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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.
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.
Health stats visible at Monitor.