metan - 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().

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Published by TiagoOlivoto almost 3 years ago

metan - 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).

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Published by TiagoOlivoto over 3 years ago

metan - 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().

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Published by TiagoOlivoto over 4 years ago

metan - 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")

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Published by TiagoOlivoto over 4 years ago

metan - 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.

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Published by TiagoOlivoto over 4 years ago

metan - 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.

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Published by TiagoOlivoto almost 5 years ago

metan - 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.

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Published by TiagoOlivoto about 5 years ago

metan - 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.

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Published by TiagoOlivoto about 5 years ago

metan -

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.

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Published by TiagoOlivoto over 5 years ago

metan - 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.

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Published by TiagoOlivoto over 5 years ago

metan - v1.8.1

• Use \doi{} markup in Rd files.
• New function gytb() to generate the Genotype by yield*trait biplot.
• New functions row_col_mean() and row_col_sum()to add a row with the mean/sum of each variable and a column with the the mean/sum for each row of a matrix or data frame.
• New functions has_zero(), remove_cols_zero(), remove_rows_zero(), select_cols_zero(), select_rows_zero(), and replace_zero() to deal with 0s in a data frame.
• Fix bug of inconsistent color legend when plotting objects of class gge.
• Include class gge and can_corr in get_model_data().
• New argument position in plot.gamem() and plot.mtsi() to control the position adjustment of the bar plot.
• New argument col.by in corr_plot() to map the color of the points by a categorical variable.
• New argument use_data in functions mgidi(), fai_blup(), and Smith_Hazel() to control which data is used (BLUPs or phenotypic means) to compute the index.
• inspect() now generate a warning if zero values are observed in data.

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Published by TiagoOlivoto over 5 years ago

metan - v1.7.0

• New functions clip_read() and clip_write() to read from the clipboard and write to the clipboard, respectively.
• New function sum_by() to compute the sum by levels of factors.
• Update wsmp.R (#7). Thank you @BartoszKozak for your contribution.
• mgidi() now allows using a fixed-effect model fitted with gafem() as input data.
• round_cols() now can be used to round whole matrices.

- R
Published by TiagoOlivoto over 5 years ago

metan - v1.6.1

• plot.mgidi() can now plot the contribution for all genotypes.
• plot_bars() and plot_factbars() now shows the values with values = TRUE
• Update the functions by using the new dplyr::across()
• Update citation field by including number and version of the published paper.

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Published by TiagoOlivoto over 5 years ago

metan - v1.6.0

New functions

• Smith_Hazel() and print.sh() and plot.sh() for computing the Smith and Hazel selection index.
• coincidence_index() for computing the coincidence index.

Minor improvements

• get_model_data() now extracts the genotypic and phenotypic variance-covariance matrix from objects of class gamem and waasb.
• fai_blup() now returns the total genetic gain and the list with the ideotypes' construction.
• mgidi() now computes the genetic gain when a mixed-model is used as input data.
• The S3 method plot() for objects of class mgidi has a new argument type = "contribution" to plot the contribution of each factor in the MGIDI index.
• plot_scores() now can produce a biplot showing other axes besides PC1 and PC2. To change the default IPCA in each axis use the new arguments first and second.

- R
Published by TiagoOlivoto almost 6 years ago

metan -

New functions

• select_rows_na() and select_cols_na() to select rows or columns with with NA values.
• mgidi() to compute the multi-trait genotype-ideotype distance index.
• plot_bars() to create bar plots quickly. Thanks to @MariaDiel for her suggestion.

Minor changes

• Deprecated functions hm_mean() and gm_mean() removed in favour of hmean() and gmean(), respectively.
• Deprecated argument rep retired in Fox(), ge_effects(), Huehn(), resp_surf(), superiority(), and Thennarasu()
• Deprecated argument verbose retired in anova_ind()
• Deprecated argument region retired in resp_surf()
• Remove dependency on dendextend by using ggplot2-based graphics in plot.wsmp().
• Update package site with pkgdown v1.5.0.
• Update documentation in ge_plot()
• Allow using fai_blup() with gamem()
• Improve checking process with inspect()
• Improve feedback for results, indicating random and fixed effects. Thanks to @NelsonJunior for his suggestion.
• plot() call on objects of class gamem, waasb and waas now returns the variable names automatically. Thanks to @MdFarhad for suggesting me this change.
• plot.gamem() and plot.waasb() have a new argument (type = "vcomp") to produce a plot showing the contribution of the variance components to the phenotypic variance
• cv_ammi(), cv_ammif(), and cv_blup() now check for missing values and unbalanced data before computing the cross-validation. (#3)

Bug fixes

• Fix problems from a recent upgrade of package tibble to version 3.0.0.
• get_model_data() now fills rows that don't matches across columns with NA. Thanks to @MdFarhad for his report.
• get_model_data() called now report mean squares, F-calculated and P-values for blocks within replicates in anova_ind().

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Published by TiagoOlivoto almost 6 years ago

metan -

Bug fixes

• Factor columns can now have custom names rather than ENV, GEN, and REP only (#2).

New functions

• gmd() a shortcut to get_model_data()
• gtb() to generate a genotype-by-trait biplot.
• gamem_met() to analyze genotypes in multi-environment trials using mixed- or random-effect models allowing unbalanced data. Thanks to @EderOliveira for his e-mail.
• has_class() to check if a class exists.
• impute_missing_val() to impute missing values in a two-way table based on Expectation-Maximization algoritms.
• non_collinear_vars() to select a set of predictors with minimal multicollinearity.
• replace_na() to replace NA values quicly.
• random_na() to generate random NA values based on a desired proportion.

Minor changes

• gge(), performs_ammi(), waas(), and waasb() now handle with unbalanced data by implementing a low-rank matrix approximation using singular value decomposition to impute missing entires. Imputation generates a warning message.
• NA values are checked and removed with a warning when computing stability indexes. Thanks to @MdFarhad for alerting me.
• New argument plot_res in path_coeff() to create a residual plot of the multiple regression model.
• Update the citation file to include the published official reference.
• Argument verbose deprecated in functions anova_ind() and split_factors()
• Argument rep deprecated in functions Fox(), Huehn(), superiority(), and Thennarasu().
• Deprecated argument means_by removed in functions can_corr() and clustering().
• Deprecated argument verbose removed in functions colindiag() and split_factors().
• Deprecated argument values removed in functions desc_stat() and find_outliers().
• Deprecated argument var removed in function desc_wider().
• Remove dependency on lattice by using ggplot2 in plot.resp_surf().
• An up-to-date cheat sheet was included.

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Published by TiagoOlivoto almost 6 years ago

metan -

New functions

• alpha_color() To get a semi-transparent color
• gafem() To analyze genotypes using fixed-effect models.
• residual_plots() A helper function to create residuals plots.
• stars_pval() To generate significance stars from p-values
• doo() An alternative to dplyr::do for doing anything

utils_stats

• cv_by() For computing coefficient of variation by levels of a factor.
• max_by() For computing maximum values by levels of a factor.
• means_by() For computing arithmetic means by levels of a factor.
• min_by() For computing minimum values by levels of a factor.
• n_by() For getting the length.
• sd_by() For computing sample standard deviation.
• sem_by() For computing standard error of the mean by levels of a factor.
• av_dev() computes the average absolute deviation.
• ci_mean() computes the confidence interval for the mean.
• cv() computes the coefficient of variation.
• hm_mean(), gm_mean() computes the harmonic and geometric means, respectively. The harmonic mean is the reciprocal of the arithmetic mean of the reciprocals. The geometric mean is the nth root of n products.
• kurt() computes the kurtosis like used in SAS and SPSS.
• range_data() Computes the range of the values.
• sd_amo(), sd_pop() Computes sample and populational standard deviation, respectively.
• sem() computes the standard error of the mean.
• skew() computes the skewness like used in SAS and SPSS.
• sum_dev() computes the sum of the absolute deviations.
• sum_sq_dev() computes the sum of the squared deviations.
• var_amo(), var_pop() computes sample and populational variance.
• valid_n() Return the valid (not NA) length of a data.

utilsrowscols

• colnames_to_lower(), colnames_to_upper(), and colnames_to_title() to translate column names to lower, upper and title cases quickly.

utilsnumstr

• all_lower_case(), all_upper_case(), and all_title_case() to translate strings vectors or character columns of a data frame to lower, upper and title cases, respectively.
• tidy_strings() Tidy up characters strings, non-numeric columns, or any selected columns in a data frame by putting all word in upper case, replacing any space, tabulation, punctuation characters by '_', and putting '_' between lower and upper cases.
• find_text_in_num() Find text fragments in columns assumed to be numeric. This is especially useful when everything() is used in argument resp to select the response variables.

New arguments

• anova_ind(), anova_joint(), performs_ammi(), waas() and waasb(), now have the argument block to analyze data from trials conducted in an alpha-lattice design. Thanks to @myaseen208 for his suggestion regarding multi-environment trial analysis with alpha-lattice designs.
• argument repel included in plot_scores() to control wheater the labels are repelled or not to avoid overlapping.

Deprecated arguments

Argument means_by was deprecated in functions can_corr() and clustering(). Use means_by() to pass data based on means of factor to these functions.

Minor changes

• Change "#000000FF" with "#FFFFFF00" in transparent_color()
• desc_stat() now handles grouped data passed from dplyr::group_by()
• plot_scores() now support objects of class waas_mean.
• Include inst/CITATION to return a reference paper with citation("metan").
• Change 'PC2' with 'PC1' in y-axis of plot_scores(type = 2) (#1)
• get_model_data() now support models of class anova_joint and gafem and extract random effects of models fitted with waasb() and gamem().
• Update plot.waasb() and plot.gamem() to show distribution of random effects.
• inspect(), cv_blup(), cv_ammif(), and cv_ammi() now generate a warning message saying that is not possible to compute cross-validation procedures in experiments with two replicates only. Thanks to @Vlatko for his email.
• plot.wsmp() now returns heatmaps created with ggplot2. Thus, we removed dependency on gplots.
• Vignettes updated

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Published by TiagoOlivoto about 6 years ago

metan - First release on CRAN

The first release of the package CRAN

- R
Published by TiagoOlivoto about 6 years ago

metan - v1.1.0

I'm very pleased to announce the release of metan 1.1.0, This is a minor release with bug fixes and new functions. The most important changes are described below.

• New function corr_stab_ind() for computing Spearman's rank correlation between stability indexes;
• New function corr_coef() for computing correlation coefficients and p-values;
• New S3 method plot.corr_coef() for creating correlation heat maps;
• New S3 method print.corr_coef() for printing correlation and p-values;
• New helper functions make_lower_tri() and make_upper_tri() for creating lower and upper triangular matrices, respectively.
• New helper function reorder_cormat() for reordering a correlation matrix according to the correlation coefficients;
• Improve usability of get_model_data() by supporting new classes of models. Now, get_model_data() can be used to get all statistics or ranks computed with the wrapper function ge_stats().
• arrange_ggplot() now support objects of class ggmatrix.
• Change the default plot theme to theme_metan()
• Update function's documentation;
• Update vignettes.

- R
Published by TiagoOlivoto over 6 years ago

metan - v1.0.1

• New function gamem() for analyzing genotypes in one-way trials using mixed-effect models;
• New function desc_wider() to convert an output of the function desc_stat() to a 'wide' format;
• New function Fox() for Stability analysis;
• New function Shukla() for stability analysis;
• New function to_factor() to quickly convert variables to factors;
• Improve usability of get_model_data() function;
• Update function's doccumentation;
• Update vignettes;

- R
Published by TiagoOlivoto over 6 years ago