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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.
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.
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.
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.