[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
  ^
```


Still it's not correct, there is no "if" before "fileExists".

Please check the original file.


Successfully deployed to following URLs:

* https://mue-491s179tg.now.sh
* https://mue.now.sh
* https://demo.muetab.xyz
* https://mue.mue.now.sh
* https://mue-git-master.mue.now.sh


I see. Shall I fix this, or do you think it's best not to go >= 1 in any circumstances? In the latter case, I'll just remove overshape.


Successfully deployed to following URLs:

* https://react-components-mwamk5atn.now.sh
* https://react-components.ludovicgueth.io
* https://react-components.ludovicgueth.now.sh
* https://react-components-git-master.ludovicgueth.now.sh


also todo: make the SET/ALIAS symbol tables persistent
also, document what's the difference between them

SET evaluates the rvalue expression, so, e.g. SET word.letter_sum=column(10);
would try to evaluate column(10), not in the context of a query, and assign a maximally unknown interval to word.letter_sum
whereas ALIAS word.letter_sum=column(10);
would assign an unevaluated expression tree to word.letter_sum, so it can be evaluated later in the context of a query.
To handle this, I keep separate evaluated and unevaluated symbol tables, where the unevaluated symbol table is used to re-write expressions with the .bind() method before passing the re-written expression to the evaluator, which is passed an evaluated symbol table, along with a vector of column values if it is being applied to a particular row of data.
This defers questions like how to deal with assignments like
foo=bar*2, bar=foo+2
which could in principle. be resolved to foo=-4, bar=-2
but a general simultaneous equation solver for arbitrary expressions seemed beyond the scope of this phase of the project.
Finitely nested assignments, like
foo=bar, bar=baz, baz=qux, qux=zyzzy, xyzzy=plugh, plugh=spam, spam=ham, ham=eggs, eggs='hello, world'
could be resolved with repeated .bind(symboltable) operations, but I leave it for the user to write that, or to write a general simultaneous equation solver if they want it (If a user/contributor wants to write such things, and determines that other expression manipulating operations would facilitate doing so, I could look into how to supply such operations)
The ALIAS, SET and SELECT commands in sql.h only bind once. (but the above assignments could have been resolved if they had been made in the opposite order, or if an ALIAS command doing those assignments was done repeatedly, so I'm not imagining a strong need to do more unless some user wants to do something more complicates than I'm anticipating)


[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)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


They are probably a left over then, did you clean your build and restarted it? (haikuporter -c)


[R/calculate_allele_frequencies.R:6:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_allele_frequencies.R#L6) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/calculate_allele_frequencies.R:8:18:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_allele_frequencies.R#L8) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
  pop_for_cpp <- population_to_vector(source_pop)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_fst.R:7:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_fst.R#L7) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop1 <- check_input_pop(pop1)
          ^~~~~~~~~~~~~~~
```
[R/calculate_fst.R:9:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_fst.R#L9) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop2 <- check_input_pop(pop2)
          ^~~~~~~~~~~~~~~
```
[R/calculate_fst.R:13:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_fst.R#L13) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_fst.R:19:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_fst.R#L19) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop1[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:20:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_fst.R#L20) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop1[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:26:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_fst.R#L26) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop2[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:27:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_fst.R#L27) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop2[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_ld.R:6:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L6) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_ld.R:12:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L12) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_ld.R:18:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L18) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 1 + findtype(pop[[i]]$chromosome1, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:19:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L19) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 1 + findtype(pop[[i]]$chromosome2, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:68:21:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L68) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        index1 <- c( (x - 1) * 2 + 1, (x - 1) * 2 + 2)
                    ^
```
[R/calculate_ld.R:69:21:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        index2 <- c( (y - 1) * 2 + 1, (y - 1) * 2 + 2)
                    ^
```
[R/calculate_ld.R:93:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L93) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
calculate_average_ld <- function(alleles_pos_1, alleles_pos_2) {
^
```
[R/calculate_ld.R:106:13:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L106) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (alleles_pos_1[a, 1]) == i && (alleles_pos_2[a, 1] == j)) {
            ^
```
[R/calculate_ld.R:110:13:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_ld.R#L110) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (alleles_pos_1[a, 2]) == i && (alleles_pos_2[a, 2] == j)) {
            ^
```
[R/calculate_marker_frequency.R:3:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_marker_frequency.R#L3) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:5:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_tajima_d.R#L5) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:24:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_tajima_d.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
calculate_tajima_d <- function(pop,
^
```
[R/calculate_tajima_d.R:95:12:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_tajima_d.R#L95) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dmax <- ( (n + 1) / (2 * n) - 1 / a1) / sqrt(e2)
           ^
```
[R/calculate_tajima_d.R:100:21:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/calculate_tajima_d.R#L100) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  p <- stats::pbeta( (d - dmin) / tmp2, b, a)
                    ^
```
[R/iso_female.R:9:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/iso_female.R#L9) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:34:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/simulate_admixture_migration.R#L34) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_1 <- population_to_vector(input_population_1)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:59:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/simulate_admixture_migration.R#L59) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_2 <- population_to_vector(input_population_2)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:72:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/simulate_admixture_migration.R#L72) *style:* **functions should have cyclomatic complexity of less than 15, this has 37.**
```r
simulate_admixture_migration <- function(input_population_1 = NA,
^
```
[R/simulate_admixture_migration.R:134:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/simulate_admixture_migration.R#L134) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_1 <- create_pop_class(selected_pop$population_1)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:135:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/simulate_admixture_migration.R#L135) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_2 <- create_pop_class(selected_pop$population_2)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:31:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/simulate_admixture.R#L31) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population <- population_to_vector(input_population)
                          ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:51:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/simulate_admixture.R#L51) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
simulate_admixture <- function(input_population = NA,
^
```
[R/simulate_admixture.R:95:25:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/R/simulate_admixture.R#L95) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct <- create_pop_class(selected_pop$population)
                        ^~~~~~~~~~~~~~~~
```
[tests/testthat/test-simulate_admixture_until.R:48:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/fe30e9f116288c88edb4d680fdc55fcba50d8820/tests/testthat/test-simulate_admixture_until.R#L48) *style:* **Commented code should be removed.**
```r
  # testthat::expect_true(fst_2 >= 0.1)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Wooow...if this is real we have SF11 before 2020... Nice Christmas gift.


Thanks! I pushed another commit, and now I think it is ok for pull request


Successfully deployed to following URLs:

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* https://www.davidegiovanni.com
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Component library for MakBit hardware projects.


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* https://nateradebaugh-react-datetime.nateradebaugh.now.sh
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@hvelarde see: https://github.com/collective/collective.cover/pull/873#issuecomment-546558818


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My congratulations!! This is awesome!! SF 11 coming soon. I think with this patch we achieved the +50 elo mark.


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nie o to chodzi

`const isValid = inputArray.every(input => input.value !== '');`


With `echo $settingsDir`, I found out that it's in /system/packages/
Haikuporter's strict mode doesn't let me use this though.
How did you do it?


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Yeah, I cleaned my patches. It works.


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* https://react-todo-app-git-master.ondrejbukartyk.now.sh


Check haikuporter source on how you can use it, hint $appsDir is the same as /system/apps (which you fixed for gamesdir


Collaborator: Review for this commit was created. [Link to review](http://217.170.125.19:40101/ui#review:id=2)


We should probably document this, at least for ourselves, since this is a change that's easy to oversee and we'll need to move this default to SimpleSAMLphp.


README file


Deployment failed with the following error:

~~~
Could not find a secret by name "CONTENTFUL_ACCESS_TOKEN"
~~~


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[R/check_param.R:74:1:](https://github.com/ropensci/beautier/blob/263548ac7711feef26f852f389ff76fd370b62a1/R/check_param.R#L74) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/init_distr.R:9:1:](https://github.com/ropensci/beautier/blob/263548ac7711feef26f852f389ff76fd370b62a1/R/init_distr.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
init_distr <- function(
^
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/263548ac7711feef26f852f389ff76fd370b62a1/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
parameter_to_xml <- function(
^
```


What an epic performance at LTC, congrats!


Deployment failed with the following error:

~~~
ENOENT: no such file or directory, stat '/tmp/RnWw7P542eI4qiVk6tUMWMQH/repo/examples/official-storybook/built-storybooks/cra-kitchen-sink'
~~~


修正多byte傳輸與%後字元多出問題


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# Performance Report

Possible performance regression was detected for benchmark.
Benchmark result of this commit is worse than the previous benchmark result exceeding threshold `0.0`.

| Benchmark suite | Current: cac48c262f65b2b14d2be34013137b4c2300469b | Previous: 053bf8dd0dbd377461126d6f20bc2263225c3aff | Ratio |
|-|-|-|-|
| `render /` | `376` ops/sec (`±161.65%`) | `372` ops/sec (`±162.84%`) | `0.9893617021276596` |
| `render /news/1` | `2580` ops/sec (`±2.01%`) | `2671` ops/sec (`±2.75%`) | `1.0352713178294575` |

This comment was automatically generated by [workflow](https://github.com/umijs/umi-server/actions?query=workflow%3Arender%20Benchmark) using [github-action-benchmark](https://github.com/marketplace/actions/continuous-benchmark).


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit 3d920826760087c60a6c4d27e5769a06207af912.

You can try again later or [upgrade](https://zeit.co/account/plan) your plan.


Pixel 4 has touch sensor on SPI bus, and interracting with i2c_msm_ctrl struct will go kaboom


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<img width="406" alt="Screenshot 2019-12-26 at 13 39 13" src="https://user-images.githubusercontent.com/534693/71476384-20d44e00-27e5-11ea-923b-59ffa4203c7c.png">


购买


出售


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`#undef pr_debug
#define pr_info pr_debug`
Good luck merging TS driver updates with this mess


成交记录


我的


Так как мы уже отходим от обычного представления и заполнения таких полей строкой нужно было реализовать при помощи интерфесов, или абстрактных классов, то есть должен быть интерфейс допустим Круглый
`interface Circle{}`
дальше в классе Backpack используем в качестве свойства:
```
class BackPack {
    List<Circle> circleItems = new ArrayList<>(); // То есть место для чего-то круглого
...
}
```
А так же добавить методы для работы с этими списками и тд


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Thank you!


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Great job!


Very nice! Now it is very clear I think for anybody to install it! :)


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Возможно abstract было бы лучше?


Абстракт?


Или создать объект который содержит эти списки


I think we already have it in place there.. It's possible to set it in `saml20-idp-hosted`..
Another option is to set a default value in the Attribute-class that is compliant with SAML2INT.. One would have to specifically set it to null or something different..
I guess it's the same discussion as with NameIDPolicy.. Where do we enforce defaults to comply with SAML2INT? I think if we want this library to be a low-level library, this is not the place to do so..


Делая вещи через наименование в ООП не очень хорошая практика, тем более что они могут быть разными, то есть я бы мог сделать `new Cylindrical("Book")`, что не есть хорошо


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-125-usfs.pantheonsite.io/)

Created multidev environment [pr-125](https://dashboard.pantheon.io/sites/41bd818c-c95f-4bfb-ae68-63c3075be556#pr-125) for usfs.


The fvim project page is: https://github.com/yatli/fvim


Zavrsen algoritam i GUI


On Windows this testcase seems to fail (tested with v8.9.0-rc2). Here's the output:
[x.jpg](https://user-images.githubusercontent.com/12746591/71476544-da332380-27e5-11ea-9d8e-79b711cfb5fe.jpg) (dimensions: 471x317)

Perhaps we could increase the tolerance to `< 30`?


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Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/uHu6vpqgggqy6cR86AOpzMzu/repo/now.json.
~~~


xD


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Ooh, that switch to upper case is going to break a few things. Out of curiosity, is there a reason for that? Personally, I find lower case easier to read, and is more friendly looking when exposed to APIs and URLs. Just my 2p :-)


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Offending files: js/vendor/jquery/jquery-ui-timepicker-addon.js


Oh, the DLL file doesn't even have to be there. You have extracted this into a separate maven package (sikulix2opencv) recently :-)


To add the environment of facs to system environment variables.It is necessary.Or the FACS.sh can not work.


@judgej at this point I'm not really considering the BC things (my shortcuts just add these uppercase), I think for the actual release those constants will just contain the 1.0 values.


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单独的


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