[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calc_K.R#L11) *style:* **Variable or function name should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calc_K.R#L12) *style:* **Variable or function name should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calc_K.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calc_K.R#L16) *style:* **Variable or function name 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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calc_K.R#L19) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calc_K.R#L23) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calc_K.R#L27) *style:* **Variable or function name should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_error.R#L15) *style:* **Variable or function name should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_error.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_error.R#L17) *style:* **Variable or function name should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_error.R#L18) *style:* **Variable or function name should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_error.R#L24) *style:* **Variable or function name 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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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:31:26:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_error.R#L31) *style:* **Put spaces around all infix operators.**
```r
  if (!relative) return(t*error)
                        ~^~
```
[R/calculate_MAT.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_MAT.R#L12) *style:* **Variable or function name should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_MAT.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_MAT.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_MAT.R#L20) *style:* **Variable or function name 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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_time.R#L13) *style:* **Variable or function name should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_time.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_time.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_time.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/calculate_time.R#L28) *style:* **Variable or function name 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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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:10:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_markers.R#L10) *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:16:35:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_markers.R#L16) *style:* **Variable or function name should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:17:35:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_markers.R#L17) *style:* **Variable or function name should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:18:35:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_markers.R#L18) *style:* **Variable or function name should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:31:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_markers.R#L31) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(J > 1e4) {
    ^
```
[R/estimate_time_markers.R:35:63:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_markers.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(2, upper_lim) )
                                                              ^
```
[R/estimate_time_phased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L2) *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:3:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc 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/estimate_time_phased.R:7:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param max_t maximum time to be considered for maximum likelihood optimization. Too large values might cause the maximum likelihood algorithm to deviate from the global maximum.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:8:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L8) *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:21:19:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L21) *warning:* **no visible global function definition for ‘get_states_phased’**
```r
  local_states <- get_states_phased(local_anc)
                  ^~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:27:21:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L27) *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:34:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L34) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(optim_pop_size == FALSE) {
    ^
```
[R/estimate_time_phased.R:41:9:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L41) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(verbose) cat(t, -sum(local_probs), "\n")
        ^
```
[R/estimate_time_phased.R:48:9:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L48) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(params[[1]] < 2) return(-Inf)
        ^
```
[R/estimate_time_phased.R:49:9:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L49) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(params[[2]] < 2) return(-Inf)
        ^
```
[R/estimate_time_phased.R:55:9:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L55) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(verbose) cat("N",params[[1]],"t", params[[2]], -sum(local_probs), "\n")
        ^
```
[R/estimate_time_phased.R:55:27:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L55) *style:* **Commas should always have a space after.**
```r
      if(verbose) cat("N",params[[1]],"t", params[[2]], -sum(local_probs), "\n")
                          ^
```
[R/estimate_time_phased.R:55:39:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_phased.R#L55) *style:* **Commas should always have a space after.**
```r
      if(verbose) cat("N",params[[1]],"t", params[[2]], -sum(local_probs), "\n")
                                      ^
```
[R/estimate_time_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_unphased.R:3:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc 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/estimate_time_unphased.R:7:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param max_t maximum time to be considered for maximum likelihood optimization. Too large values might cause the maximum likelihood algorithm to deviate from the global maximum.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_unphased.R:8:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L8) *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_unphased.R:21:19:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L21) *warning:* **no visible global function definition for ‘get_states’**
```r
  local_states <- get_states(local_anc)
                  ^~~~~~~~~~
```
[R/estimate_time_unphased.R:27:21:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L27) *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:34:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L34) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(optim_pop_size == FALSE) {
    ^
```
[R/estimate_time_unphased.R:41:9:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L41) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(verbose) cat(t, -sum(local_probs), "\n")
        ^
```
[R/estimate_time_unphased.R:48:9:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L48) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(params[[1]] < 2) return(-Inf)
        ^
```
[R/estimate_time_unphased.R:49:9:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L49) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(params[[2]] < 2) return(-Inf)
        ^
```
[R/estimate_time_unphased.R:55:9:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L55) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(verbose) cat("N",params[[1]],"t", params[[2]], -sum(local_probs), "\n")
        ^
```
[R/estimate_time_unphased.R:55:27:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L55) *style:* **Commas should always have a space after.**
```r
      if(verbose) cat("N",params[[1]],"t", params[[2]], -sum(local_probs), "\n")
                          ^
```
[R/estimate_time_unphased.R:55:39:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/estimate_time_unphased.R#L55) *style:* **Commas should always have a space after.**
```r
      if(verbose) cat("N",params[[1]],"t", params[[2]], -sum(local_probs), "\n")
                                      ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_backcross.R#L10) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_backcross.R:13:29:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_backcross.R#L13) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  jt <- 2 * H_0 * t * C * 2^(-t)
                            ^
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_di.R#L12) *style:* **Variable or function name 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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_di.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_di.R:17:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_di.R#L17) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.infinite(N)) local_k <- H_0
    ^
```
[R/number_of_junctions_di.R:19:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_di.R#L19) *style:* **Put spaces around all infix operators.**
```r
  local_j <- local_k - local_k * (1 - 1 / (2*N) - di)^t
                                           ~^~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:20:41:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_markers.R#L20) *style:* **Variable or function name 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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_markers.R#L21) *style:* **Variable or function name should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions_markers.R:25:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_markers.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(marker_distribution) < 2) {
    ^
```
[R/number_of_junctions_markers.R:30:6:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_markers.R#L30) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in 2:length(marker_distribution)) {
     ^
```
[R/number_of_junctions_markers.R:31:57:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_markers.R#L31) *style:* **Put spaces around all infix operators.**
```r
    di <- marker_distribution[i] - marker_distribution[i-1]
                                                       ~^~
```
[R/number_of_junctions_markers.R:32:27:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions_markers.R#L32) *warning:* **no visible global function definition for ‘number_of_junctions_di’**
```r
    expected_junctions <- number_of_junctions_di(N, H_0, t, di)
                          ^~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions.R#L13) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/number_of_junctions.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/RcppExports.R:4:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
simulate_backcrossing_cpp <- function(pop_size, freq_ancestor_1, total_runtime, size_in_morgan, number_of_markers, time_points, seed) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_junctions_simulate_backcrossing_cpp', PACKAGE = 'junctions', pop_size, freq_ancestor_1, total_runtime, size_in_morgan, number_of_markers, time_points, seed)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:11:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L5) *style:* **Only use double-quotes.**
```r
    .Call('_junctions_simulate_backcrossing_cpp', PACKAGE = 'junctions', pop_size, freq_ancestor_1, total_runtime, size_in_morgan, number_of_markers, time_points, seed)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:61:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L5) *style:* **Only use double-quotes.**
```r
    .Call('_junctions_simulate_backcrossing_cpp', PACKAGE = 'junctions', pop_size, freq_ancestor_1, total_runtime, size_in_morgan, number_of_markers, time_points, seed)
                                                            ^~~~~~~~~~~
```
[R/RcppExports.R:8:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
sim_fin_chrom <- function(pop_size, freq_ancestor_1, run_time, size_in_Morgan, seed, R) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:8:64:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L8) *style:* **Variable or function name should be snake_case.**
```r
sim_fin_chrom <- function(pop_size, freq_ancestor_1, run_time, size_in_Morgan, seed, R) {
                                                               ^~~~~~~~~~~~~~
```
[R/RcppExports.R:8:86:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L8) *style:* **Variable or function name should be snake_case.**
```r
sim_fin_chrom <- function(pop_size, freq_ancestor_1, run_time, size_in_Morgan, seed, R) {
                                                                                ^
```
[R/RcppExports.R:9:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_junctions_sim_fin_chrom', PACKAGE = 'junctions', pop_size, freq_ancestor_1, run_time, size_in_Morgan, seed, R)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:9:11:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L9) *style:* **Only use double-quotes.**
```r
    .Call('_junctions_sim_fin_chrom', PACKAGE = 'junctions', pop_size, freq_ancestor_1, run_time, size_in_Morgan, seed, R)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:9:49:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L9) *style:* **Only use double-quotes.**
```r
    .Call('_junctions_sim_fin_chrom', PACKAGE = 'junctions', pop_size, freq_ancestor_1, run_time, size_in_Morgan, seed, R)
                                                ^~~~~~~~~~~
```
[R/RcppExports.R:12:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
sim_inf_chrom <- function(pop_size, freq_ancestor_1, run_time, size_in_Morgan, markers, seed) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:64:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L12) *style:* **Variable or function name should be snake_case.**
```r
sim_inf_chrom <- function(pop_size, freq_ancestor_1, run_time, size_in_Morgan, markers, seed) {
                                                               ^~~~~~~~~~~~~~
```
[R/RcppExports.R:13:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_junctions_sim_inf_chrom', PACKAGE = 'junctions', pop_size, freq_ancestor_1, run_time, size_in_Morgan, markers, seed)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:13:11:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L13) *style:* **Only use double-quotes.**
```r
    .Call('_junctions_sim_inf_chrom', PACKAGE = 'junctions', pop_size, freq_ancestor_1, run_time, size_in_Morgan, markers, seed)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:13:49:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L13) *style:* **Only use double-quotes.**
```r
    .Call('_junctions_sim_inf_chrom', PACKAGE = 'junctions', pop_size, freq_ancestor_1, run_time, size_in_Morgan, markers, seed)
                                                ^~~~~~~~~~~
```
[R/RcppExports.R:16:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
sim_phased_unphased_cpp <- function(pop_size, freq_ancestor_1, total_runtime, size_in_morgan, number_of_markers, time_points, seed) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:17:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_junctions_sim_phased_unphased_cpp', PACKAGE = 'junctions', pop_size, freq_ancestor_1, total_runtime, size_in_morgan, number_of_markers, time_points, seed)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:17:11:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L17) *style:* **Only use double-quotes.**
```r
    .Call('_junctions_sim_phased_unphased_cpp', PACKAGE = 'junctions', pop_size, freq_ancestor_1, total_runtime, size_in_morgan, number_of_markers, time_points, seed)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:17:59:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L17) *style:* **Only use double-quotes.**
```r
    .Call('_junctions_sim_phased_unphased_cpp', PACKAGE = 'junctions', pop_size, freq_ancestor_1, total_runtime, size_in_morgan, number_of_markers, time_points, seed)
                                                          ^~~~~~~~~~~
```
[R/RcppExports.R:19:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/RcppExports.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_backcrossing.R:7:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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_backcrossing.R:26:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/sim_backcrossing.R#L26) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(time_points) == 1) {
    ^
```
[R/sim_backcrossing.R:27:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/sim_backcrossing.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(time_points == -1) {
      ^
```
[R/sim_fin_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/sim_fin_chrom.R#L22) *style:* **Variable or function name should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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:10:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/sim_phased_unphased.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
#' @return matrix with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:24:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/sim_phased_unphased.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(time_points) == 1) {
    ^
```
[R/sim_phased_unphased.R:25:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/sim_phased_unphased.R#L25) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(time_points == -1) {
      ^
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/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/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/unphased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc 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:18:19:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/unphased_log_likelihood.R#L18) *warning:* **no visible global function definition for ‘get_states’**
```r
  local_states <- get_states(local_anc)
                  ^~~~~~~~~~
```
[R/unphased_log_likelihood.R:24:21:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/unphased_log_likelihood.R#L24) *warning:* **no visible global function definition for ‘single_state’**
```r
    seven_states <- single_state(t = local_time, N = local_pop_size, d = di)
                    ^~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:31:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/unphased_log_likelihood.R#L31) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(t) == 1) {
    ^
```
[R/unphased_log_likelihood.R:42:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/unphased_log_likelihood.R#L42) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(t) > 1) {
    ^
```
[R/unphased_log_likelihood.R:44:8:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/unphased_log_likelihood.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in seq_along(t)) {
       ^
```
[R/util.R:12:5:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L12) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.matrix(local_anc_matrix)) {
    ^
```
[R/util.R:13:50:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L13) *style:* **Commas should always have a space after.**
```r
    local_anc <- rep(2, length(local_anc_matrix[,1]))
                                                 ^
```
[R/util.R:14:39:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L14) *style:* **Commas should always have a space after.**
```r
    homo_0 <- which(local_anc_matrix[,1] == 0 &
                                      ^
```
[R/util.R:15:42:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L15) *style:* **Commas should always have a space after.**
```r
                      (local_anc_matrix[,1] == local_anc_matrix[,2]))
                                         ^
```
[R/util.R:15:66:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L15) *style:* **Commas should always have a space after.**
```r
                      (local_anc_matrix[,1] == local_anc_matrix[,2]))
                                                                 ^
```
[R/util.R:16:39:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L16) *style:* **Commas should always have a space after.**
```r
    homo_1 <- which(local_anc_matrix[,1] == 1 &
                                      ^
```
[R/util.R:17:42:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L17) *style:* **Commas should always have a space after.**
```r
                      (local_anc_matrix[,1] == local_anc_matrix[,2]))
                                         ^
```
[R/util.R:17:66:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L17) *style:* **Commas should always have a space after.**
```r
                      (local_anc_matrix[,1] == local_anc_matrix[,2]))
                                                                 ^
```
[R/util.R:22:10:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( get_states_vector(local_anc))
         ^
```
[R/util.R:22:11:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L22) *warning:* **no visible global function definition for ‘get_states_vector’**
```r
  return( get_states_vector(local_anc))
          ^~~~~~~~~~~~~~~~~
```
[R/util.R:28:6:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in 2:length(local_anc)) {
     ^
```
[R/util.R:29:24:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L29) *style:* **Put spaces around all infix operators.**
```r
    left <- local_anc[i-1]
                      ~^~
```
[R/util.R:32:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L32) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 0 && right == 1) all_states[i-1] <- 1
      ^
```
[R/util.R:32:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L32) *style:* **Put spaces around all infix operators.**
```r
    if(left == 0 && right == 1) all_states[i-1] <- 1
                                           ~^~
```
[R/util.R:33:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L33) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 1 && right == 0) all_states[i-1] <- 2
      ^
```
[R/util.R:33:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L33) *style:* **Put spaces around all infix operators.**
```r
    if(left == 1 && right == 0) all_states[i-1] <- 2
                                           ~^~
```
[R/util.R:34:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L34) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 1 && right == 1) all_states[i-1] <- 3
      ^
```
[R/util.R:34:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L34) *style:* **Put spaces around all infix operators.**
```r
    if(left == 1 && right == 1) all_states[i-1] <- 3
                                           ~^~
```
[R/util.R:35:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L35) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 0 && right == 0) all_states[i-1] <- 4
      ^
```
[R/util.R:35:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L35) *style:* **Put spaces around all infix operators.**
```r
    if(left == 0 && right == 0) all_states[i-1] <- 4
                                           ~^~
```
[R/util.R:36:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 2 && right == 1) all_states[i-1] <- 5
      ^
```
[R/util.R:36:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L36) *style:* **Put spaces around all infix operators.**
```r
    if(left == 2 && right == 1) all_states[i-1] <- 5
                                           ~^~
```
[R/util.R:37:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L37) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 2 && right == 0) all_states[i-1] <- 6
      ^
```
[R/util.R:37:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L37) *style:* **Put spaces around all infix operators.**
```r
    if(left == 2 && right == 0) all_states[i-1] <- 6
                                           ~^~
```
[R/util.R:38:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L38) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 0 && right == 2) all_states[i-1] <- 7
      ^
```
[R/util.R:38:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L38) *style:* **Put spaces around all infix operators.**
```r
    if(left == 0 && right == 2) all_states[i-1] <- 7
                                           ~^~
```
[R/util.R:39:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L39) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 1 && right == 2) all_states[i-1] <- 8
      ^
```
[R/util.R:39:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L39) *style:* **Put spaces around all infix operators.**
```r
    if(left == 1 && right == 2) all_states[i-1] <- 8
                                           ~^~
```
[R/util.R:40:7:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L40) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(left == 2 && right == 2) all_states[i-1] <- 9
      ^
```
[R/util.R:40:45:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if(left == 2 && right == 2) all_states[i-1] <- 9
                                           ~^~
```
[R/util.R:52:48:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L52) *style:* **Commas should always have a space after.**
```r
  local_anc <- rep(2, length(local_anc_matrix[,1]))
                                               ^
```
[R/util.R:53:37:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L53) *style:* **Commas should always have a space after.**
```r
  homo_0 <- which(local_anc_matrix[,1] == 0 &
                                    ^
```
[R/util.R:54:40:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L54) *style:* **Commas should always have a space after.**
```r
                    (local_anc_matrix[,1] == local_anc_matrix[,2]))
                                       ^
```
[R/util.R:54:64:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L54) *style:* **Commas should always have a space after.**
```r
                    (local_anc_matrix[,1] == local_anc_matrix[,2]))
                                                               ^
```
[R/util.R:55:37:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L55) *style:* **Commas should always have a space after.**
```r
  homo_1 <- which(local_anc_matrix[,1] == 1 &
                                    ^
```
[R/util.R:56:40:](https://github.com/thijsjanzen/junctions/blob/51aefa07f238d13d7762ef4c88ac8320c8868e6e/R/util.R#L56) *style:* **Commas should always have a space after.**
```r
                    (local_anc_matrix[,1] == local_anc_matrix[,2]))
                                       ^
```


I forgot, In this specfic case, I would rename it ``Pending_Object`` to be consistent with  ``Unused_Object``.


Successfully aliased the URL <https://liganicer-lrska6mjt.now.sh> to the following aliases.

* https://liganicer.liganicer.now.sh
* https://liganicer-git-master.liganicer.now.sh


@JuliaRegistrator `register()`


Registration pull request created: [JuliaRegistries/General/799](https://github.com/JuliaRegistries/General/pull/799)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.2.5 -m "<description of version>" 8e1086e2cfcfb23ff7085daaad823211b4abbb7c
git push origin v0.2.5
```


which begs the question, why sizeof(queue_head) is an idiom here


@alelievr
Now it shows NO CRASH and make test RED, is there way to use green colour and rather
<img width="1414" alt="Screen Shot 2019-05-16 at 15 00 01" src="https://user-images.githubusercontent.com/20406006/57852240-534bb080-77eb-11e9-8582-7d913cc06c94.png">
show SUCCESS on NO CRASH?


Successfully aliased the URL <https://personal-lkijixwfsx.now.sh> to the following alias.

* https://www.connordav.is


If i’m  Not mistaken we also support setIfNull and “increment”, “decrement” etc don’t we ?


This blank line can be deleted.


Successfully aliased the URL <https://liganicer-myndexm5m.now.sh> to the following aliases.

* https://liganicer.liganicer.now.sh
* https://liganicer-git-master.liganicer.now.sh


For was updated too, with support for incomplete initial, condition and update expressions.


Maybe I didn't explain the problem very well. What I wanted to achieve in this case is to short-circuit on the first failure (give a response to the user calling this API) but still keep running any other computations in the background (hence `start`) for the effects.

Because computations are running in the background I need the `Deferred` to retrieve *only* the first failure, otherwise this is not possible. You can try it out by modifying `randomPutStrLn` to simulate expensive computations:

```scala
def randomPutStrLn[A](a: A): IO[Unit] =
  IO(Random.nextInt(10)).flatMap {
    case n if n % 2 == 0 => IO.sleep(Duration(n.toLong, TimeUnit.SECONDS)) *> putStrLn(a)
    case n => IO.sleep(Duration(n.toLong, TimeUnit.SECONDS)) *> IO.raiseError(Fail(s"n=$n, a=$a"))
  }
```

The real case was authorizing payments in real time where we needed to call different external paid services (that means they cost money) and whenever we get a response where we already know that the payment should be rejected we can respond to the user but since we are paying for these services we don't want to interrupt the other computations and let them keep running in the background where the results are persisted for future use. Previously we were waiting for all of these services to respond, even if we already had a response thus our service was much slower.

I presented this idea at Scala IO, hope this part of the talk makes the intent clearer: https://youtu.be/8_TWM2t97r4?t=2145

TL;DR you need `start` and `Deferred` :smiley: unless I'm missing something.


@samarV-121 yup, but kennel is not booting on implementing lz4 compression


> The changes in the blade templates causes fatal errors because the classes are called without the namespace

Wrong. Its only because you didnt update you configs.
https://github.com/HDInnovations/UNIT3D/commit/22500dbb0797b15cc26796377d3eff4bb6ed0f93


> done, i've added a bg input, refresh the page if it's not there

Thanks buddy! it work nicely ^^


Members `rtsp_ahost` and `rtsp_vhost` of `janus_streaming_rtp_source` belong in `janus_streaming_rtp_source_stream`, as they may legally differ for multiple streams of the same type.

On top of that, `ahost` is wrongly used for the video stream too, even though they are not necessarily the same.


possible addl. fields:
1. version of the queue--in case we redo the whole thing--starts at 1
2. version of this structure--same as write_class_encoder's value


We might as well create the `rpc.Client` at this point with [`rpc.NewClient`](https://golang.org/pkg/net/rpc/#NewClient) (having `d.clientConn` as input ofcourse).


олдодлолд


So if you want to put the first failure in the Deferred shouldn't it be defined before `parTraverse`? As in:

```scala
Deferred[F, Either[Throwable, A]].flatMap { d =>
  gfa.parTraverse(...)
}
```


>[...] have you considered how much refactoring it'll involve if one wants to maintain consistency?

@claird, I'd like this remark to gain a little more attention. Switching to snake_case will take lots of refactoring and time, which ought to invested elsewhere.


yes you get it right


those nodes with the same label will be in the same community


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@cnuke Could be worth it to have a counter ``Pending_Jobs`` to be able to optimize here.


Maybe, only as XXX note for now ;)


I don't understand what you did here:
  (1) it looks like you are just copying the code from above (you should not copy)
  (2) I thought we would focus first on EvoSuiteToRandoop (not the other way around)


Successfully aliased the URL <https://personal-yxeigijiyq.now.sh> to the following alias.

* https://www.connordav.is


Successfully aliased the URL <https://liganicer-r0inh4vse.now.sh> to the following aliases.

* https://liganicer.liganicer.now.sh
* https://liganicer-git-master.liganicer.now.sh


2.6.2 tag will be created in this repo by the end of june. For now there are no plan to package a iTop v2.6.2 for the community but this may change ?

With 2.6.1 a workaround would be to use `synchro_import.php --synchronize=1` if possible ? If not, we are still investigating to produce a detailed procedure.


@cnuke Would be nice to have a descriptive global constant for 16#20#.


hhh


Or a wrapper for ``Valid_Object``.


I think by changing the dependencies file you'll also need to update the paket.lock file? This seems to break the build.


dorei


size_data per 1x1 means head size on disk?  better name maybe;  also, make this 32bit and you could use htonl/ntohl on it.


@init-js This change doesn't result in skipping deletion; rather it removes a redundant deletion code path, in favor of relying on the `createTempDir` utility's shutdown hook for deletion.


Great change! 👍


@cnuke I would become more readable if ``then`` comes in a new line with same indentation as ``if``. There are other locations where this applies that I don't comment. In general, I refrain from doing this only if there is only a single condition that fits in one line.


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Commit ID	Owner

a23cad998261c81bf63aa21ac681a2e8b5303e7c	@web-flow


Iespējams varētu sadalīt 2 metodēs render un renderFromOriginal, tas tāds lieks parametrs liekas


后台怎么进入呢，/admin进不去呀


mixed palicis


ohhhhhh now I see why it works. In case of failure (with your example), the whole thing tries to cancel the other running jobs, but can't (because they are forked).


Es viņu pagaidām atstāju šādu, jo vēl neesmu izdomājis kā viņu reāli dzīvē pielietošu. Šis būs nepieciešams vienai funkcionalitātei un kad būšu ar to ticis galā, tad ticamākais šis arī mainīsies


Šo iespējams var sadalīt kaut kā, šobrīd diezgan grūti nolasāms


Ja šobrīd vispār netiek izmantots, tad kāda jēga to te atstāt


Successfully aliased the URL <https://nine-to-five-fgq855bqd.now.sh> to the following aliases.

* https://nine-to-five.conscience.now.sh
* https://nine-to-five-git-master.conscience.now.sh


Well, in this particular case it is not about the active jobs but to check if there is already a Job regarding the same pba pending.


you wrote very good,even though I don't know what it means.


Future proofing. Tas pats, kā tīkla kabelī no 8 vadiem tiek izmantoti tikai 4 :D ar domu, ka nākotnē pārējos 4us arī izmantos


To generate a self-signed certificate run, e.g., `openssl req -new -newkey rsa:4096 -x509 -sha256 -days 365 -nodes -out nginx/server.crt -keyout nginx/server.key -subj "/C=NL/ST=Utrecht/L=Utrecht/O=The Hyve/CN=localhost"`


Ah, sorry overlooked that. Nevermind.


@hlim1 Thanks, now I understand what's happening.  The problems due to undeclared variables is certainly not your problem, and I can fix those when I get back.

If you're stuck on travis errors that you cannot replicate locally, my suggestion would be that we wait on this until @adarshp is back, and meanwhile focus on the goto-elimination transformations.


Yes, that will be the case in the future when the enum values are made available in `cbe.ads`. Currently it is the only location where we actually use some specific tag value (Cbe::Tag::CACHE_TAG) in SPARK.


Tas nav īsti future proofing, tas būtu, ja nākotnē šo funkcionalitāti varētu extendod papildināsanas vajadzībām, šobrīd tas ir lieks kods


please give me the script
contact me: thompson_david_w@student.smc.edu


Maita phpstorms :D bet teorijā šeit arī īsti nevar paredzēt kāda vērtiba atnāks, jo custom placeholders, ko pēc tam developers iebaros var atgriezt da jebko. (float, int, string)

Vienīgi, varbūt by default castot uz stringu arī custom placeholderus 🤔


Right, I'll change it.


I've noticed this change introduced a minor issue in the [misc_controls_pointerlock](https://threejs.org/examples/misc_controls_pointerlock) when creating the module version of `PointerLockControls`. When starting the demo, the camera sticks now at the floor and "jumps" at the correct position as soon as the controls are enabled. In the previous version, the camera was at the correct position right from the beginning


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We have a minor bug here ! It miss a "!".

```R
js_code <- paste0("$('#", input_id, "').prop( 'disabled', ", tolower(!enable), " )")
```

PR tomorrow to correct my mistake.


왜 이파일을 수정했는지
어떤 부분이 같이 회의해야 하는가요?


Apologies, I think this was my fault. I didn't realise that `.append` returns `*this`. I thought it returned a copy of the concatenated strings.


Managed to get rid of `start`:

```
def parFailFast[A](gfa: List[IO[A]]): IO[List[A]] =
  Deferred[IO, Throwable].flatMap { d =>
    gfa.parTraverse { fa =>
      fa.onError { case e => d.complete(e).attempt.void }.recoverWith(handler).uncancelable
    }
  }
```

but with the cost of `uncancelable` (which makes it more obvious that the whole thing is uncancelable anyway) and `d.complete.attempt`, which I don't like (I'm pretty sure I could do it better with `Ref[IO, Either[Deferred[IO, Throwable], Throwable]]` or something of the sort)


[inst/doc/trees_with_root_edge.R:31:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/trees_with_root_edge.R#L31) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/walkthrough.R:11:16:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L11) *style:* **Trailing whitespace is superfluous.**
```r
    plot(tree1)
               ^
```
[inst/doc/walkthrough.R:30:50:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L30) *style:* **Trailing whitespace is superfluous.**
```r
nltts_plot(trees1, dt = 0.001, plot_nltts = TRUE,
                                                 ^
```
[inst/doc/walkthrough.R:32:50:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
nltts_plot(trees2, dt = 0.001, plot_nltts = TRUE,
                                                 ^
```
[inst/doc/walkthrough.R:42:75:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L42) *style:* **Trailing whitespace is superfluous.**
```r
plot(m1, type = "s", col = "red", lwd = 2, xlim = c(0, 1), ylim = c(0, 1),
                                                                          ^
```
[inst/doc/walkthrough.R:45:65:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L45) *style:* **Trailing whitespace is superfluous.**
```r
legend("topleft", c("trees1", "trees2"), col = c("red", "blue"),
                                                                ^
```
[inst/doc/walkthrough.R:74:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L74) *style:* **Variable or function name should be snake_case.**
```r
A <- abc_smc_nltt(
^
```
[inst/doc/walkthrough.R:85:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L85) *style:* **Variable or function name should be snake_case.**
```r
LL_B <- function(params, phy) {
^~~~
```
[inst/doc/walkthrough.R:97:3:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L97) *style:* **Variable or function name should be snake_case.**
```r
  ML <- stats::optimize(f = fun, interval = c(0, 1))
  ^~
```
[inst/doc/walkthrough.R:104:28:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L104) *style:* **Trailing whitespace is superfluous.**
```r
         lty = c(NA, 2, 2),
                           ^
```
[inst/doc/walkthrough.R:108:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L108) *style:* **Variable or function name should be snake_case.**
```r
B <- mcmc_nltt(obs, LL_B, parameters = c(0.5),
^
```
[inst/doc/walkthrough.R:108:47:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L108) *style:* **Trailing whitespace is superfluous.**
```r
B <- mcmc_nltt(obs, LL_B, parameters = c(0.5),
                                              ^
```
[inst/doc/walkthrough.R:114:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L114) *style:* **Variable or function name should be snake_case.**
```r
B.mcmc <- coda::as.mcmc(B)
^~~~~~
```
[inst/doc/walkthrough.R:119:55:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L119) *style:* **Trailing whitespace is superfluous.**
```r
  hist(A, breaks = seq(0, 1, by = 0.05), col = "grey",
                                                      ^
```
[inst/doc/walkthrough.R:124:24:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L124) *style:* **Trailing whitespace is superfluous.**
```r
         lty = c(2, 2),
                       ^
```
[inst/doc/walkthrough.R:126:55:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L126) *style:* **Trailing whitespace is superfluous.**
```r
  hist(B, breaks = seq(0, 1, by = 0.05), col = "grey",
                                                      ^
```
[inst/doc/walkthrough.R:130:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/inst/doc/walkthrough.R#L130) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/ABC_SMC.R:11:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
# @param    current                 vector       Current parameter combination for which we are determining the weight
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:12:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                   scalar       standard deviation of the perturbation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:13:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function  function     Function to calculate the prior probability of a set of parameters
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:36:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
# @brief apply the ABC routine used in our Methods in Ecology and Evolution Paper
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:43:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
# @param    statistics                    vector      A vector containing functions that take a tree as an argument and return a single scalar value (the statistic).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:44:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
# @param    simulation_function           vector      A function that implements the diversification model and returns an object of class phylo
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:45:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
# @param    init_epsilon_values           vector      A vector containing the initial threshold values for the summary statistics from the vector statistics.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:46:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_generating_function     function    Function to generate parameters from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:47:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function        function    Function to calculate the prior probability of a set of parameters (should match prior_generating_function in shape)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:48:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
# @param    number_of_particles           scalar      Number of particles to be used per iteration of the ABC-SMC algorithm.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:49:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                         scalar      Standard deviation of the perturbance distribution (perturbance distribution is a gaussian with mean 0).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:50:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
# @param    stop_rate                     scalar      If the acceptance rate drops below \code{stopRate}, stop the ABC-SMC algorithm  and assume convergence.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:51:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
# @return                                 matrix      A matrix with n columns, where n is the number of parameters you are trying to estimate.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:75:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
#'   from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:276:13:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L276) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:301:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L301) *style:* **Lines should not be more than 80 characters.**
```r
# @brief Estimate the likelihood of a given tree, provided a likelihood function, using a Monte Carlo Markov Chain
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:308:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L308) *style:* **Lines should not be more than 80 characters.**
```r
# @param    likelihood_function   function    Function that calculates the likelihood of our diversification model, given the tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:309:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:310:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:311:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L311) *style:* **Lines should not be more than 80 characters.**
```r
# @param    logtransforms         scalar      Whether to perform jumps on logtransformed parameters (TRUE) or not (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:313:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L313) *style:* **Lines should not be more than 80 characters.**
```r
# @param    burnin                scalar      Length of the burnin, default is 30% of iterations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:315:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L315) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                 scalar      Standard deviation of the jumping distribution, which is N(0, sigma).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:316:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/ABC_SMC.R#L316) *style:* **Lines should not be more than 80 characters.**
```r
# @return                         mcmc        An MCMC object, as used by the package "coda".
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:183:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/nLTTDiff.R#L183) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:257:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/nLTTDiff.R#L257) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:258:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/nLTTDiff.R#L258) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:324:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/nLTTDiff.R#L324) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:325:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/nLTTDiff.R#L325) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:326:1:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/nLTTDiff.R#L326) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_nLTT.R:36:23:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/plot_nLTT.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:51:28:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                           ^
```
[R/plot_nLTT.R:51:33:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                                ^
```
[R/plot_nLTT.R:52:28:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/plot_nLTT.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] / max( xy[, 1])      #normalize time
                           ^
```
[R/plot_nLTT.R:94:32:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/R/plot_nLTT.R#L94) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs(min( xy[, 1])) #make sure time runs from 0..T
                               ^
```
[tests/testthat/test-abc_smc_nltt.R:32:3:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/tests/testthat/test-abc_smc_nltt.R#L32) *style:* **Variable or function name should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:46:3:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/tests/testthat/test-abc_smc_nltt.R#L46) *style:* **Variable or function name should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:52:3:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/tests/testthat/test-abc_smc_nltt.R#L52) *style:* **Variable or function name should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-mcmc_nltt.R:18:3:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/tests/testthat/test-mcmc_nltt.R#L18) *style:* **Variable or function name should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:35:3:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/tests/testthat/test-mcmc_nltt.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```
[tests/testthat/test-mcmc_nltt.R:67:3:](https://github.com/richelbilderbeek/nLTT/blob/15d03a78306a54702993606bde5cb4981ddb2a97/tests/testthat/test-mcmc_nltt.R#L67) *style:* **Variable or function name should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```


Successfully aliased the URL <https://api-de-charadas-g30bedgnl.now.sh> to the following aliases.

* https://api-de-charadas.fredes.now.sh
* https://api-de-charadas-git-master.fredes.now.sh


So the next step I need to do is to put the nodes with the same tags in the same community according to the output.txt information, right?


Successfully aliased the URL <https://wp-next-from-scratch-dgo5i85y5.now.sh> to the following aliases.

* https://wp-next-from-scratch.tlock.now.sh
* https://wp-next-from-scratch-git-master.tlock.now.sh


第一次用git修改文件提交到仓库中


Successfully aliased the URL <https://lab9-q1zco3420.now.sh> to the following aliases.

* https://lab9.gyd19980910.now.sh
* https://lab9-git-master.gyd19980910.now.sh


Bravo!