In byandell/ewing: Ewing's Quantitative Population Ethology

knitr::opts_chunk$set(echo = TRUE)

Goal here is to understand better how elements of ewing package work.

library(ewing)

mysim <- init.simulation(interact = FALSE, datafile = "../../data/smallerb.xlsx")

ewing:::getOffspring(mysim, "host")
ewing:::getOffspring(mysim, "parasite")
ewing:::getOrgFeature(mysim, "parasite", "offspring" )
ewing:::getOrgFeature(mysim, "parasite", "attack" )
ewing:::getOrgInteract(mysim, "host", "parasite")
ewing:::getOrgInteract(mysim, "host", "parasite", "offspring")

str(mysim)

simres <- future.events(mysim, nstep = 10, plotit = TRUE, ageclass = FALSE)

Plot ageclasses.

for(i in seq_along(simres$plot)) print(ggplot2::autoplot(simres$plot[[i]]$ageclass))

Plot victim substrate.

for(i in seq_along(simres$plot)) print(ggplot2::autoplot(simres$plot[[i]]$substrate$victim))

Plot badguy substrate.

for(i in seq_along(simres$plot)) print(ggplot2::autoplot(simres$plot[[i]]$substrate$badguy))

Finding differences between steps.

tmp <- purrr::transpose(simres$plot)
tmp1 <- tmp$substrate[[1]]$victim
tmp2 <- tmp$substrate[[10]]$victim
tmp3 <- dplyr::intersect(tmp1,tmp2) # rows that agree
dplyr::setdiff(tmp1,tmp3)
dplyr::setdiff(tmp2,tmp3)

Look for:

dropped index (death)
NA for index (changed state)
extra NA after last (births)

compdf <- function(tmp1, tmp2) {
  # NAs are either changed (new state) or removed (died)
  m <- match(tidyr::unite(tmp1, cols, dplyr::everything())$cols,
        tidyr::unite(tmp2, cols, dplyr::everything())$cols,
        nomatch = 0)
  dplyr::bind_rows(
    list("1" = cbind(n = seq_len(nrow(tmp1)), tmp1)[m == 0,],
         "2" = cbind(n = seq_len(nrow(tmp2)), tmp2)[-m,]),
    .id = "df")
}

(cout <- compdf(tmp1,tmp2))

p1 <- simres$plot[[1]]$substrate$victim
p1$color <- "gray"
p1$color[cout[cout$df == 1, "n"]] <- "red"
p1$pchar[-cout[cout$df == 1, "n"]] <- "-"
ggplot2::autoplot(p1)

p2 <- simres$plot[[10]]$substrate$victim
p2$color <- "gray"
p2$color[cout[cout$df == 2, "n"]] <- "blue"
p2$pchar[-cout[cout$df == 2, "n"]] <- "-"
ggplot2::autoplot(p2)

Can add points to existing plots.

p <- ggplot2::autoplot(p1)
p + ggplot2::geom_text(data = cout[cout$df == 2, ],
                       ggplot2::aes(x = x, y = y, label = pchar),
                       col = "blue")

More plots

ggplot_ewing(simres)

ewing:::get.species(simres)

ggplot_current(simres, "victim")

ggplot_current(simres, "badguy")

species <- ewing:::get.species(simres)
p <- lapply(species, function(x) {
  ggplot_current(simres, x) + 
    ggplot2::ggtitle(paste(x, "on substrate"))
})
p[[1]] + p[[2]] + patchwork::plot_layout(nrow = 2)