[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calc_K.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calc_K.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calc_K.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:14:20:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calc_K.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                   C = 1) {
                   ^
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calc_K.R#L16) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calc_K.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calc_K.R#L23) *style:* **Variable and function name style should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calc_K.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_error.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_error.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_error.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_error.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:19:24:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_error.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                       C = 1,
                       ^
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_error.R#L24) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_MAT.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_MAT.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_MAT.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:15:27:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_MAT.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          C = 1) {
                          ^
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_MAT.R#L20) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_time.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_time.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_time.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_time.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:17:27:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_time.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                          C = 1) {
                          ^
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/calculate_time.R#L28) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_markers.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_markers.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_markers.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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:2:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L2) *style:* **functions should have cyclomatic complexity of less than 15, this has 49.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L2) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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:122:23:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:122:32:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:125:10:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:129:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L129) *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:130:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L130) *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:134:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L134) *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:135:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L135) *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:136:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L136) *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:171:11:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L171) *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:178:58:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_phased.R#L178) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_unphased.R#L2) *style:* **functions should have cyclomatic complexity of less than 15, this has 28.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_unphased.R#L2) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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:102:23:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_unphased.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:102:32:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_unphased.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:105:12:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_unphased.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:160:11:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_unphased.R#L160) *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:167:58:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/estimate_time_unphased.R#L167) *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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions_backcross.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_backcross.R:11:43:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions_backcross.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
                                          C = 1,
                                          ^
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions_di.R#L12) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions_di.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions_markers.R#L20) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions_markers.R#L21) *style:* **Variable and function name style should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions_markers.R:32:27:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:16:33:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                                C = 1,
                                ^
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/number_of_junctions.R#L28) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_fin_chrom.R#L22) *style:* **Variable and function name style should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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:12:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_unphased.R#L12) *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/sim_phased_with_error.R:1:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_with_error.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Individual Based Simulation of the accumulation of junctions, given phasing error
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_with_error.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. Phased data is
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:3:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_with_error.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' generated using a user-provided error rate. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:8:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_with_error.R#L8) *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_with_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_with_error.R#L9) *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_with_error.R:10:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_with_error.R#L10) *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_with_error.R:15:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_with_error.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
#' @param error_rate fraction of markers that are erroneously phased (e.g. swapped)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:16:1:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/R/sim_phased_with_error.R#L16) *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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/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)]      )
                                                         ^
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-equations.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-equations.R#L18) *style:* **Variable and function name style 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/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-marker_dist.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-marker_dist.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-marker_dist.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-marker_dist.R#L60) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-marker_dist.R#L61) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-phased-error.R:53:64:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-phased-error.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  expected_heterozygosity <- 2 * 0.5 * 0.5 * (1 - 1 / (2 * 100) ) ^ 200
                                                               ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-sims.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-sims.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-sims.R#L6) *style:* **Variable and function name style should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:7:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-sims.R#L7) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-sims.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-sims.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:31:3:](https://github.com/thijsjanzen/junctions/blob/01dd9084b3e00cbe645020dc126c09b5d9aacf02/tests/testthat/test-sims.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```


I was curious because you left `D_JSON_TEMPERATURE` in the second part of the `if` statement and since I'm learning C now (I´m on Python side, sorry!) I'm trying to figure out all I can quickly. :P


kangerrrr


Actually, speed was not different, but still the regression test failed badly. So something is different. Could be that the compilation differs from my machine to others? Or maybe I didn't preserve functionality? Not clear.

Anyway, I will need more tests after exploring some possibilities.


@dpochernin Два вопроса: 1) разобрался ли ты в функции map? 2) Ты уверен, что нет другой функции для суммирования кроме fsum из библиотеки math?


Successfully deployed to following URLs:

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* https://bnr-git-master.fdmediagroep.now.sh


[R/calc_sum_stats.R:9:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/calc_sum_stats.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
calc_sum_stats <- function(focal_tree, emp_tree = NULL) {
^
```
[R/generate_naive.R:18:4:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/generate_naive.R#L18) *style:* **Commented code should be removed.**
```r
#  oplan <- future::plan()
   ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/generate_naive.R:19:4:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/generate_naive.R#L19) *style:* **Commented code should be removed.**
```r
#  on.exit(future::plan(oplan), add = TRUE)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/generate_naive.R:21:4:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/generate_naive.R#L21) *style:* **Commented code should be removed.**
```r
#  future::plan(future::multiprocess)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/generate_naive.R:41:9:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/generate_naive.R#L41) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(is.null(found_tree)) {
        ^
```
[R/generate_naive.R:45:16:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/generate_naive.R#L45) *style:* **Use <-, not =, for assignment.**
```r
      num_tips = found_tree$Nnode + 1
               ^
```
[R/generate_naive.R:47:9:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/generate_naive.R#L47) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(num_tips >= min_tips && num_tips <= max_tips) {
        ^
```
[R/generate_naive.R:79:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/generate_naive.R#L79) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/infer_params.R:14:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 19.**
```r
infer_params <- function(number_of_particles,
^
```
[R/infer_params.R:30:16:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L30) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
  emp_stats <- calc_sum_stats(emp_tree, emp_tree)
               ^~~~~~~~~~~~~~
```
[R/infer_params.R:33:44:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L33) *warning:* **no visible binding for global variable ‘param_from_prior’**
```r
  previous_par <- t(apply(param_matrix, 1, param_from_prior))
                                           ^~~~~~~~~~~~~~~~
```
[R/infer_params.R:39:5:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L39) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(continue_from_file == TRUE) {
    ^
```
[R/infer_params.R:40:8:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L40) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in max_iter:0) {
       ^
```
[R/infer_params.R:42:9:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L42) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(file.exists(file_name) ) {
        ^
```
[R/infer_params.R:42:32:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L42) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if(file.exists(file_name) ) {
                               ^
```
[R/infer_params.R:51:18:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L51) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
    emp_stats <- calc_sum_stats(emp_tree, emp_tree)
                 ^~~~~~~~~~~~~~
```
[R/infer_params.R:84:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L84) *style:* **Lines should not be more than 80 characters.**
```r
      found_trees <- apply(candidate_particles, 1, sim_envidiv_tree, crown_age, TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_params.R:84:52:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L84) *warning:* **no visible binding for global variable ‘sim_envidiv_tree’**
```r
      found_trees <- apply(candidate_particles, 1, sim_envidiv_tree, crown_age, TRUE)
                                                   ^~~~~~~~~~~~~~~~
```
[R/infer_params.R:89:31:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L89) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
          stat_matrix[i, ] <- calc_sum_stats(found_trees[[i]], emp_tree)[1:8]
                              ^~~~~~~~~~~~~~
```
[R/infer_params.R:99:44:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/infer_params.R#L99) *warning:* **no visible binding for global variable ‘calc_fit’**
```r
        local_fit <- apply(stat_matrix, 1, calc_fit, emp_stats)
                                           ^~~~~~~~
```
[R/is_within_prior.R:5:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/is_within_prior.R#L5) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
is_within_prior <- function(params) {
^
```
[R/RcppExports.R:6:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/RcppExports.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param waterlevel_changes a vector that indicates the time points of water level changes
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/RcppExports.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:11:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/RcppExports.R#L12) *style:* **Only use double-quotes.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:49:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/RcppExports.R#L12) *style:* **Only use double-quotes.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
                                                ^~~~~~~~~
```
[R/RcppExports.R:14:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/RcppExports.R#L14) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_envidiv_tree.R:23:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/sim_envidiv_tree.R#L23) *style:* **functions should have cyclomatic complexity of less than 15, this has 32.**
```r
sim_envidiv_tree <- function(params,
^
```
[R/sim_envidiv_tree.R:33:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/sim_envidiv_tree.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
  if (is.null(seed) || is.na(seed) || length(seed) == 0) seed <- as.numeric(Sys.time())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:37:20:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/R/sim_envidiv_tree.R#L37) *warning:* **no visible global function definition for ‘generate_water’**
```r
  water_changes <- generate_water(params[6], crown_age)
                   ^~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:33:5:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/tests/testthat/test-infer_params.R#L33) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(1 == 2) {
    ^
```
[tests/testthat/test-infer_params.R:40:1:](https://github.com/thijsjanzen/enviDiv/blob/7a3faea1baad427a3f1021814d6a2357ff268d43/tests/testthat/test-infer_params.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    testthat::expect_equal(3, length(summary(vx))) # if TRUE, length(summary) = 2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://nohai-app-8katm707e.now.sh
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* https://nohai-app-git-master.nohai.now.sh


Do you think you can find something like:

```solidity
(game.status == Status.NotInPlay) == (game.player1Sender == 0)
```
for all of the statuses?


Successfully deployed to following URLs:

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it's all about karma
https://github.com/AOSiP-Devices/device_xiaomi_sdm660-common/commit/b04795b7d335b95a4bc49ea2ae47177fa4807194


This is the If Else conditional statement


@dpochernin Эту задачу можно решить без цикла. Мы ведь циклы не успели на занятии, поэтому задачи на цикл я вам не давала. Реши без цикла, пожалуйста! Тем более, что у тебя в твоем цикле максимум одна или ноль итераций, а значит сам цикл не нужен. А что нужно в такм случае?


j


Sorry to comment that so late, I just discovered browsing my email box...

That's fine but you also need to add `MinSizeRel` and `RelWithDebInfo`.


@dpochernin Чем тебе не подошед обычный метод `split`?


@dpochernin И еще: есть второе решение не переводя число в строку, работая просто с числом. Хочешь попробовать?


I would have preferred the `with` statement too, but apparently the Python 2 version of that function did not support the context manager, so I just went for the laziest solution to get it up and running for now :)


My bad, I was thinking that `Release` and `Debug` was enough. :bowing_man:


[R/calculate_allele_frequencies.R:34:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_fst.R#L78) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop1[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:79:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_fst.R#L79) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop1[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:85:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_fst.R#L85) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop2[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:86:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_fst.R#L86) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop2[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_ld.R:39:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_ld.R#L51) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 1 + findtype(pop[[i]]$chromosome1, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:52:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_ld.R#L52) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 1 + findtype(pop[[i]]$chromosome2, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:73:15:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_ld.R#L73) *warning:* **no visible global function definition for ‘calculate_average_ld’**
```r
        ld <- calculate_average_ld(g1, g2)
              ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_ld.R:93:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_ld.R#L93) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
calculate_average_ld <- function(alleles_pos_1, alleles_pos_2) {
^
```
[R/calculate_marker_frequency.R:31:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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:24:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/calculate_tajima_d.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
calculate_tajima_d <- function(pop,
^
```
[R/calculate_tajima_d.R:28:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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:72:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/simulate_admixture_migration.R#L72) *style:* **functions should have cyclomatic complexity of less than 15, this has 36.**
```r
simulate_admixture_migration <- function(input_population_1 = NA,
^
```
[R/simulate_admixture_migration.R:105:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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$population_1)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:203:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/simulate_admixture_migration.R#L203) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_2 <- create_pop_class(selected_pop$population_2)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:51:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/simulate_admixture.R#L51) *style:* **functions should have cyclomatic complexity of less than 15, this has 26.**
```r
simulate_admixture <- function(input_population = NA,
^
```
[R/simulate_admixture.R:81:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/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/31672b4c6b78209a31cbf25096906caeb3bd8dcb/R/utilities.R#L275) *warning:* **no visible binding for global variable ‘verify_individual’**
```r
  v <- unlist(lapply(pop, verify_individual))
                          ^~~~~~~~~~~~~~~~~
```


wtf


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Sure! https://github.com/cure53/DOMPurify/pull/368


I wonder if doing:

```solidity
Game memory zero = Game();
gameMap[entryHash] = zero;
```
would save gas because `player1Sender` and `player2Move` are on the same storage slot, same with `player2Sender` and `status`, so perhaps the compiler does 1 `SSTORE` per slot with the `memory zero` one instead of 2 as per your code.


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A


It is already fixed on 2c8b3243dca0c48dd05ecd7b420a7a03b3e19c93


Now could not deploy this pull request since it contains the following references to invalid secrets in the `env` sections of the `now.json` file:

* `airtable-api-key` (in env: `AIRTABLE_API_KEY)`

Add those secrets or remove them from the `env` maps in the `now.json` file.


Puzzle `20-eb4af059` disappeared from [`src/main/java/org/cactoos/http/HtKeepAliveResponse.java`](https://github.com/yegor256/cactoos-http/blob/master/src/main/java/org/cactoos/http/HtKeepAliveResponse.java), that's why I closed #74. Please, remember that the puzzle was not necessarily removed in this particular commit. Maybe it happened earlier, but we discovered this fact only now.


> For Portworx, the default cache block size is 1MB. Thus, the migration bandwidth is 10MB.
Need revision. The default cache block size is automatically found based on the assigned cache capacity for a given pool. If it is 1MB, then default migration bandwidth is set to 100 times cache block size at 100MB. This translates to 204800 512 byte sectors.


Deployment failed with the following error:

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


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Unused declaration.


不客气！互相学习和交流！


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@dpochernin Что-то ты намудрил: если я ввожу 12.1, мне выдает `No digit on second after "." in this number`. Я вижу в чем ошибка, но хочу, чтобы ты сам разобрался. Исправь!


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`curl -4 https://vincent.bernat.ch/ip`, `curl -6 https://vincent.bernat.ch/ip` ?


Update info on NorESM github development repository.


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Thanks for fixing)


@dpochernin Не правильно: у тебя все, которые делятся на 100 не високосные, даже те что делятся на 400. Т.е. у тебя условие `not (y % 400)` никогда не срабатывает


Shouldn't we cleanup all `wsrep_thd_query(thd)) ? wsrep_thd_query(thd) : "void"` constructs?


@dpochernin 👍


berigud sir hahahaha


changed {% if post.categories **==** 'blog' %}
		{% endif %}
to           {% if post.categories **contains** 'blog' %}
		{% endif %}


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Update to this commit, appearing again  [issues90](https://github.com/zevlg/telega.el/issues/90)


Fixes #18


add this one


Ok, ovo smo uradili, zajedno :)


Ovo sam uneo, mada nisam siguran kako mi pomaze. Mozemo da prodiskutujemo.


Ovo sam dodao i radi, ako neki objekat u jsonu nema text atribut ispise se "missing text" po defaultu


modify and indent content


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@dpochernin "All other is right ?" No, I checked all your homework only today


@IgorKalinovskii Можно!


Ar buvo realiai testuota 100000 simoblių 1000 000 skirtingų porų eksperimentas? Nes net ir leidžiant su sha256 algoritmu šis procesas užima 9 valandas. Gal būt reiktų mažinti reikalavimus.


Deployment failed with the following error:

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


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Deployment failed with the following error:

~~~
The chosen alias "preloader.now.sh" is already in use by another account.
~~~


usersテーブルとgroupsデーブルのアソシェーションを修正しました
1対多　多対多の関係でhas_manyを使用しました


@IgorKalinovskii Файлы лучше заканчивать знаком переноса строки (об этом тебе github красным знаком вконе этой строки говорит). Это потому, что если ты будешь добавлять еще строки в конец файла, то эта последняя строка будет тоже измененной, т.к. ты в конце строки поставил перенос строки. Но по факту (то, что видит человек) ты строку не менял


在处理事情的优先级方面


2.0.0 version published, https://github.com/shepherdwind/velocity.js/blob/master/History.md#200-2019-09-26

@timse You can upgrade to the new version, and set escape option to true. https://github.com/shepherdwind/velocity.js/blob/master/index.d.ts#L39


@IgorKalinovskii А что будет, если ты выполнишь `s.center(100)`? Попробуй! И объясни почему и где об этом написано в документации


@IgorKalinovskii 👍


Why cast?


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![](https://github.trello.services/images/mini-trello-icon.png) [2 - Добавить инициализацию даты и времени и функции для обновления и ускорения](https://trello.com/c/o1h1dvux/7-2-%D0%B4%D0%BE%D0%B1%D0%B0%D0%B2%D0%B8%D1%82%D1%8C-%D0%B8%D0%BD%D0%B8%D1%86%D0%B8%D0%B0%D0%BB%D0%B8%D0%B7%D0%B0%D1%86%D0%B8%D1%8E-%D0%B4%D0%B0%D1%82%D1%8B-%D0%B8-%D0%B2%D1%80%D0%B5%D0%BC%D0%B5%D0%BD%D0%B8-%D0%B8-%D1%84%D1%83%D0%BD%D0%BA%D1%86%D0%B8%D0%B8-%D0%B4%D0%BB%D1%8F-%D0%BE%D0%B1%D0%BD%D0%BE%D0%B2%D0%BB%D0%B5%D0%BD%D0%B8%D1%8F-%D0%B8-%D1%83%D1%81%D0%BA%D0%BE%D1%80%D0%B5%D0%BD%D0%B8%D1%8F)


Groß/Kleinschreibung


@IgorKalinovskii Правильно, но интересно то, что эту задачку можно решить в одну строку без использования `if`. Т.е. написать одну формулу, которая правильно сработает и для четных и для нечетных


paga


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Aqui a gente poderia definir
 `` char output[tamanhoSequencia * 2]; `` ?

Assim caso a sequencia tivesse por exemplo 7 algoritmos o output teria 14 espaços no maximo.

O que acha?


@IgorKalinovskii Да, можно и такое:) Если и другие решения, если преобразовывать числа в строку


Muito bom!  :rocket:  :smile:


DCA6321D2892: 树莓派_新疆_2223_有线
DCA6321D2894: 树莓派_新疆_2223_无线


`@RESOURCE[ElectricCharge` needs a closing ]


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h


nice post!!!!!!


agree


Could you double check the above `if`. Why no engine check if session setting is `STRICT`?


- **Processor**: Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz 3.19 GHz
- **RAM**: 16.0 GB
- **OS**: Windows 10 Pro 64bit
- Node.js 12.11.0

On the `eslint` repo, `--parallel` looks like 2x faster.

```
$ eslint bin lib tests/lib
Linting complete in: 19215ms
```

```
$ eslint bin lib tests/lib --parallel
Start 4
Start 10
Start 1
Start 2
Start 5
Start 7
Start 9
Start 6
Start 11
Start 3
Start 8
Finish 4
Finish 3
Finish 5
Finish 6
Finish 10
Finish 1
Finish 11
Finish 9
Finish 2
Finish 12
Finish 8
Finish 7
Linting complete in: 9113ms
```


Actually, v12.11.0. The constant `UV_FS_O_FILEMAP` was not exposed in `fs.constants` before so this won't work.


Extron device was broken by long HSync
It can accept 4.7us but doesn't accept 5.0us already.
https://github.com/MiSTer-devel/Genesis_MiSTer/issues/78


hoqqppa


Can you adjust the position without touching the HSync size?


Redundant space.


лишняя строка


надо исправить


@dpochernin Пока мало мы выучили. В седующий раз будет больше и на эти темы тоже. Вернее и эти темы и новые будут вместе. Но если знаешь уже больше, то можешь поискать задачки в интернете. Их много. Например: http://pythontutor.ru/lessons/inout_and_arithmetic_operations/problems/aplusbplusc/ или https://informatics.mccme.ru/course/view.php?id=156


@dpochernin Да, увидела


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@dpochernin 👍


@knownasilya FYI this should be considered a breaking change and released in a major (or pre-1.0 in a minor) version. it looks like this was released in v0.2.2 though, which is now breaking a lot of depending packages where CI is still running on Node.js 6 :-/


#44 should be fixed by this.


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@alfonsogarciacaro This is awesome, thanks a lot.
The [export](https://github.com/ncave/fsharp/pull/3) branch is rebased, if you want to run the `export.metadata` target for sdk 3.0 binaries (I promise to do it next time).


No <tab>s please.


Ich würde das einheitlich machen bei den Namen und Unternehmen. Sandra arbeitet ja auch bei der RedTecLab :-)


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):

> set -x && set -e && set -o pipefail && cd /tmp/0pdd20190926-4-11ditdu/kkamkou/gitmostwanted.com && pdd -v -f /tmp/20190926-12945-18acgas [1]: bash: warning: setlocale: LC_ALL: cannot change locale (UTF-8) + set -e + set -o pipefail + cd /tmp/0pdd20190926-4-11ditdu/kkamkou/gitmostwanted.com + pdd...

Please, copy and paste this stack trace to GitHub:

```
UserError
set -x && set -e && set -o pipefail && cd /tmp/0pdd20190926-4-11ditdu/kkamkou/gitmostwanted.com && pdd -v -f /tmp/20190926-12945-18acgas [1]:
bash: warning: setlocale: LC_ALL: cannot change locale (UTF-8)
+ set -e
+ set -o pipefail
+ cd /tmp/0pdd20190926-4-11ditdu/kkamkou/gitmostwanted.com
+ pdd -v -f /tmp/20190926-12945-18acgas

My version is 0.20.5
Ruby version is 2.6.0 at x86_64-linux
Reading /tmp/0pdd20190926-4-11ditdu/kkamkou/gitmostwanted.com
104 file(s) found, 56 excluded
/tmp/0pdd20190926-4-11ditdu/kkamkou/gitmostwanted.com/gitmostwanted/static/images/bg.png is a binary file (661 bytes)
/tmp/0pdd20190926-4-11ditdu/kkamkou/gitmostwanted.com/gitmostwanted/static/favicon.ico is a binary file (318 bytes)
Reading alembic.ini...
Reading LICENSE...
Reading instance.cfg.distr...
Reading .codeclimate.yml...
Reading wercker.yml...
Reading Readme.md...
Reading requirements.txt...
Reading .coveralls.yml...
Reading .gitignore...
Reading gitmostwanted.com.wsgi.distr...
Reading docker-compose.yml...
Reading gitmostwanted/blueprints/user_attitude.py...
Reading gitmostwanted/blueprints/repo_rating.py...
Reading gitmostwanted/blueprints/static_content.py...
Reading gitmostwanted/blueprints/user_profile.py...
Reading gitmostwanted/blueprints/user_oauth.py...
Puzzle 1-a36e7cf1 15/DEV at gitmostwanted/blueprints/user_oauth.py
Puzzle 2-ab6bea6a 15/DEV at gitmostwanted/blueprints/user_oauth.py
Reading gitmostwanted/blueprints/repo_trending.py...
Reading gitmostwanted/models/report.py...
Reading gitmostwanted/models/user.py...
Reading gitmostwanted/models/repo.py...
Reading gitmostwanted/app.py...
Reading gitmostwanted/config.py...
Reading gitmostwanted/static/styles.css...
Reading gitmostwanted/static/common.js...
Reading gitmostwanted/services/sentry.py...
Reading gitmostwanted/services/oauth.py...
Reading gitmostwanted/services/celery.py...
Reading gitmostwanted/services/bigquery.py...
Reading gitmostwanted/services/log.py...
Reading gitmostwanted/services/db.py...
Reading gitmostwanted/templates/index.html...
Reading gitmostwanted/templates/layout.html...
Reading gitmostwanted/templates/profile.html...
Reading gitmostwanted/templates/repository/attitude.html...
Reading gitmostwanted/templates/repository/top.html...
Reading gitmostwanted/templates/repository/details.html...
Reading gitmostwanted/templates/macros/repository.html...
Reading gitmostwanted/templates/macros/attitude.html...
Reading gitmostwanted/templates/macros/messages.html...
Reading gitmostwanted/templates/macros/navigation.html...
Reading gitmostwanted/templates/static/donations.html...
Reading gitmostwanted/templates/footer.html...
Reading gitmostwanted/tasks/repo_most_starred.py...
Reading gitmostwanted/tasks/repo_metadata.py...
Reading gitmostwanted/tasks/github.py...
Reading gitmostwanted/tasks/repo_status.py...
Reading gitmostwanted/tasks/repo_stars.py...
Puzzle 0-15c49b8d 15/DEV at gitmostwanted/tasks/repo_stars.py
Puzzle 192-ebcb75c9 60/DEV at gitmostwanted/tasks/repo_stars.py
Reading gitmostwanted/web.py...
Reading gitmostwanted/lib/regex.py...
Reading gitmostwanted/lib/bigquery/result.py...
Puzzle 0-68786374 180/DEV at gitmostwanted/lib/bigquery/result.py
Reading gitmostwanted/lib/bigquery/job.py...
Reading gitmostwanted/lib/bigquery/service.py...
ERROR: gitmostwanted/lib/bigquery/service.py; puzzle at line #17; @todo found, but puzzle can't be parsed, most probably because @todo is not followed by a puzzle marker, as this page explains: https://github.com/yegor256/pdd#how-to-format
If you can't understand the cause of this issue or you don't know how to fix it, please submit a GitHub issue, we will try to help you: https://github.com/yegor256/pdd/issues. This tool is still in its beta version and we will appreciate your feedback. Here is where you can find more documentation: https://github.com/yegor256/pdd/blob/master/README.md.
Exit code is 1

/app/objects/git_repo.rb:66:in `rescue in block in xml'
/app/objects/git_repo.rb:63:in `block in xml'
/app/vendor/ruby-2.6.0/lib/ruby/2.6.0/tempfile.rb:295:in `open'
/app/objects/git_repo.rb:62:in `xml'
/app/objects/puzzles.rb:36:in `deploy'
/app/objects/job.rb:38:in `proceed'
/app/objects/job_starred.rb:33:in `proceed'
/app/objects/job_recorded.rb:32:in `proceed'
/app/objects/job_emailed.rb:35: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'
```


1、“题目来源”修改成“课题背景”更书面化，可以再简单介绍一下此项目的应用背景；
2、需要标明课题的进度安排。


would using `time.perf_counter()` be more efficient?


Why another `#ifdef WITH_WSREP`? Similar `ifdef` is immediately following this one.


Successfully deployed to following URLs:

* https://materialize-angular-guide-42g0adv0p.now.sh
* https://materialize.workylab.com
* https://materialize-angular.workylab.com
* https://materialize-angular-guide.workylab.now.sh
* https://materialize-angular-guide-git-master.workylab.now.sh


latest


That's not correct, we pull `daffy` on the Pi, `daffy-amd64` on the laptop


This is so exciting!! So excited to see the results of this! Thanks for all your hard work!


Wooowww 🥳😱

Sent from my iPhone

> On Sep 26, 2019, at 8:29 PM, jmgabon <notifications@github.com> wrote:
>
>
> berigud sir hahahaha
>
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