Nothing
.onAttach <- function(...){
ref <- random_ref()
if (!is.null(ref)) packageStartupMessage(ref)
}
#' @importFrom pillar style_subtle
random_ref <- function(pkgname = NULL, pkgVersion = NULL, random_n = 2){
if (!is.null(pkgname) && !is.null(pkgVersion)){
headermsg <- paste0(pkgname, " v", pkgVersion, " ",
"For help: https://yulab-smu.top/treedata-book/", "\n\n")
}else{
headermsg <- NULL
}
msg <- "If you use the ggtree package suite in published research, please cite the appropriate paper(s):\n\n"
refs <- c(
ggtreeBook = paste("Guangchuang Yu. ",
"Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition).",
"Chapman and Hall/CRC. 2022, doi:10.1201/9781003279242\n"),
ggtreeCPB = paste0(
"Guangchuang Yu. ",
"Using ggtree to visualize data on tree-like structures. ",
"Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96\n"
),
ggtree_imeta = paste0("Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. ",
"Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. ",
"iMeta 2022, 1(4):e56. doi:10.1002/imt2.56\n"),
ggtreeMBE = paste0(
"Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
"Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
"Molecular Biology and Evolution. 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194\n"
),
ggtree = paste0(
"Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
"ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
"Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628\n"
),
treeio = paste0(
"LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. ",
"treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. ",
"Molecular Biology and Evolution. 2020, 37(2):599-603. doi: 10.1093/molbev/msz240\n"
),
ggtreeExtra = paste0(
"S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ",
"ggtreeExtra: Compact visualization of richly annotated phylogenetic data. ",
"Molecular Biology and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166\n"
),
ggtreeCRC = paste0(
"G Yu. ",
"Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st ed.). ",
"Chapman and Hall/CRC. 2022. ISBN: 9781032233574\n"
)
)
if (is.null(pkgname)){
refs <- paste0(sample(refs, random_n), collapse="\n")
}else{
indx <- match(pkgname, names(refs))
refs <- paste0(c(refs[indx], sample(refs[-indx], random_n)), collapse="\n")
}
if (all(nchar(refs) > 0)){
return(paste(strwrap(style_subtle(paste0(headermsg, msg, refs))), collapse = "\n"))
}else{
return(NULL)
}
}
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