Documented arguments not in \usage in Rd file 'allocate_subset_node.simulate.Rd':
  'node:' 'array:' 'value:'

Documented arguments not in \usage in Rd file 'check_data.Rd':
  'trait_correlation_threshold'

Documented arguments not in \usage in Rd file 'compute_E.simple.Rd':
  'sim' 'Sigma' 'Sigma_YY_inv'

Documented arguments not in \usage in Rd file 'compute_expectations.BM.Rd':
  'phylo:'

Documented arguments not in \usage in Rd file 'compute_expectations.scOU.Rd':
  'phylo:'

Documented arguments not in \usage in Rd file 'compute_gauss_lasso.Rd':
  'Yp'

Documented arguments not in \usage in Rd file 'compute_log_likelihood.simple.Rd':
  'Y_data' 'Sigma_YY_inv'

Documented arguments not in \usage in Rd file 'compute_mahalanobis_distance.simple.Rd':
  'Y_data' 'Sigma_YY_inv'

Documented arguments not in \usage in Rd file 'compute_residuals.simple.Rd':
  'Y_data' 'Sigma_YY_inv'

Documented arguments not in \usage in Rd file 'equivalent_shifts_values.Rd':
  'shifts' 'beta_0'

Documented arguments not in \usage in Rd file 'extract.variance_covariance.Rd':
  'what:' 'miss;'

Documented arguments not in \usage in Rd file 'find_shift_values.Rd':
  'm_Y'

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

Documented arguments not in \usage in Rd file 'init.parsimonyCost.Rd':
  'phylo'

Documented arguments not in \usage in Rd file 'init.simulate.OU.Rd':
  'phy:' 'p:'

Documented arguments not in \usage in Rd file 'init.simulate.StateAndExp.Rd':
  'phy:' 'p:'

Documented arguments not in \usage in Rd file 'is.in.ranges.Rd':
  'params'

Documented arguments not in \usage in Rd file 'merge_params_independent.Rd':
  'params_split:'

Documented arguments not in \usage in Rd file 'penalty_pBIC.Rd':
  'C'

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

Documented arguments not in \usage in Rd file 'segmentation.OU.specialCase.same_shifts.Rd':
  '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 Rd file 'qr.solve_exact.Rd':
  '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.