In your implementation, it will be `LogReceived, LogClaim`.


Successfully aliased the URL <https://wes-so-e4ce45n9h.now.sh> to the following aliases:

* https://wes.dev
* https://wes-so.wessouza.now.sh
* https://wes-so-git-master.wessouza.now.sh


| /home/foxbob/test/build/tmp/work/armv7ahf-neon-oe-linux-gnueabi/enigma2-plugin-extensions-merlininfo/2.1+gitAUTOINC+fea062666f-r0/recipe-sysroot-native/usr/bin/python-native/python: can't open file 'setup.py': [Errno 2] No such file or directory


Yes, that would make sense. Also keep in mind that the block gas limit can go down as well as up.
During the "Shanghai attacks", it was even cut by 3 to reduce the attack surface. If your cap had worked before, it may not have worked during the attacks.


What about:

> Oh, and what value will owner be if I do owner = address(2); in the constructor?


here you will have a lot of code repetition.


Are we planning to add any properties to task instance? Otherwise Array<String> should be preferable as it is more simple.


UO?WHAT IS THIS...?


The benchmark job for this commit has completed.
Here is the benchmark [report]( https://github.com/TuringLang/ContinuousBenchmarks.jl/blob/report/jobs/BMCI-0-31177c4-201907111204.report.md) and commit (TuringLang/ContinuousBenchmarks.jl@97bc6fd47982e495b49a85ab8b5da9e36fd4c63e).
The benchmark log (printed via `log_report`) can be found below.

```
```


While I understand this if it's about really complex things or entirely different interfaces.. This is just about a goddamn boolean that's also only possibly to utilize through these public methods because `diff()` is protected. Oh, and parameter `$timeOnly` of method `timeAgo` also exists, though is not used anywhere. Sorry, but sometimes I wonder why we don't argue about more serious things. :roll_eyes:


[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
  ^~~
```


Thats not a mistake
You just have no definition of drop reconfig
https://github.com/rcstar6696/android_kernel_xiaomi_clover/commit/da71a9e4e8820e6126a1d10c5561dcf34707f054


| /home/foxbob/test/build/tmp/work/armv7ahf-neon-oe-linux-gnueabi/enigma2-plugin-extensions-weatherplugin2/1.0+gitAUTOINC+b16150066c-r0/recipe-sysroot-native/usr/bin/python-native/python: can't open file 'setup.py': [Errno 2] No such file or directory


7285-UnitVentControlProblem (rraustad) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2477 of 2477 tests passed, 0 test warnings)

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


Deployment failed with the following error:

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


hsjahjasdhsaj


sanjjajajassajsajdadsads


Something along the lines of:
```
uint256 memory tip = msg.value % peers.length;

if (tip > 0) {
  uint256 memory currentownerBalance = peerMap[owner].balance;
  uint256 memory newOwnerBalance = currentownerBalance + tip;
  require(newOwnerBalance > currentOwnerBalance, 'Balance overflow!');
  peerMap[owner].balance = newOwnerBalance;
}
```


Is there an ETA for tagging this change?


you can always write a prive function for it. code repetition is ok if it increases readability


Aliasing was ignored due to a new commit existing for this branch, which will be aliased instead.


As far as I understand this will retun typeOf(string) if one of the operand is String!!


Huh, didn't know about that. Thanks for enlightening me :)


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


Successfully aliased the URL <https://nextjs-green-af0u5ja38.now.sh> to the following aliases:

* https://nextjs-green.now.sh
* https://nextjs-green.ftandcompany.now.sh
* https://nextjs-green-git-master.ftandcompany.now.sh


| /home/foxbob/test/build/tmp/work/all-oe-linux/enigma2-plugin-skins-metrix-vision/2.2+gitAUTOINC+0e6615c1b7-r0/git/locale/pl.po:1337:74: syntax error
| /home/foxbob/test/build/tmp/work/all-oe-linux/enigma2-plugin-skins-metrix-vision/2.2+gitAUTOINC+0e6615c1b7-r0/git/locale/pl.po:1337: keyword "n" unknown
| /home/foxbob/test/build/tmp/work/all-oe-linux/enigma2-plugin-skins-metrix-vision/2.2+gitAUTOINC+0e6615c1b7-r0/git/locale/pl.po:1338: end-of-line within string
| /home/foxbob/test/build/tmp/work/all-oe-linux/enigma2-plugin-skins-metrix-vision/2.2+gitAUTOINC+0e6615c1b7-r0/recipe-sysroot-native/usr/bin/msgfmt: found 3 fatal errors


Successfully aliased the URL <https://will-it-tow-bbiukcxva.now.sh> to the following aliases:

* https://will-it-tow.now.sh
* https://will-it-tow.dannyphillips.now.sh
* https://will-it-tow-git-master.dannyphillips.now.sh


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

* https://tenpercent.now.sh


Yep, with SafeMath it will be more readable.


Hmm, not sure. Would it be the same as `address(0)` as long as address is not a proper 160 bit value?


Successfully aliased the URL <https://ecommerce-nbghyq0qg.now.sh> to the following aliases:

* https://ecommerce.vigneshvilha.now.sh
* https://ecommerce-git-master.vigneshvilha.now.sh


Successfully aliased the URL <https://website-m0sywoomj.now.sh> to the following aliases:

* https://commercereads.com
* https://website.commercereads.now.sh
* https://website-git-master.commercereads.now.sh


Wow, you are always so fast :-) I'll merge it now :)


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

* https://wordfeed.now.sh


Deployment failed with the following error:

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