Package: easynem 1.0.3

easynem: Nematode Community Analysis

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>.

Authors:Wang Kunguang [aut, cre]

easynem_1.0.3.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
easynem/json (API)

# Install 'easynem' in R:
install.packages('easynem', repos = c('https://whkygl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/whkygl/easynem/issues

Datasets:
  • nemmeta - Experimental Design of Kiwifruit Cover Crops
  • nemtab - Table of soil nematode abundance in kiwifruit orchards
  • nemtax - Nematode taxonomy table

On CRAN:

Conda:

4.66 score 4 stars 76 scripts 217 downloads 43 exports 142 dependencies

Last updated from:e0c5215144. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK223
source / vignettesOK286
linux-release-x86_64OK260
macos-release-arm64OK263
macos-oldrel-arm64OK187
windows-develOK181
windows-releaseOK139
windows-oldrelOK163
wasm-releaseOK151

Exports:calc_alphacalc_betacalc_beta2calc_comparecalc_compare2calc_efcalc_ef2calc_funguildcalc_funguild2calc_lmcalc_lm2calc_mfcalc_mf2calc_nemindexcalc_tercalc_ter2easynem_examplefilter_namefilter_numgeom_encircleHSDHSD2KruskalTestKruskalTest2LSDLSD2nem_calcnem_databasenem_plotnem_transorder_factorread_nemread_nem2trans_combinetrans_formulatrans_formula_vtrans_nametrans_normtrans_rareTTestTTest2WilcoxTestWilcoxTest2

Dependencies:abindagricolaeAlgDesignbackportsbase64encbitbit64bootbroombslibcachemcarcarDataclicliprclueclustercolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkDerivdigestdoBydplyrDTevaluatefarverfastmapfontawesomeforecastFormulafracdifffsgenericsggforceggplot2ggpubrggraphggrepelggsciggsignifgluegraphlayoutsgridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvigraphisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewnlmenloptrnnetnumDerivotelpbkrtestpermutepillarpkgconfigPlotToolsplyrpolyclippolynomprettyunitsprogresspromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasreshape2rlangrmarkdownrstatixS7sassscalesshinyshinydashboardsourcetoolsspSparseMstringistringrsurvivalsystemfontsTernarytibbletidygraphtidyrtidyselecttimeDatetinytextweenrtzdburcautf8vctrsveganviridisviridisLitevroomwithrxfunxtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Class for storing alpha diversity calculation resultsalpha-class
A class to store beta diversity results (single factor)beta-class
A class to store beta diversity results (two-factor)beta2-class
Alpha diversity analysis, generating alpha-classcalc_alpha
Beta diversity analysis, generating beta-class (single factor)calc_beta
Beta diversity analysis, generating beta2-class (two-factor)calc_beta2
Multiple comparisons between treatments (single factor)calc_compare
Multiple comparisons between treatments (two-factor)calc_compare2
Calculation of energy flow in nematode communities (single factor)calc_ef
Calculation of energy flow in nematode communities (two-factor)calc_ef2
Nematode food web analysis (single factor)calc_funguild
Nematode food web analysis (two-factor)calc_funguild2
Linear regression analysis of easynem-class (single factor)calc_lm
Linear regression analysis of easynem-class (two-factor)calc_lm2
Calculating the metabolic footprint of nematodes (single factor)calc_mf
Calculating the metabolic footprint of nematodes (two-factor)calc_mf2
Calculate multiple nematode ecological indices and generate nemindex classcalc_nemindex
Trivariate analysis of nematode feeding or cp value (single factor)calc_ter
Trivariate analysis of nematode feeding or cp value (two-factor)calc_ter2
A S4 class to store multiple comparisons results (single factor).compare-class
A S4 class to store multiple comparisons results (two-factor).compare2-class
Path to example fileseasynem_example
The main experiment-level class for easynem dataeasynem-class
A S4 class to store energy flow results (single factor)ef-class
A S4 class to store energy flow results (two-factor)ef2-class
Filter easynem by column name and keep rows that match a conditionfilter_name
Filter easynem's tab by discovery rate or abundancefilter_num
Class for storing computational results of nematode functional guild analysis (single factor)funguild-class
Class for storing computational results of nematode functional guild analysis (two-factor)funguild2-class
Automatically enclose points in a polygongeom_encircle
Compute Tukey Honest Significant Differences (single factor)HSD
Compute Tukey Honest Significant Differences (two-factor)HSD2
Perform Kruskal-Wallis test on easynem meta-table by treatment (single factor)KruskalTest
Perform Kruskal-Wallis test on easynem meta-table by treatment (two-factor)KruskalTest2
A S4 class to store the linear regression analysis results (single factor)lme-class
A S4 class to store the linear regression analysis results (two-factor)lme2-class
Multiple comparisons, "Least significant difference" and Adjust P-values (single factor)LSD
Multiple comparisons, "Least significant difference" and Adjust P-values (two-factor)LSD2
A S4 class to store Metabolic footprints results (single factor)mf-class
A S4 class to store Metabolic footprints results (two-factor)mf2-class
calcnem_calc
Nematode database searchnem_database
Visualize the results of the calculationnem_plot
Visualization of beta diversity results (single factor)nem_plot,beta-method
Visualization of beta diversity results (two-factor)nem_plot,beta2-method
Visualizing the results of multiple comparisons (single factor)nem_plot,compare-method
Visualizing the results of multiple comparisons (two-factor)nem_plot,compare2-method
Visualizing the energy structure of nematode communities (single factor)nem_plot,ef-method
Visualizing the energy structure of nematode communities (two-factor)nem_plot,ef2-method
Visualizing nematode functional guild data (single factor)nem_plot,funguild-method
Visualizing nematode functional guild data (two-factor)nem_plot,funguild2-method
Visualizing the results of linear regression (single factor)nem_plot,lme-method
Visualizing the results of linear regression (two-factor)nem_plot,lme2-method
Visualizing the metabolic footprint of nematode communities (single factor)nem_plot,mf-method
Visualizing the metabolic footprint of nematode communities (two-factor)nem_plot,mf2-method
Visualizing the results of the ternary analysis (single factor)nem_plot,ter-method
Visualizing the results of the ternary analysis (two-factor)nem_plot,ter2-method
nem_transnem_trans
Class for storing nematode ecological index calculation resultsnemindex-class
Experimental Design of Kiwifruit Cover Cropsnemmeta
Table of soil nematode abundance in kiwifruit orchardsnemtab
Nematode taxonomy tablenemtax
order_factororder_factor
Build easynem-class objects from their csv fileread_nem
Build easynem-class objects from their tibble type objectread_nem2
A S4 class to store the ternary analysis results (single factor)ter-class
A S4 class to store the ternary analysis results (two-factor)ter2-class
Merge multiple columns of easynem's metatrans_combine
Formula conversion for easynem's metatrans_formula
Formula conversion for easynem's meta (Vectorization)trans_formula_v
Reorganize the easynem's tab by taxonomic nametrans_name
Normalizing the nematode abundance tabletrans_norm
Randomly rarefied OTU or ASV tables of nematodes for amplicon sequencing datatrans_rare
Perform t-test on easynem meta-table by treatment (single factor)TTest
Perform t-test on easynem meta-table by treatment (two-factor)TTest2
Perform wilcoxon-test on easynem meta-table by treatment (single factor)WilcoxTest
Perform wilcoxon-test on easynem meta-table by treatment (two-factor)WilcoxTest2