metan 1.18.0

New features

• New functions *_wd_here() to set and get the Working Directory (wd) quicky.
  • get_wd_here() gets the working directory to the path of the current script.
  • set_wd_here() sets the working directory to the path of the current script.
  • open_wd_here() open the File Explorer at the directory path of the current script.
  • open_wd() open the File Explorer at the current working directory.
• corr_coef() now can compute both linear and partial correlation, controled by the argument type.
• New function network_plot() to produce a network plot of a correlation matrix or an object computed with corr_coef().
• New functions sample_random() and sample_systematic() for random and systematic sampling, respectively.

Minor improvements

• plot.waasb() now has new arguments to control whether to show the percentage values within bars and the order of variables on the x-axis.
• corr_coef() now handles grouped data passed from group_by()
• New arguments size.varnames and col.varnames added in corr_plot().
• Fix bug in gmd(mod, "h2"), when mod is computed with random = "env".
• Include the argument repel in plot.gge().

metan 1.17.0

New features

• Implement a plot method for path_coeff_*() functions.
• New function path_coeff_seq() to implement a sequential (two chains) path analysis.
• New function prop_na() to measure the proportion of NAs in each column.
• New functions remove_cols_all_na() and remove_rows_all_na() to remove columns and rows that have all values as NAs.
• New functions ci_mean_z() and ci_mean_t() to compute z- and t-confidence intervals, respectively.
• New function set_wd_here() to set the working directory to the path of the current script.

Minor improvements

• Fix bug in rowname_to_column().
• Fix bug in mps() where stab was being rewritten with stab_res.
• Changes the object name in mgidi() example that overwrites the function.
• Fix bug with x.lab and y.lab from plot_scores(). Now it accepts an object from expression()
• plot_waasby() now accepts objects of class waas_means.
• get_model_data() now includes new options coefs, and anova for objects computed with ge_reg().
• New argument max_overlaps in plot_scores() to exclude text labels that overlap too many things.
• Improve the control over highlighted individuals in plot_scores() (shape, alpha, color, and size).

metan 1.16.0

New features

• Include new AMMI-based stability methods.
• Update ge_stats() to include the new stability methods.
• wsmp() now accepts objects computed with mps(), waas(), and waasb().

Minor improvements

• AMMI_indexes() has been deprecated in favour of ammi_indexes().
• Include formulas for the AMMI-indexes in ammi_indexes()
• Correct the number of environments in the documentation of data_ge().

metan 1.15.0

• Fix bug when calling gmd(., "data")
• Fix bug with fai_blup() when genotypes has distance as 0.
• Fix bug in inspect() when some trait has character values.
• Fix bug in gmd(model, "blupge")

metan 1.14.0

Minor improvements

• Fix bug in get_model_data() calling objects of class mgidi with what = "PCA".
• Fix bug in path_coeff() when generating sequences of direct effects depending on the constant added to the diagonal of correlation matrix.
• Improve output of gmd() for gge objects.
• New option projection in gmd() for gge objects to get the projection of each genotype in the AEC coordinates.
• Fix bug when using mtsi() with an object of class waas.

metan 1.13.0

New functions

• progress() and run_progress() for text progress bar in the terminal.
• rbind_fill_id() To implement the common pattern of do.call(rbind, dfs) with data frame identifier and filling of missing values.
• hmgv(), rpgv(), hmrpgv(), blup_indexes() to compute stability indexes based on a mixed-effect model.
• mps() and mtmps() for uni- and multivariate-based mean performance and stability in multi-environment trials.

Minor improvements

• ge_reg() now returns hypotesis testing for slope and deviations from the regression. Thanks to @LeonardoBehring and @MichelSouza for the suggestion.
• Resende_indexes() now remove NAs before computing harmonic and arithmetic means.
• Improved outputs in plot_scores that now has a highlight argument to highlight genotypes or environments by hand. Thanks to Ibrahim Elbasyoni for his suggestions.
• Licecycle badges added to the functions' documentation.
• Fix bug in clustering() when using with by argument and defacult nclust argument.
• get_model_data() now extract BLUEs from objects computed with gamem() and gamem_met(). Thanks to @MdFarhad for suggesting me this improvement.
• g_simula() and ge_simula() now have a res_eff to control the residual effect.
• mgidi() now have an optional weights argument to assign different weights for each trait in the selection process. Thanks to @MichelSouza for his suggestion.

metan 1.12.0

New functions

• get_levels_comb() to get the combination of the levels of a factor.
• g_simula() to simulate replicated genotype data.
• add_row_id() to add a column as the row id.
• remove_rownames(), column_to_rownames() and rownames_to_column() to deal
  with rownames.

Minor improvements

• New argument sel.var() in corr_ci() to filter correlations with a selected
  variable
• New arguments fill and position.fill in plot_ci() to fill correlations
  by levels of a factor variable.
• Remove deprecated arguments in arrange_ggplot() and gge().
• New argument theme in arrange_ggplot() to control the theme of the plot.
• Include by argument in gafem().
• mgid() now understands models of class gafem_grouped.
• Fix bug in get_levels() to get the levels even if the variable is not a factor.

v1.11.0

New functions

• set_union(), set_difference() and set_intersect() for set operations with many sets.
• venn_plot() to produce Venn diagrams.

Minor improvements

• gge() now have a by argument and understand data passed from group_by.
• New arguments col.stroke and size.stroke in plot.gge()
• gtb and gytb now produces biplots with lines for genotype's vectors in type = 1.
• get_model_data() now understand objects of class fai_blup and sh.

v1.10.0

Minor improvements

• gamem(), gamem_met(), and waasb() now have a by argument and understand data passed from group_by.
• mtsi() and mgidi() now returns the ranks for the contribution of each factor and understand models fitted with gamem() and waasb() using the by argument.
• plot.mtsi() and plot.mgidi() now returns a radar plot by default when using type = "contribution".
• get_model_data() now returns the genotypic and phenotypic correlation matrices from objects of class waasb and gamem.
• replace_string(), replace_number(), extract_string(), and extract_number() now accepts tidy evaluation in the new ... argument.

New functions

• get_dist() to get distance matrices from objects of class clustering.
• get_corvars() to get normal, multivariate correlated variables.
• get_covmat() to obtain covariance matrix based on variances and correlation values.
• as_numeric(), as_integer(), as_logical(), as_character(), and as_factor() to coerce variables to specific formats quickly.
• n_valid(), n_missing(), and n_unique() to count valid, missing, and unique values, respectively.
• tidy_colnames() to clean up column names. It is a shortcut to tidy_strings() applied to the column names of a data frame.
• env_stratification() to perform environment stratification using factor analysis.

v1.9.0

• New functions add_prefix() and add_suffix() to add prefixes and suffixes to variable names, respectively.
• New function select_pred() to selects a best subset of predictor variables.
• New function acv() to compute the adjusted coefficient of variation to account for the systematic dependence of variance on mean.
• New function ge_acv() to compute yield stability index based on the adjusted coefficient of variation.
• New function ge_polar() to compute yield stability index based on Power Law Residuals (POLAR) statistics.
• New function mantel_test() to performs a Mantel test between two matrices.
• New arguments prefix and suffix in concatenate() to add prefixes and suffixes to concatenated values, respectively.
• List packages providing the Rd macros in 'Imports' instead of 'Suggests' as suggested by the CRAN team.