PLNPCA_param | R Documentation |

Helper to define list of parameters to control the PLNPCA fit. All arguments have defaults.

```
PLNPCA_param(
backend = "nlopt",
trace = 1,
config_optim = list(),
inception = NULL
)
```

`backend` |
optimization back used, either "nlopt" or "torch". Default is "nlopt" |

`trace` |
a integer for verbosity. |

`config_optim` |
a list for controlling the optimizer (either "nlopt" or "torch" backend). See details |

`inception` |
Set up the parameters initialization: by default, the model is initialized with a multivariate linear model applied on log-transformed data, and with the same formula as the one provided by the user. However, the user can provide a PLNfit (typically obtained from a previous fit), which sometimes speeds up the inference. |

The list of parameters `config_optim`

controls the optimizers. When "nlopt" is chosen the following entries are relevant

"algorithm" the optimization method used by NLOPT among LD type, e.g. "CCSAQ", "MMA", "LBFGS". See NLOPT documentation for further details. Default is "CCSAQ".

"maxeval" stop when the number of iteration exceeds maxeval. Default is 10000

"ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

"xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

"ftol_abs" stop when an optimization step changes the objective function by less than ftol_abs. Default is 0.0 (disabled)

"xtol_abs" stop when an optimization step changes every parameters by less than xtol_abs. Default is 0.0 (disabled)

"maxtime" stop when the optimization time (in seconds) exceeds maxtime. Default is -1 (disabled)

When "torch" backend is used, with the following entries are relevant:

"maxeval" stop when the number of iteration exceeds maxeval. Default is 10000

"ftol_rel" stop when an optimization step changes the objective function by less than ftol multiplied by the absolute value of the parameter. Default is 1e-8

"xtol_rel" stop when an optimization step changes every parameters by less than xtol multiplied by the absolute value of the parameter. Default is 1e-6

list of parameters configuring the fit.

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