1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
#'
#' Web-based tree explorer
#'
#' This function opens up an application in a web browser for an interactive exploration of the diversity in a set of trees.
#' For further details please see the "help" tab within the application.
#'
#' @seealso For convenience, \code{treespaceServer} is also available as a separate web app which can be used from any browser (it is not necessary to have \R installed): \url{https://mkendall.shinyapps.io/treespace/}
#'
#' @author Thibaut Jombart \email{thibautjombart@@gmail.com}
#' @author Michelle Kendall \email{michelle.louise.kendall@@gmail.com}
#'
#' @import ape
#' @import scatterD3
#' @import shiny
#' @import rgl
#' @importFrom ade4 dudi.pco
#' @importFrom adegraphics s1d.barchart
#' @importFrom adegraphics s.class
#' @importFrom adegraphics s.label
#' @importFrom adephylo distTips
#' @importFrom distory dist.multiPhylo
#' @importFrom fields rdist
#' @importFrom htmlwidgets saveWidget
#' @importFrom MASS Shepard
#' @importFrom phangorn Children
#' @importFrom phangorn Descendants
#' @importFrom RLumShiny jscolorInput
#' @importFrom shinyBS bsTooltip
#' @importFrom utils packageDescription
#'
#'
#'
#' @export
treespaceServer <- function(){
## RUN APP
options(rgl.useNULL=TRUE)
runApp(system.file("shiny",package="treespace"))
return(invisible())
}
#'
#' Auxiliary functions
#'
#' These functions are not supposed to be used by the user.
#'
#' @author Thibaut Jombart \email{thibautjombart@@gmail.com}
#'
#'
#' @importFrom adegenet .readExt
#'
#' @export
.render.server.info <- function(){
renderPrint(
{
cat("\n== R version ==\n")
print(R.version)
cat("\n== Date ==\n")
print(date())
cat("\n== treespace version ==\n")
print(packageDescription("treespace", fields=c("Package", "Version", "Date", "Built")))
cat("\n== shiny version ==\n")
print(packageDescription("shiny", fields=c("Package", "Version", "Date", "Built")))
cat("\n== attached packages ==\n")
print(search())
}
) # end renderPrint
} # end .render.server.info
|
