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Prepare cross-validated Hmsc models for HPC fitting

Source: R/Mod_CV_Fit.R
Mod_CV_Fit.Rd

This function prepares cross-validated Hmsc models for fitting using HPC. It handles data preparation, model initialization, and generation of SLURM commands.

Usage

Mod_CV_Fit(
  Path_Model = NULL,
  CVName = c("CV_Dist", "CV_Large"),
  Partitions = NULL,
  EnvFile = ".env",
  InitPar = NULL,
  JobName = "CV_Models",
  Updater = list(Gamma2 = FALSE, GammaEta = FALSE),
  AlignPost = TRUE,
  ToJSON = FALSE,
  PrepSLURM = TRUE,
  MemPerCpu = NULL,
  Time = NULL,
  Path_Hmsc = NULL,
  Precision = 64,
  ...
)

Arguments

Path_Model

Character. Path to a saved model file (*.qs2).

CVName

Character vector. Column name(s) in the model input data to be used to cross-validate the models (see Mod_PrepData and Mod_GetCV). The function allows the possibility of using more than one way of assigning grid cells into cross-validation folders. If multiple names are provided, separate cross-validation models will be fitted for each cross-validation type. Currently, there are three cross-validation strategies: CV_SAC, CV_Dist, and CV_Large. Defaults to c("CV_Dist", "CV_Large").

Partitions

A vector for cross-validation created by Hmsc::createPartition or similar. Defaults to NULL, which means to use column name(s) provided in the CVName argument. If the Partitions vector is provided, the label used in the output files will be CV_Custom.

EnvFile

Character. Path to the environment file containing paths to data sources. Defaults to .env.

InitPar

a named list of parameter values used for initialization of MCMC states. See Hmsc::computePredictedValues for more information. Default: NULL.

JobName

Character. Name of the submitted job(s) for SLURM. Default: CV_Models.

Updater

named list. Which conditional updaters should be omitted? See Hmsc::computePredictedValues for more information. Defaults to list(Gamma2 = FALSE, GammaEta = FALSE) to disable the following warnings: setting updater$Gamma2=FALSE due to specified phylogeny matrix and setting updater$GammaEta=FALSE: not implemented for spatial methods 'GPP' and 'NNGP'.

AlignPost

Logical. Whether the posterior of each chains should be aligned. See Hmsc::computePredictedValues for more information. Default: TRUE.

ToJSON

Logical. Whether to convert unfitted models to JSON before saving to RDS file. Default: FALSE.

PrepSLURM

Logical. Whether to prepare SLURM command files. If TRUE (default), the SLURM commands will be saved to disk using the Mod_SLURM function.

MemPerCpu

Character. Memory allocation per CPU core. Example: "32G" for 32 gigabytes. Required — if not provided, the function throws an error.

Time

Character. Maximum allowed runtime for the job. Example: "01:00:00" for one hour. Required — if not provided, the function throws an error.

Path_Hmsc

Character. Path to the Hmsc-HPC installation.

Precision

Integer (either 32 or 64). Defines the floating-point precision mode for Hmsc-HPC sampling (–fp 32 or –fp 64). The default is 64, which is the default precision in Hmsc-HPC.

...

Additional arguments passed to the Mod_SLURM function.

Details

The function copies part of the Hmsc::computePredictedValues function, which currently does not support performing cross-validation using Hmsc-HPC.

Author

Ahmed El-Gabbas