parameters: Definition for parameters

Description Usage Arguments

View source: R/definition_function_parameters.R

Description

Here is the list of all parameters used in the package.

Usage

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parameters(age_at_capture, ages, binary, capture_method, check, data,
  death_prob, design_matrix, empty_design_matrix, empty_param_matrix_full,
  file_name, fit_original, indices, lb, maxtime, meta_param_name,
  meta_param_type, model, models_list, models_list_boot, n_boot, n_CPU,
  name_first_column, newdata, param_matrix, param_matrix_full,
  param_matrix_ini, param_names, param_str, param_values, pred_prob, print,
  print_level, save_pdf, save_rda, save_xlsx, scale, seed, sex, steps,
  surv_bin, table, ub, xtol_rel)

Arguments

age_at_capture

The age at capture

ages

A vector of ages for which to perform the interpolation

binary

A boolean indicated if the binary version of the package must be built

capture_method

A character indicating the method of capture of the elephant: "CAPTIVE", "IMM", "MILARSHI" or "STOCKADE"

check

Whether the arguments should be checked against expected types

data

The dataset to be used

death_prob

A vector of yearly probabilities of death

design_matrix

The design matrix

empty_design_matrix

The empty design matrix

empty_param_matrix_full

The empty expanded or complete parameter matrix

file_name

The file name for the exported table

fit_original

A fitted model

indices

The list of indices computed by compute_indices

lb

Lower boundary for parameter values during the optimisation (default = 0)

maxtime

Maximum time (in seconds) allowed for nloptr to fit; use Inf for best fit!

meta_param_name

The name of the meta parameter

meta_param_type

The type of subcategories for the meta parameters

model

A fitted model

models_list

The list of fitted models

models_list_boot

The list of fitted models after bootstrap

n_boot

The number of bootstrapped dataset to generate and fit

n_CPU

The number of CPU to use for fitting the bootstrapped datasets

name_first_column

The name of the first column which is taken from the row names of the table

newdata

A data frame providing the covariate values for predictions

param_matrix

The matrix storing parameter values

param_matrix_full

The expanded or complete parameter matrix

param_matrix_ini

The matrix storing initial values for the parameters

param_names

A vector of parameter names

param_str

The named vector indicating the parameter structure, that is, the type of subcategory for each meta parameter

param_values

The vector of values for the parameters

pred_prob

The predicted probability of death computed by predictor()

print

A boolean indicating whether or not to print information about potential issues

print_level

Printing setting for nloptr

save_pdf

A boolean indicating whether saving the plot as a *.pdf object or not

save_rda

A boolean indicating whether saving the model as a *.rda object or not

save_xlsx

A boolean indicating whether saving the table as a *.xlsx document or not

scale

The scaling parameter (useful if the optimisation function can only minimise)

seed

An integer giving the seed for the (pseudo-)random generator

sex

A character indicating the sex of the elephant: "males" or "females"

steps

An integer giving the number of increments for the interpolation (within each year)

surv_bin

The binary response variable taking 1 for alive and 0 for death

table

The table to be exported as *.xlsx

ub

Upper boundary for parameter values during the optimisation (default = 3)

xtol_rel

Tolerance parameter for nloptr


courtiol/SileR documentation built on May 16, 2020, 8:10 p.m.