microeco v2.3.0

• add trans_niche class
• add trans_phylo class
• support graphml format in save_network function in trans_network
• fix data offset issue in cal_betadiv of microtable class
• fix filter_taxa parameter issue in cladogram of trans_diff class
• fix freq issue in filter_taxa function
• fix standardize usage issue in trans_env class
• fix min_num_nonpara and get_angle usage issue in trans_diff
• fix normalize_pathways parameter usage issue in tax4fun2
• fix boruta repetition issue in trans_classifier
• fix GMPR sapply return issue
• fix plot_box aes inherit issue in trans_abund class
• add digits parameter in save_abund function in microtable class
• allow otu_table NULL in microtable
• check more input values and parameters in trans_func class
• check input formula in cal_manova function

microeco v2.2.0

• add cal_pathway function in trans_metab class
• add cal_pathway_enrich function in trans_metab class
• add plot_pathway_enrich function in trans_metab class
• add cal_pathway_network function in trans_metab class
• optimize cal_origin_network function class
• fix namespace issue in get_node_table function of trans_network class
• check group parameter input in trans_diff class
• trim tidle for input formula
• use linewidth instead of size in plot_heatmap function
• use linewidth for errorbar in trans_alpha class

microeco v2.1.0

• create the trans_metab class
• add soil_metab and soil_microb example data
• drop unused factor levels in sample_table of microtable
• add add_prefix parameter in tidy_taxonomy function
• delete useless format in tidy_taxonomy function
• fix ordiArrowMul issue in trans_ordination of trans_env class
• linewidth instead of size in plot_ordination of trans_env class
• extend log2FC to Estimate in plot_volcano of trans_diff
• add xtitle ytitle xlabel ylabel parameters in plot_volcano of trans_diff
• use maaslin3 method in trans_diff and trans_env classes
• add complete_cases parameter in cal_cor of trans_env class
• fix env scope bug in cal_ordination of trans_env class
• add sample_name_each parameter in subset_network of trans_network class
• add example in subset_network of trans_network class
• fix order_x length issue in trans_alpha class
• fix return in deprecated functions in trans_func class
• add label_na and weight_na parameters in get_edge_table function
• fix feature selection name matching issue in RDA
• extend plot_volcano function to methods with Factors type
• fix the add_rownames2taxonomy warning in all classes
• fix the duplicated rows issue in ancombc result of trans_diff class

microeco v2.0.0

• support running several visualization functions directly with the previous statistical functions
• update FAPROTAX version to 1.2.12 in trans_func class
• optimize the cal_func function in trans_func class
• add more transformation methods from vegan package in trans_norm class
• add remove_zero parameter in cal_func_FR function of trans_func class
• use linesize instead of size in plot_box in trans_abund class
• use linewidth in plot_scatterfit function of trans_env class
• add sample_name parameter in subset_network function in trans_network class
• add parameters for second type of points in ordination visualization
• add plot_volcano function in trans_diff class
• add_rownames2tax instead of rownames2taxonomy in microtable class

microeco v1.16.0

• add COR_return_padjust parameter in cal_network of trans_network
• fix names issue for rclr method in trans_norm
• extend by_group parameter usage to lm and lme methods in trans_alpha
• fix plot theme issue for ggplot2 v4.0 in trans_abund and trans_venn
• solve width warning for ggplot2 v4.0 in plot_bar of trans_abund
• add both option in ratio parameter of trans_venn
• add CSS_p parameter for CSS method in norm of trans_norm
• add cal_func_FR_comm function in trans_func
• optimize the naming in trans_func
• remove column with empty name in sample_table of microtable
• show input data basic info in trans_network
• add message for imcomplete order_x in trans_abund
• add legend_title parameter in plot_cor of trans_env
• fix matrix issue for NetCoMi in trans_network
• add sample_plot parameter in plot_bar of trans_abund
• update the help document

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