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labLogistics: flour and tape ordering. Data sheet handling for the stocks. Validated good chunk of priorityEffects last night.
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macroHelminth: small edits to text and figures. Will now wait for Vanessa’s input. Need to push along nestedness stuff, but have to wait until I have access to the farm cluster (pending). If I get antsy, I’ll start it on my home machine tonight. It’s not an issue of runtime, but simply of memory. Some matrices require lots of memory because all null matrices are held in memory in R. The generation of nulls is a bit time-consuming, but prohibitively so. If I can’t put a solid dent in it tonight, I’ll either parallelize my batch script for the cluster, or just code it up in Julia.
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farmCluster: Related to the above: got access to the farm cluster. Wrote bash script to run some R code. Submitted job to serial nodes (the ones I have access to). Failed. Unclear why, as it doesn’t kick anything to the log files. It’s probably some weird error on my part. However, I tried running a quick srun (they use SLURM as job manager) to just open up an interactive xterm with like 1g of memory and it bonked, citing something about my permissions. I give up for the day, but will talk to Carlos tomorrow.
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experimentIdea: asked a member of the undergrad team if we could run a small long-ish term experiment alongside the stocks that wouldn’t take too much work, but would be spatial. He said ‘no’ and laughed. Rats. I guess in the meantime, I need to figure out how to safely and effectively mark the beetles (some form of paint? White-out worked decently well, but was a bit difficult to apply).
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priorityEffects: meeting with Alan on Thursday. Discuss pmf progress, nll functions, and optimizing parameters for two species at same time.
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extinctionChapter: pushed text along. Still needs a good bit of work though.