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flexsdm: An R package for supporting a comprehensive and flexible species distribution modeling workflow

Authors: Santiago J.E. Velazco; M. Brooke Rose; André Felipe Alves de Andrade; Ignacio Minoli; Janet Franklin;

flexsdm: An R package for supporting a comprehensive and flexible species distribution modeling workflow

Abstract

What's Changed documentation for plot_max_res was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/1 documentation for enm_eval was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/2 Docu by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/3 MAE metric added by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/6 data_part function created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/7 LOOCV and BOOT partition improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/8 bloc_partition_pa function improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/9 new function 'get_block' created and importat improvments made in blo… by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/10 tune_gbm can deal with partition with several replicas :) by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/11 Tune gbm by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/12 Tune svm by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/13 Tune rf by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/14 tune_nnet addapted to work with BOOT and REP_KFOLD method by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/15 tune_mx addapted to work with BOOT and REP_KFOLD by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/16 fit_glm created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/17 fit_glm documentation improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/18 NAMESPACE and fit_glm documentation updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/19 tuen function autputs were changed by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/20 teste do andre by @andrefaa in https://github.com/sjevelazco/flexsdm/pull/21 eliminou teste by @andrefaa in https://github.com/sjevelazco/flexsdm/pull/22 threshold description was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/23 fit_glm output was changed by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/24 Fit gam by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/25 document updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/26 Fit gam by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/27 Fit by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/28 all fit and tune funciones have ability to report performance for se… by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/29 code style and documentation were updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/30 fit_rf was created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/31 fit_nnet was created and documented by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/33 dependencies updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/34 fit_mx was created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/35 documentation of fit_gau was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/36 background function was subsituted by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/37 new function created sample_pseudoabs by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/38 documentation was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/39 Pseudoa by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/40 calip_area created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/42 documentation improved and CFP cluster data added by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/43 Update enm_eval.Rd by @mrose048 in https://github.com/sjevelazco/flexsdm/pull/46 Update block_partition.Rd by @mrose048 in https://github.com/sjevelazco/flexsdm/pull/45 Update tune_nnet.Rd by @mrose048 in https://github.com/sjevelazco/flexsdm/pull/47 block_partition corrected by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/48 documentation of sdm_predict was created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/49 Predict by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/50 tune_svm updated with new sdm_eval by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/51 tune_rf updated with new sdm_eval by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/52 tune_svm updated with new sdm_eval by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/53 tune_mx updated with new sdm_eval by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/54 new data added by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/58 some auxiliary functions and bloc_partition adapted to terra by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/59 calib_area updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/60 Terra by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/61 homogenize_na updated and created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/62 Terra by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/63 plot_res addapted to terra by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/64 sample_background updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/65 Function to deal with predictor collinearity by @andrefaa in https://github.com/sjevelazco/flexsdm/pull/66 Fix to correct_colinvar by @andrefaa in https://github.com/sjevelazco/flexsdm/pull/67 Update sdm_predict.Rd by @mrose048 in https://github.com/sjevelazco/flexsdm/pull/68 Update block_partition.Rd by @mrose048 in https://github.com/sjevelazco/flexsdm/pull/69 fit_ function return data_ens by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/70 Ensemble by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/71 tryCath added to fit_svm adn fit_mx by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/72 arguments with hyperparameter added and ensemble info by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/73 documentations were updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/74 fit_formula added to fit_gbm and tune_gbm by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/75 Ensemble by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/76 formula message improved and added to all functions fit and tune by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/77 sdm_extract function by @mrose048 in https://github.com/sjevelazco/flexsdm/pull/78 documentation for sdm_extract by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/79 Ensemble by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/80 functions documentation and website were updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/81 fit_ensemble was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/82 fit ensemble was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/83 sdm_eval new version and fit_gau adapted to new sdm_eval by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/84 sdm_eval debuged by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/85 some algorithm names function were changed by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/86 document were updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/87 all functions adapted to new sdm_eval verstion by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/88 updating documentation by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/89 sdm_predict: new argument name, now if predict_area is used it will c… by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/90 Sdm predict by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/91 pkg documentation was updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/92 prefixes updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/93 partition functions were renamed by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/94 par_spatial by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/95 par_spatial by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/96 new funcion names part_spatial -> part_spat by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/97 new function for spatial partition was created :) by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/98 part_ function documentation were improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/99 documentation of some function were improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/100 part_sblock can lead with different number of partition by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/101 new name and description for part_senv by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/102 new functions names and documentation by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/103 function formalities updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/104 functions formalities were updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/105 debug to fa method in correct_colinvar by @andrefaa in https://github.com/sjevelazco/flexsdm/pull/106 new folder and script for testing functions by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/107 Test by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/109 .md was updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/110 ensemble of small model-GAM was created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/111 functions documentation were updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/112 function debuged by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/113 minor bug in fit_ensemble fixed by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/114 minor bug in fit_ensemble fixed by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/115 esm_gam was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/116 fit_gam : documentation was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/117 first_test by @iminoli-dev in https://github.com/sjevelazco/flexsdm/pull/118 esm_gam example improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/119 fit_gbm was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/120 esm_gbm was cread esm_gam documentation was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/121 esm_glm was created and other esm documentation was improved by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/122 esm_svm was created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/123 esm_net was created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/124 conditional for returning NA when none bivariate model have performan… by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/125 fit_max argument default was changed by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/126 esm_max was created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/127 documentation of several functions were updated by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/128 new function esm_gau was created by @sjevelazco in https://github.com/sjevelazco/flexsdm/pull/129 documentation of several function were updated by @sjevelazco in https://github.com/

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