Changes in version 1.4.0 (2024-08-30)                  

  - 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.

                 Changes in version 1.3.0 (2024-04-03)                  

  - 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.

                 Changes in version 1.2.0 (2023-11-03)                  

  - 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.

                 Changes in version 1.1.0 (2023-04-12)                  

  - 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.