Documented arguments not in \usage in documentation object 'allocate_subset_node.simulate':
  'node:' 'array:' 'value:'

Documented arguments not in \usage in documentation object 'check_data':
  'trait_correlation_threshold'

Documented arguments not in \usage in documentation object 'compute_E.simple':
  'sim' 'Sigma' 'Sigma_YY_inv'

Documented arguments not in \usage in documentation object 'compute_expectations.BM':
  'phylo:'

Documented arguments not in \usage in documentation object 'compute_expectations.scOU':
  'phylo:'

Documented arguments not in \usage in documentation object 'compute_gauss_lasso':
  'Yp'

Documented arguments not in \usage in documentation object 'compute_log_likelihood.simple':
  'Y_data' 'Sigma_YY_inv'

Documented arguments not in \usage in documentation object 'compute_mahalanobis_distance.simple':
  'Y_data' 'Sigma_YY_inv'

Documented arguments not in \usage in documentation object 'compute_residuals.simple':
  'Y_data' 'Sigma_YY_inv'

Documented arguments not in \usage in documentation object 'equivalent_shifts_values':
  'shifts' 'beta_0'

Documented arguments not in \usage in documentation object 'extract.variance_covariance':
  'what:' 'miss;'

Documented arguments not in \usage in documentation object 'find_shift_values':
  'm_Y'

Documented arguments not in \usage in documentation object 'go_back_to_original_process':
  'phy_original:' 'known.selection.strength:' 'sBM_variance:' 'params:'

Documented arguments not in \usage in documentation object 'init.parsimonyCost':
  'phylo'

Documented arguments not in \usage in documentation object 'init.simulate.OU':
  'phy:' 'p:'

Documented arguments not in \usage in documentation object 'init.simulate.StateAndExp':
  'phy:' 'p:'

Documented arguments not in \usage in documentation object 'is.in.ranges':
  'params'

Documented arguments not in \usage in documentation object 'merge_params_independent':
  'params_split:'

Documented arguments not in \usage in documentation object 'penalty_pBIC':
  'C'

Documented arguments not in \usage in documentation object 'segmentation.OU.specialCase.lasso':
  'conditional_law_X' 'selection.strength'

Documented arguments not in \usage in documentation object 'segmentation.OU.specialCase.same_shifts':
  'conditional_law_X' 'selection.strength'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
S3 methods shown with full name in documentation object 'qr.solve_exact':
  'qr.solve_exact'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.