In byandell/ewing: Ewing's Quantitative Population Ethology

knitr::opts_chunk$set(echo = TRUE)

library(ewing)
library(tidyverse)

data("organism.features")
data("future.host")
data("future.parasite")
data("host.parasite")
data("substrate.host")
data("substrate.parasite")

Get names of data structures.

dlist <- c("future.host",
           "future.parasite",
           "host.parasite",
           "substrate.host",
           "substrate.parasite")
dlist <- as.list(dlist)
names(dlist) <- c(dlist)
nlist <- map(dlist, function(x) {
  names(get(x))
})

We can combine (rbind) the futures by adding a column for species.

future <- bind_rows(
  host = future.host,
  parasite = future.parasite,
  .id = "species")

We can combine the substrate in a similar way, but first have to change the rownames into a column.

ftemp <- function(x) {
  out <- data.frame(subname = rownames(x), x)
  rownames(out) <- NULL
  out
}
substrate <- bind_rows(
  host = ftemp(substrate.host),
  parasite = ftemp(substrate.parasite),
  .id = "species")

Then we have 4 types of files:

• future
• substrate
• host.parasite
• organism.features

The organism.features would work better as a long table.

ftemp <- function(x, cc) {
  out <- sapply(x[cc,], as.character)
  names(out) <- NULL
  out
}
features <- bind_rows(
  host = data.frame(feature = colnames(organism.features),
                    value = ftemp(organism.features, 1)),
  parasite = data.frame(feature = colnames(organism.features),
                        value = ftemp(organism.features, 2)),
  .id = "species") %>%
  filter(!is.na(value))

The host.parasite could be appended to host with some adjustment.

• future.host has "starved" current state
• future.host has competing risks for "second.3" to "female" and "male"
• host.parasite has "parasite" current state
• host.parasite has rownames which should be "current"

Could do the following:

• add columns to future for "ovip" "feed" "offspring" "male"
• include NA entries for these for parasite
• add column to indicate what specied is parasite

Translation

Need routines to translate between formats, or adjust routines to handle this automatically.

byandell/ewing documentation built on Jan. 3, 2024, 7:27 p.m.