microeco v1.15.0

• optimize cal_preProcess function in trans_classifier class
• add by_auto_set parameter in cal_manova function of trans_beta class
• fix get.edges namespace issue in trans_network class
• extend delete_taxonomy_lineage for nested usage in trans_abund class
• set order_x_mean default FALSE in trans_diff class
• optimize significance label position for error bar in trans_alpha class
• use method param instead of cal_method in cal_cor function of trans_env class
• update the help document

microeco v1.14.0

• fix the otu_table filtering bug for negative values in tidy_dataset of microtable (thank Fernando Puente-Sánchez for the finding)
• fix asterisk usage issue in formula of linda method in trans_diff
• fix issue in parameter passing in plot_diff_bar of trans_diff
• add for_taxa_abund parameter in filter_taxa of microtable
• extend point_size to numerical variable in plot_ordination of trans_beta and trans_env
• fix the significance label issue for barerrorbar in trans_diff
• add choices parameter in plot_ordination of trans_beta
• add NMDS_matrix parameter in cal_ordination of trans_beta
• return a recreated microtable object in trans_norm
• add taxa_level parameter in cal_ordination of trans_beta
• add loading_text_prefix and loading_text_taxlevel parameter in plot_ordination of trans_beta
• add taxa_text_prefix parameter in plot_ordination of trans_env

microeco v1.13.0

• apply cal_feature_sel function to training data in trans_classifier class
• check data spliting for cal_feature_sel function in trans_classifier class
• use ytext_italic parameter instead of ylab_type_italic in plot_cor function of trans_env class
• fix ylab_italic failing issue in plot_cor function of trans_env class
• use ytext_position parameter instead of text_y_position in plot_cor function of trans_env
• add force_jaccard_binary parameter in cal_betadiv function of microtable class
• check node name attribute in trans_network class
• update help document in trans_abund class

microeco v1.12.0

• return invisible self for method chaining in each class
• add by and permutations parameters in cal_manova function of trans_beta class
• use deprecate function of lifecycle package
• replace deprecated functions of igraph package in trans_network class
• change default add_label_group argument in plot_taxa_roles function of trans_network class
• update the print function in each class
• update the document in each class
• delete biom and qiimer source package in extdata

microeco v1.11.0

• set sample.size = NULL in rarefy_samples in microtable class
• check tbl_df format for tidy_taxonomy function and all input tables in microtable class
• fix one sample error in filter_taxa of microtable class
• fix trans_comm issue for taxa_level not OTU in trans_network class
• add FlashWeave_gml param in cal_network of trans_network class
• allow factor for axis text in plot_cor in trans_env class
• remove Env factor in result table of cal_cor in trans_env class
• delete pheatmap option in plot_cor in trans_env class
• reassign res_diff table for customized use in plot_diff of trans_env class
• add facet_switch parameter in plot_heatmap of trans_abund class
• add y facet for high_level in plot_heatmap of trans_abund class
• check whether high_level and taxrank param same in trans_abund class
• fix factor and names issue in plot_tern of trans_abund class
• add anova_varequal_test param in cal_diff of trans_alpha class
• remove cal_tax4fun function in trans_func and delete tax4fun package in inst
• fix partial taxonomic info issue in FUNGuild prediction of trans_func class
• add lefse_sub_strict and lefse_sub_alpha param in trans_diff class
• add stop message for wrong use of taxa_level in some methods of trans_diff class
• update document for trans_diff, trans_alpha and trans_abund classes

microeco v1.10.0

• restructure plot_diff_abund function in trans_diff class
• add barerrorbar option in plot_type parameter of plot_alpha in trans_alpha class
• update FAPROTAX to v1.2.10
• reconstruct cal_abund function in microtable class
• add node_alledges and return_igraph parameter in subset_network of trans_network class
• optimize edge parameter in subset_network of trans_network class
• add check_edgetable and check_nodetable in private of trans_network
• fix the issue for one factor in cal_mantel and plot_cor of trans_env class
• check abnormal character for lefse method in trans_diff class
• add abundance summary for by_group in trans_diff class
• fix inherit aes issue in label mapping of plot_alpha and plot_diff_abund functions
• add OPLS-DA method in cal_ordination of trans_beta class
• support DNAbin type for rep_fasta object in microtable and trans_func class
• update the document

microeco v1.9.1

Fix the issues in examples of last release.

microeco v1.9.0

• use plot_type parameter instead of use_boxplot in plot_alpha of trans_alpha
• more plot options in plot_type parameter in plot_alpha of trans_alpha
• use add parameter instead of boxlot_add in plot_alpha of trans_alpha
• add partial parameter for partial correlation in cal_cor of trans_env
• set line_alpha = 0.5 in plot_scatterfit of trans_env
• add up_bar_width and left_bar_width parameters in plot_bar of trans_venn
• add left_bar_alpha, bottom_line_colour, bottom_line_width and bottom_background_alpha parameters in plot_bar of trans_venn
• add PLS-DA method in cal_ordination of trans_beta
• add add_sig_text_size parameter in plot_diff_abund of trans_diff
• add rf_imp_type parameter for rf in trans_diff
• add parameter passing for rf in trans_diff
• delete rf_ntree parameter in trans_diff
• update the usage of lefse_norm param in trans_diff
• compare mean when medians are same across groups in lefse of trans_diff
• check the prefix in cladogram of trans_diff
• fix R2 issue for glmm_beta method in trans_diff
• restructure the R2 output format for lme and glmm methods in trans_alpha and trans_diff
• extend tidy_taxonomy for microtable input
• rename parameter use_group to group in merge_samples function of microtable
• stop when tbl_df format data is found in microtable
• fix parameter usename_rawtaxa_notOTU NA issue in cal_network of trans_network
• import igraph >= 2.0.0

microeco v1.8.0

• rename ordination to method parameter in cal_ordination of trans_beta
• fix inherit aes issue in plot_ordination function of trans_beta
• extend measure parameter to customized matrix input in trans_beta$new
• optimize output format of ANOSIM and perMANOVA for overall test in trans_beta
• fix feature name replace issue in trans_classifier
• extend cal_caretList to no data_train case in trans_classifier
• extend model training for all samples in trans_classifier when the data is not splitted
• add plot_caretList_resamples function in trans_classifier
• add cal_caretList_resamples function in trans_classifier
• fix plot_feature_imp issue for regresssion in trans_classifier
• add rf_sig_show and show_sig_group in plot_feature_imp of trans_classifier
• add rf_feature_sig param in cal_feature_imp of trans_classifier
• delete coord_flip param in plot_feature_imp of trans_classifier
• add more definitions of metrics in cal_predict of trans_classifier
• rename max.tree param to ntree in cal_train of trans_classifier
• opt trainControl usage in trans_classifier
• add metrics definations in cal_ROC of trans_classifier
• fix R2 issue for glmm_beta method in trans_diff when no random effect is provided
• fix group factor issue for group_aggre in plot_diff_bar of trans_diff
• fix coord_flip FALSE feature order issue in plot_diff_bar of trans_diff
• add group_aggre and group_two_sep params in plot_diff_bar of trans_diff
• add add_sig param in plot_diff_bar func of trans_diff
• add documents in Return for Estimate in trans_alpha and trans_diff
• fix value scaling (< 1) minor issue in betareg in trans_diff
• fix group issue when no dataset in plot_scatterplot function of trans_env (customized usage)
• use factor inside data when by_group used in plot_cor of trans_env
• check add_abund_table input in cal_cor of trans_env
• unify Method name in statistics output of trans_alpha
• add coefplot related parameters in plot_alpha of trans_alpha
• remove redundant spaces in factors of anova in trans_alpha
• add FUNGuild_confidence param in cal_spe_func of trans_func
• only tidy the first prefix in tidy_taxonomy for multiple taxonomy names with same prefix (e.g., Kingdom level in Kraken)
• fix abund NULL issue in cal_network of trans_network
• add Std.Error for lm, lme, betareg and glmm models

microeco v1.7.1

• fix factor invalid issue for formula in trans_alpha