Design experiment

design_experiment()

Provides experimental design for the different situations corresponding to the choosen family of analysis

Format data

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 for data in agronomic analyses

format_data_PPBstats.data_agro_HA()

Check and format the data to be used by PPBstats functions for data agro HA to study local adaptation.

format_data_PPBstats.data_agro_LF()

Check and format the data to be used by PPBstats functions for data agro LF to study local adaptation.

format_data_PPBstats.data_agro_SR()

Check and format the data to be used by PPBstats functions for data agro SR to study response to selection.

format_data_PPBstats.data_network()

Check and format the data to be used by PPBstats functions for network analyses

format_data_PPBstats.data_organo_hedonic()

Check and format the data to be used by PPBstats functions for hedonic analyses

format_data_PPBstats.data_organo_napping()

Check and format the data to be used by PPBstats functions for napping analyses

HA_to_LF()

Transform home away data to local foreign data

LF_to_HA()

Transform local foreign data to home away data

Run models

model_GxE()

Run AMMI or GGE model

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_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

Check models

check_model()

Check if the model went well

check_model(<fit_model_GxE>)

Check if the GxE 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 well

check_model(<fit_model_bh_variance_intra>)

Check if the Hierarchical Bayesian variance intra 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

Mean comparisons

mean_comparisons()

Get mean comparisons from check_model object

mean_comparisons(<check_model_GxE>)

Get mean comparisons from check_model.fit_model_GxE object

mean_comparisons(<check_model_anova>)

Get mean comparisons from check_model.fit_model_anova object

mean_comparisons(<check_model_bh_GxE>)

Get mean comparisons from check_model.fit_model_bh_GxE object

mean_comparisons(<check_model_bh_intra_location>)

Get mean comparisons from check_model.fit_model_bh_intra_location object

mean_comparisons(<check_model_bh_variance_intra>)

Get mean comparisons from check_model.fit_model_bh_variance_intra object

mean_comparisons(<check_model_hedonic>)

Get mean comparisons from check_model.fit_model_hedonic object

mean_comparisons(<check_model_home_away>)

Get mean comparisons from check_model.fit_model_home_away object

mean_comparisons(<check_model_local_foreign>)

Get mean comparisons from check_model.fit_model_local_foreign object

mean_comparisons(<check_model_spatial>)

Get mean comparisons from check_model.fit_model_spatial object

mean_comparisons(<predict_the_past_model_bh_GxE>)

Get mean comparisons from predict_the_past_model_bh_GxE object

mean_comparisons_freq_anova()

mean comparisons for frequentist analysis

Parameter groups

parameter_groups()

Get groups of parameters based on multivariate analysis

parameter_groups_model_GxE()

Get matrix with variables in column and effects in row from check_model.fit_model_GxE

parameter_groups_model_anova()

Get matrix with variables in column and effects in row from check_model.fit_model_anova

parameter_groups_model_bh_GxE()

Get matrix with variables in column and effect in row from check_model.fit_model_bh_GxE

parameter_groups_model_spatial()

Get matrix with variables in column and effects in row from check_model.fit_model_spatial

Plot

plot.PPBstats

Get ggplot to visualize output within the PPBstats package

plot(<biplot_GxE>)

Get ggplot to visualize output from biplot_data.check_model_GxE

plot(<biplot_hedonic>)

Get ggplot to visualize output from biplot_data.check_model_hedonic

plot(<biplot_napping>)

Get ggplot to visualize output from biplot_data.check_model_hedonic

plot(<check_model_GxE>)

Get ggplot to visualize output from check_model.fit_model_GxE

plot(<check_model_anova>)

Get ggplot to visualize output from check_model.fit_model_anova

plot(<check_model_bh_GxE>)

Get ggplot to visualize output from check_model.fit_model_bh_GxE

plot(<check_model_bh_intra_location>)

Get ggplot to visualize output from check_model.fit_model_bh_intra_location

plot(<check_model_bh_variance_intra>)

Get ggplot to visualize output from check_model.fit_model_bh_variance_intra

plot(<check_model_hedonic>)

Get ggplot to visualize output from check_model.fit_model_hedonic

plot(<check_model_home_away>)

Get ggplot to visualize output from check_model.fit_model_home_away

plot(<check_model_local_foreign>)

Get ggplot to visualize output from check_model.fit_model_local_foreign

plot(<check_model_napping>)

Get ggplot to visualize output from check_model.fit_model_napping

plot(<check_model_spatial>)

Get ggplot to visualize output from check_model.fit_model_spatial

plot(<cross_validation_model_bh_GxE>)

Get ggplot to visualize output from cross_validation_model_bh_GxE

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 format_data_PPBstats.data_organo_hedonic

plot(<data_organo_napping>)

Plot napping object from format_data_PPBstats.data_organo_napping

plot(<mean_comparisons_model_GxE>)

Get ggplot to visualize output from mean_comparisons.check_model_GxE

plot(<mean_comparisons_model_anova>)

Get ggplot to visualize output from mean_comparisons.check_model_anova

plot(<mean_comparisons_model_bh_GxE>)

Get ggplot to visualize output from mean_comparisons.check_model_bh_GxE

plot(<mean_comparisons_model_bh_intra_location>)

Get ggplot to visualize output from mean_comparisons.check_model_bh_intra_location

plot(<mean_comparisons_model_hedonic>)

Get ggplot to visualize output from mean_comparisons.check_model_GxE

plot(<mean_comparisons_model_home_away>)

Get ggplot to visualize output from mean_comparisons.check_model_home_away

plot(<mean_comparisons_model_local_foreign>)

Get ggplot to visualize output from mean_comparisons.check_model_local_foreign

plot(<mean_comparisons_model_spatial>)

Get ggplot to visualize output from mean_comparisons.check_model_spatial

plot(<mean_comparisons_predict_the_past_model_bh_GxE>)

Get ggplot to visualize output from mean_comparisons.predict_the_past_model_bh_GxE

plot(<parameter_groups>)

Get ggplot to visualize output from parameter_groups

plot_check_freq_anova()

plot check freq anova

plot_descriptive_data()

Plot agro object from format_data_PPBstats()

plot_mean_comparisons_freq_anova()

plot mean comparisons for frequentist analysis

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

Biplot

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

Post hoc variation

post_hoc_variation()

Plot a barplot with factors' variation for each variable

post_hoc_variation_model_GxE()

Get dataframe for factors' variation for each variable from a list whose elements are output from check_model.fit_model_GxE

post_hoc_variation_model_anova()

Get dataframe for factors' variation for each variable from a list whose elements are output from check_model.fit_model_anova

post_hoc_variation_model_home_away()

Get dataframe for factors' variation for each variable from a list whose elements are output from check_model.fit_model_home_away

post_hoc_variation_model_local_foreign()

Get dataframe for factors' variation for each variable from a list whose elements are output from check_model.fit_model_local_foreign

post_hoc_variation_model_spatial()

Get dataframe for factors' variation for each variable from a list whose elements are output from check_model.fit_model_spatial

Others

splitter_d()

Some functions used in one or several functions of PPBstats

comp.parameters()

Get parameter comparisons two by two or to a given threshold based on MCMC outputs

cross_validation_model_bh_GxE()

Run complete cross validation with Hierarchical Bayesian GxE model

get.at.least.X.groups()

Get the value of type one error needed to have X groups.

get.env.info()

Get regional farms data and satellite farms data

GxE_build_interaction_matrix()

Compute interaction matrix for AMMI or GGE model