[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after an infinite number of generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:6:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:11:20:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L11) *style:* **Variable or function name should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L12) *style:* **Variable or function name should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  K <- H_0 * C * 2 * N * R / (2 * N * C + R)
  ^
```
[R/calc_K.R:19:5:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L19) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L23) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calc_K.R#L27) *style:* **Variable or function name should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the error in the estimate of the onset of hybridisation, following Equations 3 & 4 in the Supplementary information of Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:7:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param relative Boolean flag, if TRUE: return the relative error, if FALSE: return error in generations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:15:24:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L15) *style:* **Variable or function name should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L17) *style:* **Variable or function name should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L18) *style:* **Variable or function name should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_error.R:30:7:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
      ^
```
[R/calculate_error.R:30:25:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
                        ^
```
[R/calculate_MAT.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_MAT.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Function that calculates the maximum time after hybridization after which the number of junctions can still be reliably used to estimate the onset of hybridization. This is following equation 15 in Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:6:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_MAT.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:12:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_MAT.R#L12) *style:* **Variable or function name should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_MAT.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_MAT.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_MAT.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_time.R:1:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the number of junctions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 14 in Janzen et al. 2018
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:7:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:11:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' estimate_time(J = J, N = 100, R = 1000, H_0 = 0.5, C = 1)  # should be 200 again
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:13:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L13) *style:* **Variable or function name should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/calculate_time.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/estimate_time_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 1 in Janzen et al. unpublished
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:7:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:8:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:12:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' J <- number_of_junctions_markers(N = 100, H_0 = 0.5, t = 200, marker_distribution = markers)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:18:35:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L18) *style:* **Variable or function name should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L19) *style:* **Variable or function name should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_markers.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(lower_lim, upper_lim) )
                                                                      ^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
                                                        ^
```
[R/estimate_time_phased.R:108:19:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L108) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_phased.R:135:23:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:135:32:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:138:10:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L138) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:142:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:143:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L143) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:147:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:148:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L148) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:149:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L149) *style:* **Lines should not be more than 80 characters.**
```r
#' @param optim_pop_size If TRUE, population size is also optimized. Starting point of the optimizaton will then be on the given population size, and half the maximum time.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:184:11:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L184) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:191:58:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_phased.R#L191) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
                                                 ^
```
[R/estimate_time_unphased.R:12:24:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                       ^
```
[R/estimate_time_unphased.R:12:43:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                                          ^
```
[R/estimate_time_unphased.R:18:22:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- p * q * ( p * q * P[3] +
                     ^
```
[R/estimate_time_unphased.R:35:24:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                       ^
```
[R/estimate_time_unphased.R:88:19:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L88) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_unphased.R:115:23:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:115:32:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:118:12:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L118) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:175:11:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L175) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/estimate_time_unphased.R:182:58:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/estimate_time_unphased.R#L182) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_backcross.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, in a backcrossing mating scheme.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:4:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_backcross.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:10:43:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_backcross.R#L10) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_di.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected number of junctions between two markers separated by a given amount of recombination
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:3:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_di.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distance between two markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:12:36:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_di.R#L12) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_di <- function(N = Inf,
                                   ^
```
[R/number_of_junctions_di.R:13:36:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_di.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected total number of junctions in a chromosome, given the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distribution of markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:20:41:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_markers <- function(N = Inf,
                                        ^
```
[R/number_of_junctions_markers.R:21:41:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_markers.R#L21) *style:* **Variable or function name should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions_markers.R:32:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions_markers.R#L32) *warning:* **no visible global function definition for ‘number_of_junctions_di’**
```r
    expected_junctions <- number_of_junctions_di(N, H_0, t, di)
                          ^~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after t generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:6:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:13:33:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions.R#L13) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/number_of_junctions.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/optim_limits.R:5:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/optim_limits.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param calc_func function to calculate the time, should accept two arguments: upper, lower and should return a stats::optimize object with two properties: $minimum and $objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:6:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/optim_limits.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param iterations number of times the boundaries should be adjusted to obtain an estimate that is not close to the boundaries. After this number of iterations is exceeded, NA is returned
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/phased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/phased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:38:11:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/phased_log_likelihood.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/phased_log_likelihood.R:45:58:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/phased_log_likelihood.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/sim_backcrossing.R:7:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_backcrossing.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:11:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_backcrossing.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:12:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_backcrossing.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return List with five entries: average_junctions: average number of junctions over time, detected_junctions: average number of detected junctions, given the markers. markers: vector with the locations of the molecular markers, junction_distribution: distribution of junctions per time step average_heterozygosity: average heterozygosity.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_fin_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with regularly distributed markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:5:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_fin_chrom.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_fin_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:17:27:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_fin_chrom.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
sim_fin_chrom <- function (pop_size = 100,
                          ^
```
[R/sim_fin_chrom.R:22:28:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_fin_chrom.R#L22) *style:* **Variable or function name should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_inf_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with an infinite number of recombination sites.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:6:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_inf_chrom.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:7:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_inf_chrom.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param markers The number of genetic markers superimposed on the chromosome. If markers is set to -1, no markers are superimposed (faster simulation)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_inf_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_phased_unphased.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is returned.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:6:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_phased_unphased.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:7:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_phased_unphased.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:8:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_phased_unphased.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:11:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/sim_phased_unphased.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/unphased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the unphased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/unphased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:34:11:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/unphased_log_likelihood.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/unphased_log_likelihood.R:41:58:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/util.R:22:10:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( get_states_vector(local_anc))
         ^
```
[R/util.R:22:11:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L22) *warning:* **no visible global function definition for ‘get_states_vector’**
```r
  return( get_states_vector(local_anc))
          ^~~~~~~~~~~~~~~~~
```
[R/util.R:56:42:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    (local_anc_matrix[, 1 ] == local_anc_matrix[, 2]))
                                         ^
```
[R/util.R:89:29:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L89) *style:* **Variable or function name should be snake_case.**
```r
single_state <- function(t, N, d) {
                            ^
```
[R/util.R:92:36:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L92) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[1, ] <- c(1 - 1 / (2*N) - 2 * d , 2 * d, 0, 0, 0, 1 / (2*N), 0)
                                  ~^~
```
[R/util.R:92:48:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L92) *style:* **Commas should never have a space before.**
```r
  trans_matrix[1, ] <- c(1 - 1 / (2*N) - 2 * d , 2 * d, 0, 0, 0, 1 / (2*N), 0)
                                              ~^
```
[R/util.R:92:72:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L92) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[1, ] <- c(1 - 1 / (2*N) - 2 * d , 2 * d, 0, 0, 0, 1 / (2*N), 0)
                                                                      ~^~
```
[R/util.R:93:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L93) *style:* **Lines should not be more than 80 characters.**
```r
  trans_matrix[2, ] <- c(1 / (2*N), 1 - 3 * 1 / (2*N) - d, d, 2 * 1 / (2*N), 0, 0, 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:93:32:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L93) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[2, ] <- c(1 / (2*N), 1 - 3 * 1 / (2*N) - d, d, 2 * 1 / (2*N), 0, 0, 0)
                              ~^~
```
[R/util.R:93:51:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L93) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[2, ] <- c(1 / (2*N), 1 - 3 * 1 / (2*N) - d, d, 2 * 1 / (2*N), 0, 0, 0)
                                                 ~^~
```
[R/util.R:93:73:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L93) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[2, ] <- c(1 / (2*N), 1 - 3 * 1 / (2*N) - d, d, 2 * 1 / (2*N), 0, 0, 0)
                                                                       ~^~
```
[R/util.R:94:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L94) *style:* **Lines should not be more than 80 characters.**
```r
  trans_matrix[3, ] <- c(0, 2 * 1 / (2*N), 1 - 4 * 1/(2*N), 0, 2 * 1/(2*N), 0, 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:94:39:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L94) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[3, ] <- c(0, 2 * 1 / (2*N), 1 - 4 * 1/(2*N), 0, 2 * 1/(2*N), 0, 0)
                                     ~^~
```
[R/util.R:94:53:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L94) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[3, ] <- c(0, 2 * 1 / (2*N), 1 - 4 * 1/(2*N), 0, 2 * 1/(2*N), 0, 0)
                                                   ~^~
```
[R/util.R:94:54:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L94) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  trans_matrix[3, ] <- c(0, 2 * 1 / (2*N), 1 - 4 * 1/(2*N), 0, 2 * 1/(2*N), 0, 0)
                                                     ^
```
[R/util.R:94:56:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L94) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[3, ] <- c(0, 2 * 1 / (2*N), 1 - 4 * 1/(2*N), 0, 2 * 1/(2*N), 0, 0)
                                                      ~^~
```
[R/util.R:94:69:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L94) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[3, ] <- c(0, 2 * 1 / (2*N), 1 - 4 * 1/(2*N), 0, 2 * 1/(2*N), 0, 0)
                                                                   ~^~
```
[R/util.R:94:70:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L94) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  trans_matrix[3, ] <- c(0, 2 * 1 / (2*N), 1 - 4 * 1/(2*N), 0, 2 * 1/(2*N), 0, 0)
                                                                     ^
```
[R/util.R:94:72:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L94) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[3, ] <- c(0, 2 * 1 / (2*N), 1 - 4 * 1/(2*N), 0, 2 * 1/(2*N), 0, 0)
                                                                      ~^~
```
[R/util.R:95:45:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L95) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[4, ] <- c(0, 0, 0, 1 - 1 / (2*N) - d, d, 1/(2*N), 0)
                                           ~^~
```
[R/util.R:95:58:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L95) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[4, ] <- c(0, 0, 0, 1 - 1 / (2*N) - d, d, 1/(2*N), 0)
                                                        ~^~
```
[R/util.R:95:59:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L95) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  trans_matrix[4, ] <- c(0, 0, 0, 1 - 1 / (2*N) - d, d, 1/(2*N), 0)
                                                          ^
```
[R/util.R:95:61:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L95) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[4, ] <- c(0, 0, 0, 1 - 1 / (2*N) - d, d, 1/(2*N), 0)
                                                           ~^~
```
[R/util.R:96:45:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L96) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[5, ] <- c(0, 0, 0, 2 * 1 / (2*N), 1 - 3 * 1/(2*N), 0, 1 / (2*N))
                                           ~^~
```
[R/util.R:96:59:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L96) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[5, ] <- c(0, 0, 0, 2 * 1 / (2*N), 1 - 3 * 1/(2*N), 0, 1 / (2*N))
                                                         ~^~
```
[R/util.R:96:60:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L96) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  trans_matrix[5, ] <- c(0, 0, 0, 2 * 1 / (2*N), 1 - 3 * 1/(2*N), 0, 1 / (2*N))
                                                           ^
```
[R/util.R:96:62:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L96) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[5, ] <- c(0, 0, 0, 2 * 1 / (2*N), 1 - 3 * 1/(2*N), 0, 1 / (2*N))
                                                            ~^~
```
[R/util.R:96:76:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L96) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[5, ] <- c(0, 0, 0, 2 * 1 / (2*N), 1 - 3 * 1/(2*N), 0, 1 / (2*N))
                                                                          ~^~
```
[R/util.R:98:28:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L98) *style:* **Commas should never have a space before.**
```r
  trans_matrix[7, ] <- c(0 ,0, 0, 0, 0, 1 / (2*N),  1 - 1 / (2*N))
                          ~^
```
[R/util.R:98:29:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L98) *style:* **Commas should always have a space after.**
```r
  trans_matrix[7, ] <- c(0 ,0, 0, 0, 0, 1 / (2*N),  1 - 1 / (2*N))
                            ^
```
[R/util.R:98:47:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L98) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[7, ] <- c(0 ,0, 0, 0, 0, 1 / (2*N),  1 - 1 / (2*N))
                                             ~^~
```
[R/util.R:98:63:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L98) *style:* **Put spaces around all infix operators.**
```r
  trans_matrix[7, ] <- c(0 ,0, 0, 0, 0, 1 / (2*N),  1 - 1 / (2*N))
                                                             ~^~
```
[R/util.R:108:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:108:37:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
                                    ^
```
[R/util.R:116:49:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 3) cond_prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:119:45:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L119) *style:* **Commas should always have a space after.**
```r
                                     q * P[,6]
                                            ^
```
[R/util.R:122:49:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 4) cond_prob <- (p ^ 2) * ( P[1] + P[,4] + P[,7]) +
                                                ^
```
[R/util.R:122:60:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L122) *style:* **Commas should always have a space after.**
```r
  if (focal_state == 4) cond_prob <- (p ^ 2) * ( P[1] + P[,4] + P[,7]) +
                                                           ^
```
[R/util.R:122:68:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L122) *style:* **Commas should always have a space after.**
```r
  if (focal_state == 4) cond_prob <- (p ^ 2) * ( P[1] + P[,4] + P[,7]) +
                                                                   ^
```
[R/util.R:124:55:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L124) *style:* **Put spaces around all infix operators.**
```r
                                    (p ^ 4) * P[3] + p*P[,6]
                                                     ~^~
```
[R/util.R:124:59:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L124) *style:* **Commas should always have a space after.**
```r
                                    (p ^ 4) * P[3] + p*P[,6]
                                                          ^
```
[R/util.R:127:38:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L127) *style:* **Put spaces around all infix operators.**
```r
                                    2*(p ^ 2) * P[3] +
                                    ~^~
```
[R/util.R:127:39:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L127) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                                    2*(p ^ 2) * P[3] +
                                      ^
```
[R/util.R:146:1:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:146:44:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
                                           ^
```
[R/util.R:147:9:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L147) *style:* **Put spaces around all infix operators.**
```r
  q <- 1-p
       ~^~
```
[R/util.R:150:5:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L150) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(focal_state < 10) {
    ^
```
[R/util.R:151:18:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L151) *warning:* **no visible global function definition for ‘get_expectation_O_state’**
```r
    cond_prob <- get_expectation_O_state(P, p, focal_state)
                 ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:154:5:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L154) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(focal_state == 10) {
    ^
```
[R/util.R:155:50:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L155) *style:* **Put spaces around all infix operators.**
```r
    cond_prob <- 2 * p * q * P[1] + p * q * P[2] +2 * (p ^ 2) * (q ^ 2) * P[3]
                                                 ^~
```
[R/util.R:158:5:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/R/util.R#L158) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(focal_state == 11) {
    ^
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-equations.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-equations.R#L18) *style:* **Variable or function name should be snake_case.**
```r
  J <- junctions::number_of_junctions(N = 100, R = 1000,
  ^
```
[tests/testthat/test-marker_dist.R:4:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-marker_dist.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-marker_dist.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-marker_dist.R#L17) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-marker_dist.R#L60) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-marker_dist.R#L61) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-sims.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-sims.R#L5) *style:* **Variable or function name should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-sims.R#L6) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:14:46:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-sims.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    v <- rbind(v, as.numeric(v2$avgJunctions) )  # nolint
                                             ^
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-sims.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-sims.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:38:46:](https://github.com/thijsjanzen/junctions/blob/3c99e6ad3d771dd96691f89380afdaa08f8973e7/tests/testthat/test-sims.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    v <- rbind(v, as.numeric(v2$avgJunctions) )  # nolint
                                             ^
```


FTR, this is the forums post of the user who found this bug: https://openmx.ssri.psu.edu/node/4510 .


Hi,Where did you get this values?


ㅇㅇㅇㅇ


ㅇㅇㅇ


ok


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @gregoryashton, @duncanmmacleod were added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


a


Successfully aliased the URL <https://express-9v51rn83z.now.sh> to the following aliases.

* https://express.jfoggo.now.sh
* https://express-git-master.jfoggo.now.sh


> I think `s8p0` is perfectly valid. Maybe we should deprecate it in the standard?

I don't know. It's not a big problem.

But is this going so far as to be a possibility that anyone at some point could be able to exploit some auto reader vulnerability by feeding it, say, `s8p000000000000000004781774710507773 `?

Is it legitimate to request an `s999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999`?

> On 12 Jun 2019, at 16:05, Alexander Hill <notifications@github.com> wrote:
>
> I think s8p0 is perfectly valid. Maybe we should deprecate it in the standard?
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub, or mute the thread.


Successfully aliased the URL <https://react-pure-loaders-3gs437pws.now.sh> to the following aliases.

* https://react-pure-loaders.jameswlane.now.sh
* https://react-pure-loaders-git-master.jameswlane.now.sh


Created multidev environment [scicomposer#ci-559](https://dashboard.pantheon.io/sites/c2ba47eb-fd4a-436b-a2f6-28dc47557ea3#ci-559).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-559-scicomposer.pantheonsite.io/)


I believe that's a problem with the interpreter, not the standard.


AFN_FanModel (lgu1234) - Win64-Windows-10-VisualStudio-16: OK (2433 of 2433 tests passed, 11 test warnings)

Messages:\n
 * 11 tests had: ERR diffs.

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


🔥 Device tests completed (Failed) on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2758810)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/xcode11/87ed9ebfd42dca2d2d0115c323ea4b28801f74e3/2758810/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

230 tests' device not found, 0 tests passed.


these are not duplicate controls


oh la la, working so well now!
 Thanks!!


Perfect, many thanks for the information


forgot to commit Dockerfile so I cancelled CI/CD. That's why there is a red cross.


add cover.xml


TeamCity Bvcms / Build [Build 1313](https://builds.tpsdb.com/viewLog.html?buildId=6134&buildTypeId=Bvcms_Build) is now running


@mrdeep1 One more question, do you know how I can force client to use TLS_ECDHE_ECDSA_WITH_AES_128_CCM_8 cipher suite in tinydtls instead of TLS_PSK_WITH_AES_128_CCM_8?

Seems like the default is TLS_PSK_WITH_AES_128_CCM_8 .


Successfully aliased the URL <https://qdesrame-website-7t7a1rcli.now.sh> to the following aliases.

* https://qdesrame.dev
* https://www.qdesrame.dev
* https://qdesrame-website.quen2404.now.sh
* https://qdesrame-website-git-master.quen2404.now.sh


Successfully aliased the URL <https://relational-playground-r7nw4gmdq.now.sh> to the following aliases.

* https://relational-playground.michaelmior.now.sh
* https://relational-playground-git-master.michaelmior.now.sh


Issuing `SET NAMES` would break Unicode support in DBD::MariaDB, plus make DBI `quote` method insecure. And DBD::MariaDB already issue `SET NAMES utf8mb4` via C library function `mysql_options/MYSQL_SET_CHARSET_NAME`.

See also: https://metacpan.org/pod/DBD::MariaDB#UNICODE-SUPPORT
> Internally the DBD::MariaDB uses the MySQL's `utf8mb4` charset for the network communication with MariaDB and MySQL servers
> ...
> Do not try to change network charset (e.g. via SQL command `SET NAMES` manually) to anything different then UTF-8 as it would confuse underlying C library and DBD::MariaDB would misbehave (e.g. would lead to broken/insecure `quote` method or an emulated client side placeholders replacement).

`UTF-8` is in mysql protocol terminology named `utf8mb4`, not `utf8`.


TeamCity Bvcms / Build [Build 1313](https://builds.tpsdb.com/viewLog.html?buildId=6134&buildTypeId=Bvcms_Build) outcome was **FAILURE**
Summary: Exit code -1 (Step: Deploy to remote IIS (Command Line)) Build time: 00:03:42


Successfully aliased the URL <https://sergeyfilimonovcom-mzckw8svb.now.sh> to the following aliases.

* https://sergeyfilimonov.com
* https://sergeyfilimonovcom.sfilimonov.now.sh
* https://sergeyfilimonovcom-git-master.sfilimonov.now.sh


@gplssm  I tried to use `lv_to_pypsa` in order to transfer edisgo lv grids to pypsa format. But using that method introduces the problem that buses are listed in a `Line`s `bus0` or `bus1` field which do not exist.
Here the `side` parameter is passed over to the `__repr__` method. Thus the resulting bus will have `secondary` as a prefix. However that bus is not added to the bus dictionary. This raises errors in the later usage of pypsa for me.

I would be glad if you could tell me how I can export edisgo lv grids to pypsa nevertheless. Thanks
![image](https://user-images.githubusercontent.com/8457240/59359961-a011a100-8d2f-11e9-9ae5-b862a627a7d1.png)


水水水水水


Common


Aligned


xxx


Created multidev environment [scicomposer#ci-561](https://dashboard.pantheon.io/sites/c2ba47eb-fd4a-436b-a2f6-28dc47557ea3#ci-561).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-561-scicomposer.pantheonsite.io/)


Deployment failed with the following error:

~~~
The property `builds` is only allowed on Now 2.0 — please upgrade: https://zeit.co/upgrade
~~~


Successfully aliased the URL <https://vuetest-8zjewznsf.now.sh> to the following aliases.

* https://vue-test.medinazuri.now.sh
* https://vue-test-git-master.medinazuri.now.sh


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://v0-9-rescue-x-comms.pantheonsite.io/)

Created multidev environment [v0-9](https://dashboard.pantheon.io/sites/9dc3b9a0-4853-4dfd-b01f-6fe8cb0d08fd#v0-9) for rescue-x-comms.


Successfully aliased the URL <https://mainwebsite-mewkhthau.now.sh> to the following aliases.

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rm this


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* https://flight-lister.fatihtelis.now.sh
* https://flight-lister-git-master.fatihtelis.now.sh


`$Create2DB = $Connect2DB->prepare("INSERT INTO Article (name, description, created_at) VALUES (:name, :description, :created_at)");`


`$Result = $Create2DB->execute();`


`$Create2DB->bindParam(':created_at', $_POST['Created_at']);`


The bug is solved at this point.


你可以帮忙改下


ha! add Dockerfile and the green tick are there~


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* https://sergeyfilimonovcom-git-master.sfilimonov.now.sh


Successfully aliased the URL <https://ssr-demo-blfmcu2yn.now.sh> to the following aliases.

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Successfully aliased the URL <https://timdeschryverdev-3n5t6r7lh.now.sh> to the following aliases.

* https://timdeschryver.dev
* https://www.timdeschryver.dev
* https://timdeschryverdev.timdeschryver.now.sh
* https://timdeschryverdev-git-master.timdeschryver.now.sh


The behavior I saw was that the accept cancel buttons wouldn't go away, but at least parts of the form did reset when you click cancel.


@gplssm never mind. I just saw that the secondary side gets added in `mv_to_pypsa`. So I guess both methods only make sense together... Sorry I did bother you.


What does this do?


What is the risk of backward compatibility here?


🔥 Device tests completed (Failed) on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2758851)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/xcode11/6a852fdcc29c7ba7f72b63d4cddbcc7189c891a7/2758851/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

230 tests' device not found, 0 tests passed.


That's not strange, it is intended. TWRP replaces the AOSP standard recovery.
There is no recovery.img anymore for devices since A/B killed the recovery partition.
It is a normal behaviour.

I could say you trigger intentionally a strange behaviour with your "recovery partition exist" flag on devices without recovery partition.


🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2758850)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/xcode11/6a852fdcc29c7ba7f72b63d4cddbcc7189c891a7/2758850/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

230 tests' device not found, 0 tests passed.


AFN_FanModel (lgu1234) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (664 of 664 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.47%25-green.png)


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* https://react-pure-loaders.jameswlane.now.sh
* https://react-pure-loaders-git-master.jameswlane.now.sh


wrong date


Deployment failed with the following error:

~~~
You tried to create a Now 1.0 deployment. Please use Now 2.0 instead: https://zeit.co/upgrade
~~~


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @jtpdowns was added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

- @stuarteberg was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


stalePrev is always non-null. The code can probably also be simplified using Guava's Iterables.size()


Thanks for spotting that! Not sure why the CI build succeeded...

On Wed, Jun 12, 2019 at 8:52 AM George Zacharia <notifications@github.com>
wrote:

> Seems like a derp at
> https://github.com/moezbhatti/qksms/blob/e1c26d055ca1a3c2aa66cc55fd56ae262e3cdb66/android-smsmms/src/main/java/com/klinker/android/send_message/MmsReceivedService.java#L283
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/moezbhatti/qksms/commit/e1c26d055ca1a3c2aa66cc55fd56ae262e3cdb66?email_source=notifications&email_token=ABBIFANOQQI7CKV3BMEUYN3P2DWPRA5CNFSM4HXIU2S2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBAK4JJ#commitcomment-33911081>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/ABBIFAMPF7H3JLBUXJ4EHLDP2DWPRANCNFSM4HXIU2SQ>
> .
>

--
*Moez Bhatti*
Lead Developer, QKSMS
moez.bhatti@gmail.com


Congrats!


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* https://cecil.now.sh
* https://cecil-demo.now.sh
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* https://demo-git-master.cecilapp.now.sh


@nsheff I get no `NameError` even without this, at least on this command, with this commit installed (and `refgenconf` as downloaded from PyPI via this package's requirements):
```
(py3.5) vr @ ~/code/refgenie
dev└─ $ refgenie pull -c $REFGENIE -g hg38 -a bowtie2
Starting pull for 'hg38/bowtie2'
'hg38/bowtie2' archive size: 3.5GB
Downloading URL: http://refgenomes.databio.org/asset/hg38/bowtie2/archive
hg38/bowtie2:   0%|▏                                                                                | 5.71M/3.75G [00:03<21:43, 2.87MB/s]^C
The download was interrupted
Incomplete file '/home/vr/genomes/hg38/bowtie2.tar' was removed

```


Scratch the second part. Just sum up stalePrev.size() ;)


Hi I want to create an application that calculates ratios and all in Factorio with mods and it would be to know if I could use Factorio Data and or how you implemented the mods  in the database. Thanks.


In case this commit is correct and the docs are wrong, here's a docs PR: https://github.com/symfony/symfony-docs/pull/11732


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@DavideD There's already a `-s $HOME/.m2/settings-search-release.xml` in this line... I suspect your change will be ignored.


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#include <stdio.h>

#include <string.h>

#include <stdlib.h>

int main(int argc, char *argv[])
{
 int k;
 char temp;
 int i,j=0;
 int strsize = 0;
 for (i=1; i<argc; i++) {
 strsize += strlen(argv[i]);
 if (argc > i+1)
 strsize++;
 }
 char *cmdstring;
 cmdstring = malloc(strsize);
 cmdstring[0] = '\0';
 for (k=1; k<argc; k++) {
 strcat(cmdstring, argv[k]);
 if (argc > k+1)
 strcat(cmdstring, " ");
 }
 i = 0;
 j = strlen(cmdstring) - 1;
 while (i < j) {
 temp = cmdstring[i];
 cmdstring[i] = cmdstring[j];
 cmdstring[j] = temp;
 i++;
 j--;
 }
 printf("\nReverse string is :%s", cmdstring);
 return(0);

}


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* https://prezentacja-projekt-koncowy-wsb-git-master.lonwi.now.sh


Sorry for commenting on this old commit.

But this option seems to hide any 401/403 error and elastalert searches return 0 hits without any errors. Very hard to figure out why this was happening.


勤劳的upQwQ


The code changes in env/env_hdfs.cc break the build in HDFS env (build with USE_HDFS enabled). Can you please take a look?


@vlasenkoalexey Can you take a look at @dmmcerlean 's comment?


By the way, this commit does not enable MLD. The MLD side was added and enabled way earlier, with Gluon v2016.2 (2a51d94fbb06d086f1ee6b93dd343af4f37fc68c).

Since that commit the bridge on the node uses MLD queries to figure out where multicast listeners on the local wifi AP interface are and delivers multicast packets via individual wifi unicast transmissions (if there are any interested listeners for a specific multicast packet at all).

So we have had MLD on the client network side of each node for some years now. This patch now "just" extends this multicast awareness and interconnects the multicast awareness between the individual, per node client networks. To not only be able to filter and dissect multicast packets on the "last mile", the wifi AP of a node, but also before they enter and inside the mesh.


I think
"Value **y** enables HW timestamps in the packets"
or
"Value **y** enables HW packet timestamping"
would be better.


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


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* https://react-video-playlist.pjijin1.now.sh
* https://react-video-playlist-git-master.pjijin1.now.sh


considering you have a real C library you might want to think about strtoul() here


没我心情好才来修修 issue（


Successfully aliased the URL <https://liganicer-o5msn7gfo.now.sh> to the following aliases.

* https://liganicer.liganicer.now.sh
* https://liganicer-git-master.liganicer.now.sh


![](https://github.trello.services/images/mini-trello-icon.png) [Design Patterns](https://trello.com/c/ntJwe5Cl/4-design-patterns)


TeamCity SayMore / SayMore pull requests [Build *.*.344.cb2458a0ae697bcd34f8960135a3a77f227b9abb](http://build.palaso.org/viewLog.html?buildId=153733&buildTypeId=SayMore_SayMorePullRequests) outcome was **SUCCESS**
Summary: Running Build time: 00:01:41


Deployment failed with the following error:

~~~
Uploading failed. Please try again.
~~~


Where do these magic values come from for the buffer size ?
I recommend defines for this type of thing.


I suggest to change this section slightly.

First, unconditionally set ol_flags = 0;

Then, conditionally, do
  ol_flags |= PKT_RX_TIMESTAMP;
and the rest of the code.


large number - but why ?
I'd use a define I could change easily


Successfully aliased the URL <https://liganicer-4gflit221.now.sh> to the following aliases.

* https://liganicer.liganicer.now.sh
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I assume this is an import from mbed tests, its probably not worth changing for a Linux environment but, if you are so minded think about hexify and buffer sizes.


Please add a section explaining that enabling this option in configuration merely sets the validity flag in the MBUF and inserts the timestamp data - the timestamping unit still needs to be enabled separately according to the documentation of NFB products.


Please remove the comma.


The non-regression STC passed very easily.


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* https://liganicer.liganicer.now.sh
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Update


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* https://liganicer.liganicer.now.sh
* https://liganicer-git-master.liganicer.now.sh


Oh thank you for the information. So basically put, I've nothing to do when using MariaDB driver, right?


something doesn't click though because I was installing it and still getting the nameerror, but I'll give it another try. I'll take it out shortly :).


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>
>
> @alxhab: GameOverlay Z.105: Könnte man, nachdem die Bedingung erfüllt ist die Schleife abbrechen?
>
> Und danke für den Hinweis

@Cyention: Ja das geht, aber ich weiß nicht ob das so viel optimierung bringt.


line 27
`:HAS[@MODULE[MechJebCore]`
should be
`:HAS[@MODULE[ModuleCommand]`
otherwise it just applies to MJ Pod and AR202


maybe it wasn't earlier set to 0.1.2 ?


Thanks for reporting. Taking a look.


But of course, this is new now and adds a bit of complexity. Although we had multiple testers and reviewers for this, any observations, testing and feedback concerning multicast are very appreciated. I'd gladly have a look at any multicast related issues people come across.


I'll include that with the PR for #51.


The following doc(s) have been deployed to the [gatsby](https://gatsby-static-docs.pantheonsite.io/docs) Multidev environment:
- [source/content/migrate-manual.md](https://github.com/pantheon-systems/documentation/commit/fd0783971084f25a9640794e31130738168f25e7/source/content/migrate-manual.md)
- [source/content/modules-plugins-known-issues.md](https://github.com/pantheon-systems/documentation/commit/fd0783971084f25a9640794e31130738168f25e7/source/content/modules-plugins-known-issues.md)
- [source/content/platform-considerations.md](https://github.com/pantheon-systems/documentation/commit/fd0783971084f25a9640794e31130738168f25e7/source/content/platform-considerations.md)
- [source/content/required-reading.md](https://github.com/pantheon-systems/documentation/commit/fd0783971084f25a9640794e31130738168f25e7/source/content/required-reading.md)


need a "FIXME" here as well


Should say "no output" ?


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The following doc(s) have been deployed to the [wpdebuglog](https://wpdebuglog-static-docs.pantheonsite.io/docs) Multidev environment:
- [source/_partials/content/wp-debugging.html](https://github.com/pantheon-systems/documentation/commit/16f4da4d94f79e8833584fdda9f189f6ad71014b/source/_partials/content/wp-debugging.html)


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* https://relational-playground.michaelmior.now.sh
* https://relational-playground-git-master.michaelmior.now.sh


Why not grep (without -v) for kpatch-alternative?  That way we know the patch is applied.


wtf!!!!!!


Good work Boss, but on my own hardware, am thinking of sensing PV current instead of load current, using both Dcdc current and PV current for efficiency calculation.
Meanwhile still working on my 50a version .
I May not use THINGSET, as it's not fully supported . Thanks boss keep up the good work ..

![New Bitmap Image (2)](https://user-images.githubusercontent.com/36188081/59362437-57f07f80-8d2b-11e9-9dfc-e39d7115dd1a.png)


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* https://express.jfoggo.now.sh
* https://express-git-master.jfoggo.now.sh


Ah, I'm guessing it's because of powerpc


Why? i used the QP_id of the incoming RGP entry, which should map to the core being polled on


It looks like because of this "no break" we get duplicate body parameters.


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* https://rc-field-form.react-component.now.sh
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The black color will be changed soon, and user will be able to choose his own color.


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* https://liganicer.liganicer.now.sh
* https://liganicer-git-master.liganicer.now.sh


delete


@pgleeson

I have generalised the code to create the connectivity matrix for the 3 areas code.

The example below represents the connection between V1 -> V4 -> MT

![connection_matrix](https://user-images.githubusercontent.com/10345440/59362717-3ba51080-8d34-11e9-92ef-912f5348324e.jpg)

![Interareal gv](https://user-images.githubusercontent.com/10345440/59362644-1adcbb00-8d34-11e9-99a6-4d80694755ef.png)

Still to improve:
- Check that both the FF and the FB connection cannot be passed by the user
- Create the connectivity matrix from the list of regions passed by the user


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* https://liganicer.liganicer.now.sh
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We have been using semantic versioning so far, which implies vMajor.Minor.Patch - so this should be v3.10.11.  The `docs/version-control.md` has more links to details about this approach.


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Why 'static_cast<int>(*gl_lightmode)' and not 'static_cast<int>(gl_lightmode)'?


last


Model file


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* https://persistent-component.moviesom.com
* https://persistent-component.willim.nl
* https://ts-react-next-persistent-component.willemliu.now.sh
* https://ts-react-next-persistent-component-git-master.willemliu.now.sh


yes, this is an fork from mbed-crypto and modified to support the downstream consumer. I understand your comment about buffer sizes but I'm not sure what you referring to with hexify?


allQueries is a bit confusing to me. Rather name it allResults?


Yeah, my limited tests on the cube forge example show that the camera for the joining player is no longer sliding into position, but appears on the spot instead.


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It could happen that the core enqueues a WQE and then is immediately suspended, which would cause the RGP to get a wrong translation here