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

File List code_and_data.rar (md5: 73050eb6839d36696bd85ae3fabd6c8c)
data.plot.txt (md5: 0fc94d989c075f014fa0a88dcfe336c8)
data.subplot.txt (md5: 628b79084eb68ef06a577673fa809b9f)
data.tree.txt (md5: 9de3ce8e00f72728a6638e9a51546602)
BUGS.mA.annotated.txt (md5: 396e6ff35a8f02db566be9b304dc6c3c)
BUGS.mB.annotated.txt (md5: c2238f71556018781c2f0b1376a0626c)
Rcode.modelA.annotated.R (md5: 4662b653ba1fbc26a4de371d5ec6efb4)
Rcode.modelB.annotated.R (md5: a4a5ab4dfe94beb29f862d4a53ae3092)
effects.modelB.annotated.R (md5: 3f87f050daafb00fa2b5c1cfeed6f7ce)
Rcode.dsep.annotated.R (md5: 17bb4eabeee5c84a14693a766faf8af9)
claim1_bugs.txt (md5: 86a38928ffe6ffc4ed942d77f560ae70)
claim2_bugs.txt (md5: 44654a248baee405daa95bf47bf1f323)
claim3A_bugs.txt (md5: c0c6eab9e48e1c2928fe46029cc1e167)
claim3B_bugs.txt (md5: a385df60ef6da65b6572cc310fc754e8)
claim4_bugs.txt (md5: fea7e182b32ea77eb71d7295645bfca8)
claim5_bugs.txt (md5: 486ea08f4ed704ccfae27e62039458b0)
claim6_bugs.txt (md5: 46efa7b9c905c54a9d1cd77c81f09688)
claim7A_bugs.txt (md5: 8e36c5443e9a63fbf7fe52912f18dcba)
claim7B_bugs.txt (md5: c4e370e2574700c2b2b20db3e985a847)
claim8A_bugs.txt (md5: 25cbcbae615680c5731fa6a3ba294905) Description code_and_data.zip is an archive containing all data and code described below (19 files). data.plot.txt is a text file containing data at plot scale. Column definitions are: plot: plot number, 1–43 temp: mean daily temperature in °C age: tree age in years data.subplot.txt is a text file containing data at plot scale. Column definitions are: subplot: subplot number, 1–86 plot: plot number, 1–43 Nfert: nitrogen fertilization, dummy variable (1 = fertilized, 0 = control) data.tree.txt is a text file containing data at plot scale. Column definitions are: tree: tree number, 1–430 subplot: subplot number, 1–86 plot: plot number, 1–43 Pc: presence of Philidris cf. cordata, dummy variable (1 = present, 0 = absent) Hs: number of pods with Helopeltis sulawesi damage Cc: number of pods with Conopomorpha cramerella damage Npodh: number of harvested cacao pods 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.