Lightning Talk

Lilianna Martinez

The evolved Package

About the package

  • Created by Matheus Januario with help from Auler
  • This package aids in paleo-centric learning!
  • “Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries”
  • provides multiple tools to help educators apply inquiry-based learning in general evolution classes
  • compatible with other packages

What is in the package?

  • There are 10 datasets
  • There are also at least 14 unique functions

What can you do with this package?

  • Mathematical calculations
  • Graphical visualizations
  • Mathematical predictions
  • incorporate different data sets for qualitative and quantitative reasoning

Examples of some functions

Example 1

library(evolved)
library(ggplot2)
library(tidyverse)

# EX 1
timeseries_fossil |> 
  group_by(stem_age) |> 
  ggplot(aes(x = richness, fill = source)) + geom_histogram()

Example 2

library(evolved)

# EX 2
NatSelSim(w11 = 1, w12 = 1, w22 = 0.2, p0 = 0.5,n.gen = 20, 
          plot.type = "static", print.data = FALSE, knitr = TRUE)

Worked Vignette Example

About the example

  • Showing fossil occurrences
  • Comparing groups of animals
  • Visual representations

I want to learn more about a fossil/animal group! But how?

library(evolved)
library(ggplot2)
library(tidyverse)

trilob_fossil |>
  glimpse()

Next

# calculates fossil diversity through time 
div1 <- calcFossilDivTT(trilob_fossil, method = "stdmethod")
div2 <- calcFossilDivTT(ammonoidea_fossil, method = "stdmethod", bin.reso = 10)

# Comparing different bins sizes in the standard method
plot(x = div1$age, y = div1$div, type = "l", 
     xlab = "Time (Mya)", ylab = "Richness", 
     xlim = rev(range(div1$age)), col = "red") 
lines(x = div2$age, y = div2$div, col = "blue")

Next

sum(trilob_fossil$species == "Mexicella mexicana")
[1] 37

Next

Tri_pick <- trilob_fossil |> 
  filter(trilob_fossil$species == "Mexicella mexicana")

# calculates and plots the early and late boundaries associated with each taxa 
plotRawFossilOccs(data = trilob_fossil, tax.lvl = "species", sort = TRUE,
  use.midpoint = TRUE, return.ranges = FALSE, knitr = FALSE)

NEXT

hist(trilob_fossil$midpoint,
     breaks = 100, #increasing breaks to see data in a better precision
     xlab="Absolute time (Mya)", main = "Fossil Occurrence midpoints",
     
     #reversing axis to represent past -> present
     xlim = c(rev(range(trilob_fossil$midpoint))) 
     )

FINAL

library(paleobioDB)

# you can change the size of the cells using the  argument "res"
pbdb_map_occur(trilob_fossil, res = 2, cex = 0.3)
class       : SpatRaster 
size        : 84, 185, 1  (nrow, ncol, nlyr)
resolution  : 2, 2  (x, y)
extent      : -180, 190, -85.19218, 82.80782  (xmin, xmax, ymin, ymax)
coord. ref. : lon/lat WGS 84 (CRS84) (OGC:CRS84) 
source(s)   : memory
name        :  sum 
min value   :    1 
max value   : 1793

BONUS

library(paleobioDB)

Tri_pick <- trilob_fossil |> 
  filter(trilob_fossil$species == "Mexicella mexicana")

pbdb_map_occur(data = Tri_pick, res = 2, cex = 0.7)
class       : SpatRaster 
size        : 84, 185, 1  (nrow, ncol, nlyr)
resolution  : 2, 2  (x, y)
extent      : -180, 190, -85.19218, 82.80782  (xmin, xmax, ymin, ymax)
coord. ref. : lon/lat WGS 84 (CRS84) (OGC:CRS84) 
source(s)   : memory
name        : sum 
min value   :   1 
max value   :  34

References & Repos

  • [Vignette examples] (https://github.com/lmartinezgt/The-Evolved-Package-EX) by Lilianna_Martinez1@baylor.edu Github @lmartinezgt

  • CRAN (https://cran.r-project.org/web/packages/evolved/index.html)

  • Januario M, Auler J, Viol A, Rabosky D (2026). evolved: Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries. R package version 1.0.0, https://github.com/mjanuario/evolved.