diff --git a/DESCRIPTION b/DESCRIPTION index 65094246..3722e986 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: 0.14.5 +Version: 0.14.6 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre")) Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data. URL: https://jasenfinch.github.io/metabolyseR diff --git a/NEWS.md b/NEWS.md index 5e9fd4bb..9de6357a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# metabolyseR 0.14.6 + +* [`plotExplanatoryHeatmap`](https://jasenfinch.github.io/metabolyseR/reference/plotExplanatoryHeatmap.html) method for the [`Analysis`](https://jasenfinch.github.io/metabolyseR/reference/Analysis-class.html) class now returns the plot only if the number of plots is equal to 1. + +* Removed reference to the `nCores` parameter from the documentation example of [`metabolyse()`](https://jasenfinch.github.io/metabolyseR/reference/metabolyse.html). + # metabolyseR 0.14.5 * Correlation analysis results now include an absolute correlation coefficient column by which the results are also arranged in descending order. diff --git a/R/metabolyse.R b/R/metabolyse.R index b878cb14..af00f2a9 100644 --- a/R/metabolyse.R +++ b/R/metabolyse.R @@ -28,9 +28,8 @@ #' ) #' parameters(p,'modelling') <- modellingParameters('anova') #' -#' ## Change "cls" and "nCores" parameters +#' ## Change "cls" parameters #' changeParameter(p,'cls') <- 'day' -#' changeParameter(p,'nCores') <- 2 #' #' ## Run analysis using a subset of the abr1 negative mode data set #' analysis <- metabolyse(abr1$neg[,1:200], diff --git a/R/plotExplanatoryHeatmap.R b/R/plotExplanatoryHeatmap.R index 687b9ca7..0f7da093 100644 --- a/R/plotExplanatoryHeatmap.R +++ b/R/plotExplanatoryHeatmap.R @@ -493,12 +493,18 @@ setMethod('plotExplanatoryHeatmap', clusterMethod = 'ward.D2', featureNames = TRUE, featureLimit = Inf){ - x %>% + pl <- x %>% analysisResults(element = 'modelling') %>% plotExplanatoryHeatmap(threshold = threshold, distanceMeasure = distanceMeasure, clusterMethod = clusterMethod, featureNames = featureNames, - featureLimit = featureLimit) + featureLimit = featureLimit) + + if (length(pl) == 1){ + pl <- pl[[1]] + } + + return(pl) } ) diff --git a/README.Rmd b/README.Rmd index 5e3c282c..5e6f1d9e 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,7 +15,7 @@ knitr::opts_chunk$set(collapse = TRUE, # metabolyseR -[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) +[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![R-CMD-check](https://github.com/jasenfinch/metabolyseR/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metabolyseR/actions) [![codecov](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master) [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metabolyseR/blob/master/DESCRIPTION) diff --git a/README.md b/README.md index f28d427b..8e455b69 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![Lifecycle: -experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) +stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![R-CMD-check](https://github.com/jasenfinch/metabolyseR/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metabolyseR/actions) [![codecov](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master) [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metabolyseR/blob/master/DESCRIPTION) diff --git a/docs/404.html b/docs/404.html index 00f9d992..6fe14936 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/articles/index.html b/docs/articles/index.html index bed50cff..14966dd8 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/articles/metabolyseR.html b/docs/articles/metabolyseR.html index a9e4e703..b616fec7 100644 --- a/docs/articles/metabolyseR.html +++ b/docs/articles/metabolyseR.html @@ -31,7 +31,7 @@ metabolyseR - 0.14.5 + 0.14.6 @@ -89,10 +89,10 @@

Introduction

-

metabolyseR v0.14.5

+

metabolyseR v0.14.6

Jasen Finch

-

11 November, 2021

+

17 November, 2021

Source: vignettes/metabolyseR.Rmd @@ -567,32 +567,26 @@

class: cls: class occupancy: 0.667 - nCores: 4 - clusterType: FORK - transform: - TICnorm: ~ -classification: - cls: class - method: randomForest - pars: - sampling: boot - niter: 10 - nreps: 10 - strat: yes - nCores: 4 - clusterType: Fork -featureSelection: - method: fs.rf - cls: class - pars: - fs.rf: - nreps: 100 - nCores: 4 - clusterType: FORK -correlations: - method: pearson - pAdjustMethod: bonferroni - corPvalue: 0.05

+ transform: + TICnorm: ~ +classification: + cls: class + method: randomForest + pars: + sampling: boot + niter: 10 + nreps: 10 + strat: yes +featureSelection: + method: fs.rf + cls: class + pars: + fs.rf: + nreps: 100 +correlations: + method: pearson + pAdjustMethod: bonferroni + corPvalue: 0.05

This can be passed directly into an AnalysisParameters object using the following:

 paramFile <- system.file('defaultParameters.yaml',package = 'metabolyseR')
@@ -644,7 +638,7 @@ 

 
 analysis <- metabolyse(abr1$neg[,1:200],abr1$fact,p) 

 
## 
-## metabolyseR  v0.14.5 Thu Nov 11 21:33:26 2021

+## metabolyseR  v0.14.6 Wed Nov 17 10:25:14 2021
## ________________________________________________________________________________
## Parameters:
 ## pre-treatment
@@ -671,30 +665,30 @@ 

 Pre-treatment   ✓ [0.8S]
 ## Modelling …
 
-Modelling   ✓ [3.3S]
+Modelling   ✓ [3.5S]
 ## ________________________________________________________________________________
 ## 
-## Complete! [4.1S]
+## Complete! [4.4S]

Note: If a data pre-treatment step is not performed prior to modelling or correlation analysis, the raw data will automatically be used.

The analysis object containing the analysis results can be printed to provide some basic information about the results of the analysis.

 print(analysis)
## 
-## metabolyseR v0.14.5
+## metabolyseR v0.14.6
 ## Analysis:
-##  Thu Nov 11 21:33:26 2021
+##  Wed Nov 17 10:25:14 2021
 ## 
 ##  Raw Data:
 ##      No. samples = 120
 ##      No. features = 200
 ## 
 ##  Pre-treated Data:
-##      Thu Nov 11 21:33:27 2021
+##      Wed Nov 17 10:25:15 2021
 ##      No. samples = 120
 ##      No. features = 48
 ## 
 ##  Modelling:
-##      Thu Nov 11 21:33:30 2021
+##      Wed Nov 17 10:25:18 2021
 ##      Methods: randomForest
@@ -709,7 +703,7 @@ 

 analysis <- reAnalyse(analysis,parameters)
## 
-## metabolyseR v0.14.5 Thu Nov 11 21:33:30 2021
+## metabolyseR v0.14.6 Wed Nov 17 10:25:19 2021
 ## ________________________________________________________________________________
 ## Parameters:
 ## correlations
@@ -727,25 +721,25 @@ 

 
 print(analysis)

 
## 
-## metabolyseR v0.14.5
+## metabolyseR v0.14.6
 ## Analysis:
-##  Thu Nov 11 21:33:26 2021
+##  Wed Nov 17 10:25:14 2021
 ## 
 ##  Raw Data:
 ##      No. samples = 120
 ##      No. features = 200
 ## 
 ##  Pre-treated Data:
-##      Thu Nov 11 21:33:27 2021
+##      Wed Nov 17 10:25:15 2021
 ##      No. samples = 120
 ##      No. features = 48
 ## 
 ##  Modelling:
-##      Thu Nov 11 21:33:30 2021
+##      Wed Nov 17 10:25:18 2021
 ##      Methods: randomForest
 ## 
 ##  Correlations:
-##      Thu Nov 11 21:33:30 2021
+##      Wed Nov 17 10:25:19 2021
 ##      No. correlations = 140

diff --git a/docs/articles/modelling.html b/docs/articles/modelling.html index bbfd398e..c1754606 100644 --- a/docs/articles/modelling.html +++ b/docs/articles/modelling.html @@ -31,7 +31,7 @@ metabolyseR - 0.14.5 + 0.14.6
@@ -89,10 +89,10 @@

Modelling and feature selection

-

metabolyseR v0.14.5

+

metabolyseR v0.14.6

Jasen Finch

-

11 November, 2021

+

17 November, 2021

Source: vignettes/modelling.Rmd @@ -737,7 +737,7 @@

The analysis can then be executed.

analysis <- metabolyse(abr1$neg,abr1$fact,p)
 #> 
-#> metabolyseR  v0.14.5 Thu Nov 11 21:34:36 2021
+#> metabolyseR  v0.14.6 Wed Nov 17 10:26:39 2021
 #> ________________________________________________________________________________
 #> Parameters:
 #> pre-treatment
@@ -770,13 +770,13 @@ 

 #> ________________________________________________________________________________
 #> Pre-treatment …
 
-Pre-treatment   ✓ [6.3S]
+Pre-treatment   ✓ [6.9S]
 #> Modelling …
 
-Modelling   ✓ [4.3S]
+Modelling   ✓ [4.7S]
 #> ________________________________________________________________________________
 #> 
-#> Complete! [10.6S]
+#> Complete! [11.7S]

The results for the modelling can be specifically extracted using the following.

 analysisResults(analysis,'modelling')
diff --git a/docs/articles/modelling_files/figure-html/outlier-detect-1.png b/docs/articles/modelling_files/figure-html/outlier-detect-1.png
index 4cca8b27..b4fef5f2 100644
Binary files a/docs/articles/modelling_files/figure-html/outlier-detect-1.png and b/docs/articles/modelling_files/figure-html/outlier-detect-1.png differ
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 3bdcc21b..7e2e31de 100644
Binary files a/docs/articles/modelling_files/figure-html/regression-mds-1.png and b/docs/articles/modelling_files/figure-html/regression-mds-1.png differ
diff --git a/docs/articles/pre_treatment.html b/docs/articles/pre_treatment.html
index 0264c6d8..0d70bf56 100644
--- a/docs/articles/pre_treatment.html
+++ b/docs/articles/pre_treatment.html
@@ -31,7 +31,7 @@
       
       
         metabolyseR
-        0.14.5
+        0.14.6
@@ -89,10 +89,10 @@

Metabolomics data pre-treatment

-

metabolyseR v0.14.5

+

metabolyseR v0.14.6

Jasen Finch

-

11 November, 2021

+

17 November, 2021

Source: vignettes/pre_treatment.Rmd @@ -500,7 +500,7 @@

The pre-treatment routine can then be executed.

analysis <- metabolyse(abr1$neg,abr1$fact,p)
 #> 
-#> metabolyseR  v0.14.5 Thu Nov 11 21:38:26 2021
+#> metabolyseR  v0.14.6 Wed Nov 17 10:30:55 2021
 #> ________________________________________________________________________________
 #> Parameters:
 #> pre-treatment
@@ -517,24 +517,24 @@ 

 #> ________________________________________________________________________________
 #> Pre-treatment …
 
-Pre-treatment   ✓ [8.8S]
+Pre-treatment   ✓ [9.9S]
 #> ________________________________________________________________________________
 #> 
-#> Complete! [8.8S]
+#> Complete! [10S]

Printing the analysis object shows the resulting data from the pre-treatment routine.

 print(analysis)
 #> 
-#> metabolyseR v0.14.5
+#> metabolyseR v0.14.6
 #> Analysis:
-#>  Thu Nov 11 21:38:26 2021
+#>  Wed Nov 17 10:30:55 2021
 #> 
 #>  Raw Data:
 #>      No. samples = 120
 #>      No. features = 2000
 #> 
 #>  Pre-treated Data:
-#>      Thu Nov 11 21:38:34 2021
+#>      Wed Nov 17 10:31:05 2021
 #>      No. samples = 60
 #>      No. features = 1723

The pre-treated data can be extracted from the Analysis object using several methods.

diff --git a/docs/articles/quick_start.html b/docs/articles/quick_start.html index 14625566..fb4034a4 100644 --- a/docs/articles/quick_start.html +++ b/docs/articles/quick_start.html @@ -31,7 +31,7 @@ metabolyseR - 0.14.5 + 0.14.6
@@ -89,10 +89,10 @@

Quick start example analysis

-

metabolyseR v0.14.5

+

metabolyseR v0.14.6

Jasen Finch

-

11 November, 2021

+

17 November, 2021

Source: vignettes/quick_start.Rmd diff --git a/docs/authors.html b/docs/authors.html index 8b8c6849..beb96ac6 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ metabolyseR - 0.14.5 + 0.14.6
diff --git a/docs/index.html b/docs/index.html index ffee1b24..5a72de62 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@ metabolyseR - 0.14.5 + 0.14.6
@@ -239,7 +239,7 @@

Developers

Dev status

@@ -132,6 +132,14 @@

Changelog

Source: NEWS.md
+
+

+metabolyseR 0.14.6

+ +

metabolyseR 0.14.5

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index a1d4557f..00200bda 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,7 +6,7 @@ articles: modelling: modelling.html pre_treatment: pre_treatment.html quick_start: quick_start.html -last_built: 2021-11-11T21:32Z +last_built: 2021-11-17T10:23Z urls: reference: https://jasenfinch.github.io/metabolyseR//reference article: https://jasenfinch.github.io/metabolyseR//articles diff --git a/docs/reference/Analysis-class.html b/docs/reference/Analysis-class.html index 79c4a10e..b918b86e 100644 --- a/docs/reference/Analysis-class.html +++ b/docs/reference/Analysis-class.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6
diff --git a/docs/reference/AnalysisData-class.html b/docs/reference/AnalysisData-class.html index f188f2f0..c25ccca7 100644 --- a/docs/reference/AnalysisData-class.html +++ b/docs/reference/AnalysisData-class.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/AnalysisParameters-class.html b/docs/reference/AnalysisParameters-class.html index 85abcc1d..5d79ed41 100644 --- a/docs/reference/AnalysisParameters-class.html +++ b/docs/reference/AnalysisParameters-class.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/QC.html b/docs/reference/QC.html index e83bc3bb..842365c0 100644 --- a/docs/reference/QC.html +++ b/docs/reference/QC.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/RandomForest-class.html b/docs/reference/RandomForest-class.html index d2b64829..5703377d 100644 --- a/docs/reference/RandomForest-class.html +++ b/docs/reference/RandomForest-class.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/Univariate-class.html b/docs/reference/Univariate-class.html index ce1c824b..b668f5e7 100644 --- a/docs/reference/Univariate-class.html +++ b/docs/reference/Univariate-class.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/aggregate.html b/docs/reference/aggregate.html index 3342c0c5..a520531d 100644 --- a/docs/reference/aggregate.html +++ b/docs/reference/aggregate.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/analysis-accessors.html b/docs/reference/analysis-accessors.html index 70126fbd..bd0ab301 100644 --- a/docs/reference/analysis-accessors.html +++ b/docs/reference/analysis-accessors.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/analysisData.html b/docs/reference/analysisData.html index f269fc94..9bf0997b 100644 --- a/docs/reference/analysisData.html +++ b/docs/reference/analysisData.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/analysisElements.html b/docs/reference/analysisElements.html index 1d00c86a..ef5b2527 100644 --- a/docs/reference/analysisElements.html +++ b/docs/reference/analysisElements.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/analysisParameters.html b/docs/reference/analysisParameters.html index 9ca1360b..11af90de 100644 --- a/docs/reference/analysisParameters.html +++ b/docs/reference/analysisParameters.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/anova.html b/docs/reference/anova.html index 62193453..16a9a9a1 100644 --- a/docs/reference/anova.html +++ b/docs/reference/anova.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/bind.html b/docs/reference/bind.html index 1c8c1dce..6ff98dbb 100644 --- a/docs/reference/bind.html +++ b/docs/reference/bind.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/changeParameter.html b/docs/reference/changeParameter.html index b98067a8..7c28aeec 100644 --- a/docs/reference/changeParameter.html +++ b/docs/reference/changeParameter.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/cls.html b/docs/reference/cls.html index a9085e9b..85a8806f 100644 --- a/docs/reference/cls.html +++ b/docs/reference/cls.html @@ -74,7 +74,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/correction.html b/docs/reference/correction.html index 0458d37c..c4f7af25 100644 --- a/docs/reference/correction.html +++ b/docs/reference/correction.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/correlations.html b/docs/reference/correlations.html index 16c5b93b..a5c79cc3 100644 --- a/docs/reference/correlations.html +++ b/docs/reference/correlations.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/correlationsParameters.html b/docs/reference/correlationsParameters.html index 3d43d9dd..5c649a6e 100644 --- a/docs/reference/correlationsParameters.html +++ b/docs/reference/correlationsParameters.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/impute.html b/docs/reference/impute.html index 82146467..1730762e 100644 --- a/docs/reference/impute.html +++ b/docs/reference/impute.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/index.html b/docs/reference/index.html index b886870f..ed2a1cb7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/io-parameters.html b/docs/reference/io-parameters.html index f13aaa77..f5e1a4bf 100644 --- a/docs/reference/io-parameters.html +++ b/docs/reference/io-parameters.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 @@ -197,8 +197,6 @@

Examp #> class #> cls = class #> occupancy = 0.667 -#> nCores = 4 -#> clusterType = FORK #> transform #> TICnorm #> diff --git a/docs/reference/keep.html b/docs/reference/keep.html index a406ec0b..b41ef80a 100644 --- a/docs/reference/keep.html +++ b/docs/reference/keep.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/linearRegression.html b/docs/reference/linearRegression.html index 02a0d73d..6becc828 100644 --- a/docs/reference/linearRegression.html +++ b/docs/reference/linearRegression.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/metabolyse.html b/docs/reference/metabolyse.html index e1ab5bf0..88ce0442 100644 --- a/docs/reference/metabolyse.html +++ b/docs/reference/metabolyse.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 @@ -196,16 +196,15 @@

Examp ) parameters(p,'modelling') <- modellingParameters('anova') -## Change "cls" and "nCores" parameters +## Change "cls" parameters changeParameter(p,'cls') <- 'day' -changeParameter(p,'nCores') <- 2 ## Run analysis using a subset of the abr1 negative mode data set analysis <- metabolyse(abr1$neg[,1:200], abr1$fact, p) #> -#> metabolyseR v0.14.5 Thu Nov 11 21:32:32 2021 +#> metabolyseR v0.14.6 Wed Nov 17 10:24:15 2021 #> ________________________________________________________________________________ #> Parameters: #> pre-treatment @@ -224,18 +223,18 @@

Examp #> returnModels = FALSE #> ________________________________________________________________________________ #> Pre-treatment … -#> Pre-treatment ✓ [0.8S] +#> Pre-treatment ✓ [0.9S] #> Modelling … -#> Modelling ✓ [0.5S] +#> Modelling ✓ [0.6S] #> ________________________________________________________________________________ #> -#> Complete! [1.3S] +#> Complete! [1.5S] ## Re-analyse to include correlation analysis analysis <- reAnalyse(analysis, parameters = analysisParameters('correlations')) #> -#> metabolyseR v0.14.5 Thu Nov 11 21:32:33 2021 +#> metabolyseR v0.14.6 Wed Nov 17 10:24:16 2021 #> ________________________________________________________________________________ #> Parameters: #> correlations @@ -253,25 +252,25 @@

Examp print(analysis) #> -#> metabolyseR v0.14.5 +#> metabolyseR v0.14.6 #> Analysis: -#> Thu Nov 11 21:32:32 2021 +#> Wed Nov 17 10:24:15 2021 #> #> Raw Data: #> No. samples = 120 #> No. features = 200 #> #> Pre-treated Data: -#> Thu Nov 11 21:32:32 2021 +#> Wed Nov 17 10:24:16 2021 #> No. samples = 120 #> No. features = 48 #> #> Modelling: -#> Thu Nov 11 21:32:33 2021 +#> Wed Nov 17 10:24:16 2021 #> Methods: anova #> #> Correlations: -#> Thu Nov 11 21:32:33 2021 +#> Wed Nov 17 10:24:17 2021 #> No. correlations = 140 diff --git a/docs/reference/modelling-accessors.html b/docs/reference/modelling-accessors.html index 6181a346..582afd84 100644 --- a/docs/reference/modelling-accessors.html +++ b/docs/reference/modelling-accessors.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/modelling-parameters.html b/docs/reference/modelling-parameters.html index 44d28815..86d2b8a4 100644 --- a/docs/reference/modelling-parameters.html +++ b/docs/reference/modelling-parameters.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/occupancy.html b/docs/reference/occupancy.html index 7af541db..11d12072 100644 --- a/docs/reference/occupancy.html +++ b/docs/reference/occupancy.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/occupancyFilter.html b/docs/reference/occupancyFilter.html index 7ee004fa..0e920a5d 100644 --- a/docs/reference/occupancyFilter.html +++ b/docs/reference/occupancyFilter.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/parameters.html b/docs/reference/parameters.html index 7947e974..2b874a9f 100644 --- a/docs/reference/parameters.html +++ b/docs/reference/parameters.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotExplanatoryHeatmap.html b/docs/reference/plotExplanatoryHeatmap.html index 784d5ac9..a5836ca8 100644 --- a/docs/reference/plotExplanatoryHeatmap.html +++ b/docs/reference/plotExplanatoryHeatmap.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotFeature.html b/docs/reference/plotFeature.html index 7435c5be..900620fd 100644 --- a/docs/reference/plotFeature.html +++ b/docs/reference/plotFeature.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotImportance.html b/docs/reference/plotImportance.html index 61aebe60..9a676428 100644 --- a/docs/reference/plotImportance.html +++ b/docs/reference/plotImportance.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotLDA.html b/docs/reference/plotLDA.html index 1e9d2e66..240fa302 100644 --- a/docs/reference/plotLDA.html +++ b/docs/reference/plotLDA.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotMDS.html b/docs/reference/plotMDS.html index 065b7c7d..ef1c6d4c 100644 --- a/docs/reference/plotMDS.html +++ b/docs/reference/plotMDS.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotMetrics.html b/docs/reference/plotMetrics.html index 6b94c8ae..3cbcd38c 100644 --- a/docs/reference/plotMetrics.html +++ b/docs/reference/plotMetrics.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotOccupancy.html b/docs/reference/plotOccupancy.html index 6146639e..d092c6d1 100644 --- a/docs/reference/plotOccupancy.html +++ b/docs/reference/plotOccupancy.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotPCA.html b/docs/reference/plotPCA.html index fccd384c..06d9b6a6 100644 --- a/docs/reference/plotPCA.html +++ b/docs/reference/plotPCA.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotROC.html b/docs/reference/plotROC.html index 45f61080..92a1166d 100644 --- a/docs/reference/plotROC.html +++ b/docs/reference/plotROC.html @@ -73,7 +73,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotRSD.html b/docs/reference/plotRSD.html index 6342c38a..60a56bd8 100644 --- a/docs/reference/plotRSD.html +++ b/docs/reference/plotRSD.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotSupervisedRF.html b/docs/reference/plotSupervisedRF.html index bdb53a54..28e0dc2d 100644 --- a/docs/reference/plotSupervisedRF.html +++ b/docs/reference/plotSupervisedRF.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotTIC.html b/docs/reference/plotTIC.html index 38b2df39..c1c47b79 100644 --- a/docs/reference/plotTIC.html +++ b/docs/reference/plotTIC.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/plotUnsupervisedRF.html b/docs/reference/plotUnsupervisedRF.html index aec673c2..3529024a 100644 --- a/docs/reference/plotUnsupervisedRF.html +++ b/docs/reference/plotUnsupervisedRF.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/pre-treatment-parameters.html b/docs/reference/pre-treatment-parameters.html index 6426d296..001466f0 100644 --- a/docs/reference/pre-treatment-parameters.html +++ b/docs/reference/pre-treatment-parameters.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/randomForest.html b/docs/reference/randomForest.html index 404b5f93..716951ff 100644 --- a/docs/reference/randomForest.html +++ b/docs/reference/randomForest.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index ef3e6879..2c5e14e2 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -79,7 +79,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/remove.html b/docs/reference/remove.html index 97189338..bb571e3d 100644 --- a/docs/reference/remove.html +++ b/docs/reference/remove.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/rsd.html b/docs/reference/rsd.html index db023caf..1e7abd8d 100644 --- a/docs/reference/rsd.html +++ b/docs/reference/rsd.html @@ -73,7 +73,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/split.html b/docs/reference/split.html index fe87c8d2..8e294611 100644 --- a/docs/reference/split.html +++ b/docs/reference/split.html @@ -73,7 +73,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/transform.html b/docs/reference/transform.html index cd84d08d..e0e8a74b 100644 --- a/docs/reference/transform.html +++ b/docs/reference/transform.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/docs/reference/ttest.html b/docs/reference/ttest.html index ff424a64..e3e99f24 100644 --- a/docs/reference/ttest.html +++ b/docs/reference/ttest.html @@ -72,7 +72,7 @@ metabolyseR - 0.14.5 + 0.14.6 diff --git a/inst/defaultParameters.yaml b/inst/defaultParameters.yaml index e0472d69..77ac55e8 100644 --- a/inst/defaultParameters.yaml +++ b/inst/defaultParameters.yaml @@ -25,8 +25,6 @@ pre-treatment: class: cls: class occupancy: 0.667 - nCores: 4 - clusterType: FORK transform: TICnorm: @@ -39,8 +37,6 @@ classification: niter: 10 nreps: 10 strat: TRUE - nCores: 4 - clusterType: Fork featureSelection: method: fs.rf @@ -48,8 +44,6 @@ featureSelection: pars: fs.rf: nreps: 100 - nCores: 4 - clusterType: FORK correlations: method: pearson diff --git a/man/metabolyse.Rd b/man/metabolyse.Rd index b9f621f1..1b252271 100644 --- a/man/metabolyse.Rd +++ b/man/metabolyse.Rd @@ -51,9 +51,8 @@ parameters(p,'pre-treatment') <- preTreatmentParameters( ) parameters(p,'modelling') <- modellingParameters('anova') -## Change "cls" and "nCores" parameters +## Change "cls" parameters changeParameter(p,'cls') <- 'day' -changeParameter(p,'nCores') <- 2 ## Run analysis using a subset of the abr1 negative mode data set analysis <- metabolyse(abr1$neg[,1:200],