- Change URL to doi for citation

NEWS.md

@@ -1,6 +1,7 @@
 # pmd 0.2.7
 
 - CRAN
+- Change URL to doi for citation
 
 # pmd 0.2.6
 

R/data.R

@@ -21,7 +21,7 @@
 #'   \item{exact_mass}{exact mass of contaminants}
 #'   \item{type_of_contaminant}{type of contaminant}
 #'   }
-#' @source \url{https://academic.oup.com/bioinformatics/article/28/21/2856/236679}
+#' @source \url{https://doi.org/10.1093/bioinformatics/bts527}
 "MaConDa"
 
 #' A peaks list dataset containing 9 samples from 3 fish with triplicates samples for each fish from LC-MS.

README.md

@@ -30,9 +30,9 @@ Usage
 
 - For MS only data such as FT-ICR or MS imaging data, check the section of "Reactomics analysis for MS only data" in Reactomics Analysis Tutorial or this blog [post](https://yufree.cn/en/2024/05/29/reactomics-analysis-for-ms-only-data/).
 
-- [PMD analysis paper](https://www.sciencedirect.com/science/article/abs/pii/S0003267018313047). This paper proposed structure/reaction directed analysis with PMD.
+- [PMD analysis paper](https://doi.org/10.1016/j.aca.2018.10.062). This paper proposed structure/reaction directed analysis with PMD. 
 
-- [Reactomics paper](https://www.nature.com/articles/s42004-020-00403-z). This paper contained the concepts of PMD based reactomics, applications and data mining of reaction database and compounds database.
+- [Reactomics paper](https://doi.org/10.1038/s42004-020-00403-z). This paper contained the concepts of PMD based reactomics, applications and data mining of reaction database and compounds database.
 
 - [Slides](http://yufree.github.io/presentation/reactomics/pres-asms.html). This is the slides for ASMS 2020 Reboot and here is the [video](https://youtu.be/-mT3HcVygHE) of presentation. Press "P" and you will see the notes for each slide with details. Another full version of reactomics presentation for one hour presentation could be found [here](http://yufree.github.io/presentation/reactomics/pres). I will not update the conference presentation while I will add new contents for the full version of reactomics presentation whenever I have new results.
 

inst/CITATION

@@ -9,7 +9,7 @@ citEntry(
 	year = "2019",
 	issn = "0003-2670",
 	doi = "10.1016/j.aca.2018.10.062",
-	url = "https://www.sciencedirect.com/science/article/pii/S0003267018313047",
+	url = "https://doi.org/10.1016/j.aca.2018.10.062",
         author = "Miao Yu and Mariola Olkowicz and Janusz Pawliszyn",
         textVersion = paste("Miao Yu, Mariola Olkowicz, Janusz Pawliszyn",
 	"2019",
@@ -31,6 +31,6 @@ citEntry(
 	"Untargeted high-resolution paired mass distance data mining for retrieving general chemical relationships,",
 	"Communications Chemistry, 3, 157."))
 
-citFooter(paste("Some functions (e.g. getmd use xcms",
+citFooter(paste("Some functions",
                  "party algorithms, see manpages and related packages",
 	         "for respective citations."))