HSD                     Compute Tukey Honest Significant Differences
                        (single factor)
HSD2                    Compute Tukey Honest Significant Differences
                        (two-factor)
KruskalTest             Perform Kruskal-Wallis test on easynem
                        meta-table by treatment (single factor)
KruskalTest2            Perform Kruskal-Wallis test on easynem
                        meta-table by treatment (two-factor)
LSD                     Multiple comparisons, "Least significant
                        difference" and Adjust P-values (single factor)
LSD2                    Multiple comparisons, "Least significant
                        difference" and Adjust P-values (two-factor)
TTest                   Perform t-test on easynem meta-table by
                        treatment (single factor)
TTest2                  Perform t-test on easynem meta-table by
                        treatment (two-factor)
WilcoxTest              Perform wilcoxon-test on easynem meta-table by
                        treatment (single factor)
WilcoxTest2             Perform wilcoxon-test on easynem meta-table by
                        treatment (two-factor)
alpha-class             Class for storing alpha diversity calculation
                        results
beta-class              A class to store beta diversity results (single
                        factor)
beta2-class             A class to store beta diversity results
                        (two-factor)
calc_alpha              Alpha diversity analysis, generating
                        alpha-class
calc_beta               Beta diversity analysis, generating beta-class
                        (single factor)
calc_beta2              Beta diversity analysis, generating beta2-class
                        (two-factor)
calc_compare            Multiple comparisons between treatments (single
                        factor)
calc_compare2           Multiple comparisons between treatments
                        (two-factor)
calc_ef                 Calculation of energy flow in nematode
                        communities (single factor)
calc_ef2                Calculation of energy flow in nematode
                        communities (two-factor)
calc_funguild           Nematode food web analysis (single factor)
calc_funguild2          Nematode food web analysis (two-factor)
calc_lm                 Linear regression analysis of easynem-class
                        (single factor)
calc_lm2                Linear regression analysis of easynem-class
                        (two-factor)
calc_mf                 Calculating the metabolic footprint of
                        nematodes (single factor)
calc_mf2                Calculating the metabolic footprint of
                        nematodes (two-factor)
calc_nemindex           Calculate multiple nematode ecological indices
                        and generate nemindex class
calc_ter                Trivariate analysis of nematode feeding or cp
                        value (single factor)
calc_ter2               Trivariate analysis of nematode feeding or cp
                        value (two-factor)
compare-class           A S4 class to store multiple comparisons
                        results (single factor).
compare2-class          A S4 class to store multiple comparisons
                        results (two-factor).
easynem-class           The main experiment-level class for easynem
                        data
easynem_example         Path to example files
ef-class                A S4 class to store energy flow results (single
                        factor)
ef2-class               A S4 class to store energy flow results
                        (two-factor)
filter_name             Filter easynem by column name and keep rows
                        that match a condition
filter_num              Filter easynem's tab by discovery rate or
                        abundance
funguild-class          Class for storing computational results of
                        nematode functional guild analysis (single
                        factor)
funguild2-class         Class for storing computational results of
                        nematode functional guild analysis (two-factor)
geom_encircle           Automatically enclose points in a polygon
lme-class               A S4 class to store the linear regression
                        analysis results (single factor)
lme2-class              A S4 class to store the linear regression
                        analysis results (two-factor)
mf-class                A S4 class to store Metabolic footprints
                        results (single factor)
mf2-class               A S4 class to store Metabolic footprints
                        results (two-factor)
nem_calc                calc
nem_database            Nematode database search
nem_plot                Visualize the results of the calculation
nem_plot,beta-method    Visualization of beta diversity results (single
                        factor)
nem_plot,beta2-method   Visualization of beta diversity results
                        (two-factor)
nem_plot,compare-method
                        Visualizing the results of multiple comparisons
                        (single factor)
nem_plot,compare2-method
                        Visualizing the results of multiple comparisons
                        (two-factor)
nem_plot,ef-method      Visualizing the energy structure of nematode
                        communities (single factor)
nem_plot,ef2-method     Visualizing the energy structure of nematode
                        communities (two-factor)
nem_plot,funguild-method
                        Visualizing nematode functional guild data
                        (single factor)
nem_plot,funguild2-method
                        Visualizing nematode functional guild data
                        (two-factor)
nem_plot,lme-method     Visualizing the results of linear regression
                        (single factor)
nem_plot,lme2-method    Visualizing the results of linear regression
                        (two-factor)
nem_plot,mf-method      Visualizing the metabolic footprint of nematode
                        communities (single factor)
nem_plot,mf2-method     Visualizing the metabolic footprint of nematode
                        communities (two-factor)
nem_plot,ter-method     Visualizing the results of the ternary analysis
                        (single factor)
nem_plot,ter2-method    Visualizing the results of the ternary analysis
                        (two-factor)
nem_trans               nem_trans
nemindex-class          Class for storing nematode ecological index
                        calculation results
nemmeta                 Experimental Design of Kiwifruit Cover Crops
nemtab                  Table of soil nematode abundance in kiwifruit
                        orchards
nemtax                  Nematode taxonomy table
order_factor            order_factor
read_nem                Build easynem-class objects from their csv file
read_nem2               Build easynem-class objects from their tibble
                        type object
ter-class               A S4 class to store the ternary analysis
                        results (single factor)
ter2-class              A S4 class to store the ternary analysis
                        results (two-factor)
trans_combine           Merge multiple columns of easynem's meta
trans_formula           Formula conversion for easynem's meta
trans_formula_v         Formula conversion for easynem's meta
                        (Vectorization)
trans_name              Reorganize the easynem's tab by taxonomic name
trans_norm              Normalizing the nematode abundance table
trans_rare              Randomly rarefied OTU or ASV tables of
                        nematodes for amplicon sequencing data
