data-raw/workflow_diagrams/datelife_workflow_diagrams_2018.07.12.R

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

#  July, 12 2018
# datelife congruify workflow
#

# foodweb plot:
# install.packages("mvbutils")
library(mvbutils)
pdf(file = "data-raw/workflow_diagrams/use_all_calibrations_foodweb1.pdf", height = 10, width = 25)
foodweb(
  where = "package:datelife", prune = "datelife",
  border = TRUE,
  boxcolor = "aliceblue",
  textcolor = "black", cex = 1.0, lwd = 2
)
mtext("datelife function foodweb", line = 2, font = 2, cex = 1.5)
grDevices::dev.off()


# run some examples with diagram package:
# install.packages("diagram")
require(diagram)
openplotmat(main = "textbox shapes")
rx <- 0.1
ry <- 0.05
pos <- coordinates(c(1, 1, 1, 1, 1, 1, 1, 1), mx = -0.2)
textdiamond(mid = pos[1, ], radx = rx, rady = ry, lab = LETTERS[1], cex = 2, shadow.col = "lightblue")

# actual diagrams:
pdf(file = "data-raw/congruify_workflow_use_all_calibrations.pdf", height = 14)
elpos <- coordinates(c(1, rep(2, 11)))
elpos2 <- coordinates(c(1, 2, 2, rep(1, 9)))
from <- c(1, 1, 2:5, 14:19)
to <- c(2, 3, 4:7, 16:21)
nr <- length(from)
arrpos <- matrix(ncol = 2, nrow = nr)
par(mar = c(1, 1, 1, 1))
openplotmat()
for (i in 1:nr) {
  arrpos[i, ] <- straightarrow(
    to = elpos[to[i], ],
    from = elpos[from[i], ],
    lwd = 2, arr.pos = 0.6, arr.length = 0.5
  )
}
# textellipse(elpos[1,], 0.1, 0.05, lab = c("datelife_search", "function"), box.col = "white",
#               shadow.col = "black", shadow.size = 0.005, cex = 0.8)
textrect(elpos[1, ], 0.15, 0.025,
  lab = c("datelife", "function"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
texthexa(elpos[2, ], 0.15, 0.025,
  lab = c("input =", "taxon names"), box.col = "orange",
  shadow.col = "red", shadow.size = 0.005, cex = 0.8
)

texthexa(elpos[3, ], 0.15, 0.025,
  lab = c("input =", "a tree"), box.col = "#AFEEEE",
  shadow.col = "darkgreen", shadow.size = 0.005, cex = 0.9
)

textrect(elpos[4, ], 0.15, 0.025,
  lab = c("make_bold_otol_tree", "function"), box.col = "orange",
  shadow.col = "red", shadow.size = 0.005, cex = 0.8
)
textrect(elpos2[6, ], 0.3, 0.015,
  lab = c("get_all_calibrations function"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
texthexa(elpos2[10, ], 0.3, 0.015,
  lab = c("congruify with scale = NA", "output is a table of calibrations"), box.col = "green",
  shadow.col = "darkgreen", shadow.size = 0.005, cex = 0.8
)
textrect(elpos2[11, ], 0.3, 0.015,
  lab = c("geiger::PATHd8.phylo function"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
textrect(elpos2[12, ], 0.3, 0.015,
  lab = c("expand calibrations until !is.null(chronogram)"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
textrect(elpos2[13, ], 0.3, 0.025,
  lab = c("output is ONE chronogram scaled", "with secondary calibrations"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
grDevices::dev.off()

pdf(file = "data-raw/congruify_workflow_datelife_search.pdf")
elpos <- coordinates(c(1, rep(2, 6)))
elpos2 <- coordinates(c(1, 2, 1, 1, 2, 2, 1))
from <- c(2, 2, 3:12) - 1
to <- c(3, 4, 5:14) - 1
nr <- length(from)
arrposA <- matrix(ncol = 2, nrow = nr)
par(mar = c(1, 1, 1, 1))
openplotmat()
for (i in 1:nr) {
  arrposA[i, ] <- straightarrow(
    to = elpos[to[i], ],
    from = elpos[from[i], ],
    lwd = 2, arr.pos = 0.6, arr.length = 0.5
  )
}
# textellipse(elpos[1,], 0.1, 0.05, lab = c("datelife_search", "function"), box.col = "white",
#               shadow.col = "black", shadow.size = 0.005, cex = 0.8)
textrect(elpos[1, ], 0.15, 0.05,
  lab = c("datelife_search", "function"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
texthexa(elpos[2, ], 0.15, 0.05,
  lab = c("input =", "taxon names"), box.col = "pink",
  shadow.col = "red", shadow.size = 0.005, cex = 0.8
)

texthexa(elpos[3, ], 0.15, 0.05,
  lab = c("input =", "a tree"), box.col = "lightblue",
  shadow.col = "darkgreen", shadow.size = 0.005, cex = 0.9
)
# textrect (elpos2[4,], 0.3, 0.03,lab = "make_datelife_query function: process names and/or tree", box.col = "white",
#           shadow.col = "black", shadow.size = 0.005, cex = 0.9)
textrect(elpos2[4, ], 0.3, 0.03,
  lab = "get_datelife_results and inside functions", box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
texthexa(elpos2[5, ], 0.3, 0.05,
  lab = c("subset chronograms from otol"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
texthexa(elpos[9, ], 0.15, 0.05,
  lab = c("congruify", "scaling = PATHd8"), box.col = "green",
  shadow.col = "darkgreen", shadow.size = 0.005, cex = 0.8
)
texthexa(elpos[10, ], 0.15, 0.05,
  lab = c("output:", "chronograms from", "primary studies ***"), box.col = "pink",
  shadow.col = "red", shadow.size = 0.005, cex = 0.8
) # chronograms with tips found in otol only

texthexa(elpos[11, ], 0.15, 0.05,
  lab = c("output:", "chronograms scaled", "with PATHd8"), box.col = "lightblue",
  shadow.col = "darkgreen", shadow.size = 0.005, cex = 0.8
)
textrect(elpos2[10, ], 0.3, 0.05,
  lab = c("summarize_datelife_result function:", "(a) all chronograms, (b) one summary chronogram,", " (c) a table of ages, (d) citations of primary studies"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)

grDevices::dev.off()


pdf(file = "data-raw/congruify_workflow_tree_add_dates.pdf")
elpos <- coordinates(c(1, rep(3, 6)))
elpos2 <- coordinates(c(1, 3, 3, 3, rep(1, 3)))
from <- c(1, 1, 1, 2:10)
to <- c(2, 3, 4, 5:13)
nr <- length(from)
arrposA <- matrix(ncol = 2, nrow = nr)
par(mar = c(1, 1, 1, 1))
openplotmat()
for (i in 1:nr) {
  arrposA[i, ] <- straightarrow(
    to = elpos[to[i], ],
    from = elpos[from[i], ],
    lwd = 2, arr.pos = 0.6, arr.length = 0.5
  )
}
# textellipse(elpos[1,], 0.1, 0.05, lab = c("datelife_search", "function"), box.col = "white",
#               shadow.col = "black", shadow.size = 0.005, cex = 0.8)
textrect(elpos[1, ], 0.15, 0.05,
  lab = c("***tree_add_dates", "function"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
texthexa(elpos[2, ], 0.15, 0.05,
  lab = c("adding_criterion =", "random"), box.col = "plum",
  shadow.col = "violet", shadow.size = 0.005, cex = 0.8
)
texthexa(elpos[3, ], 0.15, 0.05,
  lab = c("adding_criterion =", "taxonomy"), box.col = "mistyrose",
  shadow.col = "red", shadow.size = 0.005, cex = 0.8
)
texthexa(elpos[4, ], 0.15, 0.05,
  lab = c("adding_criterion =", "tree"), box.col = "azure",
  shadow.col = "darkgreen", shadow.size = 0.005, cex = 0.8
)
textrect(elpos[7, ], 0.15, 0.05,
  lab = c("make_bold_otol_tree", "function"), box.col = "azure",
  shadow.col = "darkgreen", shadow.size = 0.005, cex = 0.8
)
texthexa(elpos[10, ], 0.15, 0.05,
  lab = c("congruify", "scaling = NA"), box.col = "green",
  shadow.col = "darkgreen", shadow.size = 0.005, cex = 0.8
)
textrect(elpos2[11, ], 0.4, 0.05,
  lab = c("date with: mrbayes, bladj, PATHd8"), box.col = "white",
  shadow.col = "black", shadow.size = 0.005, cex = 0.9
)
grDevices::dev.off()