Man pages for priviere/PPBstats
An R package to perform analysis found within PPB programmes
| add_pies | Add_pies on map or network for plot.data_agro,... |
| add_split_col | add a column to split a dataframe |
| biplot_data | Format data for biplot representation |
| biplot_data.check_model_GxE | Compute ecovalence and format PCA results for biplot |
| biplot_data.check_model_hedonic | Format data for CA biplot |
| biplot_data.check_model_napping | Format data for MFA biplot for napping model |
| check_analysis_argument | error message regadring check_model of bayesian analysis |
| check_convergence | check convergence of bayesian model |
| check_data_vec_variables | check if variable are part of the data |
| check_freq_anova | check freq anova |
| check_list_out_check_model | Check constitency of list with outputs from 'check_model' |
| check_model | Check if the model went well |
| check_model.fit_model_anova | Check if the classic anova model went well |
| check_model.fit_model_bh_GxE | Check if the Hierarchical Bayesian GxE model went well |
| check_model.fit_model_bh_intra_location | Check if the Hierarchical Bayesian intra location model went... |
| check_model.fit_model_bh_variance_intra | Check if the Hierarchical Bayesian variance intra model went... |
| check_model.fit_model_GxE | Check if the GxE model went well |
| check_model.fit_model_hedonic | Check if the hedonic model went well |
| check_model.fit_model_home_away | Check if the home away model went well |
| check_model.fit_model_local_foreign | Check if the local foreign model went well |
| check_model.fit_model_napping | Check if the napping model went well |
| check_model.fit_model_spatial | Check if the spacial model went well |
| common_functions | Some functions used in one or several functions of PPBstats |
| comp.parameters | Get parameter comparisons two by two or to a given threshold... |
| cross_validation_model_bh_GxE | Run complete cross validation with Hierarchical Bayesian GxE... |
| data_agro_HA | Data to study home and away |
| data_agro_LF | Data to study local and foreign |
| data_agro_SR_4 | data set to study response to selection from data set... |
| data_hedonic | data coming from tomatoes hedonic test: |
| data_model_bh_GxE | Simulated data set for three variables to test model_bh_GxE... |
| data_model_bh_intra_location | Simulated data set for thousand kernel weight (tkw) of bread... |
| data_model_bh_variance_intra | Simulated data set for spike weight of bread wheat to test... |
| data_model_GxE | Simulated data set for three variables to test GxE model |
| data_model_spatial | Data set for one variable to test spatial model |
| data_napping | data coming from tomatoes hedonic test: |
| data_network_bipart | Simulated data set for bipart network which represents "which... |
| data_network_unipart_location | Simulated data set for unipart network which represents... |
| data_network_unipart_sl | Simulated data set for unipart network for seed lots which... |
| design_experiment | Provides experimental design for the different situations... |
| format_data_PPBstats | Check and format the data to be used by PPBstats functions |
| format_data_PPBstats.data_agro | Check and format the data to be used by PPBstats functions... |
| format_data_PPBstats.data_agro_HA | Check and format the data to be used by PPBstats functions... |
| format_data_PPBstats.data_agro_LF | Check and format the data to be used by PPBstats functions... |
| format_data_PPBstats.data_agro_SR | Check and format the data to be used by PPBstats functions... |
| format_data_PPBstats.data_network | Check and format the data to be used by PPBstats functions... |
| format_data_PPBstats.data_organo_hedonic | Check and format the data to be used by PPBstats functions... |
| format_data_PPBstats.data_organo_napping | Check and format the data to be used by PPBstats functions... |
| format_organo | format data for organoleptic analysis |
| get.at.least.X.groups | Get the value of type one error needed to have X groups. |
| get_biplot | get ggplot object for a biplot based on output from... |
| get.caterpillar.plot | get caterpillar plot to view posterior of bayesian model |
| get.env.info | Get regional farms data and satellite farms data |
| get_mcmc_traceplot_density | get mcmc traceplot density to view posterior of bayesian... |
| get_mean_comparisons_and_Mpvalue | get mean comparisons and square matrix with pvalue from MCMC... |
| get_perpendicular_segment | get coordinate to draw perpendicular segment |
| get.significant.groups | Get significant groups of means that are significantly... |
| ggplot_discrimitiveness_vs_representativeness | Return a "discrimitiveness vs representativeness" ggplot... |
| ggplot_mean_vs_stability | Return a "mean vs stability" ggplot based on PCA object |
| ggplot_which_won_where | Return a "which won where" ggplot based on PCA object |
| ggradar_bis | ggradar_bis |
| GxE_build_interaction_matrix | Compute interaction matrix for AMMI or GGE model |
| HA_to_LF | Transform home away data to local foreign data |
| is.inside.sector | to know if a point is inside an area |
| LF_to_HA | Transform local foreign data to home away data |
| mean_comparisons | Get mean comparisons from 'check_model' object |
| mean_comparisons.check_model_anova | Get mean comparisons from 'check_model.fit_model_anova'... |
| mean_comparisons.check_model_bh_GxE | Get mean comparisons from 'check_model.fit_model_bh_GxE'... |
| mean_comparisons.check_model_bh_intra_location | Get mean comparisons from... |
| mean_comparisons.check_model_bh_variance_intra | Get mean comparisons from... |
| mean_comparisons.check_model_GxE | Get mean comparisons from 'check_model.fit_model_GxE' object |
| mean_comparisons.check_model_hedonic | Get mean comparisons from 'check_model.fit_model_hedonic'... |
| mean_comparisons.check_model_home_away | Get mean comparisons from 'check_model.fit_model_home_away'... |
| mean_comparisons.check_model_local_foreign | Get mean comparisons from... |
| mean_comparisons.check_model_spatial | Get mean comparisons from 'check_model.fit_model_spatial'... |
| mean_comparisons_freq_anova | mean comparisons for frequentist analysis |
| mean_comparisons.predict_the_past_model_bh_GxE | Get mean comparisons from 'predict_the_past_model_bh_GxE'... |
| model_anova | Run classic anova model |
| model_bh_GxE | Run Hierarchical Bayesian GxE model |
| model_bh_intra_location | Run Hierarchical Bayesian intra-location model |
| model_bh_variance_intra | Run Hierarchical Bayesian variance-intra model |
| model_GxE | Run AMMI or GGE model |
| model_hedonic | Run hedonic analysis |
| model_home_away | Run Home Away model |
| model_local_foreign | Run Local Foreign model |
| model_napping | Run napping analysis |
| model_spatial | Run spatial row and column model |
| mutlivariate | Run multivariate analysis with function from FactoMineR |
| parameter_groups | Get groups of parameters based on multivariate analysis |
| parameter_groups_model_anova | Get matrix with variables in column and effects in row from... |
| parameter_groups_model_bh_GxE | Get matrix with variables in column and effect in row from... |
| parameter_groups_model_GxE | Get matrix with variables in column and effects in row from... |
| parameter_groups_model_spatial | Get matrix with variables in column and effects in row from... |
| plot.biplot_GxE | Get ggplot to visualize output from... |
| plot.biplot_hedonic | Get ggplot to visualize output from... |
| plot.biplot_napping | Get ggplot to visualize output from... |
| plot_check_freq_anova | plot check freq anova |
| plot.check_model_anova | Get ggplot to visualize output from... |
| plot.check_model_bh_GxE | Get ggplot to visualize output from... |
| plot.check_model_bh_intra_location | Get ggplot to visualize output from... |
| plot.check_model_bh_variance_intra | Get ggplot to visualize output from... |
| plot.check_model_GxE | Get ggplot to visualize output from... |
| plot.check_model_hedonic | Get ggplot to visualize output from... |
| plot.check_model_home_away | Get ggplot to visualize output from... |
| plot.check_model_local_foreign | Get ggplot to visualize output from... |
| plot.check_model_napping | Get ggplot to visualize output from... |
| plot.check_model_spatial | Get ggplot to visualize output from... |
| plot.cross_validation_model_bh_GxE | Get ggplot to visualize output from... |
| plot.data_agro | Plot agro object from format_data_PPBstats.data_agro() |
| plot.data_agro_HA | Plot agro object from format_data_PPBstats.data_agro_HA() |
| plot.data_agro_LF | Plot agro object from format_data_PPBstats.data_agro_LF() |
| plot.data_agro_SR | Plot agro object from format_data_PPBstats.data_agro_SR() |
| plot.data_network | Plot network object from format_data_PPBstats() |
| plot.data_organo_hedonic | Plot hedonic object from... |
| plot.data_organo_napping | Plot napping object from... |
| plot_descriptive_data | Plot agro object from format_data_PPBstats() |
| plot_mean_comparisons_freq_anova | plot mean comparisons for frequentist analysis |
| plot.mean_comparisons_model_anova | Get ggplot to visualize output from... |
| plot.mean_comparisons_model_bh_GxE | Get ggplot to visualize output from... |
| plot.mean_comparisons_model_bh_intra_location | Get ggplot to visualize output from... |
| plot.mean_comparisons_model_GxE | Get ggplot to visualize output from... |
| plot.mean_comparisons_model_hedonic | Get ggplot to visualize output from... |
| plot.mean_comparisons_model_home_away | Get ggplot to visualize output from... |
| plot.mean_comparisons_model_local_foreign | Get ggplot to visualize output from... |
| plot.mean_comparisons_model_spatial | Get ggplot to visualize output from... |
| plot.mean_comparisons_predict_the_past_model_bh_GxE | Get ggplot to visualize output from... |
| plot.parameter_groups | Get ggplot to visualize output from 'parameter_groups' |
| plot.PPBstats | Get ggplot to visualize output within the PPBstats package |
| pmap | map background for plot.data_agro, plot.data_network |
| post_hoc_variation | Plot a barplot with factors' variation for each variable |
| post_hoc_variation_model_anova | Get dataframe for factors' variation for each variable from a... |
| post_hoc_variation_model_GxE | Get dataframe for factors' variation for each variable from a... |
| post_hoc_variation_model_home_away | Get dataframe for factors' variation for each variable from a... |
| post_hoc_variation_model_local_foreign | Get dataframe for factors' variation for each variable from a... |
| post_hoc_variation_model_spatial | Get dataframe for factors' variation for each variable from a... |
| PPBstats | PPBstats |
| PPBstats_interface | Run interface to use the package |
| predict_the_past_model_bh_GxE | Predict values of germplasms in environments where they have... |
| reshape_data_split_x_axis_in_col | Reshape data in a list based on nb_parameters_per_plot... |
| split_data_for_ggplot | split data into several list for a given factor and a number... |
