update fonctions
- plot.data_agro_SR
- add post hoc analysis, cf #128
- add heritability for each plot
- debug, cf #139
- debug code
- format_data_PPBstats.data_network
- for unipart seed lot network and organize_sl = TRUE: change year of seed lot to year of relation, cf #156
- unipart network for seed lots: list too deep, name the list “all_data”, cf #157
- plot.data_network
- for unipart seed lot network and organize_sl = TRUE: change year of seed lot to year of relation, cf #156
update vignette (inst/bookdown)
- update regarding changes in plot.data_agro_SR.R
- add depends on R version in DESCRIPTION file, cf #140
update fonctions
- in format data functions, stop if column with only NA, cf #98
- add shapiro test in
check_model() for frequentist models, cf #101
- check_model.fit_model_GxE
- check_model.fit_model_anova
- check_model.fit_model_hedonic
- check_model.fit_model_home_away
- check_model.fit_model_local_foreign
- check_model.fit_model_spatial
- check_freq_anova in common_function
- add shapiro test in
check_model() and points of residuals for frequentist models, cf #101
- plot.check_model_GxE
- plot.check_model_anova
- plot.check_model_hedonic
- plot.check_model_home_away
- plot.check_model_spatial
- format_organo in common_function, cf #72
- format_data_PPBstats.data_organo_hedonic, cf #72
- model_hedonic, cf #72
- biplot_data.check_model_napping, cf #72
- check_model.fit_model_napping, cf #72
- format_data_PPBstats.data_organo_napping, cf #72
- model_napping, cf #72
- plot.biplot_napping, cf #72
- plot.check_model_napping, cf #72
- add match.arg in several functions, cf #75
- implement type III anova in the models home away and local foreign, cf #133
- model_home_away
- model_local_foreign
- update ggradar in common_function
- design_experiment, cf #39
- home away and local foreign workflow: change column name group to origin to be more clear
- add grid argument, cf #88 for
- plot.data_agro_LF
- plot.data_agro_HA
add new functions
- post_hoc_variation, cf #141
- post_hoc_variation_model_GxE, cf #141
- post_hoc_variation_model_anova, cf #141
- post_hoc_variation_model_spatial, cf #141
- post_hoc_variation_model_home_away, cf #141
- post_hoc_variation_model_local_foreign, cf #141
- parameter_groups_model_anova, cf #144
- parameter_groups_model_spatial, cf #144
update RData
- new data_agro_HA and data_agro_LF, cf #146
- new data_model_spatial, cf #145
update vignette (inst/bookdown)
- some typos here and there
- add shapiro test in
check_model() and points of residuals for frequentist models, cf #101
- update hedonic and napping sections, cf #72
update webiste (inst/web_site)
- improve text
- add references, cf #36
- delete current website and move to pkgdown
update fonctions
- check and format code and roxygen part for each function, DESCRIPTION and NAMESPACE cf #97
- plot_descriptive_data in common_function regarding data_version_HA and data_version_LF
- hedonic workflow, cf #72
- add PCA + HCPC on juges
- format_data
- function in the workflow
- Rd + book
- format_data_PPBstats.data_network: take into accuont when there are not lat and long columns
- pmap in common_functions : use stamen instead of google on map, cf #90
- implement spatial analysis, cf #20
- mean comparisons with spatial model, cf #124
- delete deprecated format_data function, cf #107: format_data_PPBstats.data_agro_version
- update functions: delete all data_version argument, cf #104
- plot.data_agro
- plot.data_organo_hedonic
- plot.data_organo_napping
- plot.mean_comparisons_model_bh_intra_location
- plot.mean_comparisons_predict_the_past_model_bh_GxE
- update model following new RData, cf #104
- model_home_away
- model_local_foreign
add new functions
- HA_to_LF, cf #25
- add LF_to_HA, cf #25
- create workflow for home away model, cf #25
- model_home_away
- check_model.fit_model_home_away
- plot.check_model_home_away
- mean_comparisons.check_model_home_away
- plot.mean_comparisons_model_home_away
- create workflow for local foreign cf #25
- model_local_foreign
- check_model.fit_model_local_foreign
- plot.check_model_local_foreign
- mean_comparisons.check_model_local_foreign
- plot.mean_comparisons_model_local_foreign
- add classic anova model, cf #45
- model_anova
- check_model.fit_anova
- plot.check_model_anova
- mean_comparisons.check_model_anova
- plot.mean_comparisons_model_anova
- create new format_data function, cf #107
- format_data_PPBstats.data_agro_SR
- format_data_PPBstats.data_agro_HA
- format_data_PPBstats.data_agro_LF
- create new function to switch from HA to LF, cf #107
- create new function to plot data_agro_version, cf #104
- plot.data_agro_SR
- plot.data_agro_HA
- plot.data_agro_LF
add RData
- data_version_HA, cf #25
- data_model_spatial, cf #20
- add colum “seed_lot” in all agro data format, cf #134
- create new RData, cf #107
- data agro SR
- data agro HA
- data agro LF
- delete deprecated RData, cf #107
- data_version
- data_version_HA
- data_version_SR
update vignette (inst/bookdown)
- some typo here and there
- format section on network
- complete text and pictures, cf #36
- add generation of report, cf #81
- add correlation analysis in multivariate part, cf #114
- create one workflow per family of analysis for agro
- run cross validation of model_bh_GxE, cf #26
- add classic anova model, cf #45
- update model spatial section, cf #20
- add colum “seed_lot” in all agro data format, cf #134
- add workflow for family 4
create return report web site (inst/return_report_web_site)
- add generation of report, cf #81
update webiste (inst/web_site)
- add in contribution how to run bookdown
- update secondary functions
update fonctions
- model_bh_intra_location
- deal with vec_env_with_no_controls empty
- format_data_PPBstats.data_network :
- clean check at the beginning
- add long and lat for bipart network
- add format in vertex data for further use with plot.data_network
- delete optional column alt as it is not needed for map
- format_data_PPBstats.data_agro :
- add long and lat in option
- format_data_PPBstats.data_napping :
- plot.data_network, cf #67 :
- implement map with ggmap
- add pie on map and network
- add barplot for unipart network on location
- display in variable edges of the network for unipart sl on barplot
- display in variable edges of the network for unipart sl on map with pies
- display output from unipart location on a map
- plot.data_agro, cf #68 :
- add plot_type = “map”
- add r2 on biplot, cf #84
- add argument data_version
- ggplot_check_model_GxE : add table with % next to pie plot, cf #38
- format_data_PPBstats.data_agro_version
- add specific class for data_version_SR and data_version_MR
- common_functions
- common function for check model regarding frequentist analysis, cf #71
add new functions
- create workflow for napping, cf #72
- plot.data_organo_napping
- model_napping
- check_model.fit_model_napping
- plot.check_model_napping
- biplot_data
- plot.biplot_napping
- create workflow for hedonic, cf #72
- plot.data_organo_hedonic
- model_hedonic
- check_model.fit_model_hedonic
- plot.check_model_hedonic
- biplot_data
- plot.biplot_hedonic
- mean_comparisons.check_model_hedonic
- plot.mean_comparisons_model_hedonic
- biplot_data, cf #93
- biplot_data.check_model_GxE
- biplot_data.check_model_hedonic
- biplot_data.check_model_napping
update vignette (inst/bookdown)
- regarding change with plot.data_network
- regarding change with plot.data_agro
- regarding workflow in organoleptic analysis
- improve text
update webiste (inst/web_site)
- improve download
- add email list
- improve text
update RData
- standardize RData, cf #85
update fonctions
- format_data_PPBstats.R :
- when date, add a column with julian day, cf #65
- add type data_organo_napping and data_organo_hedonic, cf #72
- format data for data_network, cf #65
- add code regarding network_split arg
- better differentiate year, relation_year_start and relation_year_end : cf Rd
- data_agro_version done
- describe_data.data_agro.R -> plot.data_agro.R :
- add raster arg for plot_type, cf #68
- replace by plot.data_agro.R
- use plot methods for describe_data cf #79
- debugs several functions regarding tests
- plot.mean_comparisons_model_1.R
- improve display of score : cf #61
- plot.parameter_groups.R:
- model 2 ACP cluster : put in blod or color a given ind, cf #76
- design_experiment.R
- no location in title for IBD and in the data frame, cf #39
- plot.[…].R
- change arg ggplot.type to plot_type cf #69
- plot.data_agro.R, cf #68
- debug radar + simplify ggradar function to get simple appearance
- create plot with dynamic in time coming from $data_julian from format_data_PPBstats
- add raster arg + update data_GxE
- reshape_data_split_x_axis_in_col.R in common_function
- mean_comparisons.check_model_GxE.R & mean_comparisons.check_model_spatial.R
- update code regarding changes in agricolae package
- rename functions related to model (cf #54)
- model_1 -> model_bh_intra_location
- model_2 -> model_bh_GxE
- GxE -> model_GxE
- spatial -> model_spatial
- model_variance_intra -> model_bh_variance_intra
add new functions
- napping.R, cf #72
- hedonic.R, cf #72
- PPBstats_interface.R, cf #64
- /inst/shiny_interface/agro/server.R, cf #64
- /inst/shiny_interface/agro/ui.R, cf #64
- format_data_PPBstats.format_network.R, cf #65
- format_data_PPBstats.format_agro.R, cf #65
- format_data_PPBstats.format_agro_version.R, cf #65
- format_data_PPBstats.format_organo_napping.R, cf #65
- format_data_PPBstats.format_organo_hedonic.R, cf #65
- plot.data_network.R, cf #67
vignette -> inst/bookdown
- update text (cf #76, #65, #67)
- translate Rnw files to Rmd files, format to bookdown, put all files in inst/bookdown (cf #36)
- explain Skewness and Kurtosis test as well as other output from check model for frequentist analysis (cf #36)
- text and decision tree improved by Pierre, Isabelle and Camille
add new RData
- data_network_unipart_sl.RData
- data_network_unipart_location.RData
- data_network_bipart.RData
- data_version_SR
- data_version_MR
web site
- add files in inst/web_site, cf #83
update functions
- model_1.R :
- correct bug model_1 (cf #60)
- better plot for score regarding model 1 (cf #61)
- workflow regarding spatial analysis : improve and debug
- update workflow regarding variance_intra model (cf #28, #29, #30, #31, #32) but still work to do : cf #62
- plot.parameter_groups.R : split plot ACP cluster (cf #47) + update Rd in plot.PPBstats.R
- describe_data.R : create class
add new functions
- format_data_PPBstats.R
- describe_data.data_agro.R : huge refactoring, cf #68
- describe_data.data_network.R : empty from now
- multivariate.R
vignette
- update text (typo + format_data_PPBstats + cf #36, #47, #68)
- add new section on variance_intra + update workflow figure, functions table, analysis families
- update multivariate analysis section
- update contributions
update functions
- ggplot_mean_comparisons_model_1.R
- ggplot_mean_comparisons_predict_the_past_model_2.R : cf #34
- model_1.R
- fix typo (cf #53)
- rename file .R in order to have same name of files and functions
vignette
- update text, fix typo, update fig (cf #20, #34, #49)
- add section on spatial analysis
- add Rmd regarding contributions
- substitute get_ggplot() by plot() methods (#21)
- update vignette and cached results
update functions
- add add_stars_version() in ggplot_mean_comparisons_model_1.R (cf #35)
- ok + update vignette (cf #51)
update vignette
- cf #36 : add decision tree + update
- reorganise introduction of agro section
add new functions
- model_variance_intra.R
- check_model_model_variance_intra.R
- ggplot_check_model_model_variance_intra.R
- mean_comparisons_model_variance_intra.R
update function
- check_model_model_1.R : add location and year for data_env_whose_param_did_not_converge
- ggplot_parameter_groups.R & parameter_groups.R : change kmeans methods for HCPC
- ggplot_mean_comparisons_model_1.R : little debug
update vignette
- changes in text and exemple regarding functions udaptes
update functions
- predict_the_past_model_2.R : add estimated and predicted MCMC + parameter statuts
- mean_comparisons_predict_the_past_model_2.R : add parameter statuts in mean comparisons outputs
update vignette
- remind to install JAGS
- add R version
- new sections : network, agronomic, organoleptic and molecular
- add IBD analysis section
update functions
- biplot_GxE.R and ggplot_biplot_GxE.R : add interaction matrix
- GxE.R and GxE_build_interaction_matrix.R : model writing
update vignette
- regarding changes in R code
- spelling
- contributions and aknowledgement
Huge refactoring of the code in several functions for each steps of the analysis
rename function
- analyse.outputs.R becomes check_model.R
- get.parameter.groups.R becomes parameter.groups.R
- get.mean.comparisons.R becomes mean.comparisons.R
- MC.R becomes model_1.R
- FWH.R becomes model_2.R
- cross.validation.R becomes cross_validation_model_2.R
- predict.the.past.R becomes predict_the_past_model_2.R
- get.ggplot.R becomes get_ggplot.R
add new functions
biplot_GxE.R
- check_model_model_1.R
- check_model_model_2.R
check_model_GxE.R
- mean_comparisons_GxE.R
- mean_comparisons_model_1.R
- mean_comparisons_model_2.R
mean_comparisons_predict_the_past_model_2.R
- parameter_groups_GxE.R
parameter_groups_model_2.R
- ggplot_biplot_GxE.R
- ggplot_check_model_model_1.R
- ggplot_check_model_model_2.R
- ggplot_check_model_GxE.R
- ggplot_mean_comparisons_GxE.R
- ggplot_parameter_groups.R
- ggplot_cross_validation_model_2.R
- ggplot_predict_the_past_model_2.R
ggplot_mean_comparisons_predict_the_past_model_2.R
vignette
- update regarding changes in R code
#PPBstats 0.13
add new functions
- describe_data.R
- extra_functions.R
- design_experiment.R
- ggplot_which_won_where.R
- ggplot_mean_vs_stability.R
- ggplot_discrimitiveness_vs_representativeness.R
update functions
- MC.R
- get.ggplot.R: manage nb_parameters_per_plot for ggplot.type == “biplot-alpha-beta”
- get.significant.group.R
- get.PPBstats.data.R
vignette
- refactor the code
- add new sections
- update some little bugs regarding tests
update functions
- get.ggplot.R
- debug data_version regarding real data set
- update some little bugs regarding tests
update the vignette
- add example for data_version
- add example for ggplot.type = “biplot-alpha-beta”
update functions
- get.ggplot.R
- add data_2 argument
- add ggplot.type = “biplot” which is possible for model 2
- update some little bugs regarding tests
update functions
- get.ggplot.R : add data_version argument
- get.mean.comparisons.R
- predict.the.past.R : take into account when there are no parameters in the MCMC
add new functions
- AMMI.R
- AMMI_called_functions.R
vignette
- update the vignette following previous developments
#PPBstats 0.9.2
- fix little bugs
- add the presence.absence.matrix for the model in FWH, analyse.outputs and predict.the.past
- add model1.data_env_whose_param_did_not_converge in analyse.outputs and get.ggplot
- return MCMC only for parameters that converge
- possible to choose NULL for get.at.least.X.groups
- “cluster” is displayed in the legend for ggplots from get.parameter.groups
- fix huge bug in MC where the mean of the observation were not correctly done
- little changes in vignette and readme
- little changes in the comments of some functions