Merge pull request #59 from RECETOX/hotfix

added dplyr import and removed saving files

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MFAssignR
 Type: Package
 Title: An R Package for Data Preparation and Molecular Formula Assignment
-Version: 1.1.0
+Version: 1.1.1
 Author: Simeon Schum, Lynn Mazzoleni, Laura Brown
 Maintainer: Simeon Schum, <skschum@mtu.edu>
 Description: This package contains functions that can estimate

NAMESPACE

@@ -50,3 +50,4 @@ export(process_carbon_isotoping)
 export(process_sulfur)
 export(sulfur_check)
 import(ggplot2)
+importFrom(dplyr,"%>%")

R/FindRecalSeries.R

@@ -6,6 +6,7 @@
 #' @param peak_distance_threshold Float A threshold for the peak distance parameter. The closer this value is to 1, the
 #' better.
 #' @return DataFrame A filtered dataframe.
+#' @importFrom dplyr %>%
 #' @export
 filter_recal_series <- function(df, abundance_score_threshold, peak_distance_threshold) {
   df <- df %>%
@@ -54,6 +55,7 @@ compute_subsets <- function(df, n) {
 #' @param global_max Float A higher bound of the instrument m/z range.
 #'
 #' @return Coverage (in %) of a particular subset.
+#' @importFrom dplyr %>%
 #' @export
 compute_coverage <- function(subset, global_max, global_min) {
   subset <- subset %>%
@@ -128,6 +130,7 @@ compute_scores <- function(combination) {
 #' @param scores_df DataFrame A dataframe of scores.
 #'
 #' @return DataFrame A sorted dataframe containing the final score.
+#' @importFrom dplyr %>%
 #' @export
 compute_final_score <- function(scores_df) {
   final_score <- scores_df %>%
@@ -148,19 +151,18 @@ compute_final_score <- function(scores_df) {
 #' combination will be returned.
 #'
 #' @return DataFrame A dataframe of best-scoring series.
+#' @importFrom dplyr %>%
 #' @export
 find_final_series <- function(scores_df, number_of_combinations, fill_series) {
   final_series <- compute_final_score(scores_df)
 
   if (fill_series == FALSE) {
     final_series <- final_series %>%
       dplyr::slice_head(n = number_of_combinations)
-    saveRDS(final_series, "test-data/final_seriesFALSE.rds")
   } else {
     final_series <- final_series %>%
       dplyr::distinct(series, .keep_all = TRUE) %>%
       dplyr::slice_head(n = 10)
-    saveRDS(final_series, "test-data/final_seriesTRUE.rds")
   }
 
   return(final_series)

changelog.txt

@@ -1,5 +1,8 @@
 Package Updates
 
+09/12/2024 Version 1.1.1
+ - quick fix of hardcoded paths and imports [#59](https://github.com/RECETOX/MFAssignR/pull/59)
+
 09/11/2024 (Version 1.0.4 + Version 1.1.0)
 - fixed bug which caused isofiltr to fail is some subsection of input has no isotope pairs #43
 - added functions to automatically find the best set of calibrants [#44](https://github.com/RECETOX/MFAssignR/pull/44)