[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
                        ^
```
[R/calculate_MAT.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:8:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:12:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' J <- number_of_junctions_markers(N = 100, H_0 = 0.5, t = 200, marker_distribution = markers)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:18:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L18) *style:* **Variable or function name should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L19) *style:* **Variable or function name should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(lower_lim, upper_lim) )
                                                                      ^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
                                                        ^
```
[R/estimate_time_phased.R:108:19:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L108) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_phased.R:135:23:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:135:32:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:138:10:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L138) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:142:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L142) *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:143:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L143) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:147:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:148:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L148) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:149:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L149) *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:184:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L184) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:191:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L191) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
                                                 ^
```
[R/estimate_time_unphased.R:12:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                       ^
```
[R/estimate_time_unphased.R:12:43:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                                          ^
```
[R/estimate_time_unphased.R:18:22:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- p * q * ( p * q * P[3] +
                     ^
```
[R/estimate_time_unphased.R:35:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                       ^
```
[R/estimate_time_unphased.R:88:19:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L88) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_unphased.R:115:23:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:115:32:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:118:12:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L118) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:175:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L175) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/estimate_time_unphased.R:182:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L182) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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:32:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/optim_limits.R:5:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/optim_limits.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param calc_func function to calculate the time, should accept two arguments: upper, lower and should return a stats::optimize object with two properties: $minimum and $objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/optim_limits.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param iterations number of times the boundaries should be adjusted to obtain an estimate that is not close to the boundaries. After this number of iterations is exceeded, NA is returned
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:38:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/phased_log_likelihood.R:45:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/sim_backcrossing.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return List with five entries: average_junctions: average number of junctions over time, detected_junctions: average number of detected junctions, given the markers. markers: vector with the locations of the molecular markers, junction_distribution: distribution of junctions per time step average_heterozygosity: average heterozygosity.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/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:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:34:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/unphased_log_likelihood.R:41:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/util.R:22:10:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/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/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L22) *warning:* **no visible global function definition for ‘get_states_vector’**
```r
  return( get_states_vector(local_anc))
          ^~~~~~~~~~~~~~~~~
```
[R/util.R:56:42:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    (local_anc_matrix[, 1 ] == local_anc_matrix[, 2]))
                                         ^
```
[R/util.R:108:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:108:37:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
                                    ^
```
[R/util.R:116:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 3) cond_prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:122:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 4) cond_prob <- (p ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:146:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:146:44:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
                                           ^
```
[R/util.R:151:18:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L151) *warning:* **no visible global function definition for ‘get_expectation_O_state’**
```r
    cond_prob <- get_expectation_O_state(P, p, focal_state)
                 ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-equations.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-equations.R#L18) *style:* **Variable or function name should be snake_case.**
```r
  J <- junctions::number_of_junctions(N = 100, R = 1000,
  ^
```
[tests/testthat/test-marker_dist.R:4:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L17) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L60) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L61) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L5) *style:* **Variable or function name should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L6) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```


@AmanSinghRevenge aaja bc. Kahan gaye tu. Update maarunga mai. Aaja


You have plenty of time to think about it but it would also be nice to make **Blender-Version-Manager** ready for Blender 3.0 (when it is released).


Successfully aliased the URL <https://index-ogcp0tzgn.now.sh> to the following aliases:

* https://gnab.fr
* https://index.n6g7.now.sh
* https://index-git-master.n6g7.now.sh


[R/calculate_weight.R:23:6:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/calculate_weight.R#L23) *style:* **Commented code should be removed.**
```r
    #cat("weights normalized because sum was ", sum(weights), "\n")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_weight.R:34:53:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/calculate_weight.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  final_weight <- 1.0 / (sum(model_prob) * sum(vals) )
                                                    ^
```
[R/generate_water.R:48:26:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/generate_water.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      output2 <- output2[ -length(output2)] #water level has to be high
                         ^
```
[R/infer_params.R:7:1:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/infer_params.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param write_to_file (boolean) if true, intermediate output is written to file
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_params.R:19:16:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/infer_params.R#L19) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
  emp_stats <- calc_sum_stats(emp_tree, emp_tree)
               ^~~~~~~~~~~~~~
```
[R/infer_params.R:23:44:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/infer_params.R#L23) *warning:* **no visible binding for global variable ‘param_from_prior’**
```r
  previous_par <- t(apply(param_matrix, 1, param_from_prior))
                                           ^~~~~~~~~~~~~~~~
```
[R/infer_params.R:58:31:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/infer_params.R#L58) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
          stat_matrix[i, ] <- calc_sum_stats(found_trees[[i]], emp_tree)[1:4]
                              ^~~~~~~~~~~~~~
```
[R/infer_params.R:64:48:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/infer_params.R#L64) *warning:* **no visible binding for global variable ‘calc_fit’**
```r
        local_fit <- apply(results[, 8:11], 1, calc_fit, emp_stats)
                                               ^~~~~~~~
```
[R/param_from_prior.R:3:1:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/param_from_prior.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @return vector with 7 entries: extinction, sympatric speciation at high water, sympatric speciation at low water, allopatric speciation, amount of jiggle and the chosen water model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:6:1:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/RcppExports.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param waterlevel_changes a vector that indicates the time points of water level changes
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:1:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/RcppExports.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:11:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/RcppExports.R#L12) *style:* **Only use double-quotes.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:49:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/RcppExports.R#L12) *style:* **Only use double-quotes.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
                                                ^~~~~~~~~
```
[R/RcppExports.R:14:1:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/RcppExports.R#L14) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_envidiv_tree.R:35:20:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/sim_envidiv_tree.R#L35) *warning:* **no visible global function definition for ‘generate_water’**
```r
  water_changes <- generate_water(params[6], crown_age)
                   ^~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:72:7:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/R/sim_envidiv_tree.R#L72) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( length(ape::is.binary(phy_tree)) > 1) {
      ^
```
[tests/testthat/test-get_from_prior.R:14:23:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/tests/testthat/test-get_from_prior.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_gt( max(v1), 0)
                      ^
```
[tests/testthat/test-infer_params.R:4:4:](https://github.com/thijsjanzen/enviDiv/blob/8a8048482cdaa4c0c496d19316cfc32fbc3ff2a1/tests/testthat/test-infer_params.R#L4) *style:* **Commented code should be removed.**
```r
  #skip_on_cran()
   ^~~~~~~~~~~~~~
```


Gandu


What about values outside the range of `int`?  It seems that they will fall back to the TEXT approach. Maybe we could use `toLongLong()` and `sqlite3_bind_int64()` to also support 64 bit integers (which is the maximum range of SQLite's INTEGER data type).


Thank you @ptroja


Bosadiwale aaja naaa. Tere maa ki.........


Tere ma beggar


이 부분은 gets로 제한을 줄 수 없는 문제가 있다고 알고 있어서 fgets로 수정해봤어요.


I got the manual deployment working for Windows and will probably stick with it for the first release. CI is on the roadmap though.


FYI

    (str:insert characters (input-buffer-cursor minibuffer) (input-buffer minibuffer))
    ;; insert <str> <position> <str>

since june, 15th.

(I'll replace cl-strings soon enough)


Deployment failed with the following error:

~~~
An internal error occurred with ZEIT Now.
~~~


Tere ma kuta ki billa


<'a'를 <='Z'로 수정했어요.


Would you consider instead requiring the full JSON object to include `{}`? Writing JSON in webCoRE is a bit of a pain since you have to escape the braces like`\\{`, but it gives you an unambiguous `startsWith()` test. Authorization headers may not always be base 64 encoded so I wouldn't want to break requests if anyone happened to have a colon character there.


Here NPV2 seems to give roughly similar looking graph as in the DIW report


[R/calculate_allele_frequencies.R:34:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_allele_frequencies.R#L34) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/calculate_allele_frequencies.R:36:18:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_allele_frequencies.R#L36) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
  pop_for_cpp <- population_to_vector(source_pop)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_fst.R:41:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L41) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop1 <- check_input_pop(pop1)
          ^~~~~~~~~~~~~~~
```
[R/calculate_fst.R:43:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L43) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop2 <- check_input_pop(pop2)
          ^~~~~~~~~~~~~~~
```
[R/calculate_fst.R:72:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L72) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_fst.R:78:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L78) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop1[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:79:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L79) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop1[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:85:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L85) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop2[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:86:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L86) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop2[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_ld.R:39:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L39) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_ld.R:45:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L45) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_ld.R:51:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L51) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 1 + findtype(pop[[i]]$chromosome1, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:52:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L52) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 1 + findtype(pop[[i]]$chromosome2, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:73:15:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L73) *warning:* **no visible global function definition for ‘calculate_average_ld’**
```r
        ld <- calculate_average_ld(g1, g2)
              ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_marker_frequency.R:31:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_marker_frequency.R#L31) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:28:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_tajima_d.R#L28) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/iso_female.R:44:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/iso_female.R#L44) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/junctions.R:25:12:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/junctions.R#L25) *warning:* **no visible global function definition for ‘calculate_dist_junctions’**
```r
  junct <- calculate_dist_junctions(pop)
           ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:105:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L105) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_1 <- population_to_vector(input_population_1)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:130:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L130) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_2 <- population_to_vector(input_population_2)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:202:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L202) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_1 <- create_pop_class(selected_pop$population_1)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:203:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L203) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_2 <- create_pop_class(selected_pop$population_2)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:81:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture.R#L81) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population <- population_to_vector(input_population)
                          ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:142:25:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture.R#L142) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct <- create_pop_class(selected_pop$population)
                        ^~~~~~~~~~~~~~~~
```
[R/utilities.R:275:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/utilities.R#L275) *warning:* **no visible binding for global variable ‘verify_individual’**
```r
  v <- unlist(lapply(pop, verify_individual))
                          ^~~~~~~~~~~~~~~~~
```


Deployed at: https://alva-designkit-commits-5cf00.surge.sh


зачем while)


Thanks! Just fixed it :smile:


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

* https://memeadviser-api.paramt.now.sh
* https://memeadviser-api-git-master.paramt.now.sh


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


ConcurrentNavigableMap<Long, LogSegment> tail = segments.tailMap(computeBaseOffset(flushedOffset), true);
这样是不是更好理解点？


как понять с этого вывода что тут происходит)


вот пробуйте запустить вашу апликуху, как стороний пользователь и посмотрите вам все понятно что надо делать в приложении


Found it, fixed it, was an issue in a regex.


Issues/tests


Why deprecating these methods?


未ログインユーザーもreview詳細ページを見れるように設定
set_reviewを設定してリファクタリング


Successfully aliased the URL <https://nextjs-rkl2kpb8e.now.sh> to the following aliases:

* https://neojs.dev
* https://nextjs.neosiae.now.sh
* https://nextjs-git-master.neosiae.now.sh


вот тут бы я лучше сделал цикл do while(true), и внем предложил бы ввести число, и если оно коректное то выйти с цикла, если нет то продолжить цикл


Successfully aliased the URL <https://react-scroll-progress-read-ajp7g4u04.now.sh> to the following aliases:

* https://react-scroll-progress-read.faramazpat.now.sh
* https://react-scroll-progress-read-git-develop.faramazpat.now.sh


Checkmarx scan results 01 Aug 2019 15:15 UTC +03:00

High
Medium
Low
Info

New
0
0
0
0

Recurrent
0
0
0
0

Fixed
0
0
0
0

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Included commits

Commit ID	Owner

a23cad998261c81bf63aa21ac681a2e8b5303e7c	@web-flow


вас не смущает вот этот оператор?) мне кажеться надо сделать тут while цикл это как раз его случай


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

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

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

### Deployments updated

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

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


```
if (element % 2 ==0) {
  result += element;
}
```


:hourglass_flowing_sand: Waiting for custom rule data to be resolved
:point_right: click here to view a full list of the events :point_left:


:white_check_mark: All Rules (2 / 2) Passed

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

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

:point_right: click here to view a full list of the events :point_left:


will have a look asap but meanwhile maybe instead of using auth and Co what
about the scripts simply shutil.copy the dist to one's Dropbox folder?
Local paths could be handled with an ini (we would version a default
version in the scripts folder as we do with bash_default.ini)

On Thu, Aug 1, 2019, 05:50 Daniel Nunes <notifications@github.com> wrote:

> @wrye-bash/bashers <https://github.com/orgs/wrye-bash/teams/bashers>
> Requesting low-priority review on this.
>
> If this is accepted, a few things so I won't forget:
>
>    - Utumno needs to make an "official" wrye bash dropbox app - I have a
>    temporary one set up - and then change the current client id /secret to
>    that one;
>    - Is the cookie auth too invasive? It's the only was I could find to
>    make it auto login without a huge hassle from the deployer;
>    - While this only deploys nightly builds, deploying production to
>    nexus can be done in theory but the testing is a little dangerous and I
>    didn't want to be too adventurous before getting this accepted.
>
> One step closer to CI!
>
> —
> You are receiving this because you are on a team that was mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/wrye-bash/wrye-bash/commit/d38db407d62d7d230fbc4e70d66fd7d0c48f1ead?email_source=notifications&email_token=AAKNIV2CVAXBLNBMA3QAIJ3QCJFPBA5CNFSM4IIMF6ZKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBA5UZ7#commitcomment-34526015>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAKNIVYZ3D5QK4OFLDKKIH3QCJFPBANCNFSM4IIMF6ZA>
> .
>


they are already deprecated, but just via javadoc ;)


wHaTs a fOrK??


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* https://cyberbrand.xyz
* https://gatsby-functions.neosiae.now.sh
* https://gatsby-functions-git-master.neosiae.now.sh


Since you are calling updateUIBubbles in viewDidAppear, I would remove it from viewDidLoad below.
Also, consider whether you want this code in viewDidAppear or viewWillAppear. What are the pros/cons of each?


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ok, so why were they deprecated? Because it uses `java.util.Date `?


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* https://react-scroll-progress-read.faramazpat.now.sh
* https://react-scroll-progress-read-git-develop.faramazpat.now.sh


..fixes #<issue number>


I see, cool! So I guess a lot of this documentation will be general in nature (it is not shogun specific how to onboard new people onto the project)?


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* https://robert-portfolio.olivernordlund.now.sh
* https://robert-portfolio-git-master.olivernordlund.now.sh


I see the intention of this (which is good!), but my question was more: does it effectively help in a legal dispute? Is there any evidence somewhere in other projects that putting such a statement was useful?


## Plan result
production

 Plan: 1 to add, 0 to change, 0 to destroy.

Details (Click me)

Refreshing Terraform state in-memory prior to plan...
The refreshed state will be used to calculate this plan, but will not be
persisted to local or remote state storage.

------------------------------------------------------------------------

An execution plan has been generated and is shown below.
Resource actions are indicated with the following symbols:
  + create

Terraform will perform the following actions:

  + aws_ecr_repository.ci-tf
      id:             <computed>
      arn:            <computed>
      name:           "ci-tf-production"
      registry_id:    <computed>
      repository_url: <computed>

Plan: 1 to add, 0 to change, 0 to destroy.

------------------------------------------------------------------------

Note: You didn't specify an "-out" parameter to save this plan, so Terraform
can't guarantee that exactly these actions will be performed if
"terraform apply" is subsequently run.


## Plan result
staging

 Plan: 1 to add, 0 to change, 0 to destroy.

Details (Click me)

Refreshing Terraform state in-memory prior to plan...
The refreshed state will be used to calculate this plan, but will not be
persisted to local or remote state storage.

------------------------------------------------------------------------

An execution plan has been generated and is shown below.
Resource actions are indicated with the following symbols:
  + create

Terraform will perform the following actions:

  + aws_ecr_repository.ci-tf
      id:             <computed>
      arn:            <computed>
      name:           "ci-tf-staging"
      registry_id:    <computed>
      repository_url: <computed>

Plan: 1 to add, 0 to change, 0 to destroy.

------------------------------------------------------------------------

Note: You didn't specify an "-out" parameter to save this plan, so Terraform
can't guarantee that exactly these actions will be performed if
"terraform apply" is subsequently run.


## Plan result
common

 No changes. Infrastructure is up-to-date.

Details (Click me)

Refreshing Terraform state in-memory prior to plan...
The refreshed state will be used to calculate this plan, but will not be
persisted to local or remote state storage.

aws_kms_key.ps: Refreshing state... (ID: a49f3ce4-0d67-4084-95c4-8569bad53120)

------------------------------------------------------------------------

No changes. Infrastructure is up-to-date.

This means that Terraform did not detect any differences between your
configuration and real physical resources that exist. As a result, no
actions need to be performed.


Application which calculate quadratic expression.cpp

test.cpp: In function ‘int main()’:
test.cpp:49:1: error: expected ‘}’ at end of input
 }
 ^
test.cpp:49:1: error: expected ‘}’ at end of input
test.cpp:17:13: error: unused variable ‘TWOA’ [-Werror=unused-variable]
   const int TWOA = TWO * a;
             ^
test.cpp:49:1: error: expected ‘}’ at end of input
 }
 ^
cc1plus: all warnings being treated as errors

Ваш код не компилируеться


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* https://rozy.vuzero007.now.sh
* https://rozy-git-master.vuzero007.now.sh


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* https://react-scroll-progress-read.faramazpat.now.sh
* https://react-scroll-progress-read-git-develop.faramazpat.now.sh


yep!
Check out the meta examples in the develop branch to see how this looks


in practice: yes


всеравно у вас код поплыл далеко
ну да ладно. То что то у вас тяжело получаеться с выравниванием


лучше не использовать def в качестве возвращаемого методом значения, тем более что мы его не используем. Думаю тут void хорошо бы подошёл.


[R/create_all_experiments.R:99:3:](https://github.com/richelbilderbeek/pirouette/blob/bd6ddbe16ecd0ed4ab1bef4061fcbe9950f078be/R/create_all_experiments.R#L99) *warning:* **no visible global function definition for ‘check_experiments’**
```r
  check_experiments(all_experiments)
  ^~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:56:30:](https://github.com/richelbilderbeek/pirouette/blob/bd6ddbe16ecd0ed4ab1bef4061fcbe9950f078be/R/est_evidences.R#L56) *warning:* **no visible global function definition for ‘to_evidence_filename’**
```r
  evidence_fasta_filename <- to_evidence_filename(fasta_filename)
                             ^~~~~~~~~~~~~~~~~~~~
```


we do, but isnt this obvious? :)


Hello, I want to make sure that  if I want to use clean images to train my model, then I should set 'noise2noise'=FALSE, right？ And another question, I should use clean images to test, right？
Thanks!


Successfully aliased the URL <https://robert-portfolio-qq76im153.now.sh> to the following aliases:

* https://robert-portfolio.olivernordlund.now.sh
* https://robert-portfolio-git-master.olivernordlund.now.sh


fix #8


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Successfully aliased the URL <https://robert-portfolio-cq4x2i3nz.now.sh> to the following aliases:

* https://robert-portfolio.olivernordlund.now.sh
* https://robert-portfolio-git-master.olivernordlund.now.sh


Hi there,
could you please add more details on how to install the application.
also for the demo if you could provide some credentials it will be great


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @saraedum was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


Successfully aliased the URL <https://dailygratitudecom-3o25enf1n.now.sh> to the following aliases:

* https://dailygratitudecom.hello103.now.sh
* https://dailygratitudecom-git-master.hello103.now.sh


Note running


[R/calculate_weight.R:23:6:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/calculate_weight.R#L23) *style:* **Commented code should be removed.**
```r
    #cat("weights normalized because sum was ", sum(weights), "\n")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_weight.R:34:53:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/calculate_weight.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  final_weight <- 1.0 / (sum(model_prob) * sum(vals) )
                                                    ^
```
[R/generate_water.R:48:26:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/generate_water.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      output2 <- output2[ -length(output2)] #water level has to be high
                         ^
```
[R/infer_params.R:7:1:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/infer_params.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param write_to_file (boolean) if true, intermediate output is written to file
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_params.R:19:16:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/infer_params.R#L19) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
  emp_stats <- calc_sum_stats(emp_tree, emp_tree)
               ^~~~~~~~~~~~~~
```
[R/infer_params.R:23:44:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/infer_params.R#L23) *warning:* **no visible binding for global variable ‘param_from_prior’**
```r
  previous_par <- t(apply(param_matrix, 1, param_from_prior))
                                           ^~~~~~~~~~~~~~~~
```
[R/infer_params.R:58:31:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/infer_params.R#L58) *warning:* **no visible global function definition for ‘calc_sum_stats’**
```r
          stat_matrix[i, ] <- calc_sum_stats(found_trees[[i]], emp_tree)[1:4]
                              ^~~~~~~~~~~~~~
```
[R/infer_params.R:64:48:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/infer_params.R#L64) *warning:* **no visible binding for global variable ‘calc_fit’**
```r
        local_fit <- apply(results[, 8:11], 1, calc_fit, emp_stats)
                                               ^~~~~~~~
```
[R/param_from_prior.R:3:1:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/param_from_prior.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @return vector with 7 entries: extinction, sympatric speciation at high water, sympatric speciation at low water, allopatric speciation, amount of jiggle and the chosen water model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:6:1:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/RcppExports.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param waterlevel_changes a vector that indicates the time points of water level changes
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:1:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/RcppExports.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:11:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/RcppExports.R#L12) *style:* **Only use double-quotes.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:12:49:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/RcppExports.R#L12) *style:* **Only use double-quotes.**
```r
    .Call('_enviDiv_create_tree_cpp', PACKAGE = 'enviDiv', parameters, waterlevel_changes, seed, crown_age)
                                                ^~~~~~~~~
```
[R/RcppExports.R:14:1:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/RcppExports.R#L14) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_envidiv_tree.R:35:20:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/sim_envidiv_tree.R#L35) *warning:* **no visible global function definition for ‘generate_water’**
```r
  water_changes <- generate_water(params[6], crown_age)
                   ^~~~~~~~~~~~~~
```
[R/sim_envidiv_tree.R:72:7:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/R/sim_envidiv_tree.R#L72) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( length(ape::is.binary(phy_tree)) > 1) {
      ^
```
[tests/testthat/test-get_from_prior.R:14:23:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/tests/testthat/test-get_from_prior.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_gt( max(v1), 0)
                      ^
```
[tests/testthat/test-infer_params.R:4:4:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/tests/testthat/test-infer_params.R#L4) *style:* **Commented code should be removed.**
```r
  #skip_on_cran()
   ^~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:16:4:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/tests/testthat/test-infer_params.R#L16) *style:* **Commented code should be removed.**
```r
  #v <- mean(do_smc$sym_high)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:17:4:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/tests/testthat/test-infer_params.R#L17) *style:* **Commented code should be removed.**
```r
  #v2 <- table(do_smc$model)
   ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:18:4:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/tests/testthat/test-infer_params.R#L18) *style:* **Commented code should be removed.**
```r
  #testthat::expect_true(which.max(v2) == 1)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:19:4:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/tests/testthat/test-infer_params.R#L19) *style:* **Commented code should be removed.**
```r
  #q1 <- quantile(do_smc$sym_high, c(0.025, 0.975))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-infer_params.R:20:4:](https://github.com/thijsjanzen/enviDiv/blob/9881e5cb488664edc0387f1ddd0e7206c0f9ff24/tests/testthat/test-infer_params.R#L20) *style:* **Commented code should be removed.**
```r
  #testthat::expect_true(q1[[1]] < 0.5 && q1[[2]] > 0.5)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Deployed at: https://alva-designkit-commits-4294f.surge.sh


в выводе лучше напишите вместо захардкодженых значений ваши константы
```
std::cout << "Please enter coefficient b in range [" <<
                     LOWER_VALUE << "... " UPPER_VALUE << "]\n";
```
и так по всему коду


Successfully aliased the URL <https://mknepprath-next-6mqzhkmxi.now.sh> to the following aliases:

* https://mknepprath.com
* https://www.mknepprath.com
* https://mknepprath-next.mknepprath.now.sh
* https://mknepprath-next-git-master.mknepprath.now.sh


`with silence()` :D :D

well I can't really review partly because on a mobile, partly not a windows
machine so I can't even build. Green light from me and in fact as discussed
with @Infernio if you're using this, which you probably do, you can hit dev
and we can modify later

Ignore the shutil. copy idea, everyone may not have Dropbox (Linux client
especially has issues) - not sure about the "Dropbox app"?

We will have to push a beta4 as arthmoor said so we test nexus there

On Thu, Aug 1, 2019, 15:17 Mr&Mrs D <the.ubik@gmail.com> wrote:

> will have a look asap but meanwhile maybe instead of using auth and Co
> what about the scripts simply shutil.copy the dist to one's Dropbox folder?
> Local paths could be handled with an ini (we would version a default
> version in the scripts folder as we do with bash_default.ini)
>
> On Thu, Aug 1, 2019, 05:50 Daniel Nunes <notifications@github.com> wrote:
>
>> @wrye-bash/bashers <https://github.com/orgs/wrye-bash/teams/bashers>
>> Requesting low-priority review on this.
>>
>> If this is accepted, a few things so I won't forget:
>>
>>    - Utumno needs to make an "official" wrye bash dropbox app - I have a
>>    temporary one set up - and then change the current client id /secret to
>>    that one;
>>    - Is the cookie auth too invasive? It's the only was I could find to
>>    make it auto login without a huge hassle from the deployer;
>>    - While this only deploys nightly builds, deploying production to
>>    nexus can be done in theory but the testing is a little dangerous and I
>>    didn't want to be too adventurous before getting this accepted.
>>
>> One step closer to CI!
>>
>> —
>> You are receiving this because you are on a team that was mentioned.
>> Reply to this email directly, view it on GitHub
>> <https://github.com/wrye-bash/wrye-bash/commit/d38db407d62d7d230fbc4e70d66fd7d0c48f1ead?email_source=notifications&email_token=AAKNIV2CVAXBLNBMA3QAIJ3QCJFPBA5CNFSM4IIMF6ZKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBA5UZ7#commitcomment-34526015>,
>> or mute the thread
>> <https://github.com/notifications/unsubscribe-auth/AAKNIVYZ3D5QK4OFLDKKIH3QCJFPBANCNFSM4IIMF6ZA>
>> .
>>
>


merge master


Successfully aliased the URL <https://robert-portfolio-5ra4d44ga.now.sh> to the following aliases:

* https://robert-portfolio.olivernordlund.now.sh
* https://robert-portfolio-git-master.olivernordlund.now.sh


неправильно надо обрамлять оператор if скобочками, это вопервых коде стайл, а во вторых это уменьшает источник ошибок
```
if (DISCR < 0)  {
  ...
}
```


This was useful, thanks!


check [here](https://github.com/adminless/free-xonotic-data.pk3dir/releases/tag/menu.dat) for the download.


зачем эта переменная тут обьявленна?


Stylistically better to just invert the expression in the if test rather than have a do-nothing block, e.g.

 if(course.length == 2 && is_numeric(course[1])){


Successfully aliased the URL <https://nohai-app-fldrn0b8i.now.sh> to the following aliases:

* https://nohai-app.nohai.now.sh
* https://nohai-app-git-master.nohai.now.sh


я думаю читабельнее использовать groovy map constructor https://mrhaki.blogspot.com/2018/06/groovy-goodness-add-map-constructor.html


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/3afe3af2-c7d2-4b47-94bd-885d23c3937a?env_id=ibm%3Ayp%3Aeu-de "springdoc-openapi-v3 -rest-test"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/737cd688-45b8-4311-a292-a111823c3fb8 "springdoc-openapi-v3-rest-test-pipeline") deployed [springdoc-openapi-demos](https://github.com/springdoc/springdoc-openapi-demos/releases/tag/deploy-ibm-yp-eu-de-BNPP_BDDF_IT-dev-20190801-124006 "deploy-ibm-yp-eu-de-BNPP_BDDF_IT-dev-20190801-124006") to [dev](https://console.bluemix.net/apps/1530d1fa-00ae-4b10-b035-13bfb4b99020?env_id=ibm:yp:eu-de "ibm:yp:eu-de:BNPP_BDDF_IT:dev"), including this commit


Hey hoo


## Plan result
staging

 Plan: 1 to add, 0 to change, 0 to destroy.

Details (Click me)

Refreshing Terraform state in-memory prior to plan...
The refreshed state will be used to calculate this plan, but will not be
persisted to local or remote state storage.

------------------------------------------------------------------------

An execution plan has been generated and is shown below.
Resource actions are indicated with the following symbols:
  + create

Terraform will perform the following actions:

  + aws_ecr_repository.ci-tf
      id:             <computed>
      arn:            <computed>
      name:           "ci-tf-staging"
      registry_id:    <computed>
      repository_url: <computed>

Plan: 1 to add, 0 to change, 0 to destroy.

------------------------------------------------------------------------

Note: You didn't specify an "-out" parameter to save this plan, so Terraform
can't guarantee that exactly these actions will be performed if
"terraform apply" is subsequently run.


## Plan result
production

 Plan: 1 to add, 0 to change, 0 to destroy.

Details (Click me)

Refreshing Terraform state in-memory prior to plan...
The refreshed state will be used to calculate this plan, but will not be
persisted to local or remote state storage.

------------------------------------------------------------------------

An execution plan has been generated and is shown below.
Resource actions are indicated with the following symbols:
  + create

Terraform will perform the following actions:

  + aws_ecr_repository.ci-tf
      id:             <computed>
      arn:            <computed>
      name:           "ci-tf-production"
      registry_id:    <computed>
      repository_url: <computed>

Plan: 1 to add, 0 to change, 0 to destroy.

------------------------------------------------------------------------

Note: You didn't specify an "-out" parameter to save this plan, so Terraform
can't guarantee that exactly these actions will be performed if
"terraform apply" is subsequently run.


## Plan result
common

 No changes. Infrastructure is up-to-date.

Details (Click me)

Refreshing Terraform state in-memory prior to plan...
The refreshed state will be used to calculate this plan, but will not be
persisted to local or remote state storage.

aws_kms_key.ps: Refreshing state... (ID: a49f3ce4-0d67-4084-95c4-8569bad53120)

------------------------------------------------------------------------

No changes. Infrastructure is up-to-date.

This means that Terraform did not detect any differences between your
configuration and real physical resources that exist. As a result, no
actions need to be performed.


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/3afe3af2-c7d2-4b47-94bd-885d23c3937a?env_id=ibm%3Ayp%3Aeu-de "springdoc-openapi-v3 -rest-test"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/737cd688-45b8-4311-a292-a111823c3fb8 "springdoc-openapi-v3-rest-test-pipeline") deployed [springdoc-openapi-demos](https://github.com/springdoc/springdoc-openapi-demos/releases/tag/deploy-ibm-yp-eu-de-BNPP_BDDF_IT-dev-20190801-124123 "deploy-ibm-yp-eu-de-BNPP_BDDF_IT-dev-20190801-124123") to [dev](https://console.bluemix.net/apps/a80dcdf9-d860-4ce8-b4c3-4ee140ef7f7a?env_id=ibm:yp:eu-de "ibm:yp:eu-de:BNPP_BDDF_IT:dev"), including this commit


But we here state that everyone is male, doesn't this make the opposite statement?

What we did in the past for this was to have a statement that we care about gender diversity, and particularly encourage female developers to get involved. And we had a "community manager" (Lea, @lgoetz) as a person to ping. Actually just talked to Lea, and she suggested to have a list "Other people to contact" with contacts of active/former female/other-minority devs (even though someone is not contributing anymore, they still might be happy to answer emails about how to get involved etc, e.g. @oxphos). Profile pics (if existing) then also reveal a lot.


Successfully aliased the URL <https://telepathy-427okl44i.now.sh> to the following aliases:

* https://telepathy.cbcruk.now.sh
* https://telepathy-git-master.cbcruk.now.sh