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Lasso#31

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bniebuhr wants to merge 178 commits intomainNINAnor/oneimpact:mainfrom lassoNINAnor/oneimpact:lassoCopy head branch name to clipboard

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Commits on Apr 25, 2023

• add_zoi_layers: add first version of the function

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Commits on Apr 26, 2023

• data: reorganize reindeer data sorting by id and time

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Commits on May 4, 2023

• DESCRIPTION: updated dependencies

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• conditional_boyce: added function as Bram has wrote it originally

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• add_zoi_formula: first commit with structural modifications from the original function and an example

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• extract_case_strata: first commit, with some changes from the original function to work on tibbles and data.frames in general

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• filter_na_strata; first commit with documentation a a few small changes from the original function

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• net_issf: first commit, basically the same function as original

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• set_validation_sampling and set_samplimg_parms: first commit, with some changes from the original code

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• kernel_prediction: added function, equal to original

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• spat_strat: first commit, with changes from raster to terra from the original code; documented and with examples

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• spat_stat_fit_issf: first commit, changed from spat_stat_issf with small changes

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• data-raw/test_lasso: prepare data to test lasso approach

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• concordanceSomers_d: added Rd

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• conditional_maxnet: added with no modification from the original, just for testing

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• Merge branch 'main' into lasso

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Commits on May 8, 2023

• I added an example comment

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Commits on Jun 12, 2023

• extract_response_strata: changed name from extract_case_strata to response

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• add_zoi_formula: added more documentation and examples; added additional parameters

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• create_resamples: add function v1 with only random sampling so far and a vector of p - proportion of data

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• filter_na_strata: do not use na.omit - double check! also, changed extract_case_strata to extract_response_strata

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• reindeer dataset: updated from track_xyt to only tibble

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• net_logit: Added function net_logit v1 for fitting RSF with glmnet

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• net_clogit: renamed net_issf to net_clogit and standardized code to correspond to net_logit

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• removed to_do.R (old before MEE 2023 publication)

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Commits on Jun 13, 2023

• create_resamples: replaced sapply by lapply which returns lists when p is the same for all blocks

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• removed set_sampling_params(), now these are parameters from create_resamples()

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• create_resamples: implemented spatial sampling with H0 (instead of set_validation_sampling) and random sampling with H0

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• spat_strat: updated documentation

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• renamed spat_strat_fit_issf as fit_net_clogit

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Commits on Jun 14, 2023

• reindeer_annotated: added data to the package

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Commits on Jun 15, 2023

• Added somersD and AUC to the namespace

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• create_resamples: added H0 to the output list and excluded the possibility of matrix output; list argument is still kept but could be removed

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• filter_na_strata: changed example in manual

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• kernel_prediction: improved code workflow

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• fit_net_clogit: updated based on argument samples created by create_resamples, working properly

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• added example_complete_clogit running well

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• create_resamples: added printed message

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• reindeer_ssf: renamed annotated data for ssf from reindeer_annotated

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• spat_strat: improved documentation

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• fit_net_clogit: corrected sampling dataset, data instead of data_annotated

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Commits on Jun 21, 2023

• concordance: added condition to avoid a warning for rsf, when there is no (only 1) strata

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• reindeer data: added reindeer_rsf with annotated data for rsf

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• filter_na_strata: updated example using survival package

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• fit_net_logit: implemented, working for random sampling; must be re-worked when blockH0 is given

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• bag_fit_net_logit: implemented, seem to work

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• bag_lasso: implemented, seems ok

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Commits on Jun 22, 2023

• spat_strat: added H1_as_H0 parameter, tested

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• create_resamples: improved documentations of parameters

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Commits on Jun 26, 2023

• DESCRIPTION: added pROC package to use for auc

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• concordance: added proc_AUC as a wrapper to pROC::auc

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• bag_models: changed name from bag_summary/multi_issf, added summary for character variables, added summaries of validation scores and weighted validation scores

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• create_resamples: added new warnings for when too much data is removed (NAs)

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• spat_strat: added row/step id in all outputs

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• fit_net_logit: added pROC_AUC option, filtered only the relevant covariates for train-test-validate, further NA checks, removed intercept from all predictions, and added metric to the result output

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• fit_net_clogit: added pROC_AUC option, added filter for relevant covariates, added draft of bag_fir_net_clogit

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• reindeer_rsf: changed data and documentation to data from Hardangervidda wild reindeer area, data from Niebuhr et al 2023 MEE

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• variable_importance: added functions, first version from Brams code and adaptations

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• NAMESPACE: added all new functions

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Commits on Jun 28, 2023

• net_logit and net_clogit: added standardize parameter to be passed to glmnet

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• variable_importance: added variable block, samples parameter (not implemented yet); normalize in plot_importance, and plot_weights

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• fit_net_logit: added standardize parms, subsampling for only the covariates in the formula, saveRDS for saving externally; bag_fit_net_logit: added standardize, added formula, method, metric, n, me…

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• fit_net_clogit: added standardize parameter, not yet implemented

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• bag_models: removed f from parms, added n, f, method, metric, numeric_covs to output results

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• bag_predict: added function as Bram designed, issues with weighted Quantiles (all values equal)

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• bag_plot_response: added as Bram designed, added data to parms to get category levels, added zoi_shape to use functions for prediction, added ci, plot_mean, plot_median, normalize parms for plottin…

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Commits on Jul 3, 2023

• variable_importance: corrected remove_low argument in the code

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• add_zoi_formula: added more elements to the output grid

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• bag_models: corrected response var in mm_formula, added "bag" as a class

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• bag_plot_response: added "median", "mean," and "zero" to baseline options, and n_features.

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Commits on Jul 4, 2023

• rescale_coefficients: changed to UseMethods again, implemented rescale_coefficients.bag

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• concordance: removed supressWarnings from proc_AUC

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• net_logit: added penalty.factor parameter and func parameter (glmnet or cv.glmnet)

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• bag_predict: added weights correctly in the weighted quantile

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• fit_net_logit: implemented methods with adaptivelasso and decayadaptivelasso - first tests ok

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• plot_coef: first implementation

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• bag_plot_response: added n_features parm in documentation

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Commits on Jul 7, 2023

• plot_coef: added plot_type, remove_low, remove_high, show_legend parameters and implemented. Now we can make histograms and point plots with error bars

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• git_net_logit: corrected penalties for adaptive and decay adaptive lasso, completed options for parameters

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• create_resamples: corrected output for H0 in spatially stratified sampling using strata

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• bag_predict: added logit response

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• plot_response: changed as a method for class bag, from bag_plot_response

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• bag_models: added weighing funcitons

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• vignette/logit: first draft working with Lasso, AdpLasso, and DecayAdpLasso

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• net_logit: better documentation, standardized with net_clogit

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• net_clogit: implemented all parameters and steps as in net_logit

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Commits on Jul 13, 2023

• bag_fit_net_logit: added parms alpha and penalty.factor to parallel calls

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• bag_fit_net_logit: corrected a } when closing for loop

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• bag/fit_net_logit: substantial changes to make functions correspond to the logit ones

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• kernel_prediction: added strata to make sure errors do not occur

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Commits on Aug 8, 2023

• bag_models: added score2weight_mean and inv_mean function, and the second as default. Added new output in case of errors in fitting models

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• explore_blocks and explore_blocks_pre: added first version of functions

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• variable_importance: added metric parameter for when a different metric should be used to evaluate the models

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• fitting_zoi_clogit: add incomplete version of vignette

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Commits on Aug 18, 2023

• bag_models: added second warning, corrected col parameters in hte score2weight functions

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• fit_net_(c)logit: corrected typo in Ridge option

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Commits on Aug 21, 2023

• changed predictor_grid to predictor_table parameter name

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Commits on Aug 29, 2023

• bag_fit_net_clogit: corrected object name for foreach option

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Commits on Mar 26, 2024

• add_zoi_formula: add check when there is more than one type of function to be added to the formula

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• add_zoi_formula: add check when there is more than one type of function to be added to the formula

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• plot_coef: add argument order_zoi_radius and transform variables into factor for plotting

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• Merge branch 'lasso' of https://github.com/NINAnor/oneimpact into lasso

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• Merge branch 'lasso' of https://github.com/NINAnor/oneimpact into lasso

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• Merge branch 'lasso' of https://github.com/NINAnor/oneimpact into lasso

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• fitting_ZOI_logit: added first version of vignette (still to be checked and developed/shortened)

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Commits on Apr 11, 2024

• renamed functions for concordance: conditionalSomersD, conditionalAUC

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• add_zoi_formula: improve documentation and bugs

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• add_zoi_layer: improve documentation

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• explore_blocks/pre: improved documentation and added examples

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• calc_zoi_cumulative: improved code to allow for multiple layers - following the development in main branch

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• fit_net_logit: improved selecation of variables in formula, updated other functiona calls and parameters

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• fit_net_clogit: improved filter na strata, selection of data for validation, updated other functiona calls and parameters, added subset_samples in bag_fit_net_clogit

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• create_resamples: added max size blockH1 and 2, needs to be changed and implemented

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• bag_models: implemented min functions, corrected weights computation, reorganized output

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• bag_predicxt_response: corrected drop=False and added option for factor variables

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• bag_predict: changed mm_formula name

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• extract_response_strata: changed covars argument name (from other_vars)

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• plot_coef: corrected matrix multiplication, added possibililty to rescale coefficients

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• spat_strat: improved documentation

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• rescale_coefficients: corrections for bag object - now working

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• variable_importance: new implementation for concordance functions, not much speed gained

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• bag_predict_spat: added first function draft, now running

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Commits on Apr 12, 2024

• bag_load_net_clogit: added function

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• net_logit and rescale_coefficients: improved documentation

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• create_resamples: added argument max_number_blocksH0_train

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Commits on Apr 13, 2024

• changed terra and sf to suggests

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Commits on Apr 14, 2024

• bag_load_models: added function to replace bag_load_net_clogit, now to work for both logit and clogit models

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• fit_net_logit: synced output file name when out_dir_file is provided, in accordance to fit_net_clogit (using 'Resample001', for instance).

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• variable_importance: added na.action = na.pass to avoid decreasing the number of rows in the model matrix for prediction

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• fit_net_(c)logit: corrected text for removal of missing observations

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• variable_importance: added ss parameter for sample set definition; whole dataset is considered if samples is NULL. added removal of NA obs from data

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Commits on Apr 16, 2024

• DESCRIPTION: updated terra, sf, and DescTools

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Commits on Apr 19, 2024

• fit_net_clogit: correction of strata for ridge regression in adaptive Lasso

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• variable_importance and plot_importance: implemented computation and plot per block H0

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Commits on Apr 30, 2024

• fit_net_clogit: change indexing for val2 (to be doubled checked later)

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• plot_importance: added summ_strat in the documentation

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Commits on May 6, 2024

• DESCRIPTION: added maxnet as suggests

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• bag_predict_spat: corrected computation of individual predictions and summaries (median interquatile difference)

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• plot_response: updated documentation

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Commits on May 8, 2024

• DESCRIPTION: added Neri as contributor, tidyr to imports, foreach to suggests

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• bag_predict: enhanced documentation, changed argument wQ_probs to wq_probs

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• plot_response: added individual line plot arguments and arguments for color, linewidth, and alpha for lines

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• bag_predict_spat: changed weighted summaries to DescTools instead of modi, to keep all in one package

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• add_zoi_formula: added #

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• Update add_zoi_formula.R

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• Merge pull request #28 from NINAnor/bniebuhr-patch-1

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• Update fit_net_clogit.R

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• Merge pull request #1 from Neriht/Neriht-patch-1

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• Merge pull request #29 from Neriht/lasso

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• bag_plot_response: updated way to plot response for ZOI variables when all other variables are zero

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• bag_predict: updated filtering only one variable for prediction, and thrwoing aaway the rest of the matrix

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• bag_predict_spat: first version of the function

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• variable_importance: extended to boxplot as well, and barplots for blockH0

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• plot_response: changes to default linewidth and alpha for individual lines/models

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• fit_net_clogit/logit: added gamma parameter and abs() in Adaptive Lasso

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• bag_models/rescale_coefficients: exported intermediate functions

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• bag_plot_response: changed alpha and linewidth default parms for individual lines

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• variable_importance: correction for omission of logit models

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• bag_predict_spat: added support for raster inputs

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• fit_net_logit: added support for OneZoI Adaptive Lasso

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• fit_net_clogit and fit_net_logit: added onezoi, grouped lasso, and hypothesis lasso

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• fit_net_clogit and fit_net_logit: added onezoi, grouped lasso, and hypothesis lasso

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• Merge branch 'lasso' of https://github.com/NINAnor/oneimpact into lasso

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• fit_net_clogit: corrected implementation of other flavors of adaptivelasso, tested for onezoi-adaptivelasso

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• git_net_clogit: corrected conflicting index i between sample and implementation of adaptivo lasso flavors (for loop)

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• fit_net_logit: corrected conflict of name of index i

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• variable_importance - fixed issue with variable names in output table for groups

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• bag_predict_spat: added output_rescale parameter, added both IQR and QCV to the results

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• plot_response: changed default ylab to "Relative Selection Strength"

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• calc_zoi_sql: added first version

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• calc_zoi_sql: documented and added example

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• calc_zoi_sql: updated example (not completely functional yet)

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• fit_net_clogit: corrected summary when only numeric variables are included in the model; removed redundancy in ridge regression

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• fit_net_clogit: corrected condition for ridge to work correctly

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• plot_importance: added parameter scales

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Commits on Dec 18, 2024

• bag_predict_spat_vars: added 'what' parameter for choosing whether or not to predict and plot individual models, mean, and median

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Commits on Jan 19, 2025

• bag_load_models, bag_models, fit_net_clogit: corrected way to account whether variables are numeric or not

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• fit_net_clogit: added parameter value_lasso_decay to allow no penalization of non ZOI variables

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