
+                  idx = idx)
+          })
\ No newline at end of file
diff --git a/R/metabolyseR.R b/R/metabolyseR.R
index 8c37214e..75389ffd 100644
--- a/R/metabolyseR.R
+++ b/R/metabolyseR.R
@@ -7,5 +7,5 @@ globalVariables(
     'Occupancy','adjustedPvalue','adjusted.p.value','Label','response',
     '-log10(p)','DF1','Sample1','Proximity','Dimension 1','Dimension 2',
     'x','.level','sensitivity','specificity','Mode','RSD','Median','Colour',
-    'Index','TIC','y','label','batch','correction','N','term','Metric','Frequency','|r|'
+    'Index','TIC','y','label','batch','correction','N','term','Metric','Frequency','|r|','idx_1','idx_2'
   ))
diff --git a/R/modelling-accessors.R b/R/modelling-accessors.R
index aa09fec4..ad11b9d7 100644
--- a/R/modelling-accessors.R
+++ b/R/modelling-accessors.R
@@ -5,6 +5,7 @@
 #' @param cls sample information column to use
 #' @param metric importance metric for which to retrieve explanatory features
 #' @param threshold threshold below which explanatory features are extracted
+#' @param idx sample information column to use for sample names. If `NULL`, the sample row number will be used. Sample names should be unique for each row of data.
 #' @param ... arguments to parse to method for specific class
 #' @section Methods:
 #' * `binaryComparisons`: Return a vector of all possible binary comparisons for a given sample information column.
@@ -13,6 +14,7 @@
 #' * `metrics`: Retrieve the model performance metrics for a random forest analysis
 #' * `importanceMetrics`: Retrieve the available feature importance metrics for a random forest analysis.
 #' * `importance`: Retrieve feature importance results.
+#' * `proximity`: Retrieve the random forest sample proximities.
 #' * `explanatoryFeatures`: Retrieve explanatory features.
 #' @examples 
 #' library(metaboData)
@@ -40,6 +42,9 @@
 #' ## Retrieve the feature importance results
 #' importance(rf_analysis)
 #' 
+#' ## Retrieve the sample proximities
+#' proximity(rf_analysis)
+#' 
 #' ## Retrieve the explanatory features
 #' explanatoryFeatures(rf_analysis,metric = 'FalsePositiveRate',threshold = 0.05)
 #' @export
@@ -210,6 +215,98 @@ setMethod('importance',signature = 'Analysis',
 #' @rdname modelling-accessors
 #' @export
 
+setGeneric("proximity", function(x,idx = NULL) 
+  standardGeneric("proximity")
+)
+
+#' @rdname modelling-accessors
+#' @importFrom dplyr relocate
+
+setMethod('proximity',signature = 'RandomForest',
+          function(x,idx = NULL){
+            
+            group_vars <- switch(type(x),
+                                 classification = c('Response','Comparison'),
+                                 regression = 'Response',
+                                 unsupervised = NULL) %>% 
+              c(.,'Sample1','Sample2')
+            
+            proximities <- x@proximities %>% 
+              group_by_at(group_vars) %>% 
+              summarise(Proximity = mean(Proximity),
+                        .groups = 'drop')
+            
+            if (!is.null(idx)){
+              sample_idx <- x %>% 
+                clsExtract(cls = idx)
+              
+              if (any(duplicated(sample_idx))){
+                stop(str_c('Duplicated sample names found in sample information column `',
+                           idx,
+                           '`. The specified sample names should be unique to each sample.'),
+                     call. = FALSE)
+              }
+              
+              sample_idx <- sample_idx %>% 
+                tibble(idx = .) %>% 
+                rowid_to_column(var = 'row')
+              
+              proximities <- proximities %>% 
+                left_join(sample_idx,
+                          by = c('Sample1' = 'row')) %>% 
+                rename(idx_1 = idx) %>% 
+                left_join(sample_idx,
+                          by = c('Sample2' = 'row')) %>% 
+                rename(idx_2 = idx) %>% 
+                select(-Sample1,
+                       -Sample2,
+                       Sample1 = idx_1,
+                       Sample2 = idx_2) %>% 
+                relocate(Proximity,.after = Sample2)
+            }
+            
+            return(proximities)
+          }
+)
+
+#' @rdname modelling-accessors
+
+setMethod('proximity',signature = 'list',
+          function(x,idx = NULL){
+            object_classes <- x %>%
+              map_chr(class)
+            
+            if (FALSE %in% (object_classes == 'RandomForest')) {
+              message(
+                str_c('All objects contained within supplied list ',
+                      'that are not of class RandomForest will be ignored.'))
+            }
+            
+            x <- x[object_classes == 'RandomForest']
+            
+            if (length(x) > 0) {
+              x %>%
+                map(proximity,idx = idx) %>%
+                bind_rows()  
+            } else {
+              tibble()
+            }
+            
+          })
+
+#' @rdname modelling-accessors
+
+setMethod('proximity',signature = 'Analysis',
+          function(x,idx = NULL){
+            x %>% 
+              analysisResults(element = 'modelling') %>% 
+              proximity(idx = idx)
+          })
+
+
+#' @rdname modelling-accessors
+#' @export
+
 setGeneric('explanatoryFeatures', function(x,...) 
   standardGeneric("explanatoryFeatures")
 )
diff --git a/R/modellingPlots.R b/R/modellingPlots.R
index b69373b3..ff743a04 100644
--- a/R/modellingPlots.R
+++ b/R/modellingPlots.R
@@ -384,33 +384,11 @@ setMethod('plotMDS',
               } 
             }
             
-            if (x@type == 'classification') {
-              proximities <- x@proximities %>%
-                base::split(.$Comparison) %>%
-                map(~{
-                  d <- .
-                  d %>%
-                    group_by(Sample1,Sample2) %>%
-                    summarise(Proximity = mean(Proximity),.groups = 'drop') %>%
-                    spread(Sample2,Proximity) %>%
-                    ungroup() %>%
-                    select(-Sample1)
-                }) 
-              suppressWarnings({
-                mds <- proximities %>%
-                  map(~{
-                    d <- .
-                    d %>%
-                      {1 - .} %>%
-                      cmdscale() %>%
-                      as_tibble() %>%
-                      set_colnames(c('Dimension 1','Dimension 2')) 
-                  }) %>%
-                  bind_rows(.id = 'Comparison')
-              })
-              
+            mds_dimensions <- mds(x)
+            
+            if (type(x) == 'classification') {
               if (!is.null(cls)) {
-                mds <- mds %>%
+                mds_dimensions <- mds_dimensions %>%
                   base::split(.$Comparison) %>%
                   map(~{
                     comparison <- str_split(.x$Comparison[1],'~')[[1]]
@@ -429,7 +407,7 @@ setMethod('plotMDS',
               }
               
               if (!is.null(label)) {
-                mds <- mds %>%
+                mds_dimensions <- mds_dimensions %>%
                   base::split(.$Comparison) %>%
                   map(~{
                     d <- .
@@ -452,22 +430,8 @@ setMethod('plotMDS',
               }
               
             } else {
-              proximities <- x@proximities %>%
-                group_by(Sample1,Sample2) %>%
-                summarise(Proximity = mean(Proximity)) %>%
-                spread(Sample2,Proximity) %>%
-                ungroup() %>%
-                select(-Sample1)
-              
-              suppressWarnings({
-                mds <- proximities %>%
-                  {1 - .} %>%
-                  cmdscale() %>%
-                  as_tibble() %>%
-                  set_colnames(c('Dimension 1','Dimension 2'))
-              })  
               if (!is.null(cls)) {
-                mds <- mds %>%
+                mds_dimensions <- mds_dimensions %>%
                   bind_cols(x %>%
                               sinfo() %>%
                               select(cls) %>%
@@ -476,7 +440,7 @@ setMethod('plotMDS',
               }
               
               if (!is.null(label)) {
-                mds <- mds %>%
+                mds_dimensions <- mds_dimensions %>%
                   bind_cols(x %>%
                               sinfo() %>%
                               select(label))
@@ -490,7 +454,7 @@ setMethod('plotMDS',
             }
             
             pl <- scatterPlot(
-              mds,
+              mds_dimensions,
               cls,
               'Dimension 1',
               'Dimension 2',
@@ -581,32 +545,7 @@ setGeneric("plotROC", function(x, title = '', legendPosition = 'bottom')
 setMethod('plotROC',signature = 'RandomForest',
           function(x,title = '', legendPosition = 'bottom'){
             
-            if (x@type != 'classification') {
-              stop('ROC curves can only be plotted for classification!')
-            }
-            
-            preds <- x@predictions %>%
-              base::split(.$Comparison) %>%
-              map(~{
-                d <- .
-                d <- d %>%
-                  mutate(obs = factor(obs))
-                
-                suppressMessages({
-                  suppressWarnings({
-                    if (length(levels(d$obs)) > 2) {
-                      d %>%
-                        group_by(Comparison) %>%
-                        roc_curve(obs,levels(d$obs))  
-                    } else {
-                      d %>%
-                        group_by(Comparison) %>%
-                        roc_curve(obs,levels(d$obs)[1])  
-                    }  
-                  })   
-                })
-              }) %>%
-              bind_rows()
+            preds <- roc(x)
             
             meas <- x@results$measures %>%
               filter(.metric == 'roc_auc') %>%
@@ -614,9 +553,9 @@ setMethod('plotROC',signature = 'RandomForest',
                      y = 0, 
                      label = str_c('AUC: ',round(.estimate,3)))
             
-            if ('.level' %in% colnames(preds)) {
+            if ('Class' %in% colnames(preds)) {
               preds <- preds %>%
-                arrange(.level,sensitivity)
+                arrange(Class,sensitivity)
               
               pl <- preds %>%
                 ggplot() +
@@ -624,8 +563,8 @@ setMethod('plotROC',signature = 'RandomForest',
                 geom_line(
                   aes(x = 1 - specificity, 
                       y = sensitivity,
-                      group = .level,
-                      colour = .level)) +
+                      group = Class,
+                      colour = Class)) +
                 geom_text(data = meas,aes(x = x,y = y,label = label),size = 3) +
                 theme_bw() +
                 facet_wrap(~Comparison) +
@@ -635,7 +574,7 @@ setMethod('plotROC',signature = 'RandomForest',
                     title = x@results$measures$Response[1])) +
                 labs(title = title)
               
-              if ((preds$.level %>% unique() %>% length()) <= 12) {
+              if ((preds$Class %>% unique() %>% length()) <= 12) {
                 pl <- pl +
                   scale_colour_ptol()
               }  
diff --git a/R/randomForest.R b/R/randomForest.R
index 5cc55042..209da111 100644
--- a/R/randomForest.R
+++ b/R/randomForest.R
@@ -25,8 +25,8 @@ permute <- function(x,cls,rf,n = 1000){
     params$strata <- ind
     do.call(randomForest::randomForest,params)
   },.options = furrr_options(seed = runif(1) %>% 
-    {. * 100000} %>% 
-    round())) %>%
+                               {. * 100000} %>% 
+                               round())) %>%
     set_names(1:n)
   
   return(models)
@@ -35,7 +35,7 @@ permute <- function(x,cls,rf,n = 1000){
 importance <- function(x){
   x %>%
     randomForest::importance() %>%
-    {bind_cols(tibble(Feature = rownames(.)),as_tibble(.))}
+    {bind_cols(tibble(Feature = rownames(.)),as_tibble(.,.name_repair = 'minimal'))}
 }
 
 #' @importFrom randomForest margin
@@ -149,9 +149,11 @@ classificationPermutationMeasures <- function(models){
                    pred = m$predicted,
                    margin = margin(m)) %>%
               bind_cols(m$votes %>%
-                          as_tibble())
+                          as_tibble(.name_repair = 'minimal'))
           }) %>%
-            bind_rows(.id = 'Permutation') %>%
+            {
+              suppressMessages(bind_rows(.,.id = 'Permutation'))
+            } %>%
             mutate(Permutation = as.numeric(Permutation))
         }) %>%
           bind_rows(.id = 'Comparison')
@@ -352,7 +354,7 @@ unsupervised <- function(x,rf,reps,returnModels,seed,...){
   
   proximities <- models %>%
     map(.,~{.$proximity %>%
-        as_tibble() %>%
+        as_tibble(.name_repair = 'minimal') %>%
         mutate(Sample = seq_len(nrow(.))) %>%
         gather('Sample2','Proximity',-Sample) %>%
         rename(Sample1 = Sample)
@@ -476,7 +478,7 @@ classification <- function(x,
   }
   
   if (length(unique(deframe(i))) < 2) {
-   stop('Need at least two classes to do classification.',call. = FALSE) 
+    stop('Need at least two classes to do classification.',call. = FALSE) 
   }
   
   if (length(comparisons) > 0) {
diff --git a/R/roc.R b/R/roc.R
new file mode 100644
index 00000000..016ff219
--- /dev/null
+++ b/R/roc.R
@@ -0,0 +1,91 @@
+#' Receiver-operator characteristic (ROC) curves
+#' @rdname roc
+#' @description  ROC curves for out-of-bag random forest predictions.
+#' @param x S4 object of class `RandomForest`, `Analysis` or a list
+#' @return 
+#' A tibble containing the ROC curves.
+#' @examples
+#' library(metaboData)
+#' 
+#' x <- analysisData(abr1$neg[,200:300],abr1$fact) %>%
+#'        occupancyMaximum(cls = 'day') %>%
+#'        transformTICnorm()
+#'        
+#' rf <- randomForest(x,cls = 'day')
+#' 
+#' roc(rf)
+#' @export
+
+setGeneric("roc", function(x) 
+  standardGeneric("roc")
+)
+
+#' @rdname roc
+
+setMethod('roc',signature = 'RandomForest',
+          function(x){
+            
+            if (type(x) != 'classification') {
+              stop('ROC curves can only be plotted for classification!')
+            }
+            
+            roc_curves <- x@predictions %>%
+              group_by(Response,Comparison) %>% 
+              group_map(~{
+                .x <- .x %>% 
+                  mutate(obs = factor(obs)) 
+                
+                if (length(levels(.x$obs)) > 2) {
+                  .x %>%
+                    group_by(Response,Comparison) %>% 
+                    roc_curve(obs,levels(.x$obs))  
+                } else {
+                  .x %>%
+                    group_by(Response,Comparison) %>% 
+                    roc_curve(obs,levels(.x$obs)[1])  
+                } 
+              }, .keep = TRUE) %>%
+              bind_rows() %>% 
+              ungroup() 
+            
+            if ('.level' %in% colnames(roc_curves)) {
+              roc_curves <- roc_curves %>% 
+                rename(Class = .level)
+            }
+            
+            return(roc_curves)
+          })
+
+#' @rdname roc
+
+setMethod('roc',signature = 'list',
+          function(x){
+            object_classes <- x %>%
+              map_chr(class)
+            
+            if (FALSE %in% (object_classes == 'RandomForest')) {
+              message(
+                str_c('All objects contained within supplied list ',
+                      'that are not of class RandomForest will be ignored.'))
+            }
+            
+            x <- x[object_classes == 'RandomForest']
+            
+            if (length(x) > 0) {
+              x %>%
+                map(roc) %>%
+                bind_rows()  
+            } else {
+              tibble()
+            }
+            
+          })
+
+#' @rdname roc
+
+setMethod('roc',signature = 'Analysis',
+          function(x){
+            x %>% 
+              analysisResults('modelling') %>% 
+              roc()
+          })
\ No newline at end of file
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 10732abf..a475f749 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -55,6 +55,8 @@ reference:
     - ttest
     - linearRegression
     - binaryComparisons
+    - mds
+    - roc
 
   - title: Correlations
     contents:
diff --git a/docs/404.html b/docs/404.html
index 6755b37a..44d3a98f 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -32,7 +32,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://jasenfinch.github.io/metabolyseR/index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -106,7 +106,7 @@ <h1>Page not found (404)</h1>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index cca40185..6c4c2dcc 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/articles/metabolyseR.html b/docs/articles/metabolyseR.html
index f3312b42..e3440bd4 100644
--- a/docs/articles/metabolyseR.html
+++ b/docs/articles/metabolyseR.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -85,10 +85,10 @@
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Introduction</h1>
-            <h3 data-toc-skip class="subtitle">metabolyseR v0.14.8</h3>
+            <h3 data-toc-skip class="subtitle">metabolyseR v0.14.9</h3>
                         <h4 data-toc-skip class="author">Jasen Finch</h4>
             
-            <h4 data-toc-skip class="date">06 January, 2022</h4>
+            <h4 data-toc-skip class="date">27 January, 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jasenfinch/metabolyseR/blob/HEAD/vignettes/metabolyseR.Rmd" class="external-link"><code>vignettes/metabolyseR.Rmd</code></a></small>
       <div class="hidden name"><code>metabolyseR.Rmd</code></div>
@@ -634,7 +634,7 @@ <h3 id="performing-an-analysis">Performing an analysis<a class="anchor" aria-lab
 <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">analysis</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/metabolyse.html">metabolyse</a></span><span class="op">(</span><span class="va">abr1</span><span class="op">$</span><span class="va">neg</span><span class="op">[</span>,<span class="fl">1</span><span class="op">:</span><span class="fl">200</span><span class="op">]</span>,<span class="va">abr1</span><span class="op">$</span><span class="va">fact</span>,<span class="va">p</span><span class="op">)</span> </code></pre></div>
 <pre><code><span class="co">## </span>
-<span class="co"><span style="color: #0000BB;">## metabolyseR </span> <span style="color: #BB0000;">v0.14.8</span> Thu Jan  6 13:52:47 2022</span></code></pre>
+<span class="co"><span style="color: #0000BB;">## metabolyseR </span> <span style="color: #BB0000;">v0.14.9</span> Thu Jan 27 11:59:17 2022</span></code></pre>
 <pre><code><span class="co">## ________________________________________________________________________________</span></code></pre>
 <pre><code><span class="co">## <span style="color: #BBBB00;">Parameters:</span></span>
 <span class="co">## pre-treatment</span>
@@ -658,33 +658,33 @@ <h3 id="performing-an-analysis">Performing an analysis<a class="anchor" aria-lab
 <pre><code><span class="co">## ________________________________________________________________________________</span></code></pre>
 <pre><code>## 
[34mPre-treatment 
[39m…
 
-
[34mPre-treatment 
[39m    
[32m✓
[39m [0.8S]
+
[34mPre-treatment 
[39m    
[32m✓
[39m [0.7S]
 ## 
[34mModelling 
[39m…
 
[34m
-Modelling 
[39m 
[32m✓
[39m [3.6S]
+Modelling 
[39m 
[32m✓
[39m [2.4S]
 ## ________________________________________________________________________________
 ## 
-## 
[32mComplete! 
[39m[4.4S]</code></pre>
+## 
[32mComplete! 
[39m[3.1S]</code></pre>
 <p><strong>Note: If a data pre-treatment step is not performed prior to modelling or correlation analysis, the raw data will automatically be used.</strong></p>
 <p>The <code>analysis</code> object containing the analysis results can be printed to provide some basic information about the results of the analysis.</p>
 <div class="sourceCode" id="cb68"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">analysis</span><span class="op">)</span></code></pre></div>
 <pre><code><span class="co">## </span>
-<span class="co">## <span style="color: #0000BB;">metabolyseR </span><span style="color: #BB0000; font-weight: bold;">v0.14.8</span></span>
+<span class="co">## <span style="color: #0000BB;">metabolyseR </span><span style="color: #BB0000; font-weight: bold;">v0.14.9</span></span>
 <span class="co"><span style="color: #BBBB00;">## Analysis:</span></span>
-<span class="co"><span style="color: #BBBB00;">## </span>    Thu Jan  6 13:52:47 2022</span>
+<span class="co"><span style="color: #BBBB00;">## </span>    Thu Jan 27 11:59:17 2022</span>
 <span class="co">## </span>
 <span class="co">##  Raw Data:</span>
 <span class="co">##      No. samples = 120</span>
 <span class="co">##      No. features = 200</span>
 <span class="co">## </span>
 <span class="co">##  Pre-treated Data:</span>
-<span class="co">##      Thu Jan  6 13:52:47 2022</span>
+<span class="co">##      Thu Jan 27 11:59:18 2022</span>
 <span class="co">##      No. samples = 120</span>
 <span class="co">##      No. features = 48</span>
 <span class="co">## </span>
 <span class="co">##  Modelling:</span>
-<span class="co">##      Thu Jan  6 13:52:51 2022</span>
+<span class="co">##      Thu Jan 27 11:59:20 2022</span>
 <span class="co">##      Methods: randomForest</span></code></pre>
 </div>
 <div class="section level3">
@@ -699,7 +699,7 @@ <h3 id="performing-a-re-analysis">Performing a re-analysis<a class="anchor" aria
 <div class="sourceCode" id="cb71"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">analysis</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/metabolyse.html">reAnalyse</a></span><span class="op">(</span><span class="va">analysis</span>,<span class="va">parameters</span><span class="op">)</span></code></pre></div>
 <pre><code><span class="co">## </span>
-<span class="co">## <span style="color: #0000BB;">metabolyseR</span> <span style="color: #BB0000;">v0.14.8</span> Thu Jan  6 13:52:51 2022</span>
+<span class="co">## <span style="color: #0000BB;">metabolyseR</span> <span style="color: #BB0000;">v0.14.9</span> Thu Jan 27 11:59:21 2022</span>
 <span class="co">## ________________________________________________________________________________</span>
 <span class="co">## <span style="color: #BBBB00;">Parameters:</span></span>
 <span class="co">## correlations</span>
@@ -717,25 +717,25 @@ <h3 id="performing-a-re-analysis">Performing a re-analysis<a class="anchor" aria
 <div class="sourceCode" id="cb75"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">analysis</span><span class="op">)</span></code></pre></div>
 <pre><code><span class="co">## </span>
-<span class="co">## <span style="color: #0000BB;">metabolyseR </span><span style="color: #BB0000; font-weight: bold;">v0.14.8</span></span>
+<span class="co">## <span style="color: #0000BB;">metabolyseR </span><span style="color: #BB0000; font-weight: bold;">v0.14.9</span></span>
 <span class="co"><span style="color: #BBBB00;">## Analysis:</span></span>
-<span class="co"><span style="color: #BBBB00;">## </span>    Thu Jan  6 13:52:47 2022</span>
+<span class="co"><span style="color: #BBBB00;">## </span>    Thu Jan 27 11:59:17 2022</span>
 <span class="co">## </span>
 <span class="co">##  Raw Data:</span>
 <span class="co">##      No. samples = 120</span>
 <span class="co">##      No. features = 200</span>
 <span class="co">## </span>
 <span class="co">##  Pre-treated Data:</span>
-<span class="co">##      Thu Jan  6 13:52:47 2022</span>
+<span class="co">##      Thu Jan 27 11:59:18 2022</span>
 <span class="co">##      No. samples = 120</span>
 <span class="co">##      No. features = 48</span>
 <span class="co">## </span>
 <span class="co">##  Modelling:</span>
-<span class="co">##      Thu Jan  6 13:52:51 2022</span>
+<span class="co">##      Thu Jan 27 11:59:20 2022</span>
 <span class="co">##      Methods: randomForest</span>
 <span class="co">## </span>
 <span class="co">##  Correlations:</span>
-<span class="co">##      Thu Jan  6 13:52:51 2022</span>
+<span class="co">##      Thu Jan 27 11:59:21 2022</span>
 <span class="co">##      No. correlations = 140</span></code></pre>
 </div>
 <div class="section level3">
@@ -832,7 +832,7 @@ <h3 id="extracting-analysis-results">Extracting analysis results<a class="anchor
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/modelling.html b/docs/articles/modelling.html
index 08a1a680..71b72881 100644
--- a/docs/articles/modelling.html
+++ b/docs/articles/modelling.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -85,10 +85,10 @@
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Modelling and feature selection</h1>
-            <h3 data-toc-skip class="subtitle">metabolyseR v0.14.8</h3>
+            <h3 data-toc-skip class="subtitle">metabolyseR v0.14.9</h3>
                         <h4 data-toc-skip class="author">Jasen Finch</h4>
             
-            <h4 data-toc-skip class="date">06 January, 2022</h4>
+            <h4 data-toc-skip class="date">27 January, 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jasenfinch/metabolyseR/blob/HEAD/vignettes/modelling.Rmd" class="external-link"><code>vignettes/modelling.Rmd</code></a></small>
       <div class="hidden name"><code>modelling.Rmd</code></div>
@@ -733,7 +733,7 @@ <h2 id="routine-analyses">Routine analyses<a class="anchor" aria-label="anchor"
 <p>The analysis can then be executed.</p>
 <div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb59-1"><a href="#cb59-1" aria-hidden="true" tabindex="-1"></a>analysis <span class="ot">&lt;-</span> <span class="fu">metabolyse</span>(abr1<span class="sc">$</span>neg,abr1<span class="sc">$</span>fact,p)</span>
 <span id="cb59-2"><a href="#cb59-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[34m</span></span>
-<span id="cb59-3"><a href="#cb59-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; metabolyseR 
[39m 
[31mv0.14.8
[39m Thu Jan  6 13:54:01 2022</span></span>
+<span id="cb59-3"><a href="#cb59-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; metabolyseR 
[39m 
[31mv0.14.9
[39m Thu Jan 27 12:00:15 2022</span></span>
 <span id="cb59-4"><a href="#cb59-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ________________________________________________________________________________</span></span>
 <span id="cb59-5"><a href="#cb59-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[33m
[33mParameters:
[33m
[39m</span></span>
 <span id="cb59-6"><a href="#cb59-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; pre-treatment</span></span>
@@ -766,13 +766,13 @@ <h2 id="routine-analyses">Routine analyses<a class="anchor" aria-label="anchor"
 <span id="cb59-33"><a href="#cb59-33" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ________________________________________________________________________________</span></span>
 <span id="cb59-34"><a href="#cb59-34" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[34mPre-treatment 
[39m…</span></span>
 <span id="cb59-35"><a href="#cb59-35" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb59-36"><a href="#cb59-36" aria-hidden="true" tabindex="-1"></a>
[34mPre<span class="sc">-</span>treatment 
[39m    
[32m✓
[39m [<span class="fl">6.3</span>S]</span>
+<span id="cb59-36"><a href="#cb59-36" aria-hidden="true" tabindex="-1"></a>
[34mPre<span class="sc">-</span>treatment 
[39m    
[32m✓
[39m [<span class="fl">4.6</span>S]</span>
 <span id="cb59-37"><a href="#cb59-37" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[34mModelling 
[39m…</span></span>
 <span id="cb59-38"><a href="#cb59-38" aria-hidden="true" tabindex="-1"></a>
[34m</span>
-<span id="cb59-39"><a href="#cb59-39" aria-hidden="true" tabindex="-1"></a>Modelling 
[39m 
[32m✓
[39m [<span class="fl">4.4</span>S]</span>
+<span id="cb59-39"><a href="#cb59-39" aria-hidden="true" tabindex="-1"></a>Modelling 
[39m 
[32m✓
[39m [<span class="fl">3.1</span>S]</span>
 <span id="cb59-40"><a href="#cb59-40" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ________________________________________________________________________________</span></span>
 <span id="cb59-41"><a href="#cb59-41" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb59-42"><a href="#cb59-42" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[32mComplete! 
[39m[10.7S]</span></span></code></pre></div>
+<span id="cb59-42"><a href="#cb59-42" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[32mComplete! 
[39m[7.8S]</span></span></code></pre></div>
 <p>The results for the modelling can be specifically extracted using the following.</p>
 <div class="sourceCode" id="cb60"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/analysis-accessors.html">analysisResults</a></span><span class="op">(</span><span class="va">analysis</span>,<span class="st">'modelling'</span><span class="op">)</span>
@@ -842,7 +842,7 @@ <h2 id="routine-analyses">Routine analyses<a class="anchor" aria-label="anchor"
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/modelling_files/figure-html/anova-feature-1.png b/docs/articles/modelling_files/figure-html/anova-feature-1.png
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diff --git a/docs/articles/modelling_files/figure-html/binary-mds-1.png b/docs/articles/modelling_files/figure-html/binary-mds-1.png
index c987d198..6e555e6d 100644
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diff --git a/docs/articles/modelling_files/figure-html/classification-comparison-mds-roc-1.png b/docs/articles/modelling_files/figure-html/classification-comparison-mds-roc-1.png
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diff --git a/docs/articles/modelling_files/figure-html/multinomial-mds-1.png b/docs/articles/modelling_files/figure-html/multinomial-mds-1.png
index 898dec8e..e8cc701c 100644
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diff --git a/docs/articles/modelling_files/figure-html/regression-mds-1.png b/docs/articles/modelling_files/figure-html/regression-mds-1.png
index 5044ab7a..68791ea1 100644
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diff --git a/docs/articles/modelling_files/figure-html/unsupervised-feature-1.png b/docs/articles/modelling_files/figure-html/unsupervised-feature-1.png
index f3fb1c9b..be8b1882 100644
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diff --git a/docs/articles/modelling_files/figure-html/unsupervised-rf-1.png b/docs/articles/modelling_files/figure-html/unsupervised-rf-1.png
index ab56c547..7c66d01e 100644
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diff --git a/docs/articles/pre_treatment.html b/docs/articles/pre_treatment.html
index 54dbf2cf..91eefe6f 100644
--- a/docs/articles/pre_treatment.html
+++ b/docs/articles/pre_treatment.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -85,10 +85,10 @@
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Metabolomics data pre-treatment</h1>
-            <h3 data-toc-skip class="subtitle">metabolyseR v0.14.8</h3>
+            <h3 data-toc-skip class="subtitle">metabolyseR v0.14.9</h3>
                         <h4 data-toc-skip class="author">Jasen Finch</h4>
             
-            <h4 data-toc-skip class="date">06 January, 2022</h4>
+            <h4 data-toc-skip class="date">27 January, 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jasenfinch/metabolyseR/blob/HEAD/vignettes/pre_treatment.Rmd" class="external-link"><code>vignettes/pre_treatment.Rmd</code></a></small>
       <div class="hidden name"><code>pre_treatment.Rmd</code></div>
@@ -496,7 +496,7 @@ <h2 id="routine-analyses">Routine analyses<a class="anchor" aria-label="anchor"
 <p>The pre-treatment routine can then be executed.</p>
 <div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb46-1"><a href="#cb46-1" aria-hidden="true" tabindex="-1"></a>analysis <span class="ot">&lt;-</span> <span class="fu">metabolyse</span>(abr1<span class="sc">$</span>neg,abr1<span class="sc">$</span>fact,p)</span>
 <span id="cb46-2"><a href="#cb46-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[34m</span></span>
-<span id="cb46-3"><a href="#cb46-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; metabolyseR 
[39m 
[31mv0.14.8
[39m Thu Jan  6 13:58:01 2022</span></span>
+<span id="cb46-3"><a href="#cb46-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; metabolyseR 
[39m 
[31mv0.14.9
[39m Thu Jan 27 12:03:18 2022</span></span>
 <span id="cb46-4"><a href="#cb46-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ________________________________________________________________________________</span></span>
 <span id="cb46-5"><a href="#cb46-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[33m
[33mParameters:
[33m
[39m</span></span>
 <span id="cb46-6"><a href="#cb46-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; pre-treatment</span></span>
@@ -513,24 +513,24 @@ <h2 id="routine-analyses">Routine analyses<a class="anchor" aria-label="anchor"
 <span id="cb46-17"><a href="#cb46-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ________________________________________________________________________________</span></span>
 <span id="cb46-18"><a href="#cb46-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[34mPre-treatment 
[39m…</span></span>
 <span id="cb46-19"><a href="#cb46-19" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb46-20"><a href="#cb46-20" aria-hidden="true" tabindex="-1"></a>
[34mPre<span class="sc">-</span>treatment 
[39m    
[32m✓
[39m [<span class="fl">9.4</span>S]</span>
+<span id="cb46-20"><a href="#cb46-20" aria-hidden="true" tabindex="-1"></a>
[34mPre<span class="sc">-</span>treatment 
[39m    
[32m✓
[39m [<span class="fl">6.5</span>S]</span>
 <span id="cb46-21"><a href="#cb46-21" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ________________________________________________________________________________</span></span>
 <span id="cb46-22"><a href="#cb46-22" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb46-23"><a href="#cb46-23" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[32mComplete! 
[39m[9.5S]</span></span></code></pre></div>
+<span id="cb46-23"><a href="#cb46-23" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 
[32mComplete! 
[39m[6.5S]</span></span></code></pre></div>
 <p>Printing the <code>analysis</code> object shows the resulting data from the pre-treatment routine.</p>
 <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">analysis</span><span class="op">)</span>
 <span class="co">#&gt; </span>
-<span class="co">#&gt; <span style="color: #0000BB;">metabolyseR </span><span style="color: #BB0000; font-weight: bold;">v0.14.8</span></span>
+<span class="co">#&gt; <span style="color: #0000BB;">metabolyseR </span><span style="color: #BB0000; font-weight: bold;">v0.14.9</span></span>
 <span class="co"><span style="color: #BBBB00;">#&gt; Analysis:</span></span>
-<span class="co"><span style="color: #BBBB00;">#&gt; </span>    Thu Jan  6 13:58:01 2022</span>
+<span class="co"><span style="color: #BBBB00;">#&gt; </span>    Thu Jan 27 12:03:18 2022</span>
 <span class="co">#&gt; </span>
 <span class="co">#&gt;  Raw Data:</span>
 <span class="co">#&gt;      No. samples = 120</span>
 <span class="co">#&gt;      No. features = 2000</span>
 <span class="co">#&gt; </span>
 <span class="co">#&gt;  Pre-treated Data:</span>
-<span class="co">#&gt;      Thu Jan  6 13:58:10 2022</span>
+<span class="co">#&gt;      Thu Jan 27 12:03:24 2022</span>
 <span class="co">#&gt;      No. samples = 60</span>
 <span class="co">#&gt;      No. features = 1723</span></code></pre></div>
 <p>The pre-treated data can be extracted from the <code>Analysis</code> object using several methods.</p>
@@ -577,7 +577,7 @@ <h2 id="routine-analyses">Routine analyses<a class="anchor" aria-label="anchor"
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>
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diff --git a/docs/articles/pre_treatment_files/figure-html/supervised-rf-1.png b/docs/articles/pre_treatment_files/figure-html/supervised-rf-1.png
index f9d96b17..33e3124a 100644
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diff --git a/docs/articles/pre_treatment_files/figure-html/transform_RF-1.png b/docs/articles/pre_treatment_files/figure-html/transform_RF-1.png
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diff --git a/docs/articles/quick_start.html b/docs/articles/quick_start.html
index c091c1e0..00d1ac5c 100644
--- a/docs/articles/quick_start.html
+++ b/docs/articles/quick_start.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -85,10 +85,10 @@
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Quick start example analysis</h1>
-            <h3 data-toc-skip class="subtitle">metabolyseR v0.14.8</h3>
+            <h3 data-toc-skip class="subtitle">metabolyseR v0.14.9</h3>
                         <h4 data-toc-skip class="author">Jasen Finch</h4>
             
-            <h4 data-toc-skip class="date">06 January, 2022</h4>
+            <h4 data-toc-skip class="date">27 January, 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jasenfinch/metabolyseR/blob/HEAD/vignettes/quick_start.Rmd" class="external-link"><code>vignettes/quick_start.Rmd</code></a></small>
       <div class="hidden name"><code>quick_start.Rmd</code></div>
@@ -160,18 +160,18 @@ <h4 data-toc-skip class="date">06 January, 2022</h4>
 <div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">explan_feat</span>
 <span class="co">#&gt; <span style="color: #949494;"># A tibble: 379 × 10</span></span>
-<span class="co">#&gt;    Response Comparison  Feature term      df    sumsq  meansq statistic  p.value</span>
-<span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> day      1~2~3~4~5~H N341    respo…     5  3.88<span style="color: #949494;">e</span><span style="color: #BB0000;">-4</span> 7.76<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span>     137.  1.55<span style="color: #949494;">e</span><span style="color: #BB0000;">-46</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> day      1~2~3~4~5~H N133    respo…     5  7.00<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span> 1.40<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span>     126.  8.63<span style="color: #949494;">e</span><span style="color: #BB0000;">-45</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> day      1~2~3~4~5~H N163    respo…     5  6.01<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span> 1.20<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span>     117.  2.95<span style="color: #949494;">e</span><span style="color: #BB0000;">-43</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> day      1~2~3~4~5~H N1087   respo…     5  2.42<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span> 4.84<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span>      99.8 5.61<span style="color: #949494;">e</span><span style="color: #BB0000;">-40</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> day      1~2~3~4~5~H N171    respo…     5  2.25<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span> 4.50<span style="color: #949494;">e</span><span style="color: #BB0000;">-8</span>      95.7 3.84<span style="color: #949494;">e</span><span style="color: #BB0000;">-39</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> day      1~2~3~4~5~H N513    respo…     5  3.38<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span> 6.76<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span>      95.3 4.78<span style="color: #949494;">e</span><span style="color: #BB0000;">-39</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> day      1~2~3~4~5~H N1025   respo…     5  2.78<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span> 5.56<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span>      91.0 3.91<span style="color: #949494;">e</span><span style="color: #BB0000;">-38</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> day      1~2~3~4~5~H N342    respo…     5  3.71<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span> 7.41<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span>      90.3 5.32<span style="color: #949494;">e</span><span style="color: #BB0000;">-38</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> day      1~2~3~4~5~H N1083   respo…     5  5.11<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span> 1.02<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span>      89.0 1.06<span style="color: #949494;">e</span><span style="color: #BB0000;">-37</span></span>
-<span class="co">#&gt; <span style="color: #BCBCBC;">10</span> day      1~2~3~4~5~H N1085   respo…     5  1.10<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span> 2.19<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span>      83.4 1.92<span style="color: #949494;">e</span><span style="color: #BB0000;">-36</span></span>
+<span class="co">#&gt;    Response Comparison  Feature term       df   sumsq  meansq statistic  p.value</span>
+<span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> day      1~2~3~4~5~H N341    respon…     5 3.88<span style="color: #949494;">e</span><span style="color: #BB0000;">-4</span> 7.76<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span>     137.  1.55<span style="color: #949494;">e</span><span style="color: #BB0000;">-46</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> day      1~2~3~4~5~H N133    respon…     5 7.00<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span> 1.40<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span>     126.  8.63<span style="color: #949494;">e</span><span style="color: #BB0000;">-45</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> day      1~2~3~4~5~H N163    respon…     5 6.01<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span> 1.20<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span>     117.  2.95<span style="color: #949494;">e</span><span style="color: #BB0000;">-43</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> day      1~2~3~4~5~H N1087   respon…     5 2.42<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span> 4.84<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span>      99.8 5.61<span style="color: #949494;">e</span><span style="color: #BB0000;">-40</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> day      1~2~3~4~5~H N171    respon…     5 2.25<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span> 4.50<span style="color: #949494;">e</span><span style="color: #BB0000;">-8</span>      95.7 3.84<span style="color: #949494;">e</span><span style="color: #BB0000;">-39</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> day      1~2~3~4~5~H N513    respon…     5 3.38<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span> 6.76<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span>      95.3 4.78<span style="color: #949494;">e</span><span style="color: #BB0000;">-39</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> day      1~2~3~4~5~H N1025   respon…     5 2.78<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span> 5.56<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span>      91.0 3.91<span style="color: #949494;">e</span><span style="color: #BB0000;">-38</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> day      1~2~3~4~5~H N342    respon…     5 3.71<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span> 7.41<span style="color: #949494;">e</span><span style="color: #BB0000;">-7</span>      90.3 5.32<span style="color: #949494;">e</span><span style="color: #BB0000;">-38</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> day      1~2~3~4~5~H N1083   respon…     5 5.11<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span> 1.02<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span>      89.0 1.06<span style="color: #949494;">e</span><span style="color: #BB0000;">-37</span></span>
+<span class="co">#&gt; <span style="color: #BCBCBC;">10</span> day      1~2~3~4~5~H N1085   respon…     5 1.10<span style="color: #949494;">e</span><span style="color: #BB0000;">-5</span> 2.19<span style="color: #949494;">e</span><span style="color: #BB0000;">-6</span>      83.4 1.92<span style="color: #949494;">e</span><span style="color: #BB0000;">-36</span></span>
 <span class="co">#&gt; <span style="color: #949494;"># … with 369 more rows, and 1 more variable: adjusted.p.value &lt;dbl&gt;</span></span></code></pre></div>
 <p>The ANOVA has identified 379 features significantly explanatory over the infection time course. A heat map of the mean relative intensity for each class of these explanatory features can be plotted to visualise their trends between the infection time point classes.</p>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
@@ -201,7 +201,7 @@ <h4 data-toc-skip class="date">06 January, 2022</h4>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/quick_start_files/figure-html/feature_plot-1.png b/docs/articles/quick_start_files/figure-html/feature_plot-1.png
index f2040915..f9b45610 100644
Binary files a/docs/articles/quick_start_files/figure-html/feature_plot-1.png and b/docs/articles/quick_start_files/figure-html/feature_plot-1.png differ
diff --git a/docs/articles/quick_start_files/figure-html/pca-1.png b/docs/articles/quick_start_files/figure-html/pca-1.png
index 6d33c1e2..d34e0c67 100644
Binary files a/docs/articles/quick_start_files/figure-html/pca-1.png and b/docs/articles/quick_start_files/figure-html/pca-1.png differ
diff --git a/docs/articles/quick_start_files/figure-html/supervised_RF-1.png b/docs/articles/quick_start_files/figure-html/supervised_RF-1.png
index f428105c..397c5b51 100644
Binary files a/docs/articles/quick_start_files/figure-html/supervised_RF-1.png and b/docs/articles/quick_start_files/figure-html/supervised_RF-1.png differ
diff --git a/docs/authors.html b/docs/authors.html
index 17b325f8..c5036eb5 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -79,13 +79,13 @@ <h1 id="citation">Citation</h1>
 
     <p>Finch J (2022).
 <em>metabolyseR: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data</em>.
-R package version 0.14.8, <a href="https://jasenfinch.github.io/metabolyseR">https://jasenfinch.github.io/metabolyseR</a>. 
+R package version 0.14.9, <a href="https://jasenfinch.github.io/metabolyseR">https://jasenfinch.github.io/metabolyseR</a>. 
 </p>
     <pre>@Manual{,
   title = {metabolyseR: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data},
   author = {Jasen Finch},
   year = {2022},
-  note = {R package version 0.14.8},
+  note = {R package version 0.14.9},
   url = {https://jasenfinch.github.io/metabolyseR},
 }</pre>
 
@@ -100,7 +100,7 @@ <h1 id="citation">Citation</h1>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/index.html b/docs/index.html
index d44c7cad..9acbeb07 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -263,7 +263,7 @@ <h2 data-toc-skip>Dev status</h2>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/news/index.html b/docs/news/index.html
index ea905a7e..987df62e 100644
--- a/docs/news/index.html
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@@ -17,7 +17,7 @@
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -63,6 +63,13 @@ <h1 data-toc-skip>Changelog <small></small></h1>
       <small>Source: <a href="https://github.com/jasenfinch/metabolyseR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="page-header" data-toc-text="0.14.9" id="metabolyser-0149">metabolyseR 0.14.9<a class="anchor" aria-label="anchor" href="#metabolyser-0149"></a></h2>
+<ul><li><p>Suppressed name repair console message encountered during random forest permutation testing.</p></li>
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+<li><p>Added the <a href="https://jasenfinch.github.io/metabolyseR/reference/mds.html"><code>mds()</code></a> method to perform multidimensional scaling on sample proximities from the <a href="https://jasenfinch.github.io/metabolyseR/reference/RandomForest-class.html"><code>RandomForest</code></a> S4 class.</p></li>
+<li><p>Added the <a href="https://jasenfinch.github.io/metabolyseR/reference/roc.html"><code>roc()</code></a> method to calculate receiver-operator characteristic curves from the <a href="https://jasenfinch.github.io/metabolyseR/reference/RandomForest-class.html"><code>RandomForest</code></a> S4 class.</p></li>
+</ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.14.8" id="metabolyser-0148">metabolyseR 0.14.8<a class="anchor" aria-label="anchor" href="#metabolyser-0148"></a></h2>
 <ul><li><p>An error is now thrown during random forest classification when less than two classes are specified.</p></li>
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-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index b962b74b..d33f1e92 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,12 +1,12 @@
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   modelling: modelling.html
   pre_treatment: pre_treatment.html
   quick_start: quick_start.html
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+last_built: 2022-01-27T11:58Z
 urls:
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   article: https://jasenfinch.github.io/metabolyseR/articles
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
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diff --git a/docs/reference/AnalysisData-class.html b/docs/reference/AnalysisData-class.html
index f1f4e875..ccad2458 100644
--- a/docs/reference/AnalysisData-class.html
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@@ -17,7 +17,7 @@
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/reference/AnalysisParameters-class.html b/docs/reference/AnalysisParameters-class.html
index 9c8e0e79..46af2a52 100644
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@@ -17,7 +17,7 @@
       </button>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/reference/QC-1.png b/docs/reference/QC-1.png
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diff --git a/docs/reference/QC.html b/docs/reference/QC.html
index 3cd150ff..da1cd34e 100644
--- a/docs/reference/QC.html
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@@ -17,7 +17,7 @@
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
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diff --git a/docs/reference/RandomForest-class.html b/docs/reference/RandomForest-class.html
index 50b746fe..da9017e7 100644
--- a/docs/reference/RandomForest-class.html
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@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
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diff --git a/docs/reference/Univariate-class.html b/docs/reference/Univariate-class.html
index 954dd9e9..aa95c5f8 100644
--- a/docs/reference/Univariate-class.html
+++ b/docs/reference/Univariate-class.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -99,7 +99,7 @@ <h2>Slots</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
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index 621882ae..3d13f65a 100644
--- a/docs/reference/aggregate.html
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@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -156,7 +156,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/analysis-accessors.html b/docs/reference/analysis-accessors.html
index 4ef2043d..3de471ab 100644
--- a/docs/reference/analysis-accessors.html
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@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -269,7 +269,7 @@ <h2>Examples</h2>
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 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/analysisData.html b/docs/reference/analysisData.html
index 480aea6b..792a3f55 100644
--- a/docs/reference/analysisData.html
+++ b/docs/reference/analysisData.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -111,7 +111,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/analysisElements.html b/docs/reference/analysisElements.html
index 3942fc48..5e4356ae 100644
--- a/docs/reference/analysisElements.html
+++ b/docs/reference/analysisElements.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -95,7 +95,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/analysisParameters.html b/docs/reference/analysisParameters.html
index ad7d97c7..f56fb4fd 100644
--- a/docs/reference/analysisParameters.html
+++ b/docs/reference/analysisParameters.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -148,7 +148,7 @@ <h2>Examples</h2>
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 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/anova.html b/docs/reference/anova.html
index b7151125..2bfb03de 100644
--- a/docs/reference/anova.html
+++ b/docs/reference/anova.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -140,7 +140,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/bind.html b/docs/reference/bind.html
index 90354215..b95ee797 100644
--- a/docs/reference/bind.html
+++ b/docs/reference/bind.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -115,7 +115,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/changeParameter.html b/docs/reference/changeParameter.html
index cf3b2a1a..94ebec32 100644
--- a/docs/reference/changeParameter.html
+++ b/docs/reference/changeParameter.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -150,7 +150,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/cls.html b/docs/reference/cls.html
index 05ee9d49..59d0de0d 100644
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@@ -19,7 +19,7 @@
       </button>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -241,7 +241,7 @@ <h2>Examples</h2>
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 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
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@@ -17,7 +17,7 @@
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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@@ -134,7 +134,7 @@ <h2>Examples</h2>
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 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/reference/correlations.html b/docs/reference/correlations.html
index c9af15df..34e8374b 100644
--- a/docs/reference/correlations.html
+++ b/docs/reference/correlations.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -142,7 +142,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/reference/correlationsParameters.html b/docs/reference/correlationsParameters.html
index ff0d580a..8cd1dc88 100644
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@@ -17,7 +17,7 @@
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       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
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     </div>
 
@@ -102,7 +102,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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index 0cb7225d..6e123140 100644
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diff --git a/docs/reference/impute-2.png b/docs/reference/impute-2.png
index feb285e4..6eb864fa 100644
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diff --git a/docs/reference/impute-3.png b/docs/reference/impute-3.png
index 8b551ec3..db8e8b78 100644
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diff --git a/docs/reference/impute.html b/docs/reference/impute.html
index bb9eca51..acafa5cc 100644
--- a/docs/reference/impute.html
+++ b/docs/reference/impute.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -151,7 +151,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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       </footer></div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7638e125..9ec7f8ff 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -195,9 +195,17 @@ <h2 id="modelling">Modelling <a href="#modelling" class="anchor" aria-hidden="tr
         </td>
         <td><p>Linear regression</p></td>
       </tr><tr><td>
-          <p><code><a href="modelling-accessors.html">binaryComparisons()</a></code> <code><a href="modelling-accessors.html">type()</a></code> <code><a href="modelling-accessors.html">response()</a></code> <code><a href="modelling-accessors.html">metrics()</a></code> <code><a href="modelling-accessors.html">importanceMetrics()</a></code> <code><a href="modelling-accessors.html">importance()</a></code> <code><a href="modelling-accessors.html">explanatoryFeatures()</a></code> </p>
+          <p><code><a href="modelling-accessors.html">binaryComparisons()</a></code> <code><a href="modelling-accessors.html">type()</a></code> <code><a href="modelling-accessors.html">response()</a></code> <code><a href="modelling-accessors.html">metrics()</a></code> <code><a href="modelling-accessors.html">importanceMetrics()</a></code> <code><a href="modelling-accessors.html">importance()</a></code> <code><a href="modelling-accessors.html">proximity()</a></code> <code><a href="modelling-accessors.html">explanatoryFeatures()</a></code> </p>
         </td>
         <td><p>Modelling accessor methods</p></td>
+      </tr><tr><td>
+          <p><code><a href="mds.html">mds()</a></code> </p>
+        </td>
+        <td><p>Multidimensional scaling (MDS)</p></td>
+      </tr><tr><td>
+          <p><code><a href="roc.html">roc()</a></code> </p>
+        </td>
+        <td><p>Receiver-operator characteristic (ROC) curves</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="correlations">Correlations <a href="#correlations" class="anchor" aria-hidden="true"></a></h2>
           <p class="section-desc"></p>
@@ -295,7 +303,7 @@ <h2 id="miscellaneous">Miscellaneous <a href="#miscellaneous" class="anchor" ari
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/io-parameters.html b/docs/reference/io-parameters.html
index 8515613e..090a3493 100644
--- a/docs/reference/io-parameters.html
+++ b/docs/reference/io-parameters.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -148,7 +148,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/reference/keep.html b/docs/reference/keep.html
index 92d934e4..b0586288 100644
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@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -164,7 +164,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/reference/linearRegression.html b/docs/reference/linearRegression.html
index 78be6689..a3b45613 100644
--- a/docs/reference/linearRegression.html
+++ b/docs/reference/linearRegression.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -136,7 +136,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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diff --git a/docs/reference/mds.html b/docs/reference/mds.html
new file mode 100644
index 00000000..09ace6e1
--- /dev/null
+++ b/docs/reference/mds.html
@@ -0,0 +1,148 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Multidimensional scaling (MDS) — mds • metabolyseR</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Multidimensional scaling (MDS) — mds"><meta property="og:description" content="Multidimensional scaling of random forest proximities."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
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+    Articles
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+      <a href="../articles/pre_treatment.html">Metabolomics data pre-treatment</a>
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+    <li>
+      <a href="../articles/modelling.html">Modelling and feature selection</a>
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+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Multidimensional scaling (MDS)</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jasenfinch/metabolyseR/blob/HEAD/R/mds.R" class="external-link"><code>R/mds.R</code></a></small>
+    <div class="hidden name"><code>mds.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Multidimensional scaling of random forest proximities.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mds</span><span class="op">(</span><span class="va">x</span>, dimensions <span class="op">=</span> <span class="fl">2</span>, idx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
+
+<span class="co"># S4 method for RandomForest</span>
+<span class="fu">mds</span><span class="op">(</span><span class="va">x</span>, dimensions <span class="op">=</span> <span class="fl">2</span>, idx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
+
+<span class="co"># S4 method for list</span>
+<span class="fu">mds</span><span class="op">(</span><span class="va">x</span>, dimensions <span class="op">=</span> <span class="fl">2</span>, idx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
+
+<span class="co"># S4 method for Analysis</span>
+<span class="fu">mds</span><span class="op">(</span><span class="va">x</span>, dimensions <span class="op">=</span> <span class="fl">2</span>, idx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>S4 object of class <code>RandomForest</code>, <code>Analysis</code> or a list</p></dd>
+<dt>dimensions</dt>
+<dd><p>The number of dimensions by which the data are to be represented.</p></dd>
+<dt>idx</dt>
+<dd><p>sample information column to use for sample names. If <code>NULL</code>, the sample row number will be used. Sample names should be unique for each row of data.</p></dd>
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    <p>A tibble containing the scaled dimensions.</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://aberhrml.github.io/metaboData/" class="external-link">metaboData</a></span><span class="op">)</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="analysisData.html">analysisData</a></span><span class="op">(</span><span class="va">abr1</span><span class="op">$</span><span class="va">neg</span><span class="op">[</span>,<span class="fl">200</span><span class="op">:</span><span class="fl">300</span><span class="op">]</span>,<span class="va">abr1</span><span class="op">$</span><span class="va">fact</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span class="r-in">       <span class="fu"><a href="occupancyFilter.html">occupancyMaximum</a></span><span class="op">(</span>cls <span class="op">=</span> <span class="st">'day'</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span class="r-in">       <span class="fu"><a href="transform.html">transformTICnorm</a></span><span class="op">(</span><span class="op">)</span></span>
+<span class="r-in">       </span>
+<span class="r-in"><span class="va">rf</span> <span class="op">&lt;-</span> <span class="fu"><a href="randomForest.html">randomForest</a></span><span class="op">(</span><span class="va">x</span>,cls <span class="op">=</span> <span class="st">'day'</span><span class="op">)</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="fu">mds</span><span class="op">(</span><span class="va">rf</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 120 × 5</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    Response Comparison  Sample `Dimension 1` `Dimension 2`</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> day      1~2~3~4~5~H      1       -<span style="color: #BB0000;">0.012</span><span style="color: #BB0000; text-decoration: underline;">9</span>       -<span style="color: #BB0000;">0.190</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> day      1~2~3~4~5~H      2       -<span style="color: #BB0000;">0.101</span>        -<span style="color: #BB0000;">0.254</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> day      1~2~3~4~5~H      3       -<span style="color: #BB0000;">0.015</span><span style="color: #BB0000; text-decoration: underline;">6</span>        0.173 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> day      1~2~3~4~5~H      4       -<span style="color: #BB0000;">0.089</span><span style="color: #BB0000; text-decoration: underline;">6</span>        0.147 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> day      1~2~3~4~5~H      5        0.146        -<span style="color: #BB0000;">0.056</span><span style="color: #BB0000; text-decoration: underline;">6</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> day      1~2~3~4~5~H      6       -<span style="color: #BB0000;">0.132</span>         0.094<span style="text-decoration: underline;">6</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> day      1~2~3~4~5~H      7       -<span style="color: #BB0000;">0.086</span><span style="color: #BB0000; text-decoration: underline;">2</span>       -<span style="color: #BB0000;">0.195</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> day      1~2~3~4~5~H      8        0.144        -<span style="color: #BB0000;">0.091</span><span style="color: #BB0000; text-decoration: underline;">7</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> day      1~2~3~4~5~H      9        0.040<span style="text-decoration: underline;">8</span>       -<span style="color: #BB0000;">0.110</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> day      1~2~3~4~5~H     10       -<span style="color: #BB0000;">0.146</span>         0.155 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 110 more rows</span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Jasen Finch.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/metabolyse.html b/docs/reference/metabolyse.html
index c25d1d61..51990aad 100644
--- a/docs/reference/metabolyse.html
+++ b/docs/reference/metabolyse.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -127,7 +127,7 @@ <h2>Examples</h2>
 <span class="r-in">                       <span class="va">abr1</span><span class="op">$</span><span class="va">fact</span>,</span>
 <span class="r-in">                       <span class="va">p</span><span class="op">)</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">metabolyseR </span> <span style="color: #BB0000;">v0.14.8</span> Thu Jan  6 13:51:47 2022</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">metabolyseR </span> <span style="color: #BB0000;">v0.14.9</span> Thu Jan 27 11:58:32 2022</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ________________________________________________________________________________</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">Parameters:</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> pre-treatment</span>
@@ -146,18 +146,18 @@ <h2>Examples</h2>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 		returnModels = FALSE</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ________________________________________________________________________________</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Pre-treatment </span>…
</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 
<span style="color: #0000BB;">Pre-treatment </span>	<span style="color: #00BB00;">✔</span> [0.9S]</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 
<span style="color: #0000BB;">Pre-treatment </span>	<span style="color: #00BB00;">✔</span> [0.6S]</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Modelling </span>…
</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">
Modelling </span>	<span style="color: #00BB00;">✔</span> [0.6S]</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">
Modelling </span>	<span style="color: #00BB00;">✔</span> [0.7S]</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ________________________________________________________________________________</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">Complete! </span>[1.5S]</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">Complete! </span>[1.3S]</span>
 <span class="r-in">                       </span>
 <span class="r-in"><span class="co">## Re-analyse to include correlation analysis</span></span>
 <span class="r-in"><span class="va">analysis</span> <span class="op">&lt;-</span> <span class="fu">reAnalyse</span><span class="op">(</span><span class="va">analysis</span>,</span>
 <span class="r-in">                      parameters <span class="op">=</span> <span class="fu"><a href="analysisParameters.html">analysisParameters</a></span><span class="op">(</span><span class="st">'correlations'</span><span class="op">)</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">metabolyseR</span> <span style="color: #BB0000;">v0.14.8</span> Thu Jan  6 13:51:48 2022</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">metabolyseR</span> <span style="color: #BB0000;">v0.14.9</span> Thu Jan 27 11:58:33 2022</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> ________________________________________________________________________________</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">Parameters:</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> correlations</span>
@@ -175,25 +175,25 @@ <h2>Examples</h2>
 <span class="r-in"></span>
 <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">analysis</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">metabolyseR </span><span style="color: #BB0000; font-weight: bold;">v0.14.8</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">metabolyseR </span><span style="color: #BB0000; font-weight: bold;">v0.14.9</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">Analysis:</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 	Thu Jan  6 13:51:47 2022</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 	Thu Jan 27 11:58:32 2022</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 	Raw Data:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 		No. samples = 120</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 		No. features = 200</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 	Pre-treated Data:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 		Thu Jan  6 13:51:48 2022</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 		Thu Jan 27 11:58:33 2022</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 		No. samples = 120</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 		No. features = 48</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 	Modelling:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 		Thu Jan  6 13:51:48 2022</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 		Thu Jan 27 11:58:33 2022</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 		Methods: anova</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 	Correlations:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 		Thu Jan  6 13:51:48 2022</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 		Thu Jan 27 11:58:33 2022</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 		No. correlations = 140</span>
 <span class="r-in"></span>
 </code></pre></div>
@@ -210,7 +210,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/modelling-accessors.html b/docs/reference/modelling-accessors.html
index 0a175bfe..cfa0f6ae 100644
--- a/docs/reference/modelling-accessors.html
+++ b/docs/reference/modelling-accessors.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -114,6 +114,17 @@ <h1>Modelling accessor methods</h1>
 <span class="co"># S4 method for Analysis</span>
 <span class="fu">importance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 
+<span class="fu">proximity</span><span class="op">(</span><span class="va">x</span>, idx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
+
+<span class="co"># S4 method for RandomForest</span>
+<span class="fu">proximity</span><span class="op">(</span><span class="va">x</span>, idx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
+
+<span class="co"># S4 method for list</span>
+<span class="fu">proximity</span><span class="op">(</span><span class="va">x</span>, idx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
+
+<span class="co"># S4 method for Analysis</span>
+<span class="fu">proximity</span><span class="op">(</span><span class="va">x</span>, idx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span>
+
 <span class="fu">explanatoryFeatures</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span>
 
 <span class="co"># S4 method for Univariate</span>
@@ -135,6 +146,8 @@ <h2>Arguments</h2>
 <dd><p>S4 object of class <code>AnalysisData</code>,<code>RandomForest</code>, <code>Univariate</code>, <code>Analysis</code> or a list.</p></dd>
 <dt>cls</dt>
 <dd><p>sample information column to use</p></dd>
+<dt>idx</dt>
+<dd><p>sample information column to use for sample names. If <code>NULL</code>, the sample row number will be used. Sample names should be unique for each row of data.</p></dd>
 <dt>...</dt>
 <dd><p>arguments to parse to method for specific class</p></dd>
 <dt>threshold</dt>
@@ -152,6 +165,7 @@ <h2>Methods</h2>
 <li><p><code>metrics</code>: Retrieve the model performance metrics for a random forest analysis</p></li>
 <li><p><code>importanceMetrics</code>: Retrieve the available feature importance metrics for a random forest analysis.</p></li>
 <li><p><code>importance</code>: Retrieve feature importance results.</p></li>
+<li><p><code>proximity</code>: Retrieve the random forest sample proximities.</p></li>
 <li><p><code>explanatoryFeatures</code>: Retrieve explanatory features.</p></li>
 </ul></div>
 
@@ -211,6 +225,23 @@ <h2>Examples</h2>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> day      1~2~3~4~5~H N200    SelectionFrequency   1.6 <span style="color: #949494;">e</span>+ 1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,000 more rows</span></span>
 <span class="r-in"></span>
+<span class="r-in"><span class="co">## Retrieve the sample proximities</span></span>
+<span class="r-in"><span class="fu">proximity</span><span class="op">(</span><span class="va">rf_analysis</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 14,400 × 5</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    Response Comparison  Sample1 Sample2 Proximity</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> day      1~2~3~4~5~H       1       1    1     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> day      1~2~3~4~5~H       1       2    0.070<span style="text-decoration: underline;">4</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> day      1~2~3~4~5~H       1       3    0.058<span style="text-decoration: underline;">0</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> day      1~2~3~4~5~H       1       4    0.093<span style="text-decoration: underline;">0</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> day      1~2~3~4~5~H       1       5    0.055<span style="text-decoration: underline;">6</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> day      1~2~3~4~5~H       1       6    0.043<span style="text-decoration: underline;">5</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> day      1~2~3~4~5~H       1       7    0.055<span style="text-decoration: underline;">6</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> day      1~2~3~4~5~H       1       8    0.044<span style="text-decoration: underline;">1</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> day      1~2~3~4~5~H       1       9    0.106 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> day      1~2~3~4~5~H       1      10    0     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 14,390 more rows</span></span>
+<span class="r-in"></span>
 <span class="r-in"><span class="co">## Retrieve the explanatory features</span></span>
 <span class="r-in"><span class="fu">explanatoryFeatures</span><span class="op">(</span><span class="va">rf_analysis</span>,metric <span class="op">=</span> <span class="st">'FalsePositiveRate'</span>,threshold <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 35 × 5</span></span>
@@ -241,7 +272,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/modelling-parameters.html b/docs/reference/modelling-parameters.html
index 5eaab072..793ca0f3 100644
--- a/docs/reference/modelling-parameters.html
+++ b/docs/reference/modelling-parameters.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -117,7 +117,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/occupancy.html b/docs/reference/occupancy.html
index 65a74c3f..e8e84334 100644
--- a/docs/reference/occupancy.html
+++ b/docs/reference/occupancy.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -122,7 +122,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/occupancyFilter-1.png b/docs/reference/occupancyFilter-1.png
index 5d12a862..41ade7d0 100644
Binary files a/docs/reference/occupancyFilter-1.png and b/docs/reference/occupancyFilter-1.png differ
diff --git a/docs/reference/occupancyFilter-2.png b/docs/reference/occupancyFilter-2.png
index 5a12a748..d53959c0 100644
Binary files a/docs/reference/occupancyFilter-2.png and b/docs/reference/occupancyFilter-2.png differ
diff --git a/docs/reference/occupancyFilter.html b/docs/reference/occupancyFilter.html
index 91894c10..ae168a37 100644
--- a/docs/reference/occupancyFilter.html
+++ b/docs/reference/occupancyFilter.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -144,7 +144,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/parameters.html b/docs/reference/parameters.html
index 06ebc640..649ac57f 100644
--- a/docs/reference/parameters.html
+++ b/docs/reference/parameters.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -224,7 +224,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/plotExplanatoryHeatmap.html b/docs/reference/plotExplanatoryHeatmap.html
index f7123220..4ba85d72 100644
--- a/docs/reference/plotExplanatoryHeatmap.html
+++ b/docs/reference/plotExplanatoryHeatmap.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -177,7 +177,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/plotFeature-1.png b/docs/reference/plotFeature-1.png
index e2815feb..19d9a1c5 100644
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diff --git a/docs/reference/plotFeature.html b/docs/reference/plotFeature.html
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diff --git a/docs/reference/roc.html b/docs/reference/roc.html
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+    </li>
+    <li>
+      <a href="../articles/modelling.html">Modelling and feature selection</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">Changelog</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jasenfinch/metabolyseR/" class="external-link">
+    <span class="fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Receiver-operator characteristic (ROC) curves</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jasenfinch/metabolyseR/blob/HEAD/R/roc.R" class="external-link"><code>R/roc.R</code></a></small>
+    <div class="hidden name"><code>roc.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>ROC curves for out-of-bag random forest predictions.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">roc</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
+
+<span class="co"># S4 method for RandomForest</span>
+<span class="fu">roc</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
+
+<span class="co"># S4 method for list</span>
+<span class="fu">roc</span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
+
+<span class="co"># S4 method for Analysis</span>
+<span class="fu">roc</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>x</dt>
+<dd><p>S4 object of class <code>RandomForest</code>, <code>Analysis</code> or a list</p></dd>
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    <p>A tibble containing the ROC curves.</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://aberhrml.github.io/metaboData/" class="external-link">metaboData</a></span><span class="op">)</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="analysisData.html">analysisData</a></span><span class="op">(</span><span class="va">abr1</span><span class="op">$</span><span class="va">neg</span><span class="op">[</span>,<span class="fl">200</span><span class="op">:</span><span class="fl">300</span><span class="op">]</span>,<span class="va">abr1</span><span class="op">$</span><span class="va">fact</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span class="r-in">       <span class="fu"><a href="occupancyFilter.html">occupancyMaximum</a></span><span class="op">(</span>cls <span class="op">=</span> <span class="st">'day'</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
+<span class="r-in">       <span class="fu"><a href="transform.html">transformTICnorm</a></span><span class="op">(</span><span class="op">)</span></span>
+<span class="r-in">       </span>
+<span class="r-in"><span class="va">rf</span> <span class="op">&lt;-</span> <span class="fu"><a href="randomForest.html">randomForest</a></span><span class="op">(</span><span class="va">x</span>,cls <span class="op">=</span> <span class="st">'day'</span><span class="op">)</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="fu">roc</span><span class="op">(</span><span class="va">rf</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 711 × 6</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    Response Comparison  Class .threshold specificity sensitivity</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> day      1~2~3~4~5~H 1     -<span style="color: #BB0000;">Inf</span>              0              1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> day      1~2~3~4~5~H 1        0              0              1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> day      1~2~3~4~5~H 1        0.005<span style="text-decoration: underline;">03</span>        0.01           1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> day      1~2~3~4~5~H 1        0.005<span style="text-decoration: underline;">38</span>        0.02           1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> day      1~2~3~4~5~H 1        0.010<span style="text-decoration: underline;">3</span>         0.03           1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> day      1~2~3~4~5~H 1        0.010<span style="text-decoration: underline;">5</span>         0.04           1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> day      1~2~3~4~5~H 1        0.011<span style="text-decoration: underline;">7</span>         0.05           1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> day      1~2~3~4~5~H 1        0.014<span style="text-decoration: underline;">4</span>         0.06           1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> day      1~2~3~4~5~H 1        0.015<span style="text-decoration: underline;">7</span>         0.07           1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> day      1~2~3~4~5~H 1        0.022<span style="text-decoration: underline;">2</span>         0.08           1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 701 more rows</span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Jasen Finch.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/rsd.html b/docs/reference/rsd.html
index 23990630..f9752f69 100644
--- a/docs/reference/rsd.html
+++ b/docs/reference/rsd.html
@@ -18,7 +18,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -124,7 +124,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/split.html b/docs/reference/split.html
index 574fcae2..cf503323 100644
--- a/docs/reference/split.html
+++ b/docs/reference/split.html
@@ -18,7 +18,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -167,7 +167,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/transform-1.png b/docs/reference/transform-1.png
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diff --git a/docs/reference/transform-2.png b/docs/reference/transform-2.png
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diff --git a/docs/reference/transform-3.png b/docs/reference/transform-3.png
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diff --git a/docs/reference/transform-4.png b/docs/reference/transform-4.png
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diff --git a/docs/reference/transform-6.png b/docs/reference/transform-6.png
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diff --git a/docs/reference/transform-7.png b/docs/reference/transform-7.png
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diff --git a/docs/reference/transform-8.png b/docs/reference/transform-8.png
index e1c13cbc..ad093f40 100644
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diff --git a/docs/reference/transform-9.png b/docs/reference/transform-9.png
index 53478402..d4e31ff3 100644
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diff --git a/docs/reference/transform.html b/docs/reference/transform.html
index 4f090f00..7819a044 100644
--- a/docs/reference/transform.html
+++ b/docs/reference/transform.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -257,7 +257,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/ttest.html b/docs/reference/ttest.html
index 24450fcc..e9691b2b 100644
--- a/docs/reference/ttest.html
+++ b/docs/reference/ttest.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">metabolyseR</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.8</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.9</span>
       </span>
     </div>
 
@@ -147,7 +147,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer></div>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 6cae8dd2..6ca698d7 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -198,6 +198,9 @@
   <url>
     <loc>https://jasenfinch.github.io/metabolyseR/reference/linearRegression.html</loc>
   </url>
+  <url>
+    <loc>https://jasenfinch.github.io/metabolyseR/reference/mds.html</loc>
+  </url>
   <url>
     <loc>https://jasenfinch.github.io/metabolyseR/reference/metabolyse.html</loc>
   </url>
@@ -321,6 +324,9 @@
   <url>
     <loc>https://jasenfinch.github.io/metabolyseR/reference/response.html</loc>
   </url>
+  <url>
+    <loc>https://jasenfinch.github.io/metabolyseR/reference/roc.html</loc>
+  </url>
   <url>
     <loc>https://jasenfinch.github.io/metabolyseR/reference/rsd.html</loc>
   </url>
diff --git a/man/mds.Rd b/man/mds.Rd
new file mode 100644
index 00000000..de831555
--- /dev/null
+++ b/man/mds.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mds.R
+\name{mds}
+\alias{mds}
+\alias{mds,RandomForest-method}
+\alias{mds,list-method}
+\alias{mds,Analysis-method}
+\title{Multidimensional scaling (MDS)}
+\usage{
+mds(x, dimensions = 2, idx = NULL)
+
+\S4method{mds}{RandomForest}(x, dimensions = 2, idx = NULL)
+
+\S4method{mds}{list}(x, dimensions = 2, idx = NULL)
+
+\S4method{mds}{Analysis}(x, dimensions = 2, idx = NULL)
+}
+\arguments{
+\item{x}{S4 object of class \code{RandomForest}, \code{Analysis} or a list}
+
+\item{dimensions}{The number of dimensions by which the data are to be represented.}
+
+\item{idx}{sample information column to use for sample names. If \code{NULL}, the sample row number will be used. Sample names should be unique for each row of data.}
+}
+\value{
+A tibble containing the scaled dimensions.
+}
+\description{
+Multidimensional scaling of random forest proximities.
+}
+\examples{
+library(metaboData)
+
+x <- analysisData(abr1$neg[,200:300],abr1$fact) \%>\%
+       occupancyMaximum(cls = 'day') \%>\%
+       transformTICnorm()
+       
+rf <- randomForest(x,cls = 'day')
+
+mds(rf)
+}
diff --git a/man/modelling-accessors.Rd b/man/modelling-accessors.Rd
index 236f1441..2f88f176 100644
--- a/man/modelling-accessors.Rd
+++ b/man/modelling-accessors.Rd
@@ -18,6 +18,10 @@
 \alias{importance,Univariate-method}
 \alias{importance,list-method}
 \alias{importance,Analysis-method}
+\alias{proximity}
+\alias{proximity,RandomForest-method}
+\alias{proximity,list-method}
+\alias{proximity,Analysis-method}
 \alias{explanatoryFeatures}
 \alias{explanatoryFeatures,Univariate-method}
 \alias{explanatoryFeatures,RandomForest-method}
@@ -59,6 +63,14 @@ importance(x)
 
 \S4method{importance}{Analysis}(x)
 
+proximity(x, idx = NULL)
+
+\S4method{proximity}{RandomForest}(x, idx = NULL)
+
+\S4method{proximity}{list}(x, idx = NULL)
+
+\S4method{proximity}{Analysis}(x, idx = NULL)
+
 explanatoryFeatures(x, ...)
 
 \S4method{explanatoryFeatures}{Univariate}(x, threshold = 0.05)
@@ -74,6 +86,8 @@ explanatoryFeatures(x, ...)
 
 \item{cls}{sample information column to use}
 
+\item{idx}{sample information column to use for sample names. If \code{NULL}, the sample row number will be used. Sample names should be unique for each row of data.}
+
 \item{...}{arguments to parse to method for specific class}
 
 \item{threshold}{threshold below which explanatory features are extracted}
@@ -92,6 +106,7 @@ Methods for accessing modelling results.
 \item \code{metrics}: Retrieve the model performance metrics for a random forest analysis
 \item \code{importanceMetrics}: Retrieve the available feature importance metrics for a random forest analysis.
 \item \code{importance}: Retrieve feature importance results.
+\item \code{proximity}: Retrieve the random forest sample proximities.
 \item \code{explanatoryFeatures}: Retrieve explanatory features.
 }
 }
@@ -122,6 +137,9 @@ importanceMetrics(rf_analysis)
 ## Retrieve the feature importance results
 importance(rf_analysis)
 
+## Retrieve the sample proximities
+proximity(rf_analysis)
+
 ## Retrieve the explanatory features
 explanatoryFeatures(rf_analysis,metric = 'FalsePositiveRate',threshold = 0.05)
 }
diff --git a/man/roc.Rd b/man/roc.Rd
new file mode 100644
index 00000000..29f11598
--- /dev/null
+++ b/man/roc.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/roc.R
+\name{roc}
+\alias{roc}
+\alias{roc,RandomForest-method}
+\alias{roc,list-method}
+\alias{roc,Analysis-method}
+\title{Receiver-operator characteristic (ROC) curves}
+\usage{
+roc(x)
+
+\S4method{roc}{RandomForest}(x)
+
+\S4method{roc}{list}(x)
+
+\S4method{roc}{Analysis}(x)
+}
+\arguments{
+\item{x}{S4 object of class \code{RandomForest}, \code{Analysis} or a list}
+}
+\value{
+A tibble containing the ROC curves.
+}
+\description{
+ROC curves for out-of-bag random forest predictions.
+}
+\examples{
+library(metaboData)
+
+x <- analysisData(abr1$neg[,200:300],abr1$fact) \%>\%
+       occupancyMaximum(cls = 'day') \%>\%
+       transformTICnorm()
+       
+rf <- randomForest(x,cls = 'day')
+
+roc(rf)
+}
diff --git a/tests/testthat/test-mds.R b/tests/testthat/test-mds.R
new file mode 100644
index 00000000..ce75af31
--- /dev/null
+++ b/tests/testthat/test-mds.R
@@ -0,0 +1,15 @@
+d <- analysisData(abr1$neg,abr1$fact) %>%
+  keepFeatures(features = features(.)[200:250]) %>% 
+  clsAdd('sample_names',paste0(seq_len(nSamples(.)),'_a'))
+
+rf <- randomForest(d)
+
+test_that("mds works", {
+  mds_results <- mds(rf)
+  
+  expect_s3_class(mds_results,'tbl_df')
+})
+
+test_that('mds correctly ignores irrelevant objects in lists',{
+  expect_identical(mds(list(0,0)),tibble())
+})
diff --git a/tests/testthat/test-metabolyse.R b/tests/testthat/test-metabolyse.R
index cb7b5da8..d71dbc05 100644
--- a/tests/testthat/test-metabolyse.R
+++ b/tests/testthat/test-metabolyse.R
@@ -27,4 +27,7 @@ test_that('metabolyse-works', {
   expect_equal(nSamples(analysis),20)
   
   expect_s3_class(metrics(analysis),'tbl_df')
+  expect_s3_class(proximity(analysis),'tbl_df')
+  expect_s3_class(mds(analysis),'tbl_df')
+  expect_s3_class(roc(analysis),'tbl_df')
 })
diff --git a/tests/testthat/test-modellingPlots.R b/tests/testthat/test-modellingPlots.R
index f8b1faa8..139e9474 100644
--- a/tests/testthat/test-modellingPlots.R
+++ b/tests/testthat/test-modellingPlots.R
@@ -108,3 +108,14 @@ test_that('plotMDS throws an error when non RandomForest object included in list
 test_that('plotROC throws an error when non classification random forest specified',{
   expect_error(plotROC(unsupervised_rf_res))
 })
+
+test_that('plotROC works on a list of random forest objects',{
+  pl <- plotROC(classification_rf_res)
+  
+  expect_s3_class(pl,'patchwork')
+})
+
+test_that('plotROC throws an error when non RandomForest object included in list',{
+  d <- c(classification_rf_res,list('wrong'))
+  expect_error(plotROC(d))
+})
diff --git a/tests/testthat/test-randomForest.R b/tests/testthat/test-randomForest.R
index 20bda1d8..7df93496 100644
--- a/tests/testthat/test-randomForest.R
+++ b/tests/testthat/test-randomForest.R
@@ -1,7 +1,8 @@
 library(metaboData)
 
 d <- analysisData(abr1$neg,abr1$fact) %>%
-  keepFeatures(features = features(.)[200:250])
+  keepFeatures(features = features(.)[200:250]) %>% 
+  clsAdd('sample_names',paste0(seq_len(nSamples(.)),'_a'))
 
 context('randomForest')
 
@@ -17,6 +18,7 @@ test_that('random forest classification works',{
   
   rf_metrics <- metrics(rf)
   rf_importance <- importance(rf)
+  rf_proximity <- proximity(rf,idx = 'sample_names')
   
   rf_wrong <- c(rf,list('wrong'))
   
@@ -24,7 +26,17 @@ test_that('random forest classification works',{
   expect_identical(type(rf$day),'classification')
   expect_s3_class(rf_metrics,'tbl_df')
   expect_s3_class(rf_importance,'tbl_df')
+  expect_s3_class(rf_proximity,'tbl_df')
+  
+  expect_s3_class(metrics(rf_wrong),'tbl_df')
   expect_error(importance(rf_wrong))
+  expect_s3_class(proximity(rf_wrong),'tbl_df')
+  expect_error(explanatoryFeatures(rf_wrong))
+  
+  expect_equal(nrow(metrics(list(0,0))),0)
+  expect_equal(nrow(proximity(list(0,0))),0)
+  
+  expect_error(proximity(rf,idx = 'name'))
 })
 
 test_that('binary classification works',{
diff --git a/tests/testthat/test-roc.R b/tests/testthat/test-roc.R
new file mode 100644
index 00000000..6f170da0
--- /dev/null
+++ b/tests/testthat/test-roc.R
@@ -0,0 +1,3 @@
+test_that('roc correctly ignores irrelevant objects in lists',{
+  expect_identical(roc(list(0,0)),tibble())
+})
\ No newline at end of file