From 7c50aaf05a22a1b320f7bed9cbc498a1bde3b6f8 Mon Sep 17 00:00:00 2001 From: yufree Date: Tue, 14 Jan 2025 13:03:32 -0500 Subject: [PATCH] - Change URL to doi for citation --- NEWS.md | 1 + R/data.R | 2 +- README.md | 4 ++-- inst/CITATION | 4 ++-- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/NEWS.md b/NEWS.md index cb2e65c..232324b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,7 @@ # pmd 0.2.7 - CRAN +- Change URL to doi for citation # pmd 0.2.6 diff --git a/R/data.R b/R/data.R index 45901a5..70080c3 100644 --- a/R/data.R +++ b/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. diff --git a/README.md b/README.md index 9bd3b17..e6b7eaf 100644 --- a/README.md +++ b/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. diff --git a/inst/CITATION b/inst/CITATION index 377c138..2b2c777 100644 --- a/inst/CITATION +++ b/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."))