NEWS.md

In FieldSimR: Simulation of Plot Errors and Phenotypes in Plant Breeding Field Trials

FieldSimR 1.1.0

• Added a NEWS.md file to track changes to the package.

• Added argument pos_def to function rand_cor_mat to make bending of a non-positive-definite correlation matrix to a positive-definite matrix optional.

• Added example data frame df_error_bivar with plot errors for two traits across three locations generated using field_trial_error.

• Added example data frame df_gv_unstr with simulated genetic values for two traits across three environments generated using unstr_asr_input and unstr_asr_output.

• Added functionality to simulate extraneous variation to field_trial_error.

• Added internal functions spline_interp and fill_matrix to interpolate and extrapolate missing values if some NAs remain after bivariate interpolation.

• Added make_phenotypes to create phenotypes through combination of genetic values and plot errors.

• Added qq_plot to compare the theoretical quantiles of a normal distribution with the sample quantiles of the distribution of a user-defined effect.

• Added sample_variogram to create a variogram of a user-defined effect.

• Added theoretical_variogram to create a theoretical variogram.

• Added vignette compound_symmetry_GxE_demo to demonstrate the simulation of genetic values using a compound symmetry GxE model.

• Added vignette spatial_error_demo to demonstrate the simulation of plot errors and phenotypes for a multi-environment plant breeding trial.

• Added vignette unstructured_GxE_demo to demonstrate the simulation of genetic values using an unstructured GxE model.

• Removed argument env from function plot_effects.

• Replaced package fields for graphics in plot_effects by ggplot2.

• Set the complexity argument of field_trial_error by default to the maximum number of columns and rows in each environment.

• Updated Description in DESCRIPTION.

FieldSimR 1.2.0

• Argument ext_ord replaced arguments ext_col_cor and ext_row_cor in function field_trial_error.

• Factorised argument env, rep and id in functions field_trial_error, make_phenotypes, unstr_asr_output, compsym_asr_output.

• Randomisation fixed in function make_phenotypes.

• Changed default parameters for col_cor and row_cor, prop_spatial, and complexity in function field_trial_error.

• Argument plot_labels added to function plot_effects.

• Added function qq_plot to create quantile-quantile (Q-Q) plots.

• Added function sample_variogram to create sample variograms.

• Added function theoretical_variogram to create theoretical variograms.

FieldSimR 1.3.0

• Replaced all instances of _ with . in function arguments, e.g., pos.def replaced pos_def.

• Replaced all instances of n_ with n in function arguments, e.g., ntraits replaced n_traits and nenvs replaced n_envs.

• Added multi_asr_input and multi_asr_output wrapper functions for simulating genetic values based on a multiplicative model for GxE interaction.

• Added small.positive argument to function rand_cor_mat, which is passed to the bend function.

• Updated data frames to reflect the data used in the manuscript FieldSimR: An R package for simulating plot data in multi-environment field trials.

• Changed names of example data frames from df_error_bivar and df_gv_unstr to error_df_bivar and gv_df_unstr, respectively.

• Replaced rel.main.eff.A with prop.main, rel.main.eff.DD with prop.mainD, and rel.main.eff.AA with prop.mainAA in the compsym_asr_input function, since these arguments define the proportion of main effect variance, not the relative magnitude.

• prop.main was implemented instead of prop.mainA, since this argument is aligned with var, i.e., it represents the proportion of additive or total main effect variance depending on whether useVarA = TRUE or FALSE in AlphaSimR.

• Added return.effects argument to the make_phenotypes function for returning the plot errors and genetic values for each trait. The latter will be returned in randomised order when randomise = TRUE.

• Added functionality for plot_effects to display the factor block, instead of a numeric column.

• Added plot_matrix function for graphically displaying a symmetric matrix, e.g., correlation or covariance matrix, in a similar manner to the plot_effects function. This function allows the matrix to be ordered based on a dendrogram, and split into user-defined groups.

FieldSimR 1.4.0

• Added functionality to the make_phenotypes function to handle incomplete experimental designs through the new design.df argument, which accepts a data frame with individual x environment frequencies.

• Added new function struc_cor_mat for simulating structured correlation matrices with reduced rank. This function also handles user-defined base functions.

• Added new functions rand_diag_mat and skew_diag_mat for simulating diagonal variance matrices, with diagonal elements simulated randomly or with a skewed (gamma or inverse gamma) distribution, respectively.

• Added new function sample_met for sampling environments from a larger population to mimic the sampling which occurs during multi-environment trialling.

• Swapped order of rep and id arguments in compsym_asr_output and unstr_asr_output functions

• Swapped order of rep and id arguments in gv_df_unstr example data frame.

• Updated colour scheme in plot_matrix. Now prints a red-blue heatmap when a correlation matrix is supplied, or a light-dark blue heatmap when a covariance matrix is supplied.

• Updated qq_plot and plot_hist to handle a matrix as input through the df argument (converts to a data frame internally).

• Added new function group_cor_mat for simulating structured correlation matrices with multiple groups and reduced rank.

FieldSimR documentation built on Sept. 11, 2024, 6:39 p.m.