microeco v0.14.1

• fix plot_cor of trans_env for merging ggplot2 figures
• fix Fisher index in cal_alphadiv of microtable

microeco v0.14.0

• add lme and betareg models in trans_alpha and trans_diff class
• add by_ID param for trans_alpha and trans_diff class
• optimize cal_group_distance_diff params of trans_beta
• xtext_angle param in plot_diff_abund of trans_diff
• fix cal_cor of trans_env for only one feature
• restructure facet param in trans_abund
• rename cal_ordination_envfit in trans_env
• add cal_ordination_anova function in trans_env
• add filter_taxa function in microtable
• add ordered_group and sep param in trans_beta
• add by_ID param in cal_group_distance_diff of trans_beta
• update FAPROTAX to v1.2.6 in trans_func
• optimize the ggplot in trans_abund

microeco v0.13.0

1. add by_group parameter in cal_group_distance of trans_beta
2. create cal_group_distance_diff function in trans_beta
3. add by_group param in cal_mantel of trans_env
4. multi-way anova table for trans_alpha and trans_diff
5. opt input_taxaname param in trans_abund
6. fix the abundance issue in get_node_table of trans_network
7. fix bug of pheatmap in plot_heatmap of trans_abund
8. add scheirerRayHare test in trans_alpha and trans_diff
9. ancombc2 instead of ancombc in trans_diff
10. use formula instead of anova_set in cal_diff of trans_alpha

microeco v0.12.0

1. add feature number checking in trans_network
2. fix cluster space issue in plot_cor of trans_env
3. optimize group_order parameter in plot_diff_cladogram in trans_diff
4. add legend_title param in plot_heatmap of trans_abund
5. add spearman example in trans_env
6. add delete_unlinked_nodes parameter in cal_network function
7. add facet3 parameter in plot_bar and plot_heatmap function of trans_abund
8. add more measure checking in trans_beta
9. auto calculate abundance in cal_cor of trans_env if missing
10. add ANCOMBC method in trans_diff class
11. optimize trans_diff to plot abundance for all the methods
12. fix the bug in KW_dunn of trans_diff when all abund equal
13. add others abundance in alluvium of trans_abund
14. add ALDEx2_t and ALDEx2_kw methods in trans_diff
15. optimize cal_Cscore of trans_nullmodel
16. opt plot_diff_abund in trans_diff
17. add by_group param in trans_alpha for sub-group test and plotting

microeco v0.11.0

1. rename cal_cor to cor_method in trans_network$new
2. add 'bray', 'bicor', 'cclasso' and 'ccrepe' options in cor_method of trans_network$new
3. add use_WGCNA_pearson_spearman and use_NetCoMi_pearson_spearman parameters in trans_network$new
4. add plot_diff function in trans_env
5. fix the bug in get_node_table when tax_table is not available
6. move cal_sum_links and plot_sum_links functions back to trans_network class
7. fix the bug from 'Incertae_Sedis' in plot_diff_cladogram
8. check the diag of adjacency matrix in cal_network
9. add label related parameters in plot_taxa_roles of trans_network
10. rename select_samples to order_x in plot_spe_func_perc
11. fix the error when only one label in cal_sum_links
12. create plot_bar function in trans_venn
13. change COR_optimization_low_high parameter in cal_network

microeco v0.10.0

1.fix the bug for spieceasi glasso method in cal_network
2.optimize the network construction of spieceasi method
3.change cal_cor NULL for non-cor methods in trans_network
4.add errorbar_width parameter in plot_line of trans_abund
5.modify the print function in classes
6.change parameter names in plot_diff of trans_alpha
7.add label_text_size parameter in plot_diff of trans_alpha
8.fix the bug of anova when one measure is used in cal_diff of trans_alpha
9.check group names when add_sig = T in plot_diff_abund

microeco v0.9.0

1.fix the bug for wilcox test when method = "lefse" in trans_diff
2.add plot_line function for line chart in trans_abund
3.add add_sig parameter for significance label for all the methods in plot_diff_abund
4.reuse KW test for two groups in first step of lefse in trans_diff
5.add add_sig parameter in plot_diff_abund of trans_diff
6.fix the warning in cal_tax4fun
7.save reference profile and add KO names in cal_tax4fun2
8.correct the parameter in cal_manova example
9.check julia software for network_method = FlashWeave in cal_network function
10.add COR_optimization_low_high parameter in cal_network function
11.rename y_increae parameter to y_increase in plot_alpha of trans_alpha
12.optimize add_taxa_name parameter in cal_network of trans_network

microeco v0.8.0

1. optimize cal_diff and plot_alpha functions in trans_alpha class
2. add tNST method in trans_nullmodel class
3. add more differential test method in trans_diff class
4. restructure and optimize the return data and function name and structure of trans_diff class
5. optimize plot_ordination of trans_beta class to make it flexible
6. add get_adjacency_matrix function in trans_network
7. add trans_comm function in trans_network
8. use cal_powerlaw function instead of previous two functions in trans_network
9. add cal_diff function in trans_env class
10. add cal_autocor function in trans_env class
11. reshape plot_ordination function of trans_beta class
12. fix the bug in cal_manova and reshape this function of trans_beta class
13. optimize plot_scatterfit function of trans_env class for multiple groups
14. rename return data and optimize the code in trans_abund
15. rename trans_venn_com to trans_comm function in trans_venn class

microeco v0.7.5

1. add more parameters for ordination plotting in trans_env
2. optimize p value adjustment of correlation network
3. add Recall-precision plot in plot_ROC of trans_classifier
4. optimize FlashWeave network parameters input in trans_network
5. optimize network node roles plot
6. add tutorial wetsite hyperlink in the help document
7. add other_text_show and other parameter in plot_venn
8. add more checking blocks in microtable class
9. add more parameters in tidy_taxonomy function
10. add cal_preProcess function in trans_classifier
11. use get_node_table instead of cal_node_type and optimize the function
12. add network plotting with igraph and networkD3 package
13. add network method based on the beemStatic package
14. optimize cal_manova and use adonis2 instead of adonis
15. add more null models in trans_ses_betampd and trans_ses_betamntd

microeco v0.7.0

1. add trans_classifier class
2. add CCA method in trans_env class and rename functions associated with ordination.
3. optimize scaled-up methods and parameters in trans_ordination of trans_env class.
4. optimize the format of returned pathway files of cal_tax4fun2 in trans_func class.
5. optimize classes to accept null microtable object when created for external data analysis.
6. optimize text size adjustment parameters in plot_lefse_cladogram of trans_diff class
7. add taxa abundance filtering in trans_diff and trans_classifier object creating
8. add KW_dunn for Dunn's Kruskal-Wallis Multiple Comparisons in trans_alpha$cal_diff and trans_diff$new.
9. optimize KW method in trans_alpha$cal_diff and trans_diff$new.
10. add dendrogram option for clustering based on ggplot2 in plot_cor of trans_env class.
11. add colors instance
12. change use_OTUs_frequency to use_frequency in trans_venn_com function of trans_venn class.
13. fix the bug in trans_func$cal_tax4fun2_FRI()
14. fix the warnings in plot_lefse_cladogram of trans_diff class