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

microeco v1.7.0

• add cal_caretList function in trans_classifier
• add lm and glmm method for cal_diff in trans_env
• add edgeR method in trans_diff
• update FAPROTAX to v1.2.7
• add ytext_size parameter in plot_cor of trans_env
• restructure rarefy function in microtable and trans_norm
• add rarefy, eBay, deseq2 and wrench method in trans_norm
• add Significance label for all methods in trans_alpha
• extend by_group for anova formula usage in trans_alpha
• bar_full instead of bar_type param in plot_bar of trans_abund
• show all eigens in results of cal_ordination of trans_beta
• add abundance checking and calculation in trans_classifier
• set same yaxis range for by_group in plot of trans_alpha
• fix factor issue for paired comparison in trans_diff
• fix group error in lme method of cal_diff in trans_env
• fix metagenomeseq Group issue in trans_diff
• fix sample_table one column subsetting issue in trans_diff
• set factor for group and by_group in trans_alpha
• add detailed documentation for node_roles in trans_network
• fix rep_fasta load issue in new session
• fix delete_taxonomy_lineage message issue in trans_abund
• fix NA issue of COR method in trans_network

microeco v1.6.0

• add trans_norm class for data normalization and transformation
• add by_group param in cal_manova and cal_anosim of trans_beta class
• fix kw_dunn issue by space in groups for trans_alpha
• filter index with NaN in trans_alpha
• fix label issue in cal_sum_links of trans_network
• skip error indexes for non-interger data in cal_alphadiv of microtable
• fix colnames duplicate issue in plot of maaslin2 of trans_diff
• filter measure with same value for KW_dunn in trans_diff
• check NA and name matching for other_taxa in cal_cor of trans_env
• add formula for FR in cal_spe_func_perc function
• optimize DESeq2 method in trans_diff
• add reference for rc-bray in trans_nullmodel
• function stop if abund_table have very few features in plot_diff_cladogram
• Import ggplot2 >= 3.5.0

microeco v1.5.0

• optimize ancombc2 method usage in trans_diff class
• support both group and formula input for linda method in trans_diff class
• design two output formats for linda in trans_diff class
• add scale_species_ratio parameter in cal_ordination function of trans_beta class
• add loading arrow parameters for PCA in plot_ordination function of trans_beta class
• add lm method in trans_alpha and trans_diff class
• add messages for COR method in cal_network of trans_network class
• fix plot_feature_imp error in trans_classifier class
• add group parameter in cal_process of trans_nullmodel class
• fix the anova error in part of indexes with trycatch in trans_alpha class
• skip the environmental variable with only one value in trans_env class

microeco v1.4.0

• add DCA method in cal_ordination of trans_beta
• add glmm_beta option in method parameter of trans_diff
• add Pielou evenness index in cal_alphadiv function of microtable
• add heatmap for formula usage in plot_alpha of trans_alpha
• fix the ordination axis text issue in trans_env
• use Machine double.eps in pseudo count of trans_diff
• change sort_samples parameter to default FALSE in plot_bar of trans_venn
• fix tidy_taxonomy function match issue in pattern parameter
• add message for the trans_spe_func_perc func in trans_func class
• update the document of cal_alphadiv and cal_betadiv in microtable

microeco v1.3.0

• fix bug of direction in trans_ordination function of trans_env class
• add NMDS_stress_text_prefix parameter in plot_ordination function of trans_beta class
• add NMDS_stress_pos parameter in plot_ordination function of trans_beta class
• add modularity metric in cal_network_attr function of trans_network class
• add trans_spe_func_perc function in trans_func class
• force ggplot2 version >= 3.4.0
• fix text_y_order for multiple groups in plot_cor of trans_env