diff --git a/R/BIOMOD_Modeling.R b/R/BIOMOD_Modeling.R index a8751734..c08cfd5a 100644 --- a/R/BIOMOD_Modeling.R +++ b/R/BIOMOD_Modeling.R @@ -471,14 +471,14 @@ BIOMOD_Modeling <- function(bm.format, for (ii in vals) { OPT.user@options[[mod]]@args.values[[ii]] <- val } - } else if (all(grepl("_allRun", nam))){ #Check if the user create the options just for PA dataset - sep.name <- unlist(strsplit(mod,split = '[.]')) - cat("\n \n \t The options for",sep.name[1], "for '_PAx_allRun' will be given to all runs with PAx (_PAx_RUN1, _PAx_RUN2,...) \n") - for (run in vals){ - PA.set <- grep("PA|allData", unlist(strsplit(run, "_")), value = T) - if (is.null(OPT.user@options[[mod]]@args.values[[paste0("_", PA.set, "_allRun")]])){ - opt.default <- BIOMOD.options.dataset(mod = sep.name[1],typ = sep.name[2],pkg =sep.name[3], fun = sep.name[4], strategy = "default", - bm.format = bm.format, calib.lines = calib.lines) + } else if (all(grepl("_allRun", nam))) { #Check if the user create the options just for PA dataset + sep.name <- unlist(strsplit(mod, split = '[.]')) + cat("\n \n \t The options for", sep.name[1], "for '_PAx_allRun' will be given to all runs with PAx (_PAx_RUN1, _PAx_RUN2,...) \n") + for (run in vals) { + PA.set <- grep("PA|allData", unlist(strsplit(run, "_")), value = TRUE) + if (is.null(OPT.user@options[[mod]]@args.values[[paste0("_", PA.set, "_allRun")]])) { + opt.default <- BIOMOD.options.dataset(mod = sep.name[1], typ = sep.name[2], pkg =sep.name[3], fun = sep.name[4] + , strategy = "default", bm.format = bm.format, calib.lines = calib.lines) OPT.user@options[[mod]]@args.values[[run]] <- opt.default@args.values[["_allData_allRun"]] } else { OPT.user@options[[mod]]@args.values[[run]] <- OPT.user@options[[mod]]@args.values[[paste0("_", PA.set, "_allRun")]] diff --git a/README.md b/README.md index 91285c98..2ff1e442 100644 --- a/README.md +++ b/README.md @@ -57,7 +57,7 @@ devtools::install_github("biomodhub/biomod2", dependencies = TRUE) ### `biomod 4.2-5` - Modeling options & Tuning Update -**! `biomod2 4.2-5` is now available on GitHub !** +**! `biomod2 4.2-5` is now available on CRAN !** `/!\` Please **feel free to indicate if you notice some strange new behaviors** ! @@ -70,7 +70,10 @@ devtools::install_github("biomodhub/biomod2", dependencies = TRUE) #### What is new ? - `ModelsTable` and `OptionsBigboss` datasets (*note that improvement of bigboss modeling options is planned in near future*) -- [data preparation vignette](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) has been created (*questions you should ask yourself before modeling*) +- 3 new vignettes have been created : + - [data preparation](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) (*questions you should ask yourself before modeling*) + - [cross-validation](https://biomodhub.github.io/biomod2/articles/vignette_crossValidation.html) (*to prepare your own calibration / validation datasets*) + - [modeling options](https://biomodhub.github.io/biomod2/articles/vignette_dataPreparation.html) (*to help you navigate through the new way of parameterizing single models*)
diff --git a/docs/articles/news.html b/docs/articles/news.html index 7e8c7ef7..e3ff383e 100644 --- a/docs/articles/news.html +++ b/docs/articles/news.html @@ -138,15 +138,84 @@

- 2023 + 2024

-

4.2-5 Modeling options and Tuning (2023-09-12) +

4.2-5 Modeling options and Tuning (2024-05-02)

+
Major Changes
    +
  • Add print function for BIOMOD.options.dataset and +BIOMOD.models.options classes
  • +
  • Add GAM.binary.gam.gam and +GAM.binary.mgcv.bam in OptionsBigboss +dataset
  • +
  • Add checks for obs and fit parameters in +bm_FindOptimStat +
  • +
  • In bm_Tuning function : +
      +
    • add MAXENT.algorithm and MAXENT.parallel +parameters
    • +
    • be sure to update default tuning parameters if not all provided
    • +
    • fix tuning for XGBOOST and SRE +
    • +
    • fix optimization of formula
    • +
    • switch from gamSpline to gamLoess method +to tune GAM.gam.gam model, and add GAM.span +and GAM.degree parameters
    • +
    +
  • +
  • Fix multiple cases when using different settings of PA / +cross-validation / modeling options through all the different secundary +functions and BIOMOD_Modeling +
  • +
+
+
+
Minor Changes +
+
    +
  • Add vignette for cross-validation (to prepare your own +calibration / validation datasets)
  • +
  • Add vignette for modeling options (to help you navigate through +the new way of parameterizing single models)
  • +
  • Update examples and documentation
  • +
+
+
+
Bugfix +
+
    +
  • Add try and error message in call for models in +bm_RunModelsLoop +
  • +
  • Check for predictions >1000 +
  • +
  • Correct BIOMOD_EnsembleForecasting when using +data.frame +
  • +
  • Correct predictions for EMci (removing round)
  • +
+
+
+
+
+

+ 2023 +

+
+

4.2-5 Modeling options and Tuning (2023-09-12) +

+
+
Major Changes +
+
  • Reformat modeling options, how they are created and how they are given to models :
      @@ -173,7 +242,7 @@
      Major Changes -
      Minor Changes +
      Minor Changes
      • Remove BIOMOD_PresenceOnly function and add @@ -189,7 +258,7 @@
        Minor Changes -
        Bugfix +
        Bugfix
        • 4.2-4-10 : fixed wrap applied to a @@ -233,7 +302,7 @@
          Bugfix

          4.2-4 XGBOOST (2023-06-21)

          -
          Major Changes +
          Major Changes
          • added XGBOOST as a possible algorithm in @@ -242,7 +311,7 @@
            Major Changes
          -
          Minor Changes +
          Minor Changes
          • changed CV.do.full.models default value to @@ -251,7 +320,7 @@
            Minor Changes
          -
          Bugfix +
          Bugfix
          • 4.2-3-5 : @@ -285,7 +354,7 @@
            Bugfix<

            4.2-3 Cross-Validation and Pseudo-Absences (2023-05-09)

            -
            Major Changes +
            Major Changes
            • Improved pseudo-absence management: it is now possible to have @@ -301,7 +370,7 @@
              Major Changes
            -
            Minor Changes +
            Minor Changes
            • improved Documentation (get_evaluations, @@ -328,7 +397,7 @@
              Minor Changes
            -
            Bugfix +
            Bugfix
            • validation metric calculation now properly use the calibration @@ -393,7 +462,7 @@
              Internal4.2-2 Improvement patch (2023-01-13)
              -
              Major Changes +
              Major Changes
              • @@ -424,7 +493,7 @@
                Major Changes
              -
              Minor Changes +
              Minor Changes
              • Simplified maxent model names: ‘MAXENT.Phillips’ -> ‘MAXENT’ @@ -453,7 +522,7 @@
                Minor Changes
              -
              Bugfix +
              Bugfix
              • Fixed MAXENT.Phillips.2 and single variable @@ -485,14 +554,14 @@
                Internal Changes
              -

              - 2022 +

              + 2022

              4.2-1 Bugfix patch

              -
              Major Changes +
              Major Changes
              • Package sp is back into Imports due to the @@ -505,7 +574,7 @@
                Major Changes
              -
              Minor Changes +
              Minor Changes
              • Added initial_heap_size and max_heap_size @@ -515,7 +584,7 @@
                Minor Changes
              -
              Bugfix +
              Bugfix
              • Fixed MAXENT.Phillips predict method for large dataset @@ -564,7 +633,7 @@
                Internal4.2-0 Terra Update
                -
                Major Changes +
                Major Changes
                • Package now rely only on terra @@ -580,7 +649,7 @@
                  Major Changes
                -
                Minor Changes +
                Minor Changes
                • @@ -611,7 +680,7 @@
                  Minor Changes
                -
                Bugfix +
                Bugfix
                • MAXENT.Phillips models can now properly fail
                • @@ -678,10 +747,10 @@
                  Internal Changes -

                  4.1-3 +

                  4.1-3

                  -
                  Bugfix +
                  Bugfix
                  • Ensemble models that fails (e.g. EMcv with only one models) will not @@ -707,10 +776,10 @@

                    Internal Changes -

                    4.1-2 (2022-09-29) +

                    4.1-2 (2022-09-29)

                    -
                    Major changes +
                    Major changes
                    • @@ -726,7 +795,7 @@
                      Major changes
                    -
                    Minor changes +
                    Minor changes
                    • Individual EM models projected as raster are now saved with @@ -803,7 +872,7 @@
                      Miscellaneous -

                      4.1-1 (2022-08-30) +

                      4.1-1 (2022-08-30)

                      • add do.progress parameter (to render or not progress @@ -815,14 +884,14 @@

                        4.1-1 (2022-08-30)

                    -

                    4.1 (2022-07-12) +

                    4.1 (2022-07-12)

                    • fix bugs following major release 4.0
                    -

                    4.0 (2022-03-01) +

                    4.0 (2022-03-01)

                    • MAJOR RELEASE
                    • @@ -837,11 +906,11 @@

                      4.0 (2022-03-01) -

                      - 2021 +

                      + 2021

                      -

                      3.5-3 (2021-11-02) +

                      3.5-3 (2021-11-02)

                      • clean BIOMOD classes definitions and functions @@ -856,7 +925,7 @@

                        3.5-3 (2021-11-02)

                      -

                      3.5-2 (2021-10-18) +

                      3.5-2 (2021-10-18)

                      • fix BIOMOD_PresenceOnly function (previously @@ -869,11 +938,11 @@

                        3.5-2 (2021-10-18)

                      -

                      - 2018-2019 +

                      + 2018-2019

                      -

                      3.3-20 (2019-03-05) +

                      3.3-20 (2019-03-05)

                      • Remove maxent Tsurukoa because not maintained anymore (required by @@ -881,14 +950,14 @@

                        3.3-20 (2019-03-05)

                      -

                      3.3-18 (2018-07-04) +

                      3.3-18 (2018-07-04)

                      • fix the gbm multicore issue
                      -

                      3.3-17 (2018-04-23) +

                      3.3-17 (2018-04-23)

                      • correct the single presence pseudo-absences generation bug @@ -897,18 +966,18 @@

                        3.3-17 (2018-04-23)

                      -

                      - 2016 +

                      + 2016

                      -

                      3.3-6 (2016-01-14) +

                      3.3-6 (2016-01-14)

                      • add get_predictions function for ensemble models
                      -

                      3.3-5 (2016-01-04) +

                      3.3-5 (2016-01-04)

                      • MARS models are now computed throw earth package (was @@ -920,11 +989,11 @@

                        3.3-5 (2016-01-04)

                      -

                      - 2015 +

                      + 2015

                      -

                      3.3-4 (2015-11-04) +

                      3.3-4 (2015-11-04)

                      • update BIOMOD_tuning function (Frank @@ -932,7 +1001,7 @@

                        3.3-4 (2015-11-04)

                      -

                      3.3-3 (2015-10-27) +

                      3.3-3 (2015-10-27)

                      • force sampling of each level of factorial variables
                      • @@ -941,7 +1010,7 @@

                        3.3-3 (2015-10-27)

                      -

                      3.3-00 (2015-10-05) +

                      3.3-00 (2015-10-05)

                      • MAJOR RELEASE
                      • @@ -957,7 +1026,7 @@

                        3.3-00 (2015-10-05)

                      -

                      3.2-00 (2015-07-28) +

                      3.2-00 (2015-07-28)

                      • add 3 new functions in biomod2 (Frank B. @@ -975,11 +1044,11 @@

                        3.2-00 (2015-07-28)

                      -

                      - 2014 +

                      + 2014

                      -

                      3.1-59 (2014-10-23) +

                      3.1-59 (2014-10-23)

                      • add model evaluation scores plotting function
                      • @@ -988,7 +1057,7 @@

                        3.1-59 (2014-10-23)

                      -

                      3.1-53 (2014-08-06) +

                      3.1-53 (2014-08-06)

                      • new ensemble models names to be more coherent with formal models @@ -996,7 +1065,7 @@

                        3.1-53 (2014-08-06)

                      -

                      3.1-44 (2014-05-20) +

                      3.1-44 (2014-05-20)

                      • possibility to use user defined function to influence the way models @@ -1005,7 +1074,7 @@

                        3.1-44 (2014-05-20)

                      -

                      3.1-43 (2014-05-20) +

                      3.1-43 (2014-05-20)

                      • add of as.data.frame argument for @@ -1014,7 +1083,7 @@

                        3.1-43 (2014-05-20)

                      -

                      3.1-42 (2014-05-19) +

                      3.1-42 (2014-05-19)

                      • enable ensemble forecasting models selection (thanks to @@ -1023,11 +1092,11 @@

                        3.1-42 (2014-05-19)

                      -

                      - 2013 +

                      + 2013

                      -

                      3.1-17 (2013-10-23) +

                      3.1-17 (2013-10-23)

                      • add parameter to control amount of memory reserved for @@ -1040,7 +1109,7 @@

                        3.1-17 (2013-10-23)

                      -

                      3.1-1 (2013-09-04) +

                      3.1-1 (2013-09-04)

                      • limitation of package dependencies
                      • @@ -1050,7 +1119,7 @@

                        3.1-1 (2013-09-04)

                      -

                      3.0.2 (2013-07-23) +

                      3.0.2 (2013-07-23)

                      • new functions to evaluate a-posteriori models quality
                      • @@ -1059,7 +1128,7 @@

                        3.0.2 (2013-07-23)

                      -

                      3.0.0 (2013-07-01) +

                      3.0.0 (2013-07-01)

                      • MAJOR RELEASES
                      • @@ -1078,7 +1147,7 @@

                        3.0.0 (2013-07-01)

                      -

                      2.1.37 (2013-06-12) +

                      2.1.37 (2013-06-12)

                      • change (temporally?) gam default package from mgcv to @@ -1089,7 +1158,7 @@

                        2.1.37 (2013-06-12)

                      -

                      2.1.32 (2013-05-30) +

                      2.1.32 (2013-05-30)

                      • weights for user defined pseudo-absences are now supported @@ -1099,7 +1168,7 @@

                        2.1.32 (2013-05-30)

                      -

                      2.1.13 (2013-03-06) +

                      2.1.13 (2013-03-06)

                      • Add ProbDensFunc() function to package to produce nice @@ -1107,7 +1176,7 @@

                        2.1.13 (2013-03-06)

                      -

                      2.1.12 (2013-03-04) +

                      2.1.12 (2013-03-04)

                      • add rasterVis dependency for nicer biomod2 @@ -1119,7 +1188,7 @@

                        2.1.12 (2013-03-04)

                      -

                      2.1.9 (2013-02-28) +

                      2.1.9 (2013-02-28)

                      • possibility to indicate manually which data should be used for @@ -1129,7 +1198,7 @@

                        2.1.9 (2013-02-28)

                      -

                      2.1.9 (2013-02-27) +

                      2.1.9 (2013-02-27)

                      • one var modeling supported (thanks Anne O.)
                      • @@ -1138,14 +1207,14 @@

                        2.1.9 (2013-02-27)

                      -

                      2.1.8 (2013-02-25) +

                      2.1.8 (2013-02-25)

                      • response plot supports now formal models
                      -

                      2.1.0 (2013-02-21) +

                      2.1.0 (2013-02-21)

                      • MAJOR RELEASE
                      • @@ -1164,7 +1233,7 @@

                        2.1.0 (2013-02-21)

                      -

                      2.0.11 (2013-02-18) +

                      2.0.11 (2013-02-18)

                      • possibility to consider a user.defined pseudo absences selection @@ -1174,7 +1243,7 @@

                        2.0.11 (2013-02-18)

                      -

                      2.0.9 (2013-02-15) +

                      2.0.9 (2013-02-15)

                      • automatic save on hard drive of BIOMOD_Projection @@ -1182,7 +1251,7 @@

                        2.0.9 (2013-02-15)

                      -

                      2.0.8 (2013-02-14) +

                      2.0.8 (2013-02-14)

                      • @@ -1192,14 +1261,14 @@

                        2.0.8 (2013-02-14)

                      -

                      2.0.7 (2013-02-12) +

                      2.0.7 (2013-02-12)

                      • bug on weights corrected (thanks to Lugi M.)
                      -

                      2.0.3 (2013-01-18) +

                      2.0.3 (2013-01-18)

                      • deal with MAXENT categorical variables and categorical @@ -1207,7 +1276,7 @@

                        2.0.3 (2013-01-18)

                      -

                      2.0.0 (2013-01-17) +

                      2.0.0 (2013-01-17)

                      • MAJOR RELEASE
                      • diff --git a/docs/index.html b/docs/index.html index 3b42a477..e88e9079 100644 --- a/docs/index.html +++ b/docs/index.html @@ -168,7 +168,7 @@

                        biomod 4.2-5 - Modeling options & Tuning Update

                        -

                        ! biomod2 4.2-5 is now available on GitHub !

                        +

                        ! biomod2 4.2-5 is now available on CRAN !

                        /!\ Please feel free to indicate if you notice some strange new behaviors !

                        @@ -187,8 +187,16 @@

                        • ModelsTable and OptionsBigboss datasets (note that improvement of bigboss modeling options is planned in near future)
                        • +
                        • 3 new vignettes have been created : + +


                        diff --git a/vignettes/news.Rmd b/vignettes/news.Rmd index c6e8866d..3bea68e7 100644 --- a/vignettes/news.Rmd +++ b/vignettes/news.Rmd @@ -13,6 +13,41 @@ vignette: > ## Development updates +### 2024 + +#### 4.2-5 Modeling options and Tuning (2024-05-02) + +- Submitted on CRAN + +##### Major Changes + +- Add print function for `BIOMOD.options.dataset` and `BIOMOD.models.options` classes +- Add `GAM.binary.gam.gam` and `GAM.binary.mgcv.bam` in `OptionsBigboss` dataset +- Add checks for `obs` and `fit` parameters in `bm_FindOptimStat` +- In `bm_Tuning` function : + + add `MAXENT.algorithm` and `MAXENT.parallel` parameters + + be sure to update default tuning parameters if not all provided + + fix tuning for `XGBOOST` and `SRE` + + fix optimization of formula + + switch from `gamSpline` to `gamLoess` method to tune `GAM.gam.gam` model, and add `GAM.span` and `GAM.degree` parameters +- Fix multiple cases when using different settings of PA / cross-validation / modeling options through all the different secundary functions and `BIOMOD_Modeling` + + +##### Minor Changes + +- Add vignette for cross-validation (_to prepare your own calibration / validation datasets_) +- Add vignette for modeling options (_to help you navigate through the new way of parameterizing single models_) +- Update examples and documentation + +##### Bugfix + +- Add `try` and error message in call for models in `bm_RunModelsLoop` +- Check for predictions `>1000` +- Correct `BIOMOD_EnsembleForecasting` when using `data.frame` +- Correct predictions for `EMci` (removing round) + + + ### 2023 #### 4.2-5 Modeling options and Tuning (2023-09-12)