Lite #207
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Lite #207
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…24.3% more time, -34.1% env_mem)
…change in env_mem)
…re efficient to create pops_multirun_lite.R from pops.R
… use infilenames, enabling organized tracking of pops_lite raw exports to streamline subsequent analysis and data summarization.
…e_config to pass tests
…d, total_hosts, total_exposed, mortality tracker) into a function, and reduced intermediate objects.
…EI matrices, etc.) from pops_lite.R
…step naming requirements.
…ts and associated seeds.
…teration after excluding spatial_indices, soil_reservoirs, and exposed (if model_type = SI)
- update pops_lite_run to accept a config file that reads in configuration data, rather than producing the configuration data, and then running pops lite. 58.7% less memory needed.
…number of cores and iterations.
…adjusts file paths to point to the data's new location on a different workstation without requiring the config file to be recreated.
…ew root directory for input and output file paths in the config_file. This updates paths to reflect a new location on a different workstation without recreating the config_file. The default is NULL, meaning the original paths in the config_file will be used if no new path is provided.
…r quantity, allocation, and disagreement lite functions to optimize memory usage.
…ation_disagreement_lite.R function; currently keys are for pops_lite.R
…th data prep for use_rmse and use_distance.
…ement.R; instead accepts config_qad_lite_file which contains the outputs after data prep. All other analyses in this function are unchanged from quantity_allocation_disagreement.R, excluding a few time/memory improvements.
…configuration_qad_lite functions
…d configuration_qad_lite functions reduce time by 65.2% and memory allocation by 49.58%.
…When multiple_random_seed = TRUE and file_random_seeds = NULL in the config, resample seeds using number_of_iterations and generate a unique ID to track random seeds used per pops_model run. Added if/else logic to optionally include unique IDs in the pops_model output file names.
…nces of duplicate ids if a large number of runs needed
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update single-host pops to include (e.g., pops_lite, config_qad_lite, quantity_allocation_disagreement_lite.R) and modify functions (helpers.R, configuration.R) to allow for broad extent, fine-resolution PoPS forecasting.