DOI: 10.6084/m9.figshare.3568332.v1
title: Supplement 2. R code and associated source files used to generate parameters and conduct simulations based on real ecological data sets.

description: File List All Files at Once: Supplement_2.zip (MD5: b3572e87400306d7b0543dffda7edbde) Readme_Supplement2.txt (MD5: a7635149c51da79c6149ddb607823866)<br> Ekofisk.csv (MD5: 7bdbdccc30a9799e7a3b12a0bdce5dcb)<br> Ekofisk_dw.csv (MD5: dac36e965f5993986597dbfa95193d5b)<br> Norway.csv (MD5: 4f1f2a7aa772e5835588c06b35072b7c)<br> FitParameters_Ekofisk.R (MD5: 874ef4203154247252db241fd4aac852)<br> FitParameters_Norway.R (MD5: faa855f8e6adb007ef4ea505c11e576e)<br> Sim_Functions.R (MD5: 3033e9b636ce595f636baf0903dbea32)<br> Par_Ekofisk_A-B_ln.ct.eu.R (MD5: 929fd83818e148538c5d2d035bb6a41e)<br> Par_Ekofisk_A-B_ln.l1.eu.R (MD5: b02ff1a10455719ad6a9ab21804dc255)<br> Par_Ekofisk_A-B_ln.qp.bc0.R (MD5: f004464a598bb89f605c5eaad1b2ce9d)<br> Par_Ekofisk_A-B_nb.ct.eu.df.R (MD5: 9b10ad9e9d5fd2699c9d9c13ab3e0357)<br> Par_Ekofisk_A-B_nb.ct.eu.dv.R (MD5: 9b10ad9e9d5fd2699c9d9c13ab3e0357)<br> Par_Ekofisk_A-B_nb.l1.eu.df.R (MD5: b8bf67dc1ea90b8f37485ea7e3cfd1a2)<br> Par_Ekofisk_A-B_nb.l1.eu.dv.R (MD5: e0db4b3d8fbb249e6a68f36488be56e8)<br> Par_Ekofisk_A-B_nb.qp.bc0.df.R (MD5: 803b0d8a608db0948442ee7f90b40e7c)<br> Par_Ekofisk_A-B_nb.qp.bc0.dv.R (MD5: 06771f1f8f371dbae913472962622385)<br> Par_Ekofisk_B-C_ln.ct.eu.R (MD5: 41c2ae7182309da5b966e31bf643b053)<br> Par_Ekofisk_B-C_ln.l1.eu.R (MD5: 787945612f927046a9697376b1584b33)<br> Par_Ekofisk_B-C_ln.qp.bc0.R (MD5: f26014b0c0b44b6df4901d35ac149918)<br> Par_Ekofisk_B-C_nb.ct.eu.df.R (MD5: 42704fc56ef7a1e46344f26b28bf8f7d)<br> Par_Ekofisk_B-C_nb.ct.eu.dv.R (MD5: 346cbb6a5dd248d5ba4d0e0d7ba289ef)<br> Par_Ekofisk_B-C_nb.l1.eu.df.R (MD5: 9205b4131dc22c7a00bd7230a03d2e8c)<br> Par_Ekofisk_B-C_nb.l1.eu.dv.R (MD5: 1d4ea625561ae6348b448dd69e6515ee)<br> Par_Ekofisk_B-C_nb.qp.bc0.df.R (MD5: 04cfde95529281883a20519781b6d017)<br> Par_Ekofisk_B-C_nb.qp.bc0.dv.R (MD5: 04cfde95529281883a20519781b6d017)<br> Par_Ekofisk_C-D_ln.ct.eu.R (MD5: 926dcdc7862e812045fa1f7635fb25b3)<br> Par_Ekofisk_C-D_ln.l1.eu.R (MD5: 07cb5226bb8f540296a2e62f3f3a8463)<br> Par_Ekofisk_C-D_ln.qp.bc0.R (MD5: b849134b5d32d8aa0953b1dc67e04d0f)<br> Par_Ekofisk_C-D_nb.ct.eu.df.R (MD5: 79ad6bfe4b5ef65df3bed6e0129c0622)<br> Par_Ekofisk_C-D_nb.ct.eu.dv.R (MD5: 6ff650b99c02d958e5b81e1283d1063f)<br> Par_Ekofisk_C-D_nb.l1.eu.df.R (MD5: 91de46426b68a362c45f0df2e8949d7c)<br> Par_Ekofisk_C-D_nb.l1.eu.dv.R (MD5: 212eba37ffc2f7aa884c57383cb9498a)<br> Par_Ekofisk_C-D_nb.qp.bc0.df.R (MD5: 9254a0cd1a47dceeebb1ee35ab037691)<br> Par_Ekofisk_C-D_nb.qp.bc0.dv.R (MD5: 4b7bb4b8847d925ea30fe3526965c2ca)<br> Par_Norway_1-2.R (MD5: f482a356fbf64ecb6ee016752374f8d6)<br> Par_Norway_2-3.R (MD5: cf75e4fd951c8f985cdcabc59287206b)<br> Par_Norway_3-4.R (MD5: 6f1548331162aede52b0b2d5265f5ed9)<br> Par_Norway_4-5.R (MD5: 08e788943b5a8cd807265e4230f60149) Description Readme_Supplement2.txt contains information on how to run the simulations in R using the parameter files generated from real data sets and using the simulation functions provided in the file Sim_Functions.R<br> Ekofisk.csv ontains the Ekofisk data set.<br> Ekofisk_dw.csv contains dispersion weights for each species in the Ekofisk data set.<br> Norway.csv contains the Norwegian continental shelf data set. FitParameters_Ekofisk.R contains the R code for calculating fitted parameters on which simulations based on the Ekofisk data set can be run.<br> FitParameters_Norway.R contains the R code for calculating fitted parameters on which simulations based on the Ekofisk data set can be run.<br> Sim_Functions.R contains R code to calculate the test-statistics and run the simulations for a given set of parameters.<br> Par_Ekofisk_A-B_ln.ct.eu.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the lognormal distribution and using chi-squared distances.<br> Par_Ekofisk_A-B_ln.l1.eu.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the lognormal distribution and using Euclidean distances on log(x+1)-transformed data.<br> Par_Ekofisk_A-B_ln.qp.bc0.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the lognormal distribution and using Bray-Curtis dissimilarities fourth-root-transformed data.<br> Par_Ekofisk_A-B_nb.ct.eu.df.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the negative binomial/Poisson distributions with fixed overdispersion parameters and using chi-squared distances.<br> Par_Ekofisk_A-B_nb.ct.eu.dv.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the negative binomial/Poisson distributions with variable overdispersion parameters and using chi-squared distances.<br> Par_Ekofisk_A-B_nb.l1.eu.df.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the negative binomial/Poisson distributions with fixed overdispersion parameters and using Euclidean distances on log(x+1)-transformed data.<br> Par_Ekofisk_A-B_nb.l1.eu.dv.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the negative binomial/Poisson distributions with variable overdispersion parameters and using Euclidean distances on log(x+1)-transformed data.<br> Par_Ekofisk_A-B_nb.qp.bc0.df.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the negative binomial/Poisson distributions with fixed overdispersion parameters and using Bray-Curtis dissimilarities fourth-root-transformed data.<br> Par_Ekofisk_A-B_nb.qp.bc0.dv.R contains parameters in R code for running simulations based on the Ekofisk data to compare groups A and B on the basis of the negative binomial/Poisson distributions with variable overdispersion parameters and using Bray-Curtis dissimilarities fourth-root-transformed data....