Merge pull request #75 from jasenfinch/fix

v0.13.3

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Classification, Feature Selection and Correlation Analyses of Metabolomics Data
-Version: 0.13.2
+Version: 0.13.3
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Methods for pre-treatment, classification, feature selection and correlation analyses of metabolomics data.
 biocViews: Metabolomics
@@ -77,6 +77,7 @@ Collate: allGenerics.R
     rawData-method.R
     rawInfo-method.R
     reAnalyse.R
+    reexports.R
     removeMethods.R
     show-method.R
     transformMethods.R

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
 export("dat<-")
 export("preTreated<-")
 export("raw<-")
@@ -124,7 +125,6 @@ importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_all)
-importFrom(dplyr,tbl_df)
 importFrom(dplyr,ungroup)
 importFrom(e1071,naiveBayes)
 importFrom(forestControl,fpr_fs)

R/metabolyse.R

@@ -4,7 +4,6 @@
 #' @param info tibble or data.frame containing data info or meta data
 #' @param parameters an object of AnalysisParameters class containing parameters for analysis. Default calls \code{analysisParameters()}
 #' @param verbose should output be printed to the console 
-#' @importFrom magrittr %>%
 #' @importFrom methods slotNames slot
 #' @importFrom tibble tibble as_tibble 
 #' @importFrom utils packageVersion
@@ -40,7 +39,7 @@ metabolyse <- function(data,info,parameters = analysisParameters(), verbose = T)
       {capture.output(print(.))} %>%
       {
         .[1] <- yellow(.[1])
-        return(.)
+        .
       } %>%
       str_c(collapse = '\n')
     message(params)

R/reexports.R

@@ -0,0 +1,4 @@
+#' @rdname reexports
+#' @importFrom magrittr %>%
+#' @export
+magrittr::`%>%`

vignettes/metabolyseR-usage.Rmd

@@ -16,7 +16,6 @@ vignette: >
 
 ```{r,include=FALSE}
 knitr::opts_chunk$set(fig.align = 'center')
-library(magrittr)
 ```
 
 ## Introduction
@@ -27,7 +26,7 @@ Below shows the three analysis elements in that make up metabolyseR.
 
 <center>
 ```{r metabolyseRDiagram,echo=FALSE,fig.width=8}
-  DiagrammeR::grViz(readr::read_file('figures/metabolyseR.gv'))
+DiagrammeR::grViz(readr::read_file('figures/metabolyseR.gv'))
 ```
 </center>
 
@@ -555,7 +554,7 @@ The table below outlines the modelling methods currently available:
 metabolyseR:::modellingMethods(description = T) %>%
   purrr::map(tibble::as_tibble) %>%
   dplyr::bind_rows(.id = 'Method') %>%
-  {set_colnames(.,stringr::str_to_title(colnames(.)))} %>%
+  {magrittr::set_colnames(.,stringr::str_to_title(colnames(.)))} %>%
   knitr::kable()
 ```