Package: soilfoodwebs 1.0.2

soilfoodwebs: Soil Food Web Analysis

Analyzing soil food webs or any food web measured at equilibrium. The package calculates carbon and nitrogen fluxes and stability properties using methods described by Hunt et al. (1987) <doi:10.1007/BF00260580>, de Ruiter et al. (1995) <doi:10.1126/science.269.5228.1257>, Holtkamp et al. (2011) <doi:10.1016/j.soilbio.2010.10.004>, and Buchkowski and Lindo (2021) <doi:10.1111/1365-2435.13706>. The package can also manipulate the structure of the food web as well as simulate food webs away from equilibrium and run decomposition experiments.

Authors:Robert Buchkowski [aut, cre, cph], Zoë Lindo [aut], Carlos Barreto [aut]

soilfoodwebs_1.0.2.tar.gz
soilfoodwebs_1.0.2.zip(r-4.5)soilfoodwebs_1.0.2.zip(r-4.4)soilfoodwebs_1.0.2.zip(r-4.3)
soilfoodwebs_1.0.2.tgz(r-4.4-any)soilfoodwebs_1.0.2.tgz(r-4.3-any)
soilfoodwebs_1.0.2.tar.gz(r-4.5-noble)soilfoodwebs_1.0.2.tar.gz(r-4.4-noble)
soilfoodwebs_1.0.2.tgz(r-4.4-emscripten)soilfoodwebs_1.0.2.tgz(r-4.3-emscripten)
soilfoodwebs.pdf |soilfoodwebs.html✨
soilfoodwebs/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/robertwbuchkowski/soilfoodwebs/issues

Datasets:
  • Andres2016 - The soil food webs published for grazed and ungrazed plots in the Shortgrass Steppe long-term research station.
  • Holtkamp2011 - The soil food webs published along a chronosequence in the Netherlands.
  • Hunt1987 - The soil food web published for CPER
  • Koltz2018 - The soil food web published for an Arctic Tundra site
  • deRuiter1994 - The soil food webs published for conventional (CON) and integrated (INT) management at Lovinkhoeve experimental farm.
  • intro_comm - A baseline community for examples

On CRAN:

4.30 score 4 stars 4 scripts 160 downloads 24 exports 14 dependencies

Last updated 7 months agofrom:90414e71f4. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-winOKOct 26 2024
R-4.5-linuxOKOct 26 2024
R-4.4-winOKOct 26 2024
R-4.4-macOKOct 26 2024
R-4.3-winOKOct 26 2024
R-4.3-macOKOct 26 2024

Exports:Aijfcnbuild_foodwebcalc_smincalculate_inputscan_mutfeedcheckcommcheckeqmCijfcnCNsimcomanacomtrospcorrstoichdecompexptgetPARAMSJacobsindexnewnodeparameter_uncertaintyremovenodesrenamenodestabilitystability2TLcheddarTLsortwhomineralizes

Dependencies:clideSolvediagramgluelifecyclelpSolvemagrittrquadprogrlangrootSolveshapestringistringrvctrs

soilfoodweb_vignette

Robert W. Buchkowski

Rendered fromsoilfoodweb_vignette.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-05-09
Started: 2021-08-09

Readme and manuals

Help Manual

Help pageTopics
A function to calculate the nitrogen surplus or deficit each species gets from consuming another speciesAijfcn
The soil food webs published for grazed and ungrazed plots in the Shortgrass Steppe long-term research station.Andres2016
A function to compile the food web from simple data inputsbuild_foodweb
Calculate the strength of stability as smin.calc_smin
A function to calculate the inputs and outputs at equilibrium and print them for the user.calculate_inputs
Function used inside the calc_smin functioncalculate_smin
A function that identifies cannibalism and mutual feedingcan_mutfeed
A function check the community for errors before it is used in calculations.checkcomm
Check the carbon flux equilibrium output by comana.checkeqm
A utility function to calculate the consumption rate of each species on all prey assuming a type I functional response.Cijfcn
A function to simulate the dynamics over time wrapping getPARAMS and foodwebodeCNsim
A function to calculate carbon and nitrogen fluxes in the food web.comana
A function to combine trophic species.comtrosp
A function to correct the diet of trophic species.correct_diet
A function to correct stoichiometry dynamicallycorrection_function
Correct stoichiometrycorrstoich
Decomposition rates and effect of individual organismsdecompexpt
The soil food webs published for conventional (CON) and integrated (INT) management at Lovinkhoeve experimental farm.deRuiter1994
A function to simulation the food webs away from equilibrium.foodwebode
A function to get the parameters for a food web model.getPARAMS
The soil food webs published along a chronosequence in the Netherlands.Holtkamp2011
The soil food web published for CPERHunt1987
A baseline community for examplesintro_comm
Calculate Jacob's index.Jacobsindex
The soil food web published for an Arctic Tundra siteKoltz2018
Add node to the communitynewnode
Parameter uncertainty returns community with new parameters drawn from a distribution of choiceparameter_uncertainty
A function to fix production efficiency.productionadj
Remove nodes from community.removenodes
Rename a node in a community.renamenode
A function to rescale a vector.RESCALE
Calculates the stability of the food webstability
A function to run the stability analysis using the numerical simulation of the Jacobain matrix.stability2
Calculates the trophic level for each tropospeciesTLcheddar
Sorts the trophic levels from lowest to highestTLsort
Direct and indirect contributions to mineralizationswhomineralizes