# Nematode Community Analysis

## Documentation for package ‘easynem’ version 1.0.3

- DESCRIPTION file.

## Help Pages

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)