[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/util.R:22:10:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( get_states_vector(local_anc))
         ^
```
[R/util.R:22:11:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L22) *warning:* **no visible global function definition for ‘get_states_vector’**
```r
  return( get_states_vector(local_anc))
          ^~~~~~~~~~~~~~~~~
```
[R/util.R:26:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L26) *style:* **functions should have cyclomatic complexity of less than 15, this has 32.**
```r
get_states_vector <- function(local_anc) {
^
```
[R/util.R:46:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L46) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
get_states_phased <- function(local_anc_matrix) {
^
```
[R/util.R:56:42:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    (local_anc_matrix[, 1 ] == local_anc_matrix[, 2]))
                                         ^
```
[R/util.R:108:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L108) *style:* **Variable and function name style should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:108:37:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L108) *style:* **Variable and function name style should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
                                    ^
```
[R/util.R:116:49:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 3) cond_prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:122:49:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 4) cond_prob <- (p ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:146:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:146:44:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
                                           ^
```
[R/util.R:151:18:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L151) *warning:* **no visible global function definition for ‘get_expectation_O_state’**
```r
    cond_prob <- get_expectation_O_state(P, p, focal_state)
                 ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-sims.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```


This commit has not been tested yet. None of the functions inside the FileManager.php file have been tested.


Yea, no.

Pulling from a remote DB means i'm not pushing out an update for a single database edition, plus it means there's a less chance of someone forgetting to download a database update for something important.


:angry:


you can pass same `_name` here


Lets make things _**less**_ secure, good idea


Successfully aliased the URL <https://kendraio-app-qh0sxvp9b.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


Added in comments to better explain code


168168673_Issue7476 (Nigusse) - x86_64-MacOS-10.13-clang: OK (2527 of 2553 tests passed, 608 test warnings)

Messages:\n
 * 513 tests had: EIO diffs.
 * 599 tests had: ESO small diffs.
 * 395 tests had: Table small diffs.
 * 5 tests had: EDD diffs.
 * 467 tests had: MTR small diffs.
 * 17 tests had: ESO big diffs.
 * 8 tests had: MTR big diffs.
 * 21 tests had: Table big diffs.
 * 31 tests had: ZSZ small diffs.
 * 22 tests had: ERR diffs.
 * 13 tests had: SSZ small diffs.
 * 2 tests had: JSON big diffs.
 * 1 test had: AUD diffs.

Failures:\n

regression Test Summary
 * Passed: 642
 * Failed: 26

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-98.98%25-yellow.png)


There were the following issues with your Pull Request

  * Subject needs to conform to "%{type} #%{issue_number}: %{description}"
  * Subject must be equal or less than 50

Guidelines are available at https://github.com/OpenNebula/one/blob/master/share/doc/dev/COMMIT_MESSAGES.md

---
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.... The database update actually did **nothing** at all, was just laying around doing nothing. And the fact that the local database isn't right now used, maybe we should think of implementing that rather than arguing about a stupid thing.


Successfully aliased the URL <https://marchworks-pr8qesqlq.now.sh> to the following aliases:

* https://march-works.marchworks.now.sh
* https://march-works-git-master.marchworks.now.sh


Great stuff


Successfully aliased the URL <https://kendraio-app-cdmzd5jyk.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


Hey @sanderssn. I'm curious why you recommend this. Is DefinitelyTyped moving away from using the `expect` lint rule?


```java
if(running) {
    return;
}```
```java
if(running) {
    return;
}```
```java
if(running) {
    return;
}```
```java
if(running) {
    return;
}```


`@JuliaRegistrator register()`


168168673_Issue7476 (Nigusse) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2567 of 2593 tests passed, 612 test warnings)

Messages:\n
 * 534 tests had: EIO diffs.
 * 605 tests had: ESO small diffs.
 * 413 tests had: Table small diffs.
 * 468 tests had: MTR small diffs.
 * 5 tests had: EDD diffs.
 * 15 tests had: ESO big diffs.
 * 21 tests had: Table big diffs.
 * 8 tests had: MTR big diffs.
 * 46 tests had: ZSZ small diffs.
 * 12 tests had: ERR diffs.
 * 14 tests had: SSZ small diffs.
 * 2 tests had: JSON big diffs.

Failures:\n

regression Test Summary
 * Passed: 662
 * Failed: 26

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.0%25-yellow.png)


Registration pull request created: [JuliaRegistries/General/3394](https://github.com/JuliaRegistries/General/pull/3394)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.8.3 -m "<description of version>" c9f65af1391eef6b9d2fb81f68bdbf67262e8b92
git push origin v0.8.3
```


Successfully aliased the URL <https://urena-mobiliario-aquyp16it.now.sh> to the following aliases:

* https://urenamobiliario.com
* https://urena-mobiliario.raulvv.now.sh
* https://urena-mobiliario-git-master.raulvv.now.sh


I know we don't have full root cause yet just guesses. But I'm cool if you want to revert it anyways and see if the builds clear up. If it works cool that gives us root cause, if not it'll at least tell us that it's somewhere else.


In case of error, what server_free(server) is used for?


✅ Device tests passed on iOS32b on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3031874)(iOS32b): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/mono-2019-08/ae9e84aa4848f96f8f4b2e0645c9bd0956f29de1/3031874/device-tests/jenkins-results/tests/index.html) ✅

# Test results

# No tests selected.


*sigh* That must be your attempt at fixing scans overlapping, there's probably better ways of handling that you know.


This was just a test


And it did fix it. Didn't it??


while breaking a very important feature, yes.


If we make it 1 scan per time it will be _completely_ the same as what i did here


@PaulWoitaschek according to the code changes in this commit, it defaults to `0.8` by the dimens. it shouldn't have affected you :/


Tema


point is, it's supposed to scan RIGHT after the database update, not 1+ hours AFTER it.
Having the scan wait after a database update leaves a high possibility of a malicious plugin doing damage


Successfully aliased the URL <https://marchworks-3q9jg7n41.now.sh> to the following aliases:

* https://march-works.marchworks.now.sh
* https://march-works-git-master.marchworks.now.sh


Now could not deploy this pull request since the `package.json` file does not contain valid JSON.

  Click here to see the contents of `package.json`

{
  "name": "ssr2",
  "version": "1.0.0",
  "description": "Simple Example of NextJS with customized Express Server",
  "repository": {
    "private": true
  },
  "main": "server.js",
  "license": "ISC",
  "scripts": {
    "dev": "node server.js",
    "now-build": "next build",
    "build": "next build",
    "start": "NODE_ENV=production node server.js",
    "prod": "NODE_ENV=production node server.js",
    "clean": "rm -rf .next && mkdir .next"
  },
  "keywords": [],
  "author": "",
  "dependencies": {
    "@zeit/next-css": "^1.0.1",
    "bootstrap": "^4.3.1",
    "express": "^4.17.1",
    "helmet": "^3.21.0",
    "isomorphic-unfetch": "^3.0.0",
<<<<<<>>>>>> a7614f689ea9528561db8d23c8612082580c47df
  }
}


Successfully aliased the URL <https://seatsmart-remote-nw2sto3nr.now.sh> to the following aliases:

* https://remote.seatsmart.tech
* https://seatsmart-remote.now.sh
* https://seatsmart-remote.thaddeusmccleary.now.sh
* https://seatsmart-remote-git-master.thaddeusmccleary.now.sh


But it starts a scan after a scan has been started, which on 200-300 plugins and this repeated 2-3 times it will become a huge mess and will make huuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuge load on the cpu and ram


Successfully aliased the URL <https://unicorn-md-f0xproyam.now.sh> to the following aliases:

* https://unicorn-md.zrtsky.now.sh
* https://unicorn-md-git-master.zrtsky.now.sh


Successfully aliased the URL <https://itchio-godot-scraper-d2l5ssemb.now.sh> to the following aliases:

* https://itchio-godot-scraper.now.sh
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* https://itchio-godot-scraper-git-master.hiulit.now.sh


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@Sur3 I just ran your evemu trace on my PC and it picks up all the scroll wheel input...


:white_check_mark: All Rules (2 / 2) Passed

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

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

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As it looks like you don't care about cpu and ram, don't u?


idk anymore

https://gyazo.com/e1df3c58544de47ab1ea4e7fd9dc299f


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* https://www.dhk.party
* https://tech-blog.kimdhoe.now.sh
* https://tech-blog-git-master.kimdhoe.now.sh


guess what, there's better ways of handling the situation besides COMPLETELY BREAKING AN IMPORTANT FEATURE


Successfully aliased the URL <https://tikape-s19-fvgwxpkwm.now.sh> to the following aliases:

* https://tietokantojen-perusteet-s19.mooc.fi
* https://tikape-s19.mooc.now.sh
* https://tikape-s19-git-master.mooc.now.sh


opts.num = opts.num || 100;
should be better


should be psauce, the famous youtube channel


Successfully aliased the URL <https://ohjelmointi-19-7qib6k1os.now.sh> to the following aliases:

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


yep,  I would have expanded the existing command  410x_write,  but hey, we are different


Okay lets recap... You want after a database update to start another scan right? If the program's checking 300 plugins on a very low end cpu and not that much ram (let's say 4 GB of ram) and you start another scan 2 or 3 times, guess what will happen on the user pc: A) Crash B) Nothing .


Successfully aliased the URL <https://cocktail-app-6l66twgui.now.sh> to the following aliases:

* https://cocktail-app.torstendittmann.now.sh
* https://cocktail-app-git-master.torstendittmann.now.sh


Did you restart the server after the translations downloaded, as the server instructs you to (or /sponge plugins reload langswitch if you're using the current version)?
Is your server language not one of the available languages? (you can set the default to `en` in the langswitch config)
Is you language set to one unsupported (either through a geoip plugin or `/language`)?


Successfully aliased the URL <https://acueducto-6zsw1wg4k.now.sh> to the following aliases:

* https://acueducto.fobossalmeron.now.sh
* https://acueducto-git-master.fobossalmeron.now.sh


@markschmid thanks! I thought using `CURLOPT_POSTFIELDS` would set that for me...

https://www.php.net/manual/en/function.curl-setopt.php

> If value is an array, the Content-Type header will be set to multipart/form-data.

Looks like I'm wrong. :-) I'll fix, thanks!


Right! I removed the assert and will follow up in the GEOS tracker.


oh hey lets ignore the fact that we can just set a boolean to true if a scans happening and if that boolean is true RETURN, oh wait that's basically what's happened


Maybe for the tags, I would use the MISP taxonomy for false-positive:

[false-positive taxonomy](https://github.com/MISP/misp-taxonomies/blob/master/false-positive/machinetag.json)

If you see something missing, let me know.


Successfully aliased the URL <https://xadamyxyz-efhanvdw4.now.sh> to the following aliases:

* https://xadamyxyz.adamyeats.now.sh
* https://xadamyxyz-git-master.adamyeats.now.sh


168168673_Issue7476 (Nigusse) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1215 of 1215 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.12%25-green.png)


THATS BASICALLY WHAT THE BOOLEAN RUNNING WAS DOING. THE DATABASE UPDATES WERE DOING NOTHING AND YOU KNOW THAT, BUT IN FACT STILL YOU WAN'T TO HAVE THIS FEATURE JUST FOR THE SAKE OF HAVING THE FEATURE....


TeamCity Bvcms / Build [Build 1981](https://builds.tpsdb.com/viewLog.html?buildId=8293&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 92 Build time: 00:20:23


It would be amazing to release this change as babel-eslint 10.0.2 is broken which means linting via latest create-react app is broken too: https://github.com/babel/babel-eslint/issues/791


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

* https://ssr.nattapon.now.sh
* https://ssr-git-master.nattapon.now.sh


in reviewMappedRequest.js
    numberOfReviews: opts.numberOfReviews,
->
    numberOfReviews: opts.num,

current code gets the same 100 multiple times if > 100 is requested


It does work, i tested it.
It does what i need it to do, pull database updates from a REMOTE database so i can keep the database updated WITHOUT spamming the spigot resource with updates, people would get pissed if the update was just
"
**CHANGES**
  - Added a single entry to the local database
"


@MJZ1977
How about still do lazy eval if WE have the passer? Only do the full eval if THEY have the dangerous passer?


For the `_configprops.adoc` file we want to include only properties that start with `spring.sleuth.*` and `spring.zipkin.*`


Here we're passing all the dependencies for which we want to scan for configuration properties


That happens on the anti malware startup because the database isn't cached... and it wasn't working after fixing the issue of dupe scans...


This executes a script that generates the `_configprops.adoc` file


https://twitter.com/rsk0315_h4x/status/1171063681284632576 より


Hello, do you remember why this was made a `mt_note`? The applicant doesn't receive the email anymore, but the mail template was kept.


Format your manifest plox


This file contains all the attributes that our adoc files will reuse


Obrigado : ) Acabei [complicando mais do que devia](https://github.com/cuducos/go-cpf/commit/4fcfdb79db2fb7fb44a15304f3132ea7452a0a5b)!


Remember to update this with your project name


test


This file gets generated


Successfully aliased the URL <https://melon-subgraph-frontend-kp3hji8s9.now.sh> to the following aliases:

* https://monitoring.melon.network
* https://melon-subgraph-frontend.melon-project.now.sh
* https://melon-subgraph-frontend-git-master.melon-project.now.sh


This file looks exactly as in Boot. You can safely copy paste it


hmm


I mean after startup fetch the other update wasn't working


Successfully aliased the URL <https://xadamyxyz-dv1041oel.now.sh> to the following aliases:

* https://xadamyxyz.adamyeats.now.sh
* https://xadamyxyz-git-master.adamyeats.now.sh


There were the following issues with your Pull Request

  * Subject needs to conform to "%{type} #%{issue_number}: %{description}"

Guidelines are available at https://github.com/OpenNebula/one/blob/master/share/doc/dev/COMMIT_MESSAGES.md

---
This message was auto-generated by https://gitcop.com


Successfully aliased the URL <https://seatsmart-remote-m5zbbgg2s.now.sh> to the following aliases:

* https://remote.seatsmart.tech
* https://seatsmart-remote.now.sh
* https://seatsmart-remote.thaddeusmccleary.now.sh
* https://seatsmart-remote-git-master.thaddeusmccleary.now.sh


This is a fine mental model. More precisely, `/`(just a slash) is the filesystem's [root directory](http://www.linfo.org/root_directory.html), the highest-level directory that exists on your filesystem. You can list it like any other directory:

```
$ ls /
Applications
Library
Network
System
Users
Volumes
bin
cores
dev
etc
home
net
opt
private
sbin
tmp
usr
var
```

An "absolute" (rather than "relative") filepath _always_ starts with a `/`. It fully specifies the path to a file from the root directory (versus a relative path, that specifies based on the current directory). `/usr/bin/`, `/bin/`, `/usr/sbin/`, etc. are all absolute paths.


So instead of fixing it, we're just removing it entirely?
Great, great lets piss off the spigot community (and possibly even the staff)  by spamming updates for every database update, great idea


Successfully aliased the URL <https://quiet-8ntm9icn3.now.sh> to the following aliases:

* https://quiet.vincentpoulain.now.sh
* https://quiet-git-master.vincentpoulain.now.sh


Remember to include attributes for each file


It relies on template definition. Partner_to / email_to should be set.


Convert any relative paths to absolute ones via the `{project-root}` attribute


apparently num>100 does not return any data :(
nextToken is not working properly yet


Remember to add a link to the `appendix.html`


YOU DONT FUCKING UNDERSTAND WHAT IM FUCKING TALKING ABOUT....
WHEN YOU START THE PROGRAM IT STILL FETCHES IT FROM THE DATABASE AT GITHUB
I'VE JUST REMOVED THE THING WHEN THE PROGRAM'S RUNNING TO FETCH IT AGAIN


draw of sun flower


It's supposed to fetch it every few hours hence the "Auto-Update", if i update the github repo while the program is running it's going to get those updates WITHOUT having to do a thing


"Put this variable in the `env` of all child processes"


d(￣ ￣)✨


BUT THE THING IS THAT IF THE SCAN'S RUNNING THE SCANS WILL OVERLAP AND YOU WANT THE SCAN TO START AFTER THE DATABASE WAS UPDATED......


Successfully aliased the URL <https://main-site-96cdnmtjt.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


and you'd missed the proper fix majorly

boolean isCurrentlyScanning

if true don't run the update scan


Successfully aliased the URL <https://tikape-s19-9eboelqj8.now.sh> to the following aliases:

* https://tietokantojen-perusteet-s19.mooc.fi
* https://tikape-s19.mooc.now.sh
* https://tikape-s19-git-master.mooc.now.sh


You could watch this happen experimentally! Put some `echo`es in your `.bashrc`:

```
echo "Current path: $PATH"
export PATH="/usr/local/bin:$PATH"
echo "Modified path: $PATH"
```

You should see these values print when you open a new terminal!


@Vihru käännöspohja menee enkussa 9.9.6 versiossa, joka on Mi 9 laitteen uusin versio.


Updated via commit 5080947524c59342f189f3724af974fd4738b492


THAT WAS THE WHOLE FUCKING POINT OF THE RUNNING BOOLEAN WHICH PREVENTED IT....


But in fact the boolean value of the running boolean was never changed


Successfully aliased the URL <https://ohjelmointi-19-lb00iwzyj.now.sh> to the following aliases:

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


Successfully aliased the URL <https://raveled-h0mg7b0d7.now.sh> to the following aliases:

* https://raveled.michcodes.now.sh
* https://raveled-git-master.michcodes.now.sh


I made a slight mistake, BYTE wUnknow1 array shouldn't be 20, but 32!


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

* https://xadamyxyz.adamyeats.now.sh
* https://xadamyxyz-git-master.adamyeats.now.sh


Successfully aliased the URL <https://intelli-ship-f6kgx5w42.now.sh> to the following aliases:

* https://intelli-ship.vishaag.now.sh
* https://intelli-ship-git-master.vishaag.now.sh


Successfully aliased the URL <https://tech-blog-n42fr9p7z.now.sh> to the following aliases:

* https://www.dhk.party
* https://tech-blog.kimdhoe.now.sh
* https://tech-blog-git-master.kimdhoe.now.sh


Back to your `PATH`: what directory is the old version of `screen` in? Where is it in your path? What directory is the new version of `screen` in? Where is _it_ in your path?

One way to ensure Homebrew-installed `screen` launches when you just type `screen` is to ensure that Homebrew's binary directories are above the others in your path—the shell will search there first and find new `screen` before old `screen`.


Erna vil hava 1m bin ístaðin fyri 0.5m


How about adding verification to the t55 write command?


Also, cameras are adjusted, and most models stop casting shadows.


This seems to be failing for me, with the error message:

```
ERROR: /home/atl/.cache/bazel/_bazel_atl/9175df3080bb9095eb16edc46790eae0/external/io_bazel_rules_go/go/tools/coverdata/BUILD.bazel:3:1: in go_tool_library rule @io_bazel_rules_go//go/tools/coverdata:coverdata:
Traceback (most recent call last):
        File "/home/atl/.cache/bazel/_bazel_atl/9175df3080bb9095eb16edc46790eae0/external/io_bazel_rules_go/go/tools/coverdata/BUILD.bazel", line 3
                go_tool_library(name = 'coverdata')
        File "/home/atl/.cache/bazel/_bazel_atl/9175df3080bb9095eb16edc46790eae0/external/io_bazel_rules_go/go/private/rules/library.bzl", line 42, in _go_library_impl
                go.archive(go, source)
        File "/home/atl/.cache/bazel/_bazel_atl/9175df3080bb9095eb16edc46790eae0/external/io_bazel_rules_go/go/private/actions/archive.bzl", line 219, in go.archive
                sets.union(cgo_exports, *[a.cgo_exports for a...])
        File "/home/atl/.cache/bazel/_bazel_atl/9175df3080bb9095eb16edc46790eae0/external/bazel_skylib/lib/new_sets.bzl", line 184, in sets.union
                struct(_values = dicts.add(*[s._values ...]))
        File "/home/atl/.cache/bazel/_bazel_atl/9175df3080bb9095eb16edc46790eae0/external/bazel_skylib/lib/new_sets.bzl", line 184, in struct
                dicts.add(*[s._values for s in args])
        File "/home/atl/.cache/bazel/_bazel_atl/9175df3080bb9095eb16edc46790eae0/external/bazel_skylib/lib/new_sets.bzl", line 184, in dicts.add
                s._values
object of type 'list' has no field '_values'
INFO: Call stack for the definition of repository 'remote_java_tools_linux' which is a http_archive (rule definition at /home/atl/.cache/bazel/_bazel_atl/9175df3080bb9095eb16edc46790eae0/external/bazel_tools/tools/build_defs/repo/http.bzl:292:16):
```


Successfully aliased the URL <https://seatsmart-remote-7ghg1nbtw.now.sh> to the following aliases:

* https://remote.seatsmart.tech
* https://seatsmart-remote.now.sh
* https://seatsmart-remote.thaddeusmccleary.now.sh
* https://seatsmart-remote-git-master.thaddeusmccleary.now.sh


I think this template can return both local and global users, see above, so I'm not sure ``$xwiki.getUser($user.fullName)`` will return the expected user if the user is global and you are in a sub-wiki.


Thank you, got it. `email_from` is not set on the applications demo we have.


Source Map Explorer Audits (0 failures)

## Source Map Explorer Audits

### /home/circleci/repo/examples/angular/dist/example-angular/styles-es2015.js

| Label                                      | Value   | Last Value | Threshold | Success |
| ----                                       |  :---:  |   :---:    |   :---:   |  :---:  |
| src/styles.css                             |  453 B  |            |   500 B   |    ✓    |
| node_modules/style-loader/lib/addStyles.js | 9.78 KB |            |   10 KB   |    ✓    |
| node_modules/style-loader/lib/urls.js      | 2.86 KB |            |   3 KB    |    ✓    |
| src/styles.css?b364                        |  749 B  |            |   800 B   |    ✓    |
| <unmapped>                                 | 1.94 KB |            |   2 KB    |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/styles-es5.js

| Label                                      | Value   | Last Value | Threshold | Success |
| ----                                       |  :---:  |   :---:    |   :---:   |  :---:  |
| src/styles.css                             |  453 B  |            |   500 B   |    ✓    |
| node_modules/style-loader/lib/addStyles.js | 9.78 KB |            |   10 KB   |    ✓    |
| node_modules/style-loader/lib/urls.js      | 2.86 KB |            |   3 KB    |    ✓    |
| src/styles.css?b364                        |  749 B  |            |   800 B   |    ✓    |
| <unmapped>                                 | 1.94 KB |            |   2 KB    |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/main-es2015.js

| Label                                       | Value   | Last Value | Threshold | Success |
| ----                                        |  :---:  |   :---:    |   :---:   |  :---:  |
| $_lazy_route_resource lazy namespace object |  538 B  |            |   600 B   |    ✓    |
| src/app/app.component.html                  | 1.19 KB |            |  1.5 KB   |    ✓    |
| src/app/app-routing.module.ts               |  377 B  |            |   600 B   |    ✓    |
| src/app/app.component.css                   |  402 B  |            |   600 B   |    ✓    |
| src/app/app.component.ts                    |  389 B  |            |   600 B   |    ✓    |
| src/app/app.module.ts                       |  484 B  |            |   600 B   |    ✓    |
| src/environments/environment.ts             |  494 B  |            |   550 B   |    ✓    |
| src/main.ts                                 | 1.1 KB  |            |  1.5 KB   |    ✓    |
| <unmapped>                                  | 5.21 KB |            |  5.5 KB   |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/main-es5.js

| Label                                       | Value   | Last Value | Threshold | Success |
| ----                                        |  :---:  |   :---:    |   :---:   |  :---:  |
| $_lazy_route_resource lazy namespace object |  538 B  |            |   600 B   |    ✓    |
| src/app/app.component.html                  | 1.19 KB |            |  1.5 KB   |    ✓    |
| src/app/app-routing.module.ts               |  436 B  |            |   600 B   |    ✓    |
| src/app/app.component.css                   |  402 B  |            |   600 B   |    ✓    |
| src/app/app.component.ts                    |  430 B  |            |   600 B   |    ✓    |
| src/app/app.module.ts                       |  538 B  |            |   600 B   |    ✓    |
| src/environments/environment.ts             |  492 B  |            |   550 B   |    ✓    |
| src/main.ts                                 | 1.11 KB |            |  1.5 KB   |    ✓    |
| <unmapped>                                  | 5.32 KB |            |  5.5 KB   |    ✓    |

Size Checks (0 failures)

## Size Checks

| Label                                    | Value     | Last Value | Threshold | Success |
| ----                                     |   :---:   |   :---:    |   :---:   |  :---:  |
| dist/example-angular/favicon.ico         |  1.35 KB  |            |   4 KB    |    ✓    |
| dist/example-angular/index.html          |   304 B   |            |   3 KB    |    ✓    |
| dist/example-angular                     | 16.86 MB  |            |   17 MB   |    ✓    |
| dist/example-angular/main-es2015.js      |  2.8 KB   |   2.8 KB   |   3 KB    |    ✓    |
| dist/example-angular/main-es5.js         |  2.82 KB  |  2.82 KB   |   3 KB    |    ✓    |
| dist/example-angular/polyfills-es5.js    | 87.22 KB  |  87.22 KB  |   90 KB   |    ✓    |
| dist/example-angular/polyfills-es2015.js |  44.4 KB  |  44.4 KB   |   45 KB   |    ✓    |
| dist/example-angular/runtime-es2015.js   |  1.65 KB  |  1.65 KB   |  1.75 KB  |    ✓    |
| dist/example-angular/runtime-es5.js      |  1.65 KB  |  1.65 KB   |  1.75 KB  |    ✓    |
| dist/example-angular/styles-es2015.js    |  5.17 KB  |  5.17 KB   |  5.25 KB  |    ✓    |
| dist/example-angular/styles-es5.js       |  5.16 KB  |  5.16 KB   |  5.25 KB  |    ✓    |
| dist/example-angular/vendor-es2015.js    | 672.4 KB  |  672.4 KB  |  700 KB   |    ✓    |
| dist/example-angular/vendor-es5.js       | 686.07 KB | 686.07 KB  |  700 KB   |    ✓    |

Heap Snapshot Checks (0 failures)

## Heap Snapshot Checks

| Label            | Value    | Last Value   | Threshold | Success |
| ----             |  :---:   |    :---:     |   :---:   |  :---:  |
| Documents        |    5     |      5       |     5     |    ✓    |
| Frames           |    2     |      2       |     2     |    ✓    |
| JSHeapTotalSize  | 22183936 |   21659648   |           |    ✓    |
|                  |          |    +512 KB   |           |         |
| JSHeapUsedSize   | 15017072 |   15804160   |           |    ✓    |
|                  |          |   +768.64 KB |           |         |
| LayoutCount      |    2     |      2       |     5     |    ✓    |
| Nodes            |    81    |      81      |    81     |    ✓    |
| RecalcStyleCount |    3     |      3       |     6     |    ✓    |

Axe Audits (0 failures)

## Axe Audits

| Label                             | Value    | Last Value | Threshold | Success |
| ----                              |  :---:   |   :---:    |   :---:   |  :---:  |
| aria-hidden-body                  |          |            |   none    |    ✓    |
| bypass                            |          |            |   none    |    ✓    |
| color-contrast                    |          |            |   none    |    ✓    |
| document-title                    |          |            |   none    |    ✓    |
| empty-heading                     |          |            |   none    |    ✓    |
| heading-order                     |          |            |   none    |    ✓    |
| html-has-lang                     |          |            |   none    |    ✓    |
| html-lang-valid                   |          |            |   none    |    ✓    |
| image-alt                         |          |            |   none    |    ✓    |
| image-redundant-alt               |          |            |   none    |    ✓    |
| landmark-no-duplicate-banner      |          |            |   none    |    ✓    |
| landmark-no-duplicate-contentinfo |          |            |   none    |    ✓    |
| link-name                         |          |            |   none    |    ✓    |
| list                              |          |            |   none    |    ✓    |
| listitem                          |          |            |   none    |    ✓    |
| meta-viewport-large               |          |            |   none    |    ✓    |
| meta-viewport                     |          |            |   none    |    ✓    |
| page-has-heading-one              |          |            |   none    |    ✓    |
| landmark-one-main                 | moderate |  moderate  | moderate  |    ✓    |
| region                            | moderate |  moderate  | moderate  |    ✓    |

Unused Source Checks (0 failures)

## Unused Source Checks

| Label                                                  | Value  | Last Value | Threshold | Success |
| ----                                                   | :---:  |   :---:    |   :---:   |  :---:  |
| http://localhost:3000/                                 | 51.80% |   51.80%   |           |    ✓    |
| http://localhost:3000/runtime-es2015.js                | 13.93% |   13.93%   |    70%    |    ✓    |
| http://localhost:3000/styles-es2015.js                 | 49.85% |   49.85%   |    70%    |    ✓    |
| http://localhost:3000/main-es2015.js                   | 6.64%  |   6.64%    |    70%    |    ✓    |
| http://localhost:3000/polyfills-es2015.js              | 33.16% |   33.16%   |    70%    |    ✓    |
| http://localhost:3000/vendor-es2015.js                 | 53.65% |   53.65%   |    70%    |    ✓    |
| ... ///RouterModule/_EmptyOutletComponent.ngfactory.js | 27.79% |   27.79%   |    70%    |    ✓    |
| ng:///AppModule/AppComponent.ngfactory.js              | 0.02%  |   0.02%    |    70%    |    ✓    |
| ... uterModule/_EmptyOutletComponent_Host.ngfactory.js | 29.16% |   29.16%   |    70%    |    ✓    |
| ng:///AppModule/AppComponent_Host.ngfactory.js         | 0.10%  |   0.10%    |    70%    |    ✓    |
| ng:///AppModule/module.ngfactory.js                    | 0.01%  |   0.01%    |    70%    |    ✓    |

Lighthouse Audits (0 failures)

## Lighthouse Audits

| Label               | Value | Last Value | Threshold | Success |
| ----                | :---: |   :---:    |   :---:   |  :---:  |
| Performance         |   1   |     1      |     1     |    ✓    |
| Accessibility       |  100  |    100     |    100    |    ✓    |
| Best Practices      |  100  |    100     |    100    |    ✓    |
| SEO                 |  91   |     91     |    90     |    ✓    |
| Progressive Web App |  20   |     20     |    20     |    ✓    |


Size Checks (0 failures)

No Failures

Source Map Explorer Audits (0 failures)

No Failures

Heap Snapshot Checks (0 failures)

No Failures

Unused Source Checks (0 failures)

No Failures

Axe Audits (0 failures)

No Failures

Lighthouse Audits (0 failures)

No Failures


yes I restarted and yes its supported and the langswitch config is set to en.lang


Hmmm I did check the migration with subwikis and the Admin UI looked good but I will double check. Thanks


> Apart from the `eslint-disable-next-line` rule, this seems fine to me.

**i test it on windows 10 + cmd or git-bash, got error just as below**

![image](https://user-images.githubusercontent.com/998505/64540585-061fbb80-d353-11e9-9945-af42b5e2bb04.png)

```
react-grid-layout>npm run lint

> react-grid-layout@0.16.6 lint D:\code.me\github.com\react-grid-layout
> make lint

./node_modules/.bin/flow
'.' 不是内部或外部命令，也不是可运行的程序
或批处理文件。
make: *** [lint] 错误 1
npm ERR! code ELIFECYCLE
npm ERR! errno 2
npm ERR! react-grid-layout@0.16.6 lint: `make lint`
npm ERR! Exit status 2
npm ERR!
npm ERR! Failed at the react-grid-layout@0.16.6 lint script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.
```

so i think i can use `@$(BIN)/flow` instead of `./node_modules/.bin/flow`, just as `@$(BIN)/eslint --ext .js,.jsx $(LIB) $(TEST)`


By Reyhaneh Amoue


This makes it an API so it's missing a `@since`.


Same here.


the value in the config has to be a language tag like `en` or `en_US`, not a file name


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18 - Adding Up Times with Reduce/index.html

```
const [mins, secs] = timeCode.split(':').map(function(str) {
    return parseFloat(str);
```


Mergeo esto o necesita algo más?


I just realized that after using /language


Right. Adding them.


> Out of the box, Grafana dashboard comes pre-configured with a Prometheus data-source connection along with Data Flow specific widgets to monitor the streaming and/or task applications composed in a data pipeline.


jeez im dumb :P thanks! its good now!


Ehw, you're right of course. Which makes me think again about this whole design. Better have 1 codec for for all types with an embedded buffer. One sync.Pool exchange eliminated plus less pointer magic. I really appreciate you spelling this issue out @erikdubbelboer. ☺


Shouldn't one of our checkstyle tool complain for it?


The latest version that works for me is 0.18.6. 0.18.7 and subsequent versiosn all seem to produce the error above.


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Is it working ? Just sent you a linkedin message. We are stuck. Our file is encoded on upload but present in OVH console. Thanks a lot !


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Welcome


@avasuro: Awesome, thanks!! I'd like to open up a PR so we can track it if it's okay with you?


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Hi @shlomiken. This was removed as we had an ongoing effort to migrate to CodeDeploy, so the global environment should be managed with it instead.

This is important because changes to the `requirements.txt` would not be picked up by the CloudFormation stack unless you also triggered a metadata change in the EC2 instances.


Code looks good @cioan  though it would be good to test the double-layer obs group here to test the recursion.


I'd remove "started"


I think using `_is_instance_mock` would be good. All the mocks have `NonCallableMock` as parent which `_is_instance_mock` and there is also some note about `__class__` on the comment.

```
def _is_instance_mock(obj):
    # can't use isinstance on Mock objects because they override __class__
    # The base class for all mocks is NonCallableMock
    return issubclass(type(obj), NonCallableMock)
```

Something like below?

```
def _is_async_obj(obj):
    if _is_instance_mock(obj) and not isinstance(obj, AsyncMock):
        return False
    return asyncio.iscoroutinefunction(obj) or inspect.isawaitable(obj)
```


Maybe:
An alarm has already been (set|created) for that time.


This one right here, officer!


Yes


I figure man should be fixed


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Btw, clean has the same issue