[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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 $objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:6:1:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/R/optim_limits.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param iterations number of times the boundaries should be adjusted to obtain an estimate that is not close to the boundaries. After this number of iterations is exceeded, NA is returned
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:22:5:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/R/optim_limits.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(verbose) cat(lower, upper, estim$minimum, "\n")
    ^
```
[R/optim_limits.R:30:7:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/R/optim_limits.R#L30) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(verbose) cat(lower, upper, estim$minimum, "\n")
      ^
```
[R/optim_limits.R:43:7:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/R/optim_limits.R#L43) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(verbose)  cat(lower, upper, estim$minimum, "\n")
      ^
```
[R/phased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/sim_phased_with_error.R:69:4:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/R/sim_phased_with_error.R#L69) *style:* **Commented code should be removed.**
```r
#  testit::assert(all.equal(unique(phased_data$location), selected_markers))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:71:6:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/R/sim_phased_with_error.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in unique(phased_data$individual)) {
     ^
```
[R/sim_phased_with_error.R:77:7:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/R/sim_phased_with_error.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(to_flip) > 0) {
      ^
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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:53:31:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/tests/testthat/test-phased-error.R#L53) *style:* **Put spaces around all infix operators.**
```r
  expected_heterozygosity <- 2*0.5*0.5 * (1 - 1 / (2*100) )^200
                             ~^~
```
[tests/testthat/test-phased-error.R:53:35:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/tests/testthat/test-phased-error.R#L53) *style:* **Put spaces around all infix operators.**
```r
  expected_heterozygosity <- 2*0.5*0.5 * (1 - 1 / (2*100) )^200
                                 ~^~
```
[tests/testthat/test-phased-error.R:53:53:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/tests/testthat/test-phased-error.R#L53) *style:* **Put spaces around all infix operators.**
```r
  expected_heterozygosity <- 2*0.5*0.5 * (1 - 1 / (2*100) )^200
                                                   ~^~
```
[tests/testthat/test-phased-error.R:53:58:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/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-phased-error.R:55:6:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/tests/testthat/test-phased-error.R#L55) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in unique(true_data$individual)) {
     ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/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/05a0f0323098bf36c671da04824832b8fd499e51/tests/testthat/test-sims.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```


Successfully aliased the URL <https://accharplanner-mhucqfwc4.now.sh> to the following aliases:

* https://accharplanner.amoeba.now.sh
* https://accharplanner-git-master.amoeba.now.sh


Does php magic __wakeup() also qualify for this case?


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Successfully aliased the URL <https://entrepreneur-site-next-m7hetniga.now.sh> to the following aliases:

* https://entrepreneur-site-next.hacker-tom.now.sh
* https://entrepreneur-site-next-git-master.hacker-tom.now.sh


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:

* `firebase_parking_config` (in env: `firebase_parking_config)`
* `google_maps_api_key` (in env: `google_maps_api_key)`

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


Successfully aliased the URL <https://instaclone-67otfpgpk.now.sh> to the following aliases:

* https://instaclone.foxterinogg.now.sh
* https://instaclone-git-master.foxterinogg.now.sh


WaterToAirHP6323 (rraustad) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2590 of 2593 tests passed, 10 test warnings)

Messages:\n
 * 6 tests had: EIO diffs.
 * 1 test had: ERR diffs.
 * 3 tests had: ESO big diffs.
 * 1 test had: MTR big diffs.
 * 1 test had: Table big diffs.
 * 7 tests had: BND diffs.
 * 3 tests had: ESO small diffs.
 * 5 tests had: MTR small diffs.
 * 4 tests had: Table small diffs.

Failures:\n

regression Test Summary
 * Passed: 685
 * Failed: 3

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.88%25-yellow.png)


Corrupt nif file.


TeamCity Bvcms / Build [Build 2013](https://builds.tpsdb.com/viewLog.html?buildId=8361&buildTypeId=Bvcms_Build) is now running


Ther playfair cipher program is being written which is divided into various modules


The following doc(s) have been deployed to the [circlecidl](https://circlecidl-static-docs.pantheonsite.io/docs) Multidev environment:
- [.circleci/config.yml](https://github.com/pantheon-systems/documentation/commit/560fe87f617017296029b282194d1374da0a3b80/.circleci/config.yml)


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

* https://reshadow.dev
* https://reshadow.now.sh
* https://reshadow.lttb.now.sh
* https://reshadow-git-master.lttb.now.sh


is still necessary to update the changelog manually? I thought there are tools for automating this if we use conventional commits


take it to Slack, please, under #prod-edu, gentlemen. Meet you over there.


Successfully aliased the URL <https://next-portfolio-g0tq7ebv2.now.sh> to the following aliases:

* https://tim-soft.now.sh
* https://timellenberger.now.sh
* https://timellenberger.com
* https://next-portfolio.tim-soft.now.sh
* https://next-portfolio-git-master.tim-soft.now.sh


CoolingTowerPlantComponent (Myoldmopar) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2592 of 2593 tests passed, 4 test warnings)

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

Failures:\n

integration Test Summary
 * Passed: 672
 * Failed: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.96%25-yellow.png)


"C:\Program Files\Java\jdk1.8.0_201\bin\java.exe" -ea -Didea.test.cyclic.buffer.size=1048576 "-javaagent:C:\Program Files\JetBrains\IntelliJ IDEA 2018.3.3\lib\idea_rt.jar=64467:C:\Program Files\JetBrains\IntelliJ IDEA 2018.3.3\bin" -Dfile.encoding=UTF-8 -classpath "C:\Program Files\JetBrains\IntelliJ IDEA 2018.3.3\lib\idea_rt.jar;C:\Program Files\JetBrains\IntelliJ IDEA 2018.3.3\plugins\junit\lib\junit-rt.jar;C:\Program Files\JetBrains\IntelliJ IDEA 2018.3.3\plugins\junit\lib\junit5-rt.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\charsets.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\deploy.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\access-bridge-64.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\cldrdata.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\dnsns.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\jaccess.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\jfxrt.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\localedata.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\nashorn.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\sunec.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\sunjce_provider.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\sunmscapi.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\sunpkcs11.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\ext\zipfs.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\javaws.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\jce.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\jfr.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\jfxswt.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\jsse.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\management-agent.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\plugin.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\resources.jar;C:\Program Files\Java\jdk1.8.0_201\jre\lib\rt.jar;D:\mateusz\Pobrane\kółko i krzyżyk\tic-tac-toe-master\tasks\out\test\classes;D:\mateusz\Pobrane\kółko i 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191aa8c73e4f393759ed\netty-resolver-4.1.38.Final.jar;C:\Users\mateu\.gradle\caches\modules-2\files-2.1\io.netty\netty-common\4.1.38.Final\6f8aae763f743d91fb1ba1e9011dae0ef4f6ff34\netty-common-4.1.38.Final.jar;C:\Users\mateu\.gradle\caches\modules-2\files-2.1\org.ow2.asm\asm\5.0.4\da08b8cce7bbf903602a25a3a163ae252435795\asm-5.0.4.jar" com.intellij.rt.execution.junit.JUnitStarter -ideVersion5 -junit4 com.crud.tasks.trello.client.TrelloClientTest

java.lang.AssertionError:
Expected :1
Actual   :0
 <Click to see difference>

	at org.junit.Assert.fail(Assert.java:88)
	at org.junit.Assert.failNotEquals(Assert.java:834)
	at org.junit.Assert.assertEquals(Assert.java:645)
	at org.junit.Assert.assertEquals(Assert.java:631)
	at com.crud.tasks.trello.client.TrelloClientTest.shouldFetchTrelloBoards(TrelloClientTest.java:60)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
	at org.mockito.internal.runners.DefaultInternalRunner$1.run(DefaultInternalRunner.java:79)
	at org.mockito.internal.runners.DefaultInternalRunner.run(DefaultInternalRunner.java:85)
	at org.mockito.internal.runners.StrictRunner.run(StrictRunner.java:39)
	at org.mockito.junit.MockitoJUnitRunner.run(MockitoJUnitRunner.java:163)
	at org.junit.runner.JUnitCore.run(JUnitCore.java:137)
	at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:68)
	at com.intellij.rt.execution.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:47)
	at com.intellij.rt.execution.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:242)
	at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:70)

[MockitoHint] TrelloClientTest.shouldFetchTrelloBoards (see javadoc for MockitoHint):
[MockitoHint] 1. Unused... -> at com.crud.tasks.trello.client.TrelloClientTest.shouldFetchTrelloBoards(TrelloClientTest.java:54)
[MockitoHint]  ...args ok? -> at com.crud.tasks.trello.client.TrelloClient.getTrelloBoards(TrelloClient.java:44)

java.lang.NullPointerException
	at com.crud.tasks.trello.client.TrelloClientTest.shouldCreateCard(TrelloClientTest.java:90)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
	at org.mockito.internal.runners.DefaultInternalRunner$1.run(DefaultInternalRunner.java:79)
	at org.mockito.internal.runners.DefaultInternalRunner.run(DefaultInternalRunner.java:85)
	at org.mockito.internal.runners.StrictRunner.run(StrictRunner.java:39)
	at org.mockito.junit.MockitoJUnitRunner.run(MockitoJUnitRunner.java:163)
	at org.junit.runner.JUnitCore.run(JUnitCore.java:137)
	at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:68)
	at com.intellij.rt.execution.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:47)
	at com.intellij.rt.execution.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:242)
	at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:70)

[MockitoHint] TrelloClientTest.shouldCreateCard (see javadoc for MockitoHint):
[MockitoHint] 1. Unused... -> at com.crud.tasks.trello.client.TrelloClientTest.shouldCreateCard(TrelloClientTest.java:85)
[MockitoHint]  ...args ok? -> at com.crud.tasks.trello.client.TrelloClient.createNewCard(TrelloClient.java:65)

Process finished with exit code -1


@samdark This line is duplicated.


Cool!


Successfully aliased the URL <https://static-fun-r80yt43q9.zeit.sh> to the following aliases:

* https://static.fun
* https://*.static.fun
* https://static-fun.zeit.sh
* https://static-fun-git-master.zeit.sh


Lmao


Successfully aliased the URL <https://20192pirogi-5sddjs0ml.now.sh> to the following aliases:

* https://20192pirogi.ivanshport98.now.sh
* https://20192pirogi-git-dev.ivanshport98.now.sh


Atualizar


I mean specifically how corrupted, if we know? e.g. exported wrong, somehow the file got truncated, or what? Is there some specific things that happen to nif files that can cause them to become corrupt?


Awesome, thanks :)!


curious if you prefer the previous form better, same, worse than the form i asked for.  I personally think this reads better.  But i'm amenable to new ideas around these new constructs.


No. yeah, I know some libraries.
I haven't introduced them yet..


WaterToAirHP6323 (rraustad) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

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


Successfully aliased the URL <https://orbittas-react-develop-l8iwdh1ho.now.sh> to the following aliases:

* https://orbittas-react-develop.jesusrojasweb.now.sh
* https://orbittas-react-develop-git-master.jesusrojasweb.now.sh


Successfully aliased the URL <https://kendraio-app-hve7ys1p8.now.sh> to the following aliases:

* https://dev.app.kendra.io
* https://kendraio-app.kendraio.now.sh
* https://kendraio-app-git-develop.kendraio.now.sh


Successfully aliased the URL <https://aremycolorsaccessible-e27ybojkd.now.sh> to the following aliases:

* https://aremycoloursaccessible.com
* https://aremycolorsaccessible.com
* https://www.aremycolorsaccessible.com
* https://www.aremycoloursaccessible.com
* https://aremycolorsaccessible.sitaggart.now.sh
* https://aremycolorsaccessible-git-master.sitaggart.now.sh


WaterToAirHP6323 (rraustad) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (9 of 9 tests passed, 0 test warnings)

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


Successfully aliased the URL <https://coderplex-db4gvt80f.now.sh> to the following aliases:

* https://coderplex-app.now.sh
* https://coderplex.coderplex.now.sh
* https://coderplex-git-develop.coderplex.now.sh


TeamCity Glyssen / Glyssen pull requests [Build *.*.494.b3080a6614271ed509b5f99b1aa8e96517112bd1](https://build.palaso.org/viewLog.html?buildId=162400&buildTypeId=Glyssen_GlyssenPullRequests2) outcome was **SUCCESS**
Summary: Tests passed: 2256, ignored: 19 Build time: 00:09:12


CoolingTowerPlantComponent (Myoldmopar) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

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


Successfully aliased the URL <https://main-site-rhvxzvksd.now.sh> to the following aliases:

* https://fcc-mcr.now.sh
* https://main-site.fcc-mcr.now.sh
* https://main-site-git-master.fcc-mcr.now.sh


all kinds  of js framework demo


Successfully aliased the URL <https://just-another-todo-app-nobnmotkky.now.sh> to the following alias:

* https://just-another-todo-app.now.sh


CoolingTowerPlantComponent (Myoldmopar) - x86_64-Linux-Ubuntu-18.04-custom_check: Build Failed

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.png)


Successfully aliased the URL <https://mcdcdpportal-d71kmfovv.now.sh> to the following aliases:

* https://mcd-cdp-portal.mkr-js-prod.now.sh
* https://mcd-cdp-portal-git-develop.mkr-js-prod.now.sh


Зазвичай пишуть клас з елементом __list до <ul>, а до елементів списку пишуть __item або __list-item, а до посилань __list-link або __link


Successfully aliased the URL <https://gtn-shadowfeed-qwr9pjxom.now.sh> to the following aliases:

* https://shadowfeed.ajessen.com
* https://gtn-shadowfeed.andrewtyl.now.sh
* https://gtn-shadowfeed-git-master.andrewtyl.now.sh


I think the big issue is that left and right are 0. You should be able to leave top and bottom as they are already.

To streamline, you should be able to do:
if (left == 0 && right == 0)
{
   left = windowRect.left + 8;
   right = windowRect.right - 8;
}
// Titlebar height is weird
bottom += (windowRect.bottom - windowRect.top) / 2;


** talos, little endian POWER9, 64bit userland
```shell-session
uname -a
Linux hydra 5.2.11-gentoo #1 SMP Sat Aug 31 11:47:25 PDT 2019 ppc64le POWER9, altivec supported PowerNV T2P9D01 REV 1.01 GNU/Linux
ya@hydra ~/src/cpuid2cpuflags:<ppc> $ ./hwcap-dump
hwcap:00000000dc0065c2
hwcap2:00000000bee00000
ya@hydra ~/src/cpuid2cpuflags:<ppc> $ ./cpuid2cpuflags
CPU_FLAGS_PPC: altivec vsx vsx3
```


Let's do md so that it's easier to have one system.


The following doc(s) have been deployed to the [circlecidl](https://circlecidl-static-docs.pantheonsite.io/docs) Multidev environment:
- [.circleci/config.yml](https://github.com/pantheon-systems/documentation/commit/560fe87f617017296029b282194d1374da0a3b80/.circleci/config.yml)


Sure, that would be good. Feel free to re-add any additions you made. I didn't think about the readme when I merged. Sorry about that!


Я би краще добавив якийсь клас наприклад title  title--primary чи title--secondary і його стилізував, тому що на сайті може бути дуже багато тегів h2


Yes, that's the better way.


Successfully aliased the URL <https://nextjs-5e454hhfs.now.sh> to the following aliases:

* https://nextjs.mamal72.now.sh
* https://nextjs-git-master.mamal72.now.sh


@alberts2 can say what was wrong with this file - I don't do art related stuff.


Agreed, you can remove this line.


Successfully aliased the URL <https://mood-kzkbxd7xt.now.sh> to the following aliases:

* https://mood.rgrannell2.now.sh
* https://mood-git-master.rgrannell2.now.sh


Successfully aliased the URL <https://simple-tumbling20s-eegcdphzp.now.sh> to the following aliases:

* https://simple-tumbling20s.attiecyril.now.sh
* https://simple-tumbling20s-git-master.attiecyril.now.sh


不管有沒enableUrlAuth 都做了多餘的動作, 肯定不好
而且date_default_timezone_set沒有回復到本來的值, 會造成bug


Huh. I didn't know arrow functions preserved the `this` context. Interesting. Updated 7061465


Successfully aliased the URL <https://theglandergithubio-aj3x3krxz.now.sh> to the following aliases:

* https://glander.now.sh
* https://theglandergithubio.theglander.now.sh
* https://theglandergithubio-git-master.theglander.now.sh


![негадай](https://user-images.githubusercontent.com/53939052/64633275-8ef63000-d403-11e9-83fb-9d3cd11343ce.jpg)


默認是false好一點吧? 跟下面一致


Yeah that's that they're most useful for. Obviously what you had was fine, just didn't know if you ran into a situation that the arrow function didn't work. So wanted to be sure it wasn't a work around for maybe a larger issue that's all 👍


чача с сыром


Successfully aliased the URL <https://security-checklist-pxj2xr8yj.now.sh> to the following aliases:

* https://securitycheckli.st
* https://security-checklist.niceboy.now.sh
* https://security-checklist-git-master.niceboy.now.sh


配列をお洒落にした


Ah, right.  Footer PR seems like it should be its own thing (and isn't finished yet anyway).  But I'll put this one into 0.3.14.


Hi @jclem, I saw you involved in the GitHub Actions for Elixir (thank you for that) so I thought I would fast track this bug to you (if this is out of place, I apologize and feel free to ignore it). I have accidentally configured the Virtual Machine to an invalid name (in the line above). When I did that, the action got stuck:

https://github.com/elixir-ecto/ecto_sql/commit/e9f93ea4cd096d6a2ca46aba7b5979075ec5e9a9/checks

I guess users will always find new ways to break stuff. 😅

Thank you!


Mistake


this is a tough widget to get working correctly for all cases because depending on whether it is clicked or set, the object containing it has different values...


改成
```
if (isset($_POST['authMethod'])) {
    $options['authMethod'] = trim($_POST['authMethod']);
}
if (!empty($_POST['authPrimaryKey'])) {
    $options['authPrimaryKey'] = trim($_POST['authPrimaryKey']);
}
```
會不會易讀一點?


img1 краще записати як модифікатор, типу portfolio__galery__photo-box--img1
але краще читається якщо писати словами:
portfolio__galery__photo-box--first-img
portfolio__galery__photo-box--second-img
portfolio__galery__photo-box--third-img

А я би замінив img на bg


Hello, why u delete the ionic Auth Tutorial? Where i can find it?