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
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soilfoodwebs_1.0.2.tgz(r-4.4-any)soilfoodwebs_1.0.2.tgz(r-4.3-any)
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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'))

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:

24 exports 4 stars 1.10 score 14 dependencies 4 scripts 203 downloads

Last updated 5 months agofrom:90414e71f4. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 27 2024
R-4.5-win	OK	Aug 27 2024
R-4.5-linux	OK	Aug 27 2024
R-4.4-win	OK	Aug 27 2024
R-4.4-mac	OK	Aug 27 2024
R-4.3-win	OK	Aug 27 2024
R-4.3-mac	OK	Aug 27 2024

Exports:Aijfcn build_foodweb calc_smin calculate_inputs can_mutfeed checkcomm checkeqm Cijfcn CNsim comana comtrosp corrstoich decompexpt getPARAMS Jacobsindex newnode parameter_uncertainty removenodes renamenode stability stability2 TLcheddar TLsort whomineralizes

Dependencies:cli deSolve diagram glue lifecycle lpSolve magrittr quadprog rlang rootSolve shape stringi stringr vctrs

soilfoodweb_vignette

Robert W. Buchkowski

Rendered fromsoilfoodweb_vignette.Rmdusingknitr::rmarkdownon Aug 27 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A function to calculate the nitrogen surplus or deficit each species gets from consuming another species	Aijfcn
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 inputs	build_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 function	calculate_smin
A function that identifies cannibalism and mutual feeding	can_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 foodwebode	CNsim
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 dynamically	correction_function
Correct stoichiometry	corrstoich
Decomposition rates and effect of individual organisms	decompexpt
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 CPER	Hunt1987
A baseline community for examples	intro_comm
Calculate Jacob's index.	Jacobsindex
The soil food web published for an Arctic Tundra site	Koltz2018
Add node to the community	newnode
Parameter uncertainty returns community with new parameters drawn from a distribution of choice	parameter_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 web	stability
A function to run the stability analysis using the numerical simulation of the Jacobain matrix.	stability2
Calculates the trophic level for each tropospecies	TLcheddar
Sorts the trophic levels from lowest to highest	TLsort
Direct and indirect contributions to mineralizations	whomineralizes