NEWS.md

In priviere/PPBstats: An R package to perform analysis found within PPB programmes

PPBstats 0.27 under development

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

PPBstats 0.26

• 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

PPBstats 0.25

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
• HA_to_LF
• LF_to_HA
• 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

PPBstats 0.24

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 :
  • delete code arg
• 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

PPBstats 0.23

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
  • debug when NA in row
• 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

rename and reformat RData

following change of model name:

• data_GxE -> data_model_GxE
• data_model_1 -> data_model_bh_intra_location
• data_model_2 -> data_model_bh_GxE
• data_variance_intra -> data_model_bh_variance_intra

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

PPBstats 0.22

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

PPBstats 0.21

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

update RData

• Add the date in format of data #48

• add new functions that implement spatial analysis (cf #20)

  • spatial.R
  • check_model.fit_model_spatial.R
  • plot.check_model_spatial.R
  • mean_comparisons.check_model_spatial.R
  • plot.mean_comparisons_model_spatial.R

vignette

• update text, fix typo, update fig (cf #20, #34, #49)
• add section on spatial analysis
• add Rmd regarding contributions

PPBstats 0.20

• substitute get_ggplot() by plot() methods (#21)
• update vignette and cached results

PPBstats 0.19

update functions

• add add_stars_version() in ggplot_mean_comparisons_model_1.R (cf #35)
• ok + update vignette (cf #51)

PPBstats 0.18

update vignette

• cf #36 : add decision tree + update
• reorganise introduction of agro section

PPBstats 0.17

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

PPBstats 0.16

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

PPBstats 0.15

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

PPBstats 0.14

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

delete functions

• ggplot_LSDgroup

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

rename function

• AMMI.R becomes GxE.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

PPBstats 0.12

• delete all the pdf in the file that are generated by Rnw in order to earn space on github

• change the nomenclature of the version

PPBstats 0.11.1

• update some little bugs regarding tests

update functions

• get.ggplot.R
  • debug data_version regarding real data set

PPBstats 0.11.0

• update some little bugs regarding tests

update the vignette

• add example for data_version
• add example for ggplot.type = "biplot-alpha-beta"

PPBstats 0.10.2

update functions

• get.ggplot.R
  • add data_2 argument
  • add ggplot.type = "biplot" which is possible for model 2

PPBstats 0.10.1

• 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

add new data set

• data_version.RData

PPBstats 0.10.0

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

PPBstats 0.9.1

• little changes in vignette and readme
• little changes in the comments of some functions

PPBstats 0.9

• first version on Github

priviere/PPBstats documentation built on May 6, 2021, 1:20 a.m.