| 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 |
| 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) |
| 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) |
| LSD |
Multiple comparisons, "Least significant difference" and Adjust P-values (single factor) |
| LSD2 |
Multiple comparisons, "Least significant difference" and Adjust P-values (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) |
| 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 |
| nem_calc |
calc |
| nem_database |
Nematode database search |
| nem_plot |
Visualize the results of the calculation |
| nem_plot-method |
Visualization of beta diversity results (single factor) |
| nem_plot-method |
Visualization of beta diversity results (two-factor) |
| nem_plot-method |
Visualizing the results of multiple comparisons (single factor) |
| nem_plot-method |
Visualizing the results of multiple comparisons (two-factor) |
| nem_plot-method |
Visualizing the energy structure of nematode communities (single factor) |
| nem_plot-method |
Visualizing the energy structure of nematode communities (two-factor) |
| nem_plot-method |
Visualizing nematode functional guild data (single factor) |
| nem_plot-method |
Visualizing nematode functional guild data (two-factor) |
| nem_plot-method |
Visualizing the results of linear regression (single factor) |
| nem_plot-method |
Visualizing the results of linear regression (two-factor) |
| nem_plot-method |
Visualizing the metabolic footprint of nematode communities (single factor) |
| nem_plot-method |
Visualizing the metabolic footprint of nematode communities (two-factor) |
| nem_plot-method |
Visualizing the results of the ternary analysis (single factor) |
| nem_plot-method |
Visualizing the results of the ternary analysis (two-factor) |
| 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 |
| 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 |
| 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) |
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