adj                     Calculate the correlation adjacacency matrix.
adj,matrix,ANY-method   Calculate the adjacency matrix of 'norm' by
                        correlation with matrix as input.
adj,mina,ANY-method     Calculate the adjacency matrix of 'norm' by
                        correlation with 'mina' class object as input.
adj_method_list         List of adjacency matix calculation methods/
                        orrelations supported in 'adj'
bs_pm                   Inferring the network of different group of
                        samples and test significance by permutation.
bs_pm,mina,ANY-method   Inferring the network of different group of
                        samples and test significance by permutation.
check_mina              Check the tab and des file. Return TRUE if they
                        are NULL or both quantitative and descriptive
                        files of same samples are included (i.e. the
                        object is valid).
check_mina_de           Check the object and return TRUE if the object
                        includes descriptive table contains the same
                        samples as quantitative table.
check_mina_qu           Check the object and return TRUE if the object
                        includes quantitative table.
cls_tab                 Get the slot 'cls_tab'.
com_dis                 Calculate the community dissimilarity /
                        distance matrix.
com_dis,matrix,ANY-method
                        Calculate the community dissimilarity /
                        distance matrix of the input matrix.
com_dis,mina,ANY-method
                        Calculate the community dissimilarity /
                        distance matrix of 'norm' with 'mina' class
                        object as input.
com_dis_list            List of dissimilarity / distance supported in
                        'com_dis'. Dissimilarity / distance should be
                        specified by exact string match.
com_plot                Visulization of components distance /
                        dissimilarity in k dimension.
com_plot,mina,ANY-method
                        Visulization of components distance /
                        dissimilarity in k dimension.
com_r2                  Calculate the unexplained variance ratio using
                        formula indicated in: Anderson, M.J. 2001. A
                        new method for non-parametric multivariate
                        analysis of variance. Austral Ecology, 26:
                        32-46.
com_r2,mina,ANY-method
                        Function for unexplained variance ratio
                        calculation indicated in Anderson, M.J. 2001. A
                        new method for non-parametric multivariate
                        analysis of variance. Austral Ecology, 26:
                        32-46.
cp_cor                  Function for correlation coefficient
                        calculation.
data-hmp                Internal testing data of HMP project, including
                        quantitative table (hmp_otu) and descriptive
                        table (hmp_des) for testing.
data-maize              Internal testing data of maize project,
                        vegetative stage samples only, including
                        quantitative table (maize_asv.rds) and
                        descriptive table (maize_des.txt) for testing.
des<-                   Setter and getter for the slot 'des', which is
                        the description and meta data of rows in 'tab'.
dis<-                   Setter and getter for the slot 'dis'.
dis_bs                  Getter for the slots 'dis_bs', 'dis_pm' and
                        'dis_stat'.
dmr                     Dimensionality reduction of community
                        dissimilarity / distance for visulization.
dmr,matrix-method       Dimensionality reduction of the distance
                        matrix.
dmr,mina-method         Dimensionality reduction of the 'dis' included
                        in mina.
fit_tabs                Filter the quantitative and descriptive table
                        to make them have the same samples, the
                        intersect samples will be remained.
fit_tabs,mina-method    Filter the quantitative and descriptive table
                        to make them have the same samples, samples
                        present in both tables are remained. If 'norm'
                        table exist in the 'mina' object, descriptive
                        table will be filtered again to only keep
                        samples present in 'norm'.
get_net_cls_tab         Get the cluster table 'cls_tab' from
                        quantitative table 'norm' and network
                        clustering results 'cls'.
get_net_cls_tab,matrix,data.frame-method
                        Get the cluster table 'cls_tab' from
                        quantitative table 'norm' and network
                        clustering results 'cls'.
get_r2                  Same function as 'com_r2' with matrix and
                        corresponding descriptive table as input.
get_r2,matrix,ANY,ANY-method
                        Function for unexplained variance ratio
                        calculation indicated in Anderson, M.J. 2001. A
                        new method for non-parametric multivariate
                        analysis of variance. Austral Ecology, 26:
                        32-46.
get_rep                 Get the representative community members by
                        extracting the most abundant and prevalent
                        compositions.
get_rep,mina-method     Get the representative community members.
hmp_des                 Design file for HMP project, including 2711
                        samples in total.
hmp_otu                 OTU table of HMP project, data downloaded from
                        https://www.hmpdacc.org/hmp/HMQCP/
maize_asv               ASV table of maize project, vegetative stage
                        samples only.
maize_asv2              Subset of ASV table of maize project, ASVs
                        appear in less than 100 samples were filtered
                        for later analysis.
maize_des               Design file of maize project, vegetative stage
                        samples only, including 528 samples in total.
maize_des2              Subset of design file of maize project, 313
                        samples are included.
mina-class              Class "mina" includes the quantitative table
                        and descriptive table.
net_cls                 Network clustering of sparsed adjacacency
                        matrix.
net_cls,matrix,ANY-method
                        Network clustering based on the sparsed
                        adjacacency matrix.
net_cls,mina,ANY-method
                        Network clustering based on the sparsed
                        adjacacency matrix.
net_cls_tab             Get the cluster table 'cls_tab' from 'norm' and
                        'cls'.
net_cls_tab,mina-method
                        Get the cluster table 'cls_tab' from
                        quantitative table 'norm' and network
                        clustering results 'cls'.
net_dis                 Calculate the network distance of 'multi' and
                        test the significance when 'perm' is defined.
net_dis,mina,ANY-method
                        Calculate the network distance of 'multi' and
                        test the significance when 'perm' is defined.
net_dis_indi            Calculate the network distance of bootstrap and
                        permutation when appliable.
net_dis_pcoa            Visulization of spectra network distance as
                        PCoA.
net_dis_plot            Visulization of network distance, average
                        distances are used for tile plot.
net_grp_cmp             Compare the group features between networks.
net_node_cmp            Compare the node features between networks.
norm<-                  Setter and getters for the slot 'norm',
                        normalized 'tab' matrix.
norm_tab                Normalize the slot 'tab' for later analysis.
norm_tab,matrix,character-method
                        Normalize the quantitative matrix.
norm_tab,mina,ANY-method
                        Normalize the quantitative table with mina
                        input.
norm_tab_method_list    List of normalization methods supported in
                        'norm_tab'
pcoa_plot               Visulization of components distance /
                        dissimilarity in k dimension.
tab<-                   Setter and getter for the slot 'tab'.
tina                    TINA community dissimilarity used in 'com_dis'.
                        Function for 'tina' dissimilarity/distance
                        calculation. Modified from Schmidt et al.,
                        2016.
tina,matrix-method      Function for 'tina' dissimilarity calculation.
                        Modified from Schmidt et al., 2016. Person and
                        Spearman could be used for correlation and
                        weighted and unweighted Jaccard could be used
                        for similarity calculation.
