Fire, flowering phenology, and fitness of Liatris and Solidago

Here are the code and data for the manuscript:

“Flowering phenology responds to fire and influences reproductive success “

CODE: R script completeAsterphenAnalysis.R replicates the data analysis and produces Figures 2 and 3. The R script reads the csv file below. Figure 1 in the manuscript is a conceptual figure generated using Adobe Illustrator. 

This analysis was generated using R version 3.5.1

Required R packages:

FNN: Alina Beygelzimer, Sham Kakadet, John Langford, Sunil Arya, David Mount and Shengqiao Li (2013). FNN: Fast Nearest Neighbor Search Algorithms and Applications. R package version 1.1. https://CRAN.R-project.org/package=FNN

ggpubr: Alboukadel Kassambara (2019). ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 0.2.1.
https://CRAN.R-project.org/package=ggpubr

lubridate: Garrett Grolemund, Hadley Wickham (2011). Dates and Times Made Easy with lubridate. Journal of Statistical Software,
40(3), 1-25. URL http://www.jstatsoft.org/v40/i03/.

mateable: Stuart Wagenius, Danny Hanson and Amy Waananen (2016). mateable: Tools to Assess Mating Potential in Space and Time.
R package version 0.3.1. https://CRAN.R-project.org/package=mateable

tidy verse: Hadley Wickham (2017). tidyverse: Easily Install and Load the ‘Tidyverse’. R package version 1.2.1.
https://CRAN.R-project.org/package=tidyverse

DATA: The ascii comma-separated-values file solLiaPhenCtNew.csv, contains phenological and reproductive measures for burned and unburned Liatris aspera and Solidago speciosa from 2016-2018.

Fields include:

uniqueID: unique identifier for each row, generated from a combination of plantID and year that observations were conducted (character)

plantID: unique name for each individual plant in the dataset, plants may be associated with multiple rows of data if they were observed in multiple years (character)

year: year the observations were taken (numeric)

flagNo: flag number is the field identifier for each individual, not a unique identifier for each row of data (numeric)

unit: west or east, indicates the placement of each individual plant in either the east or west management unit of the preserve. Burns were conducted on the west in 2016 and east in 2018 (character)

startDate: day of year that an individual plant first released pollen and was receptive to pollination (date)

doneDate: first day of year that an individual plant was done releasing pollen and no longer receptive to pollination (date)

hdInflCt: count of flowering heads per individual plant (Liatris) or count of flowering stems (Solidago) (numeric)

full: count of full achenes from x-ray images of a random sample of achenes from each individual plant (numeric)

empty: count of empty achenes from x-ray images of a random sample of achenes from each individual plant (numeric)

species: either Solidago or Liatris (character)