Merge pull request #42 from jasenfinch/devel

v0.7.7

.github/workflows/R-CMD-check.yaml

@@ -21,8 +21,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
+          #- {os: windows-latest, r: 'release'}
+          #- {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MFassign
 Title: Molecular Formula Assignment for High Resolution metabolomics
-Version: 0.7.6
+Version: 0.7.7
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Molecular formula assignment for high resolution metabolomics.
 Depends: R (>= 3.5.0),
@@ -30,7 +30,7 @@ Remotes: jasenfinch/mzAnnotation,
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Collate:
         'allGenerics.R'
         'allClasses.R'

R/addMFs.R

@@ -20,7 +20,7 @@ addMFs <- function(rel,MF,identMF = T){
    relations[,chr_columns] <- relations[,chr_columns] %>%
      {
        .[is.na(.)] <- ''
-       return(.)
+       .
      }
 
   relations <- relations %>%
@@ -36,7 +36,7 @@ addMFs <- function(rel,MF,identMF = T){
   relations[,chr_columns] <- relations[,chr_columns] %>%
     {
       .[is.na(.)] <- ''
-      return(.)
+      .
     }
 
   relations <- relations %>%

R/assignMFs.R

@@ -16,10 +16,10 @@
 #'
 #' @export
 
-assignMFs <- function(dat,parameters,verbose = T) {
+assignMFs <- function(dat,parameters,verbose = TRUE) {
   options(digits = 10)
 
-  if (verbose == T) {
+  if (verbose == TRUE) {
     startTime <- proc.time()
     message(blue('\nMFassign '),red(str_c('v',packageVersion('MFassign') %>% as.character())),' ',date())
     message(rep('_',console_width()))
@@ -28,7 +28,7 @@ assignMFs <- function(dat,parameters,verbose = T) {
       {.[-1]} %>%
       {
         .[1] <- yellow(.[1])
-        return(.)
+        .
       } %>%
       str_c(collapse = '\n')
     message(params)

R/prepCorrelations-method.R

@@ -11,36 +11,24 @@ setMethod('prepCorrelations',signature = 'Assignment',
 
             correlations <- correlations %>%
               mutate(Mode1 = str_split_fixed(Feature1,'@',2) %>% 
-                       as_tibble() %>% 
-                       select(V1) %>% 
-                       unlist() %>% 
+                       .[,1] %>%
                        str_sub(1,1),
                      Mode2 = str_split_fixed(Feature2,'@',2) %>% 
-                       as_tibble() %>% 
-                       select(V1) %>% 
-                       unlist() %>% 
+                       .[,1] %>%
                        str_sub(1,1),
                      `m/z1` = str_split_fixed(Feature1,'@',2) %>% 
-                       as_tibble() %>% 
-                       select(V1) %>% 
-                       unlist() %>% 
+                       .[,1] %>% 
                        str_replace_all('[:alpha:]','') %>% 
                        as.numeric(),
                      `m/z2` = str_split_fixed(Feature2,'@',2) %>% 
-                       as_tibble() %>% 
-                       select(V1) %>% 
-                       unlist() %>% 
+                       .[,1] %>% 
                        str_replace_all('[:alpha:]','') %>% 
                        as.numeric(),
                      RetentionTime1 = str_split_fixed(Feature1,'@',2) %>% 
-                       as_tibble() %>% 
-                       select(V2) %>%
-                       unlist() %>%
+                       .[,2] %>%
                        as.numeric(),
                      RetentionTime2 = str_split_fixed(Feature2,'@',2) %>% 
-                       as_tibble() %>% 
-                       select(V2) %>%
-                       unlist() %>%
+                       .[,2] %>%
                        as.numeric(),
                      ID = 1:nrow(.)
               ) %>%

README.md

@@ -1,14 +1,16 @@
 # MFassign
 
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) 
+<!-- badges: start -->
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
  [![R build status](https://github.com/jasenfinch/MFassign/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/MFassign/actions)
 [![Coverage Status](https://img.shields.io/codecov/c/github/jasenfinch/MFassign/master.svg)](https://codecov.io/github/jasenfinch/MFassign?branch=master) 
 [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/MFassign/blob/master/DESCRIPTION)
-
+<!-- badges: end -->
+
 An R package for molecular formula assignment in high resolution metabolomics
 
 ### Installation
 
 ``` r
 devtools::install_github('jasenfinch/MFassign')
-```
+```

tests/testthat/test-assignMFs.R

@@ -4,7 +4,7 @@ context('assignMFs')
 p <- assignmentParameters('FIE')
 p@nCores <- 2
 
-assignment <- assignMFs(peakData,p,verbose = FALSE)
+assignment <- assignMFs(peakData,p,verbose = TRUE)
 
 test_that('assignMFs works',{
   expect_true(class(assignment) == "Assignment")