Merge pull request #81 from jasenfinch/devel

v0.14.4

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
-Version: 0.14.3
+Version: 0.14.4
 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

NEWS.md

@@ -1,3 +1,7 @@
+# metabolyseR 0.14.4
+
+* Console output from [`imputeAll()`](https://jasenfinch.github.io/metabolyseR/reference/impute.html) now suppressed.
+
 # metabolyseR 0.14.3
 
 * Temporarily added [jasenfinch/missForest](https://github.com/jasenfinch/missForest) as a remote until [stekhoven/missForest](https://github.com/stekhoven/missForest) pull request [#25](https://github.com/stekhoven/missForest/pull/25) is resolved.

R/impute.R

@@ -84,11 +84,11 @@ setMethod('imputeAll',signature = 'AnalysisData',
 
             da[da == 0] <- NA
 
-            suppressWarnings({
-              capture.output({
-                da <- missForest(da,parallelize = parallel)
-              })  
-            })
+            capture.output(
+              suppressMessages(
+                da <- missForest(da,parallelize = parallel) 
+              )
+            )
 
             dat(d_to_impute) <- as_tibble(da$ximp)
 
@@ -137,7 +137,8 @@ setMethod('imputeClass',signature = 'AnalysisData',
                   keepClasses(cls = cls,classes = .x) %>%
                   imputeAll(occupancy = occupancy,seed = seed,parallel = 'no')
               },
-              .options = furrr_options(seed = seed))
+              .options = furrr_options(seed = seed,
+                                       stdout = FALSE))
 
             d <- d %>%
               bindRows() %>%

README.Rmd

@@ -20,6 +20,7 @@ knitr::opts_chunk$set(collapse = TRUE,
 [![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)
 [![DOI](https://zenodo.org/badge/88983134.svg)](https://zenodo.org/badge/latestdoi/88983134)
+[![GitHub release](https://img.shields.io/github/release/jasenfinch/metabolyseR.svg)](https://GitHub.com/jasenfinch/metabolyseR/releases/)
 <!-- badges: end -->
 
 > **A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.**

README.md

@@ -11,6 +11,8 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
 [![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)
 [![DOI](https://zenodo.org/badge/88983134.svg)](https://zenodo.org/badge/latestdoi/88983134)
+[![GitHub
+release](https://img.shields.io/github/release/jasenfinch/metabolyseR.svg)](https://GitHub.com/jasenfinch/metabolyseR/releases/)
 <!-- badges: end -->
 
 > **A tool kit for pre-treatment, modelling, feature selection and
@@ -21,9 +23,9 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
 This package provides a tool kit of methods for metabolomics analyses
 that includes:
 
-  - data pre-treatment
-  - multivariate and univariate modelling/data mining techniques
-  - correlation analysis
+-   data pre-treatment
+-   multivariate and univariate modelling/data mining techniques
+-   correlation analysis
 
 ## Installation
 
@@ -168,7 +170,7 @@ anova_results <- d %>%
 ```
 
 A table of the significantly explanatory features can be extracted with
-a bonferroni correction adjusted p value \< 0.05 using:
+a bonferroni correction adjusted p value &lt; 0.05 using:
 
 ``` r
 explan_feat <- explanatoryFeatures(anova_results,threshold = 0.05)
@@ -177,18 +179,18 @@ explan_feat <- explanatoryFeatures(anova_results,threshold = 0.05)
 ``` r
 explan_feat
 #> # A tibble: 379 × 10
-#>    Response Comparison  Feature term        df   sumsq  meansq statistic  p.value
-#>    <chr>    <chr>       <chr>   <chr>    <dbl>   <dbl>   <dbl>     <dbl>    <dbl>
-#>  1 day      1~2~3~4~5~H N341    response     5 3.88e-4 7.76e-5     137.  1.55e-46
-#>  2 day      1~2~3~4~5~H N133    response     5 7.00e-5 1.40e-5     126.  8.63e-45
-#>  3 day      1~2~3~4~5~H N163    response     5 6.01e-5 1.20e-5     117.  2.95e-43
-#>  4 day      1~2~3~4~5~H N1087   response     5 2.42e-6 4.84e-7      99.8 5.61e-40
-#>  5 day      1~2~3~4~5~H N171    response     5 2.25e-7 4.50e-8      95.7 3.84e-39
-#>  6 day      1~2~3~4~5~H N513    response     5 3.38e-6 6.76e-7      95.3 4.78e-39
-#>  7 day      1~2~3~4~5~H N1025   response     5 2.78e-6 5.56e-7      91.0 3.91e-38
-#>  8 day      1~2~3~4~5~H N342    response     5 3.71e-6 7.41e-7      90.3 5.32e-38
-#>  9 day      1~2~3~4~5~H N1083   response     5 5.11e-5 1.02e-5      89.0 1.06e-37
-#> 10 day      1~2~3~4~5~H N1085   response     5 1.10e-5 2.19e-6      83.4 1.92e-36
+#>    Response Comparison  Feature term      df    sumsq  meansq statistic  p.value
+#>    <chr>    <chr>       <chr>   <chr>  <dbl>    <dbl>   <dbl>     <dbl>    <dbl>
+#>  1 day      1~2~3~4~5~H N341    respo…     5  3.88e-4 7.76e-5     137.  1.55e-46
+#>  2 day      1~2~3~4~5~H N133    respo…     5  7.00e-5 1.40e-5     126.  8.63e-45
+#>  3 day      1~2~3~4~5~H N163    respo…     5  6.01e-5 1.20e-5     117.  2.95e-43
+#>  4 day      1~2~3~4~5~H N1087   respo…     5  2.42e-6 4.84e-7      99.8 5.61e-40
+#>  5 day      1~2~3~4~5~H N171    respo…     5  2.25e-7 4.50e-8      95.7 3.84e-39
+#>  6 day      1~2~3~4~5~H N513    respo…     5  3.38e-6 6.76e-7      95.3 4.78e-39
+#>  7 day      1~2~3~4~5~H N1025   respo…     5  2.78e-6 5.56e-7      91.0 3.91e-38
+#>  8 day      1~2~3~4~5~H N342    respo…     5  3.71e-6 7.41e-7      90.3 5.32e-38
+#>  9 day      1~2~3~4~5~H N1083   respo…     5  5.11e-5 1.02e-5      89.0 1.06e-37
+#> 10 day      1~2~3~4~5~H N1085   respo…     5  1.10e-5 2.19e-6      83.4 1.92e-36
 #> # … with 369 more rows, and 1 more variable: adjusted.p.value <dbl>
 ```