[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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:9:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L9) *warning:* **no visible global function definition for ‘single_state_inf’**
```r
  seven_states <- single_state_inf(local_time, d = di)
                  ^~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:10:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L10) *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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L129) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_cond_prob_vector_phased_inf <- function(info_vector,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:151:23:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L151) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:151:32:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L151) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:154:10:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L154) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:158:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L158) *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:159:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L159) *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:163:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L163) *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:164:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L164) *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:165:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L165) *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:200:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L200) *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:207:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L207) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_phased.R:257:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L257) *style:* **Lines should not be more than 80 characters.**
```r
#' estimates the time since admixture, given unphased ancestry data and assuming infinite population size.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:258:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L258) *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:259:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L259) *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:262:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L262) *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:263:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L263) *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:296:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L296) *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:303:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L303) *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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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:21:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L21) *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:35:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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:102:23:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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:13:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L13) *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_markers.R:20:41:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L61) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-phased-error.R:53:64:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-phased-error.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  expected_heterozygosity <- 2 * 0.5 * 0.5 * (1 - 1 / (2 * 100) ) ^ 200
                                                               ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/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/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```


@cmb69 Do you have anything against this commit? I'd like to push it to upstream.


hola, le falta el archiv .env necesito para probarlo estoy haciendo un estudio para hacer un sistema similar


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FixMinFieldsAndIdfEd (JasonGlazer) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (674 of 675 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 674
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.41%25-green.png)


Actually, I take back my previous comments.

I read `Vec2` but was thinking **`kurbo::Point`**. The `Point` is in *Canvas Space*, but a `Vec2` is just a pair of floats so it should be fine to implement `From<Vector>` for `Vec2`.


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[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/terminus-build-tools-plugin/master/assets/images/visit-site-36.png)](https://pr-31-darwin-d8-composer-project.pantheonsite.io/)

Created multidev environment [pr-31](https://dashboard.pantheon.io/sites/52355ac1-d072-476c-a395-9c94b630e74e#pr-31) for darwin-d8-composer-project.


@dalehenrich Can you please review this backport of fix for #547?  Done at the request of @LisaAlmarode.


This works but by accident. `=` is the assignment operator, so you're overwriting the value of `num` with `0` here. Because you only enter this branch after you've determined that `num > 0`, it's doesn't break anything, but it's also not correct.

You'd want:
```javascript
if (num > 0) {
  return true;
} else if (num === 0) {
  return false;
} else {
  return false;
}
```

Since `===` and `<` involve the same block of code, you could also do:

```javascript
if (num > 0) {
  return true;
} else {
  return false;
}
```

But then, because `num > 0` as an expression evaluates to `true` or `false` directly, you could instead write

```javascript
function isPositive(num) {
  return num > 0;
}
```


FixMinFieldsAndIdfEd (mjwitte) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (675 of 676 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 675
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.43%25-green.png)


Related to: backdrop/backdrop-issues#2843


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Так будет намного проще и с данными работать, и ошибки обрабатывать


Thanks a lot for this! This was important :rocket:.


IDE folding did hide this from me...


hvacVRFRefactor (mitchute) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1266 of 1266 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-43.57%25-green.png)


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А если у тебя будет не только парсинг фолловеров, но и других данных, ты так и будешь копипастить?)
Сделай реюзабельную функцию Decode с помощью Jeneric'а, которой будешь передавать json, а она возвращать данные


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Force unwrap?????????? Удали)


Если обязательное поле, установи еще через конструктор и сделай let


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В отдельную приватную функцию


@JuliaRegistrator register


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Registration pull request created: [JuliaRegistries/General/7842](https://github.com/JuliaRegistries/General/pull/7842)

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 v0.2.1 -m "<description of version>" d8dcf978e346daa54b24aadf75ecc2120e8cb276
git push origin v0.2.1
```


@lfantoniosi Hey Luis, first of all thank you for these great projects! If you could answer a few questions about the RGB2VGA converter, please send me an email! You can find my address on my github profile.


> Please specify how much rupee bruh

fuck lmao
i edited in phone and pulled into pc
looks like i pressed the wrong key


Excuse me, I didn't elaborate muchon your code, but maybe repohead-details-container needs to be changed to repohead too?


This ensures that upon first boot efl apps like epad et al are using the proper matching icon theme instead of the default elm theme. That has been an issue every since the e-devs added those elm FDO icons to the elementary theme.


I asked internally an opinion (privacy / breakage / breakage only as workaround etc)


<!-- PMABOT:SPACE -->
This commit contains trailing whitespace, what is prohibited in phpMyAdmin. Please check our [Developer guidelines](https://github.com/phpmyadmin/phpmyadmin/wiki/Developer_guidelines#Indentation) for more information.

Offending files: remote


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verwijderd*


look this is a note @oskasf


You could reuse PLEX_VERSION in PLEX_URL


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because threat list creatures start engage mode when threat is added, not when combat is entered

(think fireball cast end vs fireball impact)


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Not sure about the latest exact version available for raspbian, but it should be 3.X - which make it incompatible with newer versions of python-qbittorrent


Good! Thanks for the pointer.


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![Difference between blocks](https://raw.githubusercontent.com/belmont-admin/lightshow/a39123aea66d254380897542fc835c8c787d7f5b/.github/makecode/blocksdiff.png)


Это количество букв в символе left_chevron


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I got an Error with *URL contains XSS injection attempt* for my URL: `http://localhost:3001/api/management/users?onlyActive=true`.
The query string part `onlyActive=` was caught by regex.


If you think something is wrong, please create PR with fix and test-case showing the problem


TeamCity Bvcms / Build [Build 3398](https://builds.tpsdb.com/viewLog.html?buildId=11319&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 224 Build time: 00:26:57


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you can return here right away


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

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

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

### Deployments updated

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

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


why u did this?


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@imod I suggest that you delete this commit's orphaned branch and the other ones too.


It does, but say if you start a restore and turn off your device, after 10 minutes the restore pauses and doesn't start back until you turn on the screen


because we don't need the rest?


Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/zy1RnwcNWKT8Gy49mTemnIby/repo/now.json.
~~~


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Build version: __`3.3.0-master.1107`__ :crossed_fingers: [`master`](https://github.com/streamich/md-mdast/tree/master) on [*CircleCI*](https://circleci.com/gh/streamich/md-mdast/1107) :tada:


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The reason I went with a fixed number of chunks is that it is theoretically required.
Le'ts say you have the following constraint: `new Constraint('<', '999999')`. If you'd compare that to `9.9`, `9.9` would always be higher because `9999999` is actually `9999999.0` 😄
I guess we could work with an `INF` constant. Lower bound would be `INF` instead of `0` and upper would be `INF` as well instead of `9999999.9999999.9999999.9999999.9999999`. When comparing in the e.g. autoload.php case, those boundaries can be ignored because they always evaluate to `true`.


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It might be eaiser to understand the test if you just returns the result of the checkPropTypes(So basically you're using checkProps as a shorthand helper).
Inside your test callback, you can take that result into a variable, error then expect it to be undefined.


@zlzleking 다시 수정 했음


So no bounds would evaluate to `INF` for both, lower and upper 🤷♂ 😄


@rmackay9 May I suggest two ideias?

1) Network access level do Lua Scripts.

I guess that some companion computers are used with vehicles to do simple tasks, not only external sensors or more substantial processing then the flight controller. They allow users to put the Vehicle in Guided mode and control them by their application decisions.

If such logic could be run in through Lua scripts safely, some native applications could raise. For example, I cite the case my own use of some copters, and RPIs only do provide the network for scripts that creates a decentralized group of UAVs to follow themselves. The onboard processing did require nothing special, but each coper exchange simple data with the other do decide the leader.

Just for saying, the esp32 has enough room to provide a TCP/IP stack and a radio. I think Lua scripts could put Ardupilot in the "Internet of the Drones" and easily allow small swarms without a central controller.

I briefly chat with @WickedShell weeks ago, and I understood that it is not a devel queue yet. (Please, correct me if I am wrong)

2) Motorcycle style balance motor vehicle

Does anyone think in Ardupilot riding bikes? [Example   ](https://www.youtube.com/watch?v=4UHLRmYNDMQ):-)


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used Loss "mean squared error".
In the final output layer we did not apply an activation function, just get the outputs directly from the previous layer.


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可以的我的哥


`.btn`とスタイルの重複になるので、paddingの指定は不要かな！


test


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## レビュー時に確認して欲しいこと
- labelタグとinputタグはどう紐付いているのか(なぜlabelタグをクリックするとinputタグが反応するか等)
- 余裕あればinputタグをlabelタグではさむパターンとそれぞれが独立してるパターンどちらでも書けることについて言及


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So by importing the RIGHT imports, by adding instances to .add code, etc., I made IntelliJ capable of actually executing the programming I wrote for the website.


fix bug:when use sandbox to create lports,Error NoneType object is not iterable


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 Comment on e439bc5

2020-01-15 07:56IST@home_kolumnin


Issue7187 (dareumnam) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: Tests Failed (2238 of 2643 tests passed, 253 test warnings)

Messages:\n
 * 648 tests had: EIO diffs.
 * 401 tests had: ESO small diffs.
 * 305 tests had: Table small diffs.
 * 237 tests had: ESO big diffs.
 * 57 tests had: MTR big diffs.
 * 295 tests had: Table big diffs.
 * 10 tests had: EDD diffs.
 * 427 tests had: MTR small diffs.
 * 308 tests had: ZSZ small diffs.
 * 89 tests had: ERR diffs.
 * 254 tests had: SSZ small diffs.
 * 23 tests had: SSZ big diffs.
 * 99 tests had: MDD diffs.
 * 101 tests had: MTD diffs.
 * 99 tests had: RDD diffs.
 * 5 tests had: MAP diffs.
 * 22 tests had: ZSZ big diffs.
 * 12 tests had: BND diffs.
 * 2 tests had: JSON big diffs.
 * 2 tests had: AUD diffs.

Failures:\n

regression Test Summary
 * Passed: 286
 * Failed: 405

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-84.68%25-red.png)


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Registration pull request created: [JuliaRegistries/General/7946](https://github.com/JuliaRegistries/General/pull/7946)

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

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```
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git push origin v0.5.1
```


The same


Dependency Update


Надо посмотреть дерево диалогов у Фален (мне кажется так её имя правильно читать, но с именами собственными вообще никаких правил нет, так что это чисто моё субъективное), Gentle осторожно, нежно. Что бы понять как перевести надо увидеть контекст.


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[R/calc_sum_stats.R:69:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/calc_sum_stats.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
  output[10] <- phyloTop::ILnumber(focal_tree) # number of internal nodes with a single child
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_reference_table.R:35:8:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/create_reference_table.R#L35) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(focal_model in 1:3) {
       ^
```
[R/create_reference_table.R:48:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/create_reference_table.R#L48) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:49:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/create_reference_table.R#L49) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:50:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/create_reference_table.R#L50) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_reference_table.R:51:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/create_reference_table.R#L51) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/generate_from_prior.R:14:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_from_prior.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
generate_from_prior <- function(number_of_particles = 1000,
^
```
[R/generate_from_prior.R:24:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_from_prior.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(emp_tree)) {
    ^
```
[R/generate_from_prior.R:27:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_from_prior.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(crown_age)) {
    ^
```
[R/generate_naive.R:13:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_naive.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
generate_naive <- function(number_of_particles = 1000,
^
```
[R/generate_naive.R:22:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_naive.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(emp_tree)) {
    ^
```
[R/generate_naive.R:25:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_naive.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(crown_age)) {
    ^
```
[R/generate_stack.R:13:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_stack.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
generate_stack <- function(number_of_replicates = 1000,
^
```
[R/generate_stack.R:22:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_stack.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(emp_tree)) {
    ^
```
[R/generate_stack.R:25:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_stack.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(crown_age)) {
    ^
```
[R/generate_stack.R:29:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_stack.R#L29) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(parameters)) {
    ^
```
[R/generate_stack.R:53:9:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_stack.R#L53) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(x[6] == 4) {
        ^
```
[R/generate_stack.R:54:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_stack.R#L54) *style:* **Lines should not be more than 80 characters.**
```r
        found_tree <- TreeSim::sim.bd.age(age = crown_age, numbsim = 1, lambda = x[2], mu = x[1], complete = FALSE)[[1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/generate_stack.R:55:14:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_stack.R#L55) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        while(is.numeric(found_tree)) {
             ^
```
[R/generate_stack.R:56:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/generate_stack.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
          found_tree <- TreeSim::sim.bd.age(age = crown_age, numbsim = 1, lambda = x[2], mu = x[1], complete = FALSE)[[1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_params.R:16:16:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/infer_params.R#L16) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
  emp_stats <- calc_sum_stats(emp_tree, emp_tree)
               ^~~~~~~~~~~~~~
```
[R/infer_params.R:19:44:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/infer_params.R#L19) *warning:* **no visible binding for global variable ‘param_from_prior’**
```r
  previous_par <- t(apply(param_matrix, 1, param_from_prior))
                                           ^~~~~~~~~~~~~~~~
```
[R/infer_params.R:74:44:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/infer_params.R#L74) *warning:* **no visible binding for global variable ‘calc_fit’**
```r
        local_fit <- apply(stat_matrix, 1, calc_fit, emp_stats)
                                           ^~~~~~~~
```
[R/infer_params.R:76:22:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/infer_params.R#L76) *warning:* **no visible global function definition for ‘calc_fit’**
```r
        local_fit <- calc_fit(stat_matrix, emp_stats)
                     ^~~~~~~~
```
[R/infer_params.R:102:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/infer_params.R#L102) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
get_next_par <- function(number_of_particles = 1000,
^
```
[R/is_within_prior.R:5:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/is_within_prior.R#L5) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
is_within_prior <- function(params) {
^
```
[R/read_reference_table.R:1:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/read_reference_table.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' collect reference table based on previously generated reference tables for each model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:3:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/read_reference_table.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param return_full_table should the function only return summary stats, or also parameters?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:10:6:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/read_reference_table.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in 1:3) {
     ^
```
[R/read_reference_table.R:27:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/read_reference_table.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!return_full_table) {
    ^
```
[R/read_reference_table.R:29:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/read_reference_table.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
    ref_table <- dplyr::select(reference_table, c("nltt", "gamma", "mbr", "num_lin",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:30:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/read_reference_table.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
                                           "beta", "colless", "sackin", "ladder", "cherries", "ILnumber",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/read_reference_table.R:32:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/read_reference_table.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
                                           "spectr_eigen", "spectr_asymmetry", "spectr_peakedness"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:16:20:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/sim_envidiv_tree.R#L16) *warning:* **no visible global function definition for ‘generate_water’**
```r
  water_changes <- generate_water(params[6], crown_age)
                   ^~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:23:1:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/R/sim_envidiv_tree.R#L23) *style:* **functions should have cyclomatic complexity of less than 15, this has 32.**
```r
sim_envidiv_tree <- function(params,
^
```
[tests/testthat/test-generate_naive.R:9:5:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/tests/testthat/test-generate_naive.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(1 == 2) {
    ^
```
[tests/testthat/test-infer_params.R:37:6:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/tests/testthat/test-infer_params.R#L37) *style:* **Commented code should be removed.**
```r
  #  future::plan(future::multiprocess())
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:47:6:](https://github.com/thijsjanzen/enviDiv/blob/dd4cf7882dac7fbcaca7edf648eacc823672ec1d/tests/testthat/test-infer_params.R#L47) *style:* **Commented code should be removed.**
```r
  #  testthat::expect_equal(mean(do_smc$sym_high), birth_rate, tolerance = 0.1)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


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IsNetCore30OnwardsTarget -> IsNetCore3OnwardsTarget ?


# Specs execution successful
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### Plans updated

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---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
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Bamboo specs have been successfully imported and the following deployment projects have been updated.

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


TODO: double check if this is still needed with hydra-base - probably not since hashing is now with unit_id rather than unit_name


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@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/7989](https://github.com/JuliaRegistries/General/pull/7989)

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 v1.0.0 -m "<description of version>" 1e4c2fc5cbb015b20ba53c4f96a8e9503a8bb3cc
git push origin v1.0.0
```


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fautes d'orthographes à piquer les yeux


Contacted Eric James at NOAA for guidance on original intention for ID(36)=2 and told to remove - not needed - grib1 never tested anyways.


A RequestCycleListener will trigger too often (e.g. for resources and non Wicket Ajax responses), so I don't think it is the right place to hook into.


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* https://stage.tylerfreeman.dev
* https://next-9.tylerfrmn5.now.sh
* https://next-9-git-master.tylerfrmn5.now.sh


This doesn't need to be classified as a builder anymore, I was trying to get a 2 stage build running, but it's not required.

so it should read `FROM node:13` not `FROM node:13 as builder` and for neatness sake, bin the comment above too


Why are you duplicating CspNonceHeaderResponse?


Successfully deployed to following URLs:

* https://seimani-only-2020-3z4t0j8jm.now.sh
* https://seimani-only-2020.now.sh
* https://seimani-only-2020.gao.now.sh
* https://seimani-only-2020-git-master.gao.now.sh


This is a test, its not really important. Also, this commit is from 2012 :D


Maybe this case line is not necessary, it seems that this type is deprecated now: https://golang.org/pkg/encoding/json/#InvalidUTF8Error


Scheduling-Min-AirFlow-For-VAV-Boxes (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (675 of 676 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 675
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.42%25-green.png)


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~