Nematode Community Analysis
Class for storing alpha diversity calculation results
A class to store beta diversity results (single factor)
A class to store beta diversity results (two-factor)
Alpha diversity analysis, generating alpha-class
Beta diversity analysis, generating beta-class (single factor)
Beta diversity analysis, generating beta2-class (two-factor)
Multiple comparisons between treatments (single factor)
Multiple comparisons between treatments (two-factor)
Calculation of energy flow in nematode communities (single factor)
Calculation of energy flow in nematode communities (two-factor)
Nematode food web analysis (single factor)
Nematode food web analysis (two-factor)
Linear regression analysis of easynem-class (single factor)
Linear regression analysis of easynem-class (two-factor)
Calculating the metabolic footprint of nematodes (single factor)
Calculating the metabolic footprint of nematodes (two-factor)
Calculate multiple nematode ecological indices and generate nemindex c...
Trivariate analysis of nematode feeding or cp value (single factor)
Trivariate analysis of nematode feeding or cp value (two-factor)
A S4 class to store multiple comparisons results (single factor).
A S4 class to store multiple comparisons results (two-factor).
Path to example files
The main experiment-level class for easynem data
A S4 class to store energy flow results (single factor)
A S4 class to store energy flow results (two-factor)
Filter easynem by column name and keep rows that match a condition
Filter easynem's tab by discovery rate or abundance
Class for storing computational results of nematode functional guild a...
Class for storing computational results of nematode functional guild a...
Automatically enclose points in a polygon
Compute Tukey Honest Significant Differences (single factor)
Compute Tukey Honest Significant Differences (two-factor)
Perform Kruskal-Wallis test on easynem meta-table by treatment (single...
Perform Kruskal-Wallis test on easynem meta-table by treatment (two-fa...
A S4 class to store the linear regression analysis results (single fac...
A S4 class to store the linear regression analysis results (two-factor...
Multiple comparisons, "Least significant difference" and Adjust P-valu...
Multiple comparisons, "Least significant difference" and Adjust P-valu...
A S4 class to store Metabolic footprints results (single factor)
A S4 class to store Metabolic footprints results (two-factor)
calc
Nematode database search
Visualization of beta diversity results (single factor)
Visualization of beta diversity results (two-factor)
Visualizing the results of multiple comparisons (single factor)
Visualizing the results of multiple comparisons (two-factor)
Visualizing the energy structure of nematode communities (single facto...
Visualizing the energy structure of nematode communities (two-factor)
Visualizing nematode functional guild data (single factor)
Visualizing nematode functional guild data (two-factor)
Visualizing the results of linear regression (single factor)
Visualizing the results of linear regression (two-factor)
Visualizing the metabolic footprint of nematode communities (single fa...
Visualizing the metabolic footprint of nematode communities (two-facto...
Visualizing the results of the ternary analysis (single factor)
Visualizing the results of the ternary analysis (two-factor)
Visualize the results of the calculation
nem_trans
Class for storing nematode ecological index calculation results
order_factor
Build easynem-class objects from their csv file
Build easynem-class objects from their tibble type object
A S4 class to store the ternary analysis results (single factor)
A S4 class to store the ternary analysis results (two-factor)
Merge multiple columns of easynem's meta
Formula conversion for easynem's meta (Vectorization)
Formula conversion for easynem's meta
Reorganize the easynem's tab by taxonomic name
Normalizing the nematode abundance table
Randomly rarefied OTU or ASV tables of nematodes for amplicon sequenci...
Perform t-test on easynem meta-table by treatment (single factor)
Perform t-test on easynem meta-table by treatment (two-factor)
Perform wilcoxon-test on easynem meta-table by treatment (single facto...
Perform wilcoxon-test on easynem meta-table by treatment (two-factor)
Provides a built-in Nemaplex database for nematodes, which can be used to search for various nematodes. Also supports various nematode community and functional analyses such as nematode diversity, maturity index, metabolic footprint, and functional guild. The methods are based on <https://shiny.wur.nl/ninja/>, Bongers, T. (1990) <doi:10.1007/BF00324627>, Ferris, H. (2010) <doi:10.1016/j.ejsobi.2010.01.003>, Wan, B. et al. (2022) <doi:10.1016/j.soilbio.2022.108695>, and Van Den Hoogen, J. et al. (2019) <doi:10.1038/s41586-019-1418-6>.