microeco v1.2.2

• fix error bar width issue in plot_line of trans_abund
• fix sample abund zero issue after feature filtering in tidy_dataset
• update trans_alpha help document

microeco v1.2.0

• add heatmap for formula usage in plot_diff_bar of trans_diff
• add remove_unknown parameter in trans_diff
• add line options for mean-se plot in trans_alpha class
• add add_sig_label_num_dec parameter in plot_alpha of trans_alpha
• add anova_post_test parameter in cal_diff of trans_alpha
• add closeness and eigenvector centrality in get_node_table of trans_network class
• add circlize method in plot_sum_links of trans_network
• add filter_env, trans and na.value parameters in plot_cor of trans_env
• fix sample selection in trans_nullmodel
• fix italic in plot_taxa_roles in trans_network
• fix cal_sum_links tax extraction when taxa_level is not OTU
• use delete_taxonomy_lineage & delete_taxonomy_prefix params in trans_abund class
• fix default zero removing issue of groups in KW_dunn method of trans_alpha
• fix relative abundance string bug in gexf file in trans_network
• fix relativeabundance null for Genus gexf file in trans_network
• rename simplify_names to keep_full_name in plot_diff_bar of trans_diff

microeco v1.1.0

• fix the bug of node roles calculation in trans_network class

microeco v1.0.0

• add cal_anosim function in trans_beta class
• fix KW_dunn bug when groups have hyphen in trans_alpha class
• extend p_adjust_method to KW_dunn in trans_alpha class
• add alpha param in cal_diff of trans_alpha class
• extend alpha param to anova letters in trans_diff class
• add ggpairs param in cal_autocor of trans_env class
• fix show_taxa select bug in trans_ordination of trans_env class
• check use_taxa_num in plot_diff_cladogram func of trans_diff class
• optimize trans_venn & delete redundant params
• KW_dunn letter ordered by medians from high to low
• optimize filter_thres parameter in trans_diff class
• fix group value NAN return NA bug in trans_alpha class
• add standardize param in trans_env class
• extend filter_thres param to more methods in trans_diff class
• add filter_thres param in cal_cor of trans_env class
• add 'none' in plot_type param of plot_cor in trans_env class
• add xtext_angle param in plot_cor of trans_env class
• add Unassigned in pattern param of tidy_taxonomy function
• add check_taxa_abund, check_microtable and check_tax_level functions

microeco v0.20.0

• fix lefse lda result feature name bug in trans_diff class
• fix abs bug of lefse in trans_diff class
• optimize y_start and y_increase params in trans_alpha class

microeco v0.19.5

• fix func_add_groups bug of FAPROTAX in cal_spe_func of trans_func class
• update check_abund_table function in microtable class

microeco v0.19.0

• add glmm method in trans_diff and trans_alpha
• restructure lme method in cal_diff of trans_alpha
• add maaslin2 method in trans_diff and cal_cor of trans_env
• add transformation parameter in trans_diff
• add color_group_map param in plot_diff_bar of trans_diff
• add SRS method in rarefy_samples of microtable
• add coord_flip param in plot_bar of trans_abund
• add clustering_plot parameter in plot_bar of trans_abund
• allow petal_color multiple values in plot_venn of trans_venn
• add return_model parameter in cal_diff of trans_alpha
• more data checking in plot_cor of trans_env
• default character2numeric FALSE in trans_env
• add return_model parameter in cal_diff of trans_alpha
• update example dataset.RData

microeco v0.17.0

• add save_table function in microtable class
• add ggnested method for nested legend in plot_bar of trans_abund
• add plot_radar function in trans_abund
• add plot_donut function in trans_abund
• create plot_tern function in trans_abund
• add add_label function in plot_pie of trans_abund
• add cal_NST_convert function in trans_nullmodel
• fix y axis bug in plot_bar of trans_abund
• create inner expand_colors function to expand more colors automatically
• interpolate colors when not enough in trans_abund, trans_alpha and trans_beta
• add ggraph_node_text parameter in plot_network function
• check input data format of microtable
• set default color_values in plot_sum_links function
• delete color_palette_20 variable
• rename use_colors to color_values in plot_clustering function of trans_beta
• reset default color_values in plot_bar of trans_abund
• fix add_rownames2taxonomy for tax_table NULL in microtable
• add Github and Issues link in microeco help document
• rename all xtext_type_hor parameters to xtext_angle in trans_abund
• delete ylab_title parameter in plot_bar of trans_abund
• move igraph from 'Suggest' to 'Import'

microeco v0.16.0

• add random_network function in trans_network
• add linda method in trans_diff
• rename cal_tNST to cal_NST and add pNST method
• fix plot_group_order bug in plot_group_distance function
• add group_morestats param in trans_abund
• default cluster_walktrap for directed network in cal_module
• parameters pass to bootstrap_p in cal_powerlaw
• add stop message for only one biomarker in lefse
• update document of each class
• add more messages in plot_diff_cladogram
• fix group subset drop issue of data.frame in cal_manova
• more check on add_data in trans_env
• simplify p_adjust_method in trans_diff
• update example dataset, i.e. microtable object
• add a help document of microeco

microeco v0.15.0

• support regression in trans_classifier
• add plot_feature_imp func in trans_classifier
• KW_dunn default letter instead of asterisk in trans_alpha and trans_diff
• merge_all param to support mpa format in save_abund of microtable
• add lm_equation param in plot_scatterfit of trans_env
• fix coverage issue in microtable
• more options in Upset plot in trans_venn
• add perc param in cal_spe_func_perc of trans_func
• add merge_by in cal_abund and sep in save_abund
• fix group passing bug in trans_beta
• fix index checking in cal_ordination of trans_env
• warning for NA in cal_spe_func
• stop for no edge in cal_network of trans_network
• adjust default p_adjust_type in cal_cor of trans_env
• support dataset NULL in trans_diff
• support dataset and network_method NULL in trans_network
• rename ANCOMBC to ancombc2 in trans_diff
• add DESeq2 method in trans_diff
• fix plot_diff_abund issue for ancombc2 in trans_diff