1. Yes, I have tested it, and it works fine. It overrides the default timeout (5min) passed via 'junit.jupiter.execution.timeout.default' in build.gradle.kts
2. The test is already part of the slowTest suite. I needed to increase the timeout because, even if testSlow was executing fine in my machine (this specific test takes a bit more than 4min ), it was failing in GitHub CI testSlow due to a timeout in this test, so I thought the best solution to unblock the situation was to increase the timeout in this test (there was already a comment "a bit slow" there), to make sure it does not fail in GitHub
3. The query runs fine, it just seems that the default 5min timeout might not be enough for this test in some environments. Maybe 10min is too much and we should set something in between.


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This is just so the application know to user PostgreSQL in production as the default is sqlite


I think the event name should be used instead of a separate keybinding name because if I have to define a keybinding, I also want to broadcast it to all the game objects that listen to that keybinding.

Which means if I have to make a new keybinding by the name `MOVE_FORWARD`, I am better off using the system if I make an event named `MoveForwardEvent` and make the input manager send that event forward to all the objects that handle that event when the W or the Up arrow key is pressed.

So a suitable architecture is as follows:
```cpp
class InputManager
{
    HashMap<Key, EventType> m_KeyEventMap;
    // Stores which event to be triggered if a key is pressed. E.g the map can look like:
    // {
	//		W => RunForward,
	//		UpArrow => RunForward, (notice the the EventType is not unique)
 	//		Escape => Quit
    // }

	fireKeyEvent(Key, sync | deferred); // Sends a call/deferred call from event manager if the Key value exists in our map. This is called from the Windows message handler. Default to using call instead of deferred for now.

	friend class GameWindow; // Because the GameWindow has the message handler and only that class can call fireKeyEvent()
public:
    addKeyEvents(LuaTextResourceFile); // Populates the m_KeyEventMap from the Lua script
	changeKeyEvent(Key, EventType); // Useful when the player binds different keys to the same events
	removeKeyEvent(Key, EventType); // Remvoe an entry from our hashmap
}
```


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That checkbox and the `view_modes ul` have nothing to do with a `textarea`; it is jus twhat shows up at the top of the dialog  window / overlay after you click on the `Preview` link (that may or not be directly attached to a `textarea`).


Done, thank you.


Thanks for the clarifications, I already forgot that the whole class was tagged as "slow" :). Regarding 3, was it taking more than 5 minutes before the change?


[Régis Hanol posted](https://review.discourse.org/t/fix-disallow-c-as-a-tag/7750/2):

That one definitely needs a test 😉


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[Régis Hanol posted](https://review.discourse.org/t/fix-disallow-none-as-a-category-slug/7749/2):

That one needs at test 😉


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Great & considerate commits for those who are unable to download these sources in common manners.


![](https://github.trello.services/images/mini-trello-icon.png) [Documentaçao JavaDoc](https://trello.com/c/wcG0wCPm/5-documenta%C3%A7ao-javadoc)


Yes I know that. I mean until the decision is made on whether these dialogs are per text area or not (and the code moved around in PHP files) I don't really want to touch that code - it's still in flux.


TeamCity Identity and Access Management / Identity - RoleManagementAPI [Build 650-IDAM-307-Api-add-rol](https://teamcity.nice.org.uk/viewLog.html?buildId=63129&buildTypeId=IdentityandAccessManagement_RoleManagementAPI) outcome was **SUCCESS**
Summary: Tests passed: 57 Build time: 00:04:49


change all text color to azure
- html, body
- .navbar-light .navbar-brand
- .navbar-light .navbar-nav .nav-link


Attribut checked dans un bouton !


Deploy preview for _website_ ready!

Built with commit da1d625bb749ef417db06cf8b3f6adba691043bb

https://static-bootstrap-site-dsly79vuu.now.sh


cancel


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How to use it?


also fixes #2140 occasionally


RIght, you can do a #ifdef GL_TEXTURE_EXTERNAL_OES then


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Lock file was updated while fixing PHP 7.4. Should be fine now.


Should be `argument.getDetails().equals("details")`


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@paddybyers  VCDiffCodeTableWriterImpl is the class I had to extract stuff from to be used by the decoder. It is a simple change but it does not get loaded by default 'cause of the size of the file.


Shouldn't this line be `FilterFeature filterFeature = (FilterFeature) table.getFeature(DataTableFeatureKey.FILTER);` similar to how the sort meta is obtained?


![](https://github.trello.services/images/mini-trello-icon.png) [Testes JUnit da classe Metodo](https://trello.com/c/jyHlBIuJ/37-testes-junit-da-classe-metodo)


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🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3315533)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/d16-5/fa7e04052c4b10941850ae05ef2361584e50af55/3315533/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>9 tests failed, 104 tests passed.</summary>

## Failed tests

 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/Debug: Failed
 * link all/iOS Unified 64-bits - device/Release: TimedOut
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): TimedOut
 * link sdk/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): TimedOut
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Failed
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/Release: TimedOut
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): TimedOut
 * [xUnit] Mono BCL tests group 3/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): TimedOut
 * mscorlib/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Failed
</details>


hardcoded path to /usr/local ?


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signed apk: [armv7](https://www.dropbox.com/s/c41vjbou7hizle5/input-master-9f0f1b18196ea47d5bf6982ab24793a73336ff38-armv7-signed.apk?dl=0) (SDK: [android-5](https://github.com/lutraconsulting/input-sdk/releases/tag/android-5))


[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after an infinite number of generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:11:20:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:14:20:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                   C = 1) {
                   ^
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  K <- H_0 * C * 2 * N * R / (2 * N * C + R)
  ^
```
[R/calc_K.R:19:5:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L23) *style:* **Variable and function name style should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the error in the estimate of the onset of hybridisation, following Equations 3 & 4 in the Supplementary information of Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param relative Boolean flag, if TRUE: return the relative error, if FALSE: return error in generations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:15:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:19:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                       C = 1,
                       ^
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L24) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_error.R:30:7:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
      ^
```
[R/calculate_error.R:30:25:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
                        ^
```
[R/calculate_MAT.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Function that calculates the maximum time after hybridization after which the number of junctions can still be reliably used to estimate the onset of hybridization. This is following equation 15 in Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:12:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:15:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          C = 1) {
                          ^
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_time.R:1:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the number of junctions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 14 in Janzen et al. 2018
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:11:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' estimate_time(J = J, N = 100, R = 1000, H_0 = 0.5, C = 1)  # should be 200 again
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:13:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:17:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                          C = 1) {
                          ^
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/estimate_time_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 1 in Janzen et al. unpublished
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:8:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:12:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' J <- number_of_junctions_markers(N = 100, H_0 = 0.5, t = 200, marker_distribution = markers)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:18:35:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(lower_lim, upper_lim) )
                                                                      ^
```
[R/estimate_time_phased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L2) *style:* **functions should have cyclomatic complexity of less than 15, this has 49.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
                                                        ^
```
[R/estimate_time_phased.R:9:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L9) *warning:* **no visible global function definition for ‘single_state_inf’**
```r
  seven_states <- single_state_inf(local_time, d = di)
                  ^~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:10:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L10) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_phased.R:122:23:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:122:32:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:125:10:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:129:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L129) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_cond_prob_vector_phased_inf <- function(info_vector,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:151:23:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L151) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:151:32:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L151) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:154:10:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L154) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:158:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L158) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:159:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:163:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L163) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:164:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L164) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:165:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L165) *style:* **Lines should not be more than 80 characters.**
```r
#' @param optim_pop_size If TRUE, population size is also optimized. Starting point of the optimizaton will then be on the given population size, and half the maximum time.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:200:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L200) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:207:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L207) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_phased.R:257:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L257) *style:* **Lines should not be more than 80 characters.**
```r
#' estimates the time since admixture, given unphased ancestry data and assuming infinite population size.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:258:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L258) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:259:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L259) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:262:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L262) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:263:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L263) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:296:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L296) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:303:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L303) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L2) *style:* **functions should have cyclomatic complexity of less than 15, this has 28.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
                                                 ^
```
[R/estimate_time_unphased.R:12:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                       ^
```
[R/estimate_time_unphased.R:12:43:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                                          ^
```
[R/estimate_time_unphased.R:18:22:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- p * q * ( p * q * P[3] +
                     ^
```
[R/estimate_time_unphased.R:21:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L21) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_unphased.R:35:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                       ^
```
[R/estimate_time_unphased.R:102:23:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:102:32:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:105:12:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:160:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L160) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/estimate_time_unphased.R:167:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L167) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_backcross.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, in a backcrossing mating scheme.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:4:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_backcross.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:10:43:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_backcross.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_backcross.R:11:43:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_backcross.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
                                          C = 1,
                                          ^
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_di.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected number of junctions between two markers separated by a given amount of recombination
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:3:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_di.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distance between two markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:12:36:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_di.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_di <- function(N = Inf,
                                   ^
```
[R/number_of_junctions_di.R:13:36:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_di.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected total number of junctions in a chromosome, given the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distribution of markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:13:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L13) *warning:* **no visible global function definition for ‘number_of_junctions_di’**
```r
    expected_junctions <- number_of_junctions_di(N, H_0, t, di)
                          ^~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:20:41:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_markers <- function(N = Inf,
                                        ^
```
[R/number_of_junctions_markers.R:21:41:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L21) *style:* **Variable and function name style should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after t generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:13:33:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:16:33:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                                C = 1,
                                ^
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/optim_limits.R:5:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/optim_limits.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param calc_func function to calculate the time, should accept two arguments: upper, lower and should return a stats::optimize object with two properties: $minimum and $objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/optim_limits.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param iterations number of times the boundaries should be adjusted to obtain an estimate that is not close to the boundaries. After this number of iterations is exceeded, NA is returned
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/phased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/phased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:38:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/phased_log_likelihood.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/phased_log_likelihood.R:45:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/phased_log_likelihood.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/sim_backcrossing.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_backcrossing.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:11:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_backcrossing.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:12:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_backcrossing.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return List with five entries: average_junctions: average number of junctions over time, detected_junctions: average number of detected junctions, given the markers. markers: vector with the locations of the molecular markers, junction_distribution: distribution of junctions per time step average_heterozygosity: average heterozygosity.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with regularly distributed markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:5:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:17:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
sim_fin_chrom <- function (pop_size = 100,
                          ^
```
[R/sim_fin_chrom.R:22:28:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L22) *style:* **Variable and function name style should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_inf_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with an infinite number of recombination sites.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_inf_chrom.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_inf_chrom.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param markers The number of genetic markers superimposed on the chromosome. If markers is set to -1, no markers are superimposed (faster simulation)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_inf_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is returned.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:8:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:12:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:1:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Individual Based Simulation of the accumulation of junctions, given phasing error
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Phased data is
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:3:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' generated using a user-provided error rate. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:8:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:10:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:15:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
#' @param error_rate fraction of markers that are erroneously phased (e.g. swapped)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:16:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the unphased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:34:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/unphased_log_likelihood.R:41:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-equations.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-equations.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
  J <- junctions::number_of_junctions(N = 100, R = 1000,
  ^
```
[tests/testthat/test-marker_dist.R:4:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L60) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L61) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-phased-error.R:53:64:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-phased-error.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  expected_heterozygosity <- 2 * 0.5 * 0.5 * (1 - 1 / (2 * 100) ) ^ 200
                                                               ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L6) *style:* **Variable and function name style should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:7:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L7) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:31:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```


signed apk: [arm64_v8a](https://www.dropbox.com/s/fkkmysq2bw3iona/input-master-9f0f1b18196ea47d5bf6982ab24793a73336ff38-arm64_v8a-signed.apk?dl=0) (SDK: [android-5](https://github.com/lutraconsulting/input-sdk/releases/tag/android-5))


Successfully deployed to following URLs:

* https://givto-kmajqttjq.now.sh
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make it 15% .


Good idea - I have changed it.


vngkj


shopping center


хорошо


Successfully deployed to following URLs:

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* https://daim.now.sh
* https://daim.damienrobinson.now.sh
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hey dude, i have problems with rift explorer with league say always rift need to retart, say the same i test 10x :(
maybe problem with new patch?


Ne pourrait-on pas ajouter Unknown et ainsi supprimer l'argument i_gpd_known de handleRxGpdId?


Chỗ này viết thừa và sai


Successfully deployed to following URLs:

* https://test-slick-slider-brznygf3s.now.sh
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* https://test-slick-slider-git-master.vadimneshadim.now.sh


doesn't matter, it's the same currently :D but feel free to change it


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* https://frontend-boilerplate-ieyckur8f.now.sh
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That is right. I removed misleading code.


@davidcarlisle Hello again :) ...don't forget to remove atveryend, intcalc, selinput from oberdiek.tex


Successfully deployed to following URLs:

* https://test-slick-slider-dbroztsfy.now.sh
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* https://test-slick-slider-git-master.vadimneshadim.now.sh


Looks like @alip is back online. Could be a good idea to archive rather than remove broken links.


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


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

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

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

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

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


Il doit y avoir moyen de ce passer de se flag, mais il ne faut pas oublier le cas ou le gpd est connu mais que l'on ne peut pas savoir si la cle est bonne ou mauvaise.

Sébastien

________________________________
De : Lionel Ains <notifications@github.com>
Envoyé : jeudi 12 décembre 2019 13:16
À : Legrandgroup/libezsp <libezsp@noreply.github.com>
Cc : Sebastien MARION <sebastien.marion@legrand.fr>; Author <author@noreply.github.com>
Objet : Re: [Legrandgroup/libezsp] fix issue #12 (fbb79b3)

Ne pourrait-on pas ajouter Unknown et ainsi supprimer l'argument i_gpd_known de handleRxGpdId?

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`assert(0 && "Invalid literal type");` ([like in](https://github.com/kinetiknz/cubeb/blob/6f2420de8f155b10330cf973900ac7bdbfee589d/src/cubeb_audiotrack.c#L121) **cubeb**) wold've worked for Clang as well. **sirit** [already has](https://github.com/KhronosGroup/SPIRV-Headers/blob/2c512180ca03b5d4f56283efc85745775b45fdc4/tools/buildHeaders/jsoncpp/dist/json/json.h#L1995) something similar within dependencies.


rsdf


remove hello.


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![](https://github.trello.services/images/mini-trello-icon.png) [Make sure the Plugin Manager can handle cases when all module responses are not present](https://trello.com/c/5Q7n16gH/1-make-sure-the-plugin-manager-can-handle-cases-when-all-module-responses-are-not-present)


+1 for adding the aria-labels :-)


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As for the semantics of the remove/add:
An `a` is for changing location and a `button` is for an action.
In this case, the add or remove is an action, so the `a`'s should be `buttons`.


Deployment failed with the following error:

~~~
An unexpected internal error occurred
~~~


Works, wonderful!


Hey Zack,
If you are going to introduce `scope="col"`, like you did below with the th's, then it's best to don't add the `role="presentation"`.
role="presentation" removes all semantics from the table, and then the scope isn't announced. I think adding the scope is a good thing, then the sortable stuff also makes more sense.
So leave out the `role="presentation"`


Thats all to keep it proper working in 9.3?


super, přesně pomocí pseudoelementů by se tohle mělo řešit 😉


hi


c


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Přidala bych ještě bílou barvu pozadí na `.hlavniobsah` už pro mobil, ne až v desktopu 🙂


@JoeMatt Can be already updated to main ruby-git master branch. :)