checkRd: (-1) compute_actualization_matrix_ultrametric.Rd:25: Lost braces; missing escapes or markup?
    25 | matrix of the (I_p - exp(-A * (h - t_pa(j))))_{j node}.
       |                                               ^
checkRd: (-1) compute_sum_var_diff.Rd:18: Lost braces; missing escapes or markup?
    18 | \code{compute_sum_var_diff} computes sum_{e edge} ell_j * Var[X_j - X_pa(j) | Y]
       |                                          ^
checkRd: (-1) find_grid_alpha.Rd:45: Lost braces; missing escapes or markup?
    45 | 2*ln(2)*quantile(d_ij)/factor_up_alpha < t_{1/2} < factor_down_alpha * ln(2) * h_tree
       |                                            ^
checkRd: (-1) incidence_matrix_actualization_factors.Rd:28: Lost braces; missing escapes or markup?
    28 | (1 - exp(-alpha * (t_i - t_pa(j) - nu_j * l_j)))_{i tip, j node}.
       |                                                  ^
checkRd: (-1) init.parsimonyCost.Rd:24: Lost braces; missing escapes or markup?
    24 | (1 - Ind(k=p)_{1<=p<=nclus})*Inf (where Inf * 0 = 0)
       |               ^
checkRd: (-1) init.parsimonyNumber.Rd:23: Lost braces; missing escapes or markup?
    23 | At a tip i in state k, the line-vector is initialized as follow : Ind(k=p)_{1<=p<=nclus}
       |                                                                            ^
checkRd: (-1) is.in.ranges.Rd:28-34: Lost braces
    28 | is.finite.params.BM <- function(params) {
       |                                         ^
checkRd: (-1) is.in.ranges.Rd:29-31: Lost braces
    29 |   if (params$root.state$random) {
       |                                 ^
checkRd: (-1) is.in.ranges.Rd:31-33: Lost braces
    31 |   } else {
       |          ^
checkRd: (-1) is.in.ranges.Rd:36-44: Lost braces
    36 | is.finite.params.BM.randroot <- function(params) {
       |                                                  ^
checkRd: (-1) is.in.ranges.Rd:39-41: Lost braces
    39 |         is.finite(params$root.state$var.root) ) {
       |                                                 ^
checkRd: (-1) is.in.ranges.Rd:41-43: Lost braces
    41 |   } else {
       |          ^
checkRd: (-1) is.in.ranges.Rd:46-53: Lost braces
    46 | is.finite.params.BM.fixedroot <- function(params) {
       |                                                   ^
checkRd: (-1) is.in.ranges.Rd:48-50: Lost braces
    48 |          is.finite(params$root.state$value.root) ) {
       |                                                    ^
checkRd: (-1) is.in.ranges.Rd:50-52: Lost braces
    50 |   } else {
       |          ^
checkRd: (-1) is.in.ranges.Rd:55-63: Lost braces
    55 | is.finite.params.OU <- function(stationary.root, shifts_at_nodes, alpha_known){
       |                                                                               ^
checkRd: (-1) is.in.ranges.Rd:56-58: Lost braces
    56 |   if (stationary.root && shifts_at_nodes && alpha_known) {
       |                                                          ^
checkRd: (-1) is.in.ranges.Rd:58-60: Lost braces
    58 |   } else if (stationary.root && shifts_at_nodes) {
       |                                                  ^
checkRd: (-1) is.in.ranges.Rd:60-62: Lost braces
    60 |   } else {
       |          ^
checkRd: (-1) is.in.ranges.Rd:65-73: Lost braces
    65 | is.finite.params.OU.specialCase <- function(params) {
       |                                                     ^
checkRd: (-1) is.in.ranges.Rd:68-70: Lost braces
    68 |         is.finite(params$root.state$var.root) ) {
       |                                                 ^
checkRd: (-1) is.in.ranges.Rd:70-72: Lost braces
    70 |   } else {
       |          ^
checkRd: (-1) is.in.ranges.Rd:75-84: Lost braces
    75 | is.finite.params.OU.stationary.root_AND_shifts_at_nodes <- function(params) {
       |                                                                             ^
checkRd: (-1) is.in.ranges.Rd:79-81: Lost braces
    79 |         is.finite(params$selection.strength)) {
       |                                               ^
checkRd: (-1) is.in.ranges.Rd:81-83: Lost braces
    81 |   } else {
       |          ^