### TinyCI build failure:
[make -j 3] returned [2]:
```[  0%] Built target json11
[  9%] Built target box2d
[ 36%] Built target sp2freetype
[ 42%] Built target lua
[ 72%] Built target bullet
Scanning dependencies of target Fuseblaze
[ 72%] Building CXX object CMakeFiles/Fuseblaze.dir/src/editor/editorHandle.cpp.o
[ 72%] Building CXX object CMakeFiles/Fuseblaze.dir/src/editor/editor.cpp.o
[ 72%] Building CXX object CMakeFiles/Fuseblaze.dir/src/editor/prototype.cpp.o
CMakeFiles/Fuseblaze.dir/build.make:134: recipe for target 'CMakeFiles/Fuseblaze.dir/src/editor/editorHandle.cpp.o' failed
CMakeFiles/Fuseblaze.dir/build.make:158: recipe for target 'CMakeFiles/Fuseblaze.dir/src/editor/prototype.cpp.o' failed
CMakeFiles/Fuseblaze.dir/build.make:110: recipe for target 'CMakeFiles/Fuseblaze.dir/src/editor/editor.cpp.o' failed
CMakeFiles/Makefile2:182: recipe for target 'CMakeFiles/Fuseblaze.dir/all' failed
Makefile:83: recipe for target 'all' failed

In file included from /data/tinyci_build/daid/Fuseblaze/src/editor/editorHandle.cpp:2:0:
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h: In member function 'virtual void Prototype::destroyHandles()':
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h:19:39: error: cannot convert 'sp::P<sp::Node>' to 'sp::Node*' in initialization
         for(Node* child : getChildren())
                                       ^
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h: In member function 'virtual sp::P<sp::Node> Prototype::getHandle(sp::Vector2d)':
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h:25:39: error: cannot convert 'sp::P<sp::Node>' to 'sp::Node*' in initialization
         for(Node* child : getChildren())
                                       ^
In file included from /data/tinyci_build/daid/Fuseblaze/src/editor/editor.cpp:3:0:
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h: In member function 'virtual void Prototype::destroyHandles()':
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h:19:39: error: cannot convert 'sp::P<sp::Node>' to 'sp::Node*' in initialization
         for(Node* child : getChildren())
                                       ^
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h: In member function 'virtual sp::P<sp::Node> Prototype::getHandle(sp::Vector2d)':
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h:25:39: error: cannot convert 'sp::P<sp::Node>' to 'sp::Node*' in initialization
         for(Node* child : getChildren())
                                       ^
In file included from /data/tinyci_build/daid/Fuseblaze/src/editor/prototype.cpp:1:0:
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h: In member function 'virtual void Prototype::destroyHandles()':
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h:19:39: error: cannot convert 'sp::P<sp::Node>' to 'sp::Node*' in initialization
         for(Node* child : getChildren())
                                       ^
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h: In member function 'virtual sp::P<sp::Node> Prototype::getHandle(sp::Vector2d)':
/data/tinyci_build/daid/Fuseblaze/src/editor/prototype.h:25:39: error: cannot convert 'sp::P<sp::Node>' to 'sp::Node*' in initialization
         for(Node* child : getChildren())
                                       ^
/data/tinyci_build/daid/Fuseblaze/src/editor/editor.cpp: In member function 'sp::Vector2d Editor::toWorld(sp::Vector2d)':
/data/tinyci_build/daid/Fuseblaze/src/editor/editor.cpp:159:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
make[2]: *** [CMakeFiles/Fuseblaze.dir/src/editor/editorHandle.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [CMakeFiles/Fuseblaze.dir/src/editor/prototype.cpp.o] Error 1
make[2]: *** [CMakeFiles/Fuseblaze.dir/src/editor/editor.cpp.o] Error 1
make[1]: *** [CMakeFiles/Fuseblaze.dir/all] Error 2
make: *** [all] Error 2
```


hello world. Python is my favourite snake.
R is my favourite letter.


that's a whoops! I'll force remove it—sorry


It seems (at keast with cmake version 3.10.2) that no space is inserted between the strings in the message. I saw this statement displays "Versions for sphinx-build ()and sphinx-quickstart ()do not match" (when Spinx was not installed).


Was this `1U` -> `1UL` change necessary? `1U` was pretty much the same across the board for all builds, `1UL` is now 64-bit in 64-bit linux builds, but it's still 32 bits when building for Windows (64 or 32 bit builds).


I cant build it on intellij. So not tried it.


Ah, thanks, I did indeed forget about this :)


Thanks @FayCross . I've checked with NVDA now and as always it's not consistent :-(
As far as my testing goes if I use the Apple iPad voice over functionality in the continuous reading mode then as it went through the buttons it just said button for the next, back and full screen buttons and now that I've added the aria label code to xenith it reads those values and so says next and back etc.
With NVDA if I tabbed to those buttons before the code change it would still say next and back but I think picking up from the title values. However if I simply hovered over the buttons rather than tab to them then NVDA would say the other buttons but not Next, Previous and Full screen. However with the changes in place it does say those buttons.
So bottom line it can't hurt and has helped to add the aria labels but perhaps this hasn't come to light before because if most testing is on a desktop/laptop with tabbing then it probably was saying the basic title values.


Hi, This is Nutakki. I have gone through your file gender detection which is really good. Here are few questions.
How can we specify an object for example a photograph of a house to the neural networks?
How can we use in Pytorch instead of Keras?
Can't we do in RNN rather than CNN?
If you have any suggestions you can give as a comment.


select a file from file manager and the file is not playing gives a toast error playing track


Oh, I see, `in` is now T, seems like this will not work on Windows properly, you will need `1ULL` (which is always 64-bit regardless of build type)


しまった、スペルミスった^q^


Why were these `using` lines added?


Closes: #40


🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2784234)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/d16-2/4ccab3326c0ee9205b7ca92fff6c4df75574f7b3/2784234/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>5 tests failed, 37 tests' device not found, 188 tests passed.</summary>

## Failed tests

 * monotouch-test/iOS Unified 64-bits - device/Debug: TimedOut (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7fb863c8ff10): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): TimedOut (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7faf3bc66390): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
 * monotouch-test/iOS Unified 64-bits - device/Release (all optimizations): TimedOut (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7f872cec39b0): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
 * System.Xml/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): TimedOut (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7fe1aa9a8c90): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
 * [NUnit] Mono BCL tests group 1/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): TimedOut (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7fc5464faa30): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
</details>


I followed the above mentioned steps but it got stuck by showing
Invalid htif write: address 0000000000000008
Invalid htif write: address 000000000000000c
Invalid htif write: address 0000000000000010
Invalid htif write: address 0000000000000014
Invalid htif write: address 0000000000000018
Invalid htif write: address 000000000000001c
Invalid htif write: address 0000000000000020
Invalid htif write: address 0000000000000024
Invalid htif write: address 0000000000000028
Invalid htif write: address 000000000000002c
Invalid htif write: address 0000000000000030
Invalid htif write: address 0000000000000034
Invalid htif write: address 0000000000000038
Invalid htif write: address 000000000000003c

any idea why ?


Successfully aliased the URL <https://urql-testapi-todos-bdsbe942e.now.sh> to the following aliases.

* https://urql-testapi-todos.philpl.now.sh
* https://urql-testapi-todos-git-master.philpl.now.sh


Beträge werden jetzt auf 2 Kommastellen gerundet


This branch is not yet stable.  We are porting zheap code to the undoprocessing branch (work is still in progress)


Successfully aliased the URL <https://musiikin-teoria-material-5q8qt17f3.now.sh> to the following aliases.

* https://musiikin-teoria.now.sh
* https://musiikin-teoria-material.mooc.now.sh
* https://musiikin-teoria-material-git-master.mooc.now.sh


Successfully aliased the URL <https://repl-gafvw9ry8.now.sh> to the following aliases.

* https://repl.teleporthq.io
* https://repl.teleport-dev.now.sh
* https://repl-git-master.teleport-dev.now.sh


Successfully aliased the URL <https://urql-testapi-todos-4q1a3nzzb.now.sh> to the following aliases.

* https://urql-testapi-todos.philpl.now.sh
* https://urql-testapi-todos-git-master.philpl.now.sh


Fix Bugs and new aesthetics.


@jow- @lucize That's weird. Bumping `ABI_VERSION` was supposed to trigger rebuild of all dependent packages


Rengeteg negatív visszajelzés volt az interaktív telepítő miatt, illetve tesztelés során nekem is sikerült belefutni hibákba.
Maradunk egyelőre mindenképp "one-click" telepítőnél.


split


maybe for now an email to dev mailing list so anyone interested to be aware


Successfully aliased the URL <https://steelepro-1mnbuj3dr.now.sh> to the following aliases.

* https://steele.pro
* https://steelepro.ynnoj.now.sh
* https://steelepro-git-master.ynnoj.now.sh


I don't think this is useful.
I don't see where you call it.

And in many case you will have 2 ports open.


Successfully aliased the URL <https://urql-testapi-todos-8kg0xzuin.now.sh> to the following aliases.

* https://urql-testapi-todos.philpl.now.sh
* https://urql-testapi-todos-git-master.philpl.now.sh


ZEIT Now cannot deploy this project to production due to following domain related issues:

 * `google.com`(for alias `google.com`) is not found inside your account. [Add it](https://zeit.co/dashboard/akurulk-qlspvp/domains?action=add&domain=google.com).
 * `arunoda.google.com`(for alias `arunoda.google.com`) is not found inside your account. [Add it](https://zeit.co/dashboard/akurulk-qlspvp/domains?action=add&domain=arunoda.google.com).
 * `iogoogle.com`(for alias `iogoogle.com`) is not found inside your account. [Add it](https://zeit.co/dashboard/akurulk-qlspvp/domains?action=add&domain=iogoogle.com).
 * `simple1234.com`(for alias `simple1234.com`) is not found inside your account. [Add it](https://zeit.co/dashboard/akurulk-qlspvp/domains?action=add&domain=simple1234.com).


## Pirate stuff
Butt stuff.


Comment on the commit as a whole.


Sajnálom, hogy gondot okozott ez a változtatás. Kíváncsi lennék mik voltak a konkrét hibák. Ahogy nézem issue nem készült ezekre.


Deployment failed with the following error:

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


Successfully aliased the URL <https://simple-now-app-r8msulswm.now.sh> to the following aliases.

* https://simple-now-app.akurulk-qlspvp.now.sh
* https://simple-now-app-git-master.akurulk-qlspvp.now.sh


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/1475](https://github.com/JuliaRegistries/General/pull/1475)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.2 -m "<description of version>" fb887f41d274063d71ff556ec3de4c11088a26a9
git push origin v0.1.2
```


cc: @RobBlackwell


Successfully aliased the URL <https://pay-overview-gqetfthsuz.now.sh> to the following alias.

* https://payroll.vacuumlabs.com


PR: https://github.com/curl/curl/pull/4025


增加模块说明


@mdiluz Do we really need to walk the tree? Couldn't we just use `IOPRIO_WHO_PGRP` instead of `IOPRIO_WHO_PROCESS` below? The parent process will have `PID == PGID`, all children will inherit the parents `PGID`.


and b020f4b66714062da1dee2c52018419f87dab053


I guess a proper logging (i.e. different levels and globally valid configuration, e.g., print intervals) instead of simple print outs is useful then. Feel free to open a new issue or change `display_sensors_task.cpp` as well as `mqtt_publish_task.cpp` accordingly 🙂


Successfully aliased the URL <https://sjoerdpennings-jyocmqtl7.now.sh> to the following aliases.

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


Ok


excuse me. why not use clang?


Successfully aliased the URL <https://cviceni-test-bch4o1b6e.now.sh> to the following aliases.

* https://cviceni-test.historylab.now.sh
* https://cviceni-test-git-master.historylab.now.sh


indexOf() : 메서드에 문자열을 입력하면 위치에따라 숫자로 반환한다.

int indexOf(String s){
return number;}


[R/calc_required_node_time.R:50:18:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_required_node_time.R#L50) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:51:16:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_required_node_time.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_required_node_time.R:66:18:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_required_node_time.R#L66) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           mu / ( (lambda - mu) *
                 ^
```
[R/calc_required_node_time.R:67:16:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_required_node_time.R#L67) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
           exp( (lambda - mu) * t))
               ^
```
[R/calc_summary_statistics.R:25:15:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_summary_statistics.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  output <- c( calc_beta(focal_tree),
              ^
```
[R/calc_summary_statistics.R:43:26:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_summary_statistics.R#L43) *warning:* **no visible global function definition for ‘calc_all_stats’**
```r
  sum_stats_true_tree <- calc_all_stats(true_tree)
                         ^~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:45:50:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_summary_statistics.R#L45) *warning:* **no visible binding for global variable ‘calc_all_stats’**
```r
  if (!verbose) sum_stats_trees <- lapply(trees, calc_all_stats)
                                                 ^~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:46:61:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_summary_statistics.R#L46) *warning:* **no visible binding for global variable ‘calc_all_stats’**
```r
  if (verbose) sum_stats_trees <-  pbapply::pblapply(trees, calc_all_stats)
                                                            ^~~~~~~~~~~~~~
```
[R/calc_time_spent_at_node.R:53:36:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_time_spent_at_node.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                   ^
```
[R/calc_time_spent_at_node.R:53:57:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_time_spent_at_node.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  ( (lambda - mu) * exp( (lambda - mu) * t))
                                                        ^
```
[R/calc_time_spent_at_node.R:69:37:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_time_spent_at_node.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                    ^
```
[R/calc_time_spent_at_node.R:69:58:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/calc_time_spent_at_node.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ( (lambda - mu) * exp( (lambda - mu) * t))
                                                         ^
```
[R/create_equal_alignment.R:15:23:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/create_equal_alignment.R#L15) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  num_emp_subs <- sum(calc_dist(focal_alignment, root_sequence))
                      ^~~~~~~~~
```
[R/create_equal_alignment.R:17:13:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/create_equal_alignment.R#L17) *warning:* **no visible global function definition for ‘calc_tree_height’**
```r
  t_mrca <- calc_tree_height(input_tree)
            ^~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:27:24:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/create_equal_alignment.R#L27) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                       ^~~~~~~~~
```
[R/create_equal_alignment.R:34:26:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/create_equal_alignment.R#L34) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                         ^~~~~~~~~
```
[R/RcppExports.R:5:1:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/RcppExports.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_nodeSub_get_p_m_rcpp', PACKAGE = 'nodeSub', eig, branch_length, rate)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:11:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/RcppExports.R#L5) *style:* **Only use double-quotes.**
```r
    .Call('_nodeSub_get_p_m_rcpp', PACKAGE = 'nodeSub', eig, branch_length, rate)
          ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:46:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/RcppExports.R#L5) *style:* **Only use double-quotes.**
```r
    .Call('_nodeSub_get_p_m_rcpp', PACKAGE = 'nodeSub', eig, branch_length, rate)
                                             ^~~~~~~~~
```
[R/RcppExports.R:7:1:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/RcppExports.R#L7) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:63:5:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L63) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:63:10:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L63) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
         ^~~~~~~~~~~~
```
[R/sim_dual_independent.R:76:5:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L76) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:76:10:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L76) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
         ^~~~~~~~~~~~
```
[R/sim_dual_independent.R:96:42:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L96) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:99:23:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L99) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_dual_independent.R:99:34:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_independent.R#L99) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:91:28:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L91) *warning:* **no visible binding for global variable ‘draw_bases’**
```r
  vx <- sapply(parent_seq, draw_bases, trans_matrix)
                           ^~~~~~~~~~
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L112) *style:* **Variable or function name should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:124:19:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L124) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:127:21:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L127) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:153:29:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L153) *warning:* **no visible global function definition for ‘make_transition_matrix’**
```r
  node_transition_matrix <- make_transition_matrix(node_mut_rate_double)
                            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_linked.R:179:7:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L179) *style:* **Variable or function name should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:179:12:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L179) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
           ^~~~~~~~~~~~
```
[R/sim_dual_linked.R:199:42:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L199) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_linked.R:202:23:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_linked.R#L202) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L64) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:64:10:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L64) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
         ^~~~~~~~~~~~
```
[R/sim_dual_parent.R:83:22:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L83) *warning:* **no visible global function definition for ‘get_index’**
```r
      local_index <- get_index(edge, parent, offspring)
                     ^~~~~~~~~
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L86) *style:* **Variable or function name should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:86:12:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L86) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
           ^~~~~~~~~~~~
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:108:23:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_dual_parent.R#L108) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_normal.R#L31) *style:* **Variable or function name should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_normal.R#L43) *style:* **Variable or function name should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_normal.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_normal.R#L67) *style:* **Variable or function name should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:67:10:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_normal.R#L67) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig, rate)
         ^~~~~~~~~~~~
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_normal.R:84:23:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/sim_normal.R#L84) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/util.R#L2) *style:* **Variable or function name should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/util.R#L20) *style:* **Variable or function name should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/util.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:44:12:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/util.R#L44) *warning:* **no visible global function definition for ‘fast.table’, Did you mean 'as.table'?**
```r
    ddd <- fast.table(data)
           ^~~~~~~~~~
```
[R/util.R:96:10:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/util.R#L96) *warning:* **no visible global function definition for ‘get_p_m_rcpp’**
```r
  res <- get_p_m_rcpp(eig, branch_length, rate)
         ^~~~~~~~~~~~
```
[R/util.R:97:4:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/util.R#L97) *style:* **Commented code should be removed.**
```r
  #res <- slow_matrix(eig, branch_length, rate)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:117:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/R/util.R#L117) *style:* **Variable or function name should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-calc-dist.R:19:26:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                         ^
```
[tests/testthat/test-calc-dist.R:19:60:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-calc-dist.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_error( calc_dist(seq_node_sub$alignment) )
                                                           ^
```
[tests/testthat/test-create_equal_alignment.R:18:26:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-create_equal_alignment.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testthat::expect_equal( length(seq_alt$alignment),
                         ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-dual_independent.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-dual_parent.R#L9) *style:* **Variable or function name should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-dual-linked.R#L9) *style:* **Variable or function name should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-sim_normal.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-substitution.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-substitution.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-substitution.R#L29) *style:* **Variable or function name should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eig_q,
    ^
```
[tests/testthat/test-substitution.R:84:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-substitution.R#L84) *style:* **Variable or function name should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:87:21:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-substitution.R#L87) *style:* **Variable or function name should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:94:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-substitution.R#L94) *style:* **Variable or function name should be snake_case.**
```r
  P1 <- nodeSub::slow_matrix(eig = eig_q,
  ^~
```
[tests/testthat/test-substitution.R:98:3:](https://github.com/thijsjanzen/nodeSub/blob/e06660004092d14e8d36f7ff0b8cc126a1e472ec/tests/testthat/test-substitution.R#L98) *style:* **Variable or function name should be snake_case.**
```r
  P2 <- get_p_matrix(branch_length, eig_q, rate)
  ^~
```


Congrats!


Successfully aliased the URL <https://musiikin-teoria-material-151wm34oc.now.sh> to the following aliases.

* https://musiikin-teoria.now.sh
* https://musiikin-teoria-material.mooc.now.sh
* https://musiikin-teoria-material-git-master.mooc.now.sh


не указано авторство


закоментированный код нужно убирать


что это за метод который находится за телом??


`|| undefined` is redundant. It would be `undefined` in parcel if it's not returned in the response.


проверено


tato prop tu je zbytocne nie?


For readability;
```
  float getEvCompensation(float refEv) const
  {
      float ev = getEv();
      if(ev == -1)
          return 1.0f;

      return std::pow(2.0f, ev - refEv);
  }
```


Successfully aliased the URL <https://urql-testapi-todos-o4im63xvm.now.sh> to the following aliases.

* https://urql-testapi-todos.philpl.now.sh
* https://urql-testapi-todos-git-master.philpl.now.sh


Successfully aliased the URL <https://effector-gvatj8wjf.now.sh> to the following aliases.

* https://effector.now.sh
* https://effector.zerobias.now.sh
* https://effector-git-master.zerobias.now.sh


@Tristar7 https://docs.microsoft.com/dotnet/api/system.console?view=netframework-4.8#unicode-support-for-the-console

TL;DR, displaying all UTF-8 characters instead of limiting yourself to the codepage of your language. Allows people to put special symbols in bot names and those are displayed properly.


ddsffdd


Successfully aliased the URL <https://laneconsultingco-mihrfe59f.now.sh> to the following aliases.

* https://laneconsulting.co
* https://www.laneconsulting.co
* https://laneconsultingco.jameswlane.now.sh
* https://laneconsultingco-git-master.jameswlane.now.sh


takto to máme u všech notifikací,  tu props tam posílá `Notification.jsx` komponenta


не понятно для чего вообще нам нужен этот html файл, если на него нельзя попасть даже через url


`DOCUMENTATION.md` only documents the usage of our adapter which has not changed.
IX has only a set of predefined tests which doesn't test private deals.


Thank you very much for the feedback. New version 99014d22fecae0f257676039ff5ec9936487b06f .


aha ok


Successfully aliased the URL <https://steelepro-nj7dtalga.now.sh> to the following aliases.

* https://steele.pro
* https://steelepro.ynnoj.now.sh
* https://steelepro-git-master.ynnoj.now.sh


Successfully aliased the URL <https://jameswlanecom-b3vdffqk2.now.sh> to the following aliases.

* https://jameswlane.com
* https://www.jameswlane.com
* https://jameswlanecom.jameswlane.now.sh
* https://jameswlanecom-git-master.jameswlane.now.sh


не понятный файл


нужно убрать закоментированный код


проверено


Successfully aliased the URL <https://jameswlanecom-41e0510va.now.sh> to the following aliases.

* https://jameswlane.com
* https://www.jameswlane.com
* https://jameswlanecom.jameswlane.now.sh
* https://jameswlanecom-git-master.jameswlane.now.sh


Successfully aliased the URL <https://jwlcloud-6tp0lz293.now.sh> to the following aliases.

* https://jwl.cloud
* https://www.jwl.cloud
* https://jwlcloud.jameswlane.now.sh
* https://jwlcloud-git-master.jameswlane.now.sh


Thanks for the new useful convention


Hi @panva , currently we are using library version 5.3.0 and we are not planning to upgrade to 6.x. Can we have this fix in 5.3.X version? I am ready to provide you MR for same.


synchronized (connectedUserList) { } 삭제
사유1 : 각 클라이언트들이 LOGOUT 프로토콜을 통해 connectedUserList에 접근해서 각자 다른값을 지움
사유2 : synchronized (hm) { } 로 인해 여러 스레드가 동시다발적으로 접근불가


Successfully aliased the URL <https://nordnet-ui-5qdk5kj97.now.sh> to the following aliases.

* https://nordnet-ui.nordnet1.now.sh
* https://nordnet-ui-git-master.nordnet1.now.sh


사용하지 않는 멤버변수로 삭제


Successfully aliased the URL <https://urql-testapi-todos-ggvyvtuuh.now.sh> to the following aliases.

* https://urql-testapi-todos.philpl.now.sh
* https://urql-testapi-todos-git-master.philpl.now.sh


Hm, how could this slip in? ;-)


[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after an infinite number of generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:11:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L11) *style:* **Variable or function name should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L12) *style:* **Variable or function name should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  K <- H_0 * C * 2 * N * R / (2 * N * C + R)
  ^
```
[R/calc_K.R:19:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L19) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L23) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L27) *style:* **Variable or function name should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the error in the estimate of the onset of hybridisation, following Equations 3 & 4 in the Supplementary information of Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param relative Boolean flag, if TRUE: return the relative error, if FALSE: return error in generations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:15:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L15) *style:* **Variable or function name should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L17) *style:* **Variable or function name should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L18) *style:* **Variable or function name should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_error.R:30:7:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
      ^
```
[R/calculate_error.R:30:25:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
                        ^
```
[R/calculate_MAT.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Function that calculates the maximum time after hybridization after which the number of junctions can still be reliably used to estimate the onset of hybridization. This is following equation 15 in Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:12:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L12) *style:* **Variable or function name should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_time.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the number of junctions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 14 in Janzen et al. 2018
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' estimate_time(J = J, N = 100, R = 1000, H_0 = 0.5, C = 1)  # should be 200 again
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:13:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L13) *style:* **Variable or function name should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/estimate_time_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 1 in Janzen et al. unpublished
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:8:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:12:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' J <- number_of_junctions_markers(N = 100, H_0 = 0.5, t = 200, marker_distribution = markers)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:18:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L18) *style:* **Variable or function name should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L19) *style:* **Variable or function name should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(lower_lim, upper_lim) )
                                                                      ^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
                                                        ^
```
[R/estimate_time_phased.R:108:19:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L108) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_phased.R:135:23:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:135:32:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:138:10:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L138) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:142:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:143:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L143) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:147:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:148:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L148) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:149:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L149) *style:* **Lines should not be more than 80 characters.**
```r
#' @param optim_pop_size If TRUE, population size is also optimized. Starting point of the optimizaton will then be on the given population size, and half the maximum time.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:184:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L184) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:191:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L191) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
                                                 ^
```
[R/estimate_time_unphased.R:12:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                       ^
```
[R/estimate_time_unphased.R:12:43:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                                          ^
```
[R/estimate_time_unphased.R:18:22:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- p * q * ( p * q * P[3] +
                     ^
```
[R/estimate_time_unphased.R:35:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                       ^
```
[R/estimate_time_unphased.R:88:19:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L88) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_unphased.R:115:23:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:115:32:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:118:12:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L118) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:175:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L175) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/estimate_time_unphased.R:182:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L182) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, in a backcrossing mating scheme.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:4:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:10:43:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L10) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected number of junctions between two markers separated by a given amount of recombination
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distance between two markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:12:36:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L12) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_di <- function(N = Inf,
                                   ^
```
[R/number_of_junctions_di.R:13:36:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected total number of junctions in a chromosome, given the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distribution of markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:20:41:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_markers <- function(N = Inf,
                                        ^
```
[R/number_of_junctions_markers.R:21:41:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L21) *style:* **Variable or function name should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions_markers.R:32:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L32) *warning:* **no visible global function definition for ‘number_of_junctions_di’**
```r
    expected_junctions <- number_of_junctions_di(N, H_0, t, di)
                          ^~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after t generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:13:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L13) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/optim_limits.R:5:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/optim_limits.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param calc_func function to calculate the time, should accept two arguments: upper, lower and should return a stats::optimize object with two properties: $minimum and $objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/optim_limits.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param iterations number of times the boundaries should be adjusted to obtain an estimate that is not close to the boundaries. After this number of iterations is exceeded, NA is returned
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:38:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/phased_log_likelihood.R:45:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/sim_backcrossing.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:12:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return List with five entries: average_junctions: average number of junctions over time, detected_junctions: average number of detected junctions, given the markers. markers: vector with the locations of the molecular markers, junction_distribution: distribution of junctions per time step average_heterozygosity: average heterozygosity.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with regularly distributed markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:5:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:17:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
sim_fin_chrom <- function (pop_size = 100,
                          ^
```
[R/sim_fin_chrom.R:22:28:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L22) *style:* **Variable or function name should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with an infinite number of recombination sites.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param markers The number of genetic markers superimposed on the chromosome. If markers is set to -1, no markers are superimposed (faster simulation)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is returned.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:8:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the unphased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:34:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/unphased_log_likelihood.R:41:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/util.R:22:10:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( get_states_vector(local_anc))
         ^
```
[R/util.R:22:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L22) *warning:* **no visible global function definition for ‘get_states_vector’**
```r
  return( get_states_vector(local_anc))
          ^~~~~~~~~~~~~~~~~
```
[R/util.R:56:42:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    (local_anc_matrix[, 1 ] == local_anc_matrix[, 2]))
                                         ^
```
[R/util.R:108:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:108:37:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
                                    ^
```
[R/util.R:116:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 3) cond_prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:122:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 4) cond_prob <- (p ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:146:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:146:44:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
                                           ^
```
[R/util.R:151:18:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L151) *warning:* **no visible global function definition for ‘get_expectation_O_state’**
```r
    cond_prob <- get_expectation_O_state(P, p, focal_state)
                 ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-equations.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-equations.R#L18) *style:* **Variable or function name should be snake_case.**
```r
  J <- junctions::number_of_junctions(N = 100, R = 1000,
  ^
```
[tests/testthat/test-marker_dist.R:4:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L17) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L60) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L61) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L5) *style:* **Variable or function name should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L6) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```


I was thinking of extending it, which would not trigger include. But that's easily solvable. However I do feel converting several cases of `class_eval` in the gem would greatly ease monkey patching the gem.

The full picture is a little obscure: https://gitlab.com/gitlab-org/gitlab-ee/issues/328#note_179567510


Reverting to this commit...


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* https://experimentwithcom-git-master.jameswlane.now.sh


> @jow- @lucize That's weird. Bumping `ABI_VERSION` was supposed to trigger rebuild of all dependent packages

https://git.openwrt.org/?p=openwrt/staging/jow.git;a=commitdiff;h=56d908703eee9b0ea207b853646030e6922b1efc


More PUBG FPS confirmed


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@PranovD Can we upgrade to tensorflow v1.14.0 ?


Failed to alias deployment. Blab.
* Learn more at the-url

http://localhost:3000/github/deployment?deploymentId=dpl_3FSenprTkH9Kkfp1SUnwtX565r4Y


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hey


Добавил


удалил


tsts


Hi, I found the problem, the Player.WardrobeCharacterNames remain undefined if the Player.Wardrobe is not null
this small change should fix it:
https://github.com/NoneNoname/Bondage-College/commit/443f6582eeeb86bb7c4582e3242b6add0ac583c8


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hi zcat ,i have a puzzle ,i can't compile this project successfully,cause there is no defintaion of function current_time(),how to solve it?

error: implicit declaration of function ‘current_time’


ok, i guess problem is gone.


Open


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Show


Since `com.kuhrusty` doesn't (yet?) reference a live domain, but you've been known to go by "bozo", how about changing the package to `clown.kuhrusty`? ;)


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it's virtual function from ChangeListener. It's part of JUCE code, i guess.