parameters: Definition for parameters

In courtiol/SileR: Survival Analysis of Elephants Using an Extension of the William Siler's Framework

Description

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

Usage

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.