| adj | Calculate the correlation adjacacency matrix. |
| adj_accessor | Setter for the slot 'adj' and 'adj_sig', the adjacency matrix... |
| adj-matrix | Calculate the adjacency matrix of 'norm' by correlation with... |
| adj_method_list | List of adjacency matix calculation methods/ orrelations... |
| adj-mina | Calculate the adjacency matrix of 'norm' by correlation with... |
| bs_pm | Inferring the network of different group of samples and test... |
| bs_pm_accessor | Setter and getter for the slot 'multi' and 'perm'. |
| bs_pm-mina | Inferring the network of different group of samples and test... |
| check_mina | Check the tab and des file. Return TRUE if they are NULL or... |
| check_mina_de | Check the object and return TRUE if the object includes... |
| check_mina_qu | Check the object and return TRUE if the object includes... |
| cls | Get the slot 'cls'. |
| cls_accessor | Setter for the slot 'cls'. |
| cls_tab | Get the slot 'cls_tab'. |
| cls_tab_accessor | Setter for the slot 'cls_tab'. |
| com_dis | Calculate the community dissimilarity / distance matrix. |
| com_dis_list | List of dissimilarity / distance supported in 'com_dis'.... |
| com_dis-matrix | Calculate the community dissimilarity / distance matrix of... |
| com_dis-mina | Calculate the community dissimilarity / distance matrix of... |
| com_plot | Visulization of components distance / dissimilarity in k... |
| com_plot-mina | Visulization of components distance / dissimilarity in k... |
| com_r2 | Calculate the unexplained variance ratio using formula... |
| com_r2-mina | Function for unexplained variance ratio calculation indicated... |
| cp_cor | Function for correlation coefficient calculation. |
| data-hmp | Internal testing data of HMP project, including quantitative... |
| data-maize | Internal testing data of maize project, vegetative stage... |
| des_accessor | Setter and getter for the slot 'des', which is the... |
| dis_accessor | Setter and getter for the slot 'dis'. |
| dis_stat_accessor | Getter for the slots 'dis_bs', 'dis_pm' and 'dis_stat'. |
| dmr | Dimensionality reduction of community dissimilarity /... |
| dmr_accessor | Setter and getter for the slot 'dmr'. |
| dmr-matrix | Dimensionality reduction of the distance matrix. |
| dmr-mina | Dimensionality reduction of the 'dis' included in mina. |
| filter_mat | Function for filtering of matrix, rows present in less than... |
| fit_tabs | Filter the quantitative and descriptive table to make them... |
| fit_tabs-mina | Filter the quantitative and descriptive table to make them... |
| get_contrast | Get the contrast between two networks / adjacency matrices. |
| get_contrast_grp | Get the contrast of groups of nodes between two... |
| get_dis_df | Function for getting distance data frame from 'dist'. |
| get_ja | Get the Jaccard distance between two networks / adjacency... |
| get_ja0 | Get the Jaccard0 distance between two networks / adjacency... |
| get_ja0_grp | Get the Jaccard0 distance between two networks / adjacency... |
| get_ja_grp | Get the Jaccard distance between two networks / adjacency... |
| get_net_cls_tab | Get the cluster table 'cls_tab' from quantitative table... |
| get_net_cls_tab-matrix-data.frame-method | Get the cluster table 'cls_tab' from quantitative table... |
| get_r2 | Same function as 'com_r2' with matrix and corresponding... |
| get_r2-mat | Function for unexplained variance ratio calculation indicated... |
| get_rep-matrix | Get the representative community members by extracting the... |
| get_rep-mima | Get the representative community members. |
| get_spectra | Function for calculation of eigenvalue of given matrix. |
| get_stat | Function for distance statistic and significance test. |
| hmp_des | Design file for HMP project, including 2711 samples in total. |
| hmp_otu | OTU table of HMP project, data downloaded from... |
| maize_asv | ASV table of maize project, vegetative stage samples only. |
| maize_asv2 | Subset of ASV table of maize project, ASVs appear in less... |
| maize_des | Design file of maize project, vegetative stage samples only,... |
| maize_des2 | Subset of design file of maize project, 313 samples are... |
| mat_or_NULL-class | Modified from... |
| mina-class | Class "mina" includes the quantitative table and descriptive... |
| net_cls | Network clustering of sparsed adjacacency matrix. |
| net_cls-matrix | Network clustering based on the sparsed adjacacency matrix. |
| net_cls-mina | 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... |
| net_dis | Calculate the network distance of 'multi' and test the... |
| net_dis_accessor | Setter for the slots 'dis_bs', 'dis_pm' and 'dis_stat'. |
| net_dis_indi | Calculate the network distance of bootstrap and permutation... |
| net_dis-mina | Calculate the network distance of 'multi' and test the... |
| net_dis_pcoa | Visulization of spectra network distance as PCoA. |
| net_dis_plot | Visulization of network distance, average distances are used... |
| net_grp_cmp | Compare the group features between networks. |
| net_node_cmp | Compare the node features between networks. |
| norm_accessor | Setter and getters for the slot 'norm', normalized 'tab'... |
| norm_by_raref | Function for normalization by rarefying the samples into the... |
| norm_by_total | Function for normalization, by total number of the reads in... |
| norm_tab | Normalize the slot 'tab' for later analysis. |
| norm_tab-matrix | Normalize the quantitative matrix. |
| norm_tab_method_list | List of normalization methods supported in 'norm_tab' |
| norm_tab-mina | Normalize the quantitative table with mina input. |
| pcoa_plot | Visulization of components distance / dissimilarity in k... |
| rarefaction_subsample | Rarefaction subsample function, one sample, modified from a... |
| re_format_AP | Convert APResult (apcluster output) to dataframe. |
| re_format_MCL | Convert mcl (mcl output) to dataframe. |
| sim_par | Function for community similarity calculation used by 'tina',... |
| sparcc | Function for 'sparcc' correlation calculation. Modified from... |
| tab_accessor | Setter and getter for the slot 'tab'. |
| tina | TINA community dissimilarity used in 'com_dis'. Function for... |
| tina-matrix-method | Function for 'tina' dissimilarity calculation. Modified from... |
