| alpha-class | Class for storing alpha diversity calculation results |
| beta2-class | A class to store beta diversity results (two-factor) |
| beta-class | A class to store beta diversity results (single factor) |
| calc_alpha | Alpha diversity analysis, generating alpha-class |
| calc_beta | Beta diversity analysis, generating beta-class (single... |
| 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... |
| calc_ef2 | Calculation of energy flow in nematode communities... |
| 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... |
| calc_mf2 | Calculating the metabolic footprint of nematodes (two-factor) |
| calc_nemindex | Calculate multiple nematode ecological indices and generate... |
| calc_ter | Trivariate analysis of nematode feeding or cp value (single... |
| calc_ter2 | Trivariate analysis of nematode feeding or cp value... |
| compare2-class | A S4 class to store multiple comparisons results... |
| compare-class | A S4 class to store multiple comparisons results (single... |
| easynem-class | The main experiment-level class for easynem data |
| easynem_example | Path to example files |
| ef2-class | A S4 class to store energy flow results (two-factor) |
| ef-class | A S4 class to store energy flow results (single factor) |
| filter_name | Filter easynem by column name and keep rows that match a... |
| filter_num | Filter easynem's tab by discovery rate or abundance |
| funguild2-class | Class for storing computational results of nematode... |
| funguild-class | Class for storing computational results of nematode... |
| geom_encircle | Automatically enclose points in a polygon |
| 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... |
| KruskalTest2 | Perform Kruskal-Wallis test on easynem meta-table by... |
| lme2-class | A S4 class to store the linear regression analysis results... |
| lme-class | A S4 class to store the linear regression analysis results... |
| LSD | Multiple comparisons, "Least significant difference" and... |
| LSD2 | Multiple comparisons, "Least significant difference" and... |
| mf2-class | A S4 class to store Metabolic footprints results (two-factor) |
| mf-class | A S4 class to store Metabolic footprints results (single... |
| nem_calc | calc |
| nem_database | Nematode database search |
| nemindex-class | Class for storing nematode ecological index calculation... |
| nemmeta | Experimental Design of Kiwifruit Cover Crops |
| nem_plot | Visualize the results of the calculation |
| nem_plot-beta2-method | Visualization of beta diversity results (two-factor) |
| nem_plot-beta-method | Visualization of beta diversity results (single factor) |
| nem_plot-compare2-method | Visualizing the results of multiple comparisons (two-factor) |
| nem_plot-compare-method | Visualizing the results of multiple comparisons (single... |
| nem_plot-ef2-method | Visualizing the energy structure of nematode communities... |
| nem_plot-ef-method | Visualizing the energy structure of nematode communities... |
| nem_plot-funguild2-method | Visualizing nematode functional guild data (two-factor) |
| nem_plot-funguild-method | Visualizing nematode functional guild data (single factor) |
| nem_plot-lme2-method | Visualizing the results of linear regression (two-factor) |
| nem_plot-lme-method | Visualizing the results of linear regression (single factor) |
| nem_plot-mf2-method | Visualizing the metabolic footprint of nematode communities... |
| nem_plot-mf-method | Visualizing the metabolic footprint of nematode communities... |
| nem_plot-ter2-method | Visualizing the results of the ternary analysis (two-factor) |
| nem_plot-ter-method | Visualizing the results of the ternary analysis (single... |
| nemtab | Table of soil nematode abundance in kiwifruit orchards |
| nemtax | Nematode taxonomy table |
| nem_trans | nem_trans |
| 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 |
| ter2-class | A S4 class to store the ternary analysis results (two-factor) |
| ter-class | A S4 class to store the ternary analysis results (single... |
| 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... |
| TTest | Perform t-test on easynem meta-table by treatment (single... |
| TTest2 | Perform t-test on easynem meta-table by treatment... |
| WilcoxTest | Perform wilcoxon-test on easynem meta-table by treatment... |
| WilcoxTest2 | Perform wilcoxon-test on easynem meta-table by treatment... |
