This dataset contains all data and code necessary to reproduce the analysis described under the heading "Experiment 3" in the manuscript:

Taliercio, E., Eickholt, D., Read, Q. D., Carter, T., Waldeck, N., & Fallen, B. (2023). Parental choice and seed size impact the uprightness of progeny from interspecific Glycine hybridizations. Crop Science. https://doi.org/10.1002/csc2.21015

The attached files are:

• G_max_G_soja_seedweight_seedcolor_analysis.Rmd: RMarkdown notebook containing all analysis code. The CSV data files should be placed in a subdirectory called data within the working directory from which the notebook is rendered.

• G_max_G_soja_seedweight_seedcolor_analysis.html: Rendered HTML output from RMarkdown notebook, including figures, tables, and explanatory text.

• counts_seedwt.csv: CSV file containing the number of progeny selected and average 100-seed weight data for each combination of cross, size class, and replicate. Columns are:

  • F3_location: text identifier of F3 nursery location, either "CLA" or "FF"
  • plot: numeric ID of plot
  • pop: numeric ID of population
  • max: name of G. max parent
  • soja: name of G. soja parent
  • F2_location: text identifier of F2 nursery location, either "Caswell" or "Hugo"
  • n_planted: number of seeds planted (raw)
  • n_selected: number of progeny selected
  • size_ordered: seed size class, to be converted to an ordered factor
  • size_combined: seed size class aggregated to fewer unique levels
  • ave_100sw: average 100-seed weight for the given size class
  • n_planted_trials: number of seeds planted rounded to nearest integer

• seedcolor.csv: CSV file with additional data on number of seeds of each color by population. Columns are:

  • cross: text identifier of cross
  • line: text identifier of line
  • light: number of light seeds
  • mid: number of mid-green seeds
  • brown: number of brown seeds
  • dark: number of dark or black seeds
  • population: identifier of population type (F2 derived or selected)
  • max: name of G. max parent
  • n_total: sum of the light, mid, brown, and dark columns
  • soja: name of G. soja parent

The data processing and analysis pipeline in the RMarkdown notebook includes:

• Importing the data (slightly cleaned version is provided)
• Creating boxplots of proportion selected by cross, nursery location, and size class
• Fitting logistic GLMM to estimate the probability of selection as a function of parent, 100-seed weight, and their interactions
• Extracting and plotting random effect estimates from model
• Calculating and plotting estimated marginal means from model
• Taking contrasts between pairs of estimated marginal means and trends
• Calculating Bayes Factors associated with the contrasts
• Generating figures and tables for all above results
• Additional seed color analysis: importing data (slightly cleaned version is provided)
• Additional seed color analysis: drawing exploratory bar plot
• Additional seed color analysis: fitting multinomial GLM modeling the proportion of seeds with each color as a function of population
• Additional seed color analysis: generating expected value predictions from GLM and taking contrasts
• Additional seed color analysis: creating figures and tables for model results

This research was funded by CRIS 6070-21220-069-00D, United Soybean Board Project # 2333-203-0101, and falls under National Program NP301.

• Resource Title: RMarkdown document with all analysis code.

  File Name: G_max_G_soja_seedweight_seedcolor_analysis.Rmd




• Resource Title: Rendered HTML version of notebook.

  File Name: G_max_G_soja_seedweight_seedcolor_analysis.html




• Resource Title: Progeny counts and seed weight data.

  File Name: counts_seedwt.csv




• Resource Title: Seed color counts data.

  File Name: seedcolor.csv