Appendix C. Details of the d-sep procedure as applied to models A and B.

Details of the d-sep procedure as applied to models A and B

Supplement 1. The data as well as the R and WinBUGS code to conduct the analyses.

<h2>File List</h2><p> <a href="Supp1Files/code_and_data.rar">code_and_data.rar</a> (md5: 73050eb6839d36696bd85ae3fabd6c8c)<br> <a href="Supp1Files/data.plot.txt">data.plot.txt</a> (md5: 0fc94d989c075f014fa0a88dcfe336c8)<br> <a href="Supp1Files/data.subplot.txt">data.subplot.txt</a> (md5: 628b79084eb68ef06a577673fa809b9f)<br> <a href="Supp1Files/data.tree.txt">data.tree.txt</a> (md5: 9de3ce8e00f72728a6638e9a51546602)<br> <a href="Supp1Files/BUGS.mA.annotated.txt">BUGS.mA.annotated.txt</a> (md5: 396e6ff35a8f02db566be9b304dc6c3c)<br> <a href="Supp1Files/BUGS.mB.annotated.txt">BUGS.mB.annotated.txt</a> (md5: c2238f71556018781c2f0b1376a0626c)<br> <a href="Supp1Files/Rcode.modelA.annotated.R">Rcode.modelA.annotated.R</a> (md5: 4662b653ba1fbc26a4de371d5ec6efb4)<br> <a href="Supp1Files/Rcode.modelB.annotated.R">Rcode.modelB.annotated.R</a> (md5: a4a5ab4dfe94beb29f862d4a53ae3092)<br> <a href="Supp1Files/effects.modelB.annotated.R">effects.modelB.annotated.R</a> (md5: 3f87f050daafb00fa2b5c1cfeed6f7ce)<br> <a href="Supp1Files/Rcode.dsep.annotated.R">Rcode.dsep.annotated.R</a> (md5: 17bb4eabeee5c84a14693a766faf8af9)<br> <a href="Supp1Files/claim1_bugs.txt">claim1_bugs.txt</a> (md5: 86a38928ffe6ffc4ed942d77f560ae70)<br> <a href="Supp1Files/claim2_bugs.txt">claim2_bugs.txt</a> (md5: 44654a248baee405daa95bf47bf1f323)<br> <a href="Supp1Files/claim3A_bugs.txt">claim3A_bugs.txt</a> (md5: c0c6eab9e48e1c2928fe46029cc1e167)<br> <a href="Supp1Files/claim3B_bugs.txt">claim3B_bugs.txt</a> (md5: a385df60ef6da65b6572cc310fc754e8)<br> <a href="Supp1Files/claim4_bugs.txt">claim4_bugs.txt</a> (md5: fea7e182b32ea77eb71d7295645bfca8)<br> <a href="Supp1Files/claim5_bugs.txt">claim5_bugs.txt</a> (md5: 486ea08f4ed704ccfae27e62039458b0)<br> <a href="Supp1Files/claim6_bugs.txt">claim6_bugs.txt</a> (md5: 46efa7b9c905c54a9d1cd77c81f09688)<br> <a href="Supp1Files/claim7A_bugs.txt">claim7A_bugs.txt</a> (md5: 8e36c5443e9a63fbf7fe52912f18dcba)<br> <a href="Supp1Files/claim7B_bugs.txt">claim7B_bugs.txt</a> (md5: c4e370e2574700c2b2b20db3e985a847)<br> <a href="Supp1Files/claim8A_bugs.txt">claim8A_bugs.txt</a> (md5: 25cbcbae615680c5731fa6a3ba294905) </p><h2>Description</h2><div> <p>code_and_data.zip is an archive containing all data and code described below (19 files).</p> <p>data.plot.txt is a text file containing data at plot scale. Column definitions are:</p> <ol> <li>plot: plot number, 1–43</li> <li>temp: mean daily temperature in °C</li> <li>age: tree age in years</li> </ol> <p>data.subplot.txt is a text file containing data at plot scale. Column definitions are:</p> <ol> <li>subplot: subplot number, 1–86</li> <li>plot: plot number, 1–43</li> <li>Nfert: nitrogen fertilization, dummy variable (1 = fertilized, 0 = control)</li> </ol> <p>data.tree.txt is a text file containing data at plot scale. Column definitions are:</p> <ol> <li>tree: tree number, 1–430</li> <li>subplot: subplot number, 1–86</li> <li>plot: plot number, 1–43</li> <li>Pc: presence of <i>Philidris</i> cf. <i>cordata</i>, dummy variable (1 = present, 0 = absent)</li> <li>Hs: number of pods with <i>Helopeltis sulawesi</i> damage</li> <li>Cc: number of pods with <i>Conopomorpha cramerella</i> damage</li> <li>Npodh: number of harvested cacao pods</li> </ol> <p>The data files BUGS.mA.annotated.txt and BUGS.mB.annotated.txt contain the BUGS code for models A and B respectively. These BUGS files, as well as the data files (files 1 to 3) have to be in the working directory of R when running the R code contained in the files Rcode.modelA.annotated.R and Rcode.modelB.annotated.R. The R package R2WinBUGS is needed as its function bugs() is called upon by the R code to run the models. The R code to compute the direct and indirect effects in model B is contained in effects.modelB.annotated.R. This code will only run if model B was run successfully, which causes the samples of the posterior distribution to be available in the R workspace. Rcode.dsep.annotated.R contains the R code to compute d-sep test for models A and B. It runs the BUGS code associated with the independence claims implied by model A and B, which is contained in the files claim1_bugs.txt, claim2_bugs.txt, claim3A_bugs.txt, claim3B_bugs.txt, claim4_bugs.txt, claim5_bugs.txt, claim6_bugs.txt, claim7A_bugs.txt, claim7B_bugs.txt, and claim8A_bugs.txt.</p> <p></p> </div

Appendix B. Posterior predictive diagnostic plots for the univariate models within path models A and B.

Posterior predictive diagnostic plots for the univariate models within path models A and B

Data_BosemBaillod_JournalAppliedEcology

Data collected in the field and used for the analysis. Column description: "Landscape" is the ID of the wheat field within a 500m radius landscape. "Sampling_Year" is the year of the data collection. "Within_field_position" denotes the transects where arthropods have been collected. "Aphid_density" and "Predator_density" are aggregated numbers of aphids and predators respectively, collected at each transect. "Predator_Prey_ratio" is the ratio between predator and prey numbers. "Parasitism_rate" is the proportion of parasitized aphids. The remaining columns are the landscape variables crop Shannon diversity (SHDI), field border length in kilometers (FBL_Km), grassy field boundary length in kilometers (GBL_Km) and the annual change in aphid host habitats (%_ΔHab)

Effects of plant size and covariables on species richness (SR) of herbivores (H) and their natural enemies (NE).

<p>Species richness of herbivores and natural enemies refer to five plant individuals per plot (N = 84 plots). Species richness of natural enemies (in total and of ectophagous vs. endophagous prey/hosts) were sqrt-transformed. Parameter weights (pw) refer to a delta 2 AICc range. Explanatory variables and interactions with a parameter weight > 0.5 were considered as important for the relevant response variable and are shown in <b>bold</b>. Estimates (est) with standard errors (SE) were assessed from the summary table of the lme-model with the lowest AICc including all explanatory variables with a parameter weight > 0.5 and are centred and standardised to improve their interpretability. Empty cells refer to variables which were not involved in the relevant full model.</p

Effects of plant size and covariables on species richness of ectophagous and endophagous arthropods.

<p>Effects of plant size on species richness of (a) ectophagous and (d) endophagous herbivores and of (b, e) their respective natural enemies. Additionally, effects of important covariables representing the amount of food resource for (c, f) natural enemies are shown. SR = species richness, H = herbivores, NE = natural enemies. Species richness of herbivores and natural enemies refer to five plant individuals per plot (N = 84 plots). Axes of variables were transformed corresponding to analyses (species richness of natural enemies: sqrt-transformation). Data points in (c, f) were jittered. Predictions derive from the lme-model with the lowest AICc including all explanatory variables with a parameter weight > 0.5.</p

Effects of plant size and covariables on species richness of leaf associated arthropods.

<p>Effects of plant size on species richness of (a) leaf associated herbivores and (c) their natural enemies. Additionally, effects of important covariables representing the amount of food resource for (b) herbivores and (d) for their natural enemies are shown. SR = species richness, H = herbivores, NE = natural enemies. Leaf biomass as well as species richness of herbivores and natural enemies refer to five plant individuals per plot (N = 84 plots). Axes of variables were transformed corresponding to analyses (species richness of leaf associated herbivores and species richness of their natural enemies: sqrt-transformation, leaf biomass: log-transformation). Data points in (d) were jittered. Predictions derive from the lme-model with the lowest AICc including all explanatory variables with a parameter weight > 0.5.</p