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

I updated the Github team because of this commit.

- @mwilson8 was added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

- @oblute, @benhuff were added to this feedstock maintenance team.

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

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

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


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

end of the stream or a document separator is expected at line 12, column 1:
    -
    ^

</details>


After this change, this materialization test can be supported by both `SubstitutionVisitor` and `AbstractMaterializedViewRule`. The plans of optimized results are both correct but little bit different.
I made this switch to circle `SubstitutionVisitor` thus don't affect existing checking for matching by `AbstractMaterializedViewRule`


if AddressSpaceSpecConnectorEndpoint#port is zero, then we shouldn't we assume the IANA registered port number for AMQP or AMQPS.


Слишком длинное название, каждый раз писать его везде, сократил его тут


Need to have this in master, because of an internal error!
Still have this line of code: def authenticate(self, nonce, request):

Why isn't it installed by pip install?


Don't forget to decrement the automated patch version too!

Call `python -m avalon --version` to see what it's at, and subtract this number at the `Builds since previous minor version` note.


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

InterpreterError at template.tasks[0]: unknown context value push

</details>


Successfully aliased the URL <https://frontend-dkmpzo4jg.now.sh> to the following aliases:

* https://niyonapp-staging.now.sh
* https://niyonapp.now.sh
* https://niyon-frontend-dev.now.sh
* https://frontend.labseu2-niyon.now.sh
* https://frontend-git-master.labseu2-niyon.now.sh


Ну это как Google сокращать до G.


Small detail: Do you really need `clone` here? This should also work (syntax supported in node 8.6+):

```ts
const options = {
  ...this.fetchOptions,
  body
};
```


Looks good to me.


Successfully aliased the URL <https://kstar-mrmw6674g.now.sh> to the following aliases:

* https://kstar.hanterokun.now.sh
* https://kstar-git-master.hanterokun.now.sh


Why do we need this?


displaying 4 rows instead of 3, revert removed code to fix it


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


I know right, the title completely tells you what happened too!


You deleted the review form!! Argh!


This is my first GitHub practical.


Delete


Just merged it 0.0
Now it's at `5.4.53`.


莫得问题


Please add `filter_horizontal` for Programs.
https://docs.djangoproject.com/en/1.11/ref/contrib/admin/#django.contrib.admin.ModelAdmin.filter_horizontal


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/2a5207e2-89be-466c-b44e-8a0f12c9ebe3?env_id=ibm%3Ayp%3Aus-south "cloud-native-toolchain-tutorial-20190909104000014"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/58668daf-a47d-43d3-ae7a-2e58b918a13a "sample-cloud-native-toolchain-tutorial-20190909104000014") deployed [cloud-native-toolchain-tutorial-app](https://github.com/santjaqo/cloud-native-toolchain-tutorial-app/releases/tag/deploy-ibm-yp-us-south-SGaitan-nl.ibm.com-dev-20190910-093532 "deploy-ibm-yp-us-south-SGaitan-nl.ibm.com-dev-20190910-093532") to [dev](https://console.bluemix.net/apps/3df33e57-a793-47de-aeef-868c02be4126?env_id=ibm:yp:us-south "ibm:yp:us-south:SGaitan@nl.ibm.com:dev"), including this commit


So.. we actually need to add a line `VERSION_PATCH -= 53` at the `Builds since previous minor version` section ?


Do we need to add queryset here?


I was able to reproduce it.
Removed `downdetector.com` from `###_evidon-barrier-wrapper` and added:
```
xn--allestrungen-9ib.at,xn--allestrungen-9ib.ch,xn--allestrungen-9ib.de,allestoringen.be,allestoringen.nl,downdetector.ae,downdetector.ca,downdetector.cl,downdetector.co.nz,downdetector.co.za,downdetector.com,downdetector.com.ar,downdetector.com.au,downdetector.com.br,downdetector.dk,downdetector.es,downdetector.fi,downdetector.fr,downdetector.hk,downdetector.ie,downdetector.in,downdetector.it,downdetector.jp,downdetector.mx,downdetector.no,downdetector.pl,downdetector.pt,downdetector.ru,downdetector.se,downdetector.sg,downdetector.co.uk,downdetector.web.tr#%#document.cookie = "_evidon_consent_cookie=1; path=/;";
```


|`hivemq-extension-sdk/src/main/java/com/hivemq/extension/sdk/api/client/ClientContext.java:23`|
|---|
revert this reformat change please


[R/create_pbd_params_selector.R:5:1:](https://github.com/richelbilderbeek/becosys/blob/7a0ae73765ac1e095f6f17fb4874b5c52b927152/R/create_pbd_params_selector.R#L5) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
create_pbd_params_selector <- function(
^
```
[R/is_pbd_params_selector.R:13:1:](https://github.com/richelbilderbeek/becosys/blob/7a0ae73765ac1e095f6f17fb4874b5c52b927152/R/is_pbd_params_selector.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
is_pbd_params_selector <- function(x) {
^
```
[R/mbd_calc_max_lik.R:31:1:](https://github.com/richelbilderbeek/becosys/blob/7a0ae73765ac1e095f6f17fb4874b5c52b927152/R/mbd_calc_max_lik.R#L31) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
mbd_calc_max_lik <- function(
^
```
[R/mbd_sim.R:15:1:](https://github.com/richelbilderbeek/becosys/blob/7a0ae73765ac1e095f6f17fb4874b5c52b927152/R/mbd_sim.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
mbd_sim <- function(
^
```
[R/pbd_calc_max_lik.R:32:1:](https://github.com/richelbilderbeek/becosys/blob/7a0ae73765ac1e095f6f17fb4874b5c52b927152/R/pbd_calc_max_lik.R#L32) *style:* **functions should have cyclomatic complexity of less than 15, this has 32.**
```r
pbd_calc_max_lik <- function(
^
```
[R/pbd_find_scenario.R:27:1:](https://github.com/richelbilderbeek/becosys/blob/7a0ae73765ac1e095f6f17fb4874b5c52b927152/R/pbd_find_scenario.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 93.**
```r
pbd_find_scenario <- function(
^
```
[R/pbd_numspec_quantile_checked.R:6:1:](https://github.com/richelbilderbeek/becosys/blob/7a0ae73765ac1e095f6f17fb4874b5c52b927152/R/pbd_numspec_quantile_checked.R#L6) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
pbd_numspec_quantile_checked <- function(
^
```
[R/pbd_sim_checked.R:16:1:](https://github.com/richelbilderbeek/becosys/blob/7a0ae73765ac1e095f6f17fb4874b5c52b927152/R/pbd_sim_checked.R#L16) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
pbd_sim_checked <- function(
^
```


## 没啥问题


resolves #53


Unfortunately I think I do, `fetchOptions` is an object, you might end up mutating references inside of it…


This needs a `try... catch` because it errors on `formNode is not a node` - yet still works...


OJBK


Using webpack or other bundlers, only one file from `node-fetch` will end up in your bundle, this one: https://github.com/bitinn/node-fetch/blob/master/browser.js


|`hivemq-extension-sdk/src/main/java/com/hivemq/extension/sdk/api/client/ClientContext.java:55`|
|---|
revert this reformat change please


If you want it to reset the patch to 0, yeah.  It'll automatically increment that number with each commit. So there's been 53 commits since 5.3.0.


|`hivemq-extension-sdk/src/main/java/com/hivemq/extension/sdk/api/client/ClientContext.java:45`|
|---|
revert this reformat change please


|`hivemq-extension-sdk/src/main/java/com/hivemq/extension/sdk/api/client/ClientContext.java:65`|
|---|
revert this reformat change please


for some reason this workaround doesn't work for me.. I tried deleting the node_modules directory altogether and doing an npm install. any clue?


wow!!


|`line 103`|
|---|
revert this reformat change please


Successfully aliased the URL <https://mcdcdpportal-6gxjmtqt1.now.sh> to the following aliases:

* https://mcd-cdp-portal.mkr-js-prod.now.sh
* https://mcd-cdp-portal-git-develop.mkr-js-prod.now.sh


|`hivemq-extension-sdk/src/main/java/com/hivemq/extension/sdk/api/client/ClientContext.java:113`|
|---|
revert this reformat change please


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

* https://kstar.hanterokun.now.sh
* https://kstar-git-master.hanterokun.now.sh


Probably it's a wrong solution. WIll think to propose a better solution?


![](https://github.trello.services/images/mini-trello-icon.png) [Hot key "Shift" for multiple select.](https://trello.com/c/fofXoLSk/26-hot-key-shift-for-multiple-select)


gmfe v2


With the latest version in master `CUDALDFLAGS` are `-L${CUDA_INSTALL_PATH}/lib64 -lcudart` according to your output it seems to be ` -L/lib64 -lcuda` (could it be that `rt` is cutoff at the end?) So you I guess you missed to set `CUDA_INSTALL_PATH`. Can you check that?


@link DisconnectInboundInterceptor


Le load te permet de faire la requête mais pour récupérer les users il vaut mieux faire un subscribe sur this.userService.entities$ comme ça si un autre component fait un patch tu auras quand même la mise à jour de la liste des utilisateurs.

Et pense à faire le takeUntil(this.destroy$)  à chaque subscribe :)


Successfully aliased the URL <https://kstar-nerellm67.now.sh> to the following aliases:

* https://kstar.hanterokun.now.sh
* https://kstar-git-master.hanterokun.now.sh


### TinyCI build failure:
Missing artifact: [EmptyEpsilon-win32.zip] after build


Successfully aliased the URL <https://static-qclfe6vht.now.sh> to the following aliases:

* https://statik.now.sh
* https://static.typi.tk
* https://thesorrymind.now.sh
* https://static.ooh.now.sh
* https://static-git-master.ooh.now.sh


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* https://stickajones.org
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hey bro error in admin sql query


Successfully aliased the URL <https://traitors-jt4awzim5.now.sh> to the following aliases:

* https://traitors.torngabeng.now.sh
* https://traitors-git-master.torngabeng.now.sh


Successfully aliased the URL <https://italian-b0qsuok9v.now.sh> to the following aliases:

* https://italian.kejender.now.sh
* https://italian-git-master.kejender.now.sh


This breaks compatibility with Android < API Level 26, because startForegroundService is supported starting from Android O


Зделал я все как вы говорите а что дальше то нечего не работает зделай мини видео что трудно что-ли


盼能发布最新一版到pypi去, 谢谢 @duanhongyi


So, for hot fixing this, I will just add this line plus bumping version to `5.4.1` in one more commit, and release it as `5.4.1`. So the automated patch version will also be at `5.4.1`, correct ?


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* https://static-git-master.ooh.now.sh


### TinyCI build failure:
[cmake .. -DSERIOUS_PROTON_DIR=../../SeriousProton -DCMAKE_TOOLCHAIN_FILE=../cmake/mingw.toolchain] returned [1]:
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7-Zip [64] 16.02 : Copyright (c) 1999-2016 Igor Pavlov : 2016-05-21
p7zip Version 16.02 (locale=C,Utf16=off,HugeFiles=on,64 bits,4 CPUs Intel(R) Atom(TM) CPU  330   @ 1.60GHz (106C2),ASM)

Scanning the drive for archives:
1 file, 952358 bytes (931 KiB)

Extracting archive: drmingw.7z
--
Path = drmingw.7z
Type = 7z
Physical Size = 952358
Headers Size = 735
Method = LZMA:23
Solid = +
Blocks = 1

Everything is Ok

Folders: 5
Files: 18
Size:       3142091
Compressed: 952358
-- ENABLE_CRASH_LOGGER is ON
-- Configuring incomplete, errors occurred!
See also "/data/tinyci_build/daid/EmptyEpsilon/_build_win32/CMakeFiles/CMakeOutput.log".

CMake Error at CMakeLists.txt:22 (message):
  DRMINGW_ROOT was not set.  Unable to continue

```


Nice ASCII art :D


updated cannot be empty

(posts and posts[0].post_date or blog.write_date).replace


修改test文件


Successfully aliased the URL <https://surname-site-8mhp2n6bm.now.sh> to the following aliases:

* https://stickajones.org
* https://surname-site.keplersj.now.sh
* https://surname-site-git-master.keplersj.now.sh


Successfully aliased the URL <https://static-28cpt9bxj.now.sh> to the following aliases:

* https://statik.now.sh
* https://static.typi.tk
* https://thesorrymind.now.sh
* https://static.ooh.now.sh
* https://static-git-master.ooh.now.sh


Successfully aliased the URL <https://static-ejd5p3pj5.now.sh> to the following aliases:

* https://statik.now.sh
* https://static.typi.tk
* https://thesorrymind.now.sh
* https://static.ooh.now.sh
* https://static-git-master.ooh.now.sh


Вот


[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calc_K.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calc_K.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calc_K.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:14:20:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calc_K.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                   C = 1) {
                   ^
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calc_K.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  K <- H_0 * C * 2 * N * R / (2 * N * C + R)
  ^
```
[R/calc_K.R:19:5:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calc_K.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calc_K.R#L23) *style:* **Variable and function name style should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calc_K.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_error.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_error.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_error.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_error.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:19:24:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_error.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                       C = 1,
                       ^
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_error.R#L24) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_error.R:30:7:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_MAT.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_MAT.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_MAT.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:15:27:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_MAT.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          C = 1) {
                          ^
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_MAT.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_time.R:1:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_time.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_time.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_time.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_time.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:17:27:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_time.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                          C = 1) {
                          ^
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/calculate_time.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/estimate_time_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_markers.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_markers.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_markers.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_markers.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(lower_lim, upper_lim) )
                                                                      ^
```
[R/estimate_time_phased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L2) *style:* **functions should have cyclomatic complexity of less than 15, this has 49.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
                                                        ^
```
[R/estimate_time_phased.R:108:19:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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:122:23:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:122:32:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:125:10:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:129:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L129) *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:130:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L130) *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:134:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L134) *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:135:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L135) *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:136:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L136) *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:171:11:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L171) *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:178:58:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_phased.R#L178) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_unphased.R#L2) *style:* **functions should have cyclomatic complexity of less than 15, this has 28.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_unphased.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
                                                 ^
```
[R/estimate_time_unphased.R:12:24:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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:102:23:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_unphased.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:102:32:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_unphased.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:105:12:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_unphased.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:160:11:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_unphased.R#L160) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/estimate_time_unphased.R:167:58:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/estimate_time_unphased.R#L167) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions_backcross.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_backcross.R:11:43:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions_backcross.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
                                          C = 1,
                                          ^
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions_di.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_di <- function(N = Inf,
                                   ^
```
[R/number_of_junctions_di.R:13:36:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions_di.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions_markers.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_markers <- function(N = Inf,
                                        ^
```
[R/number_of_junctions_markers.R:21:41:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions_markers.R#L21) *style:* **Variable and function name style should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions_markers.R:32:27:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:16:33:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                                C = 1,
                                ^
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/number_of_junctions.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/optim_limits.R:5:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_fin_chrom.R#L22) *style:* **Variable and function name style should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_unphased.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:12:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_unphased.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:1:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Individual Based Simulation of the accumulation of junctions, given phasing error
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Phased data is
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:3:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' generated using a user-provided error rate. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:8:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:10:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:15:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
#' @param error_rate fraction of markers that are erroneously phased (e.g. swapped)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:16:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:69:4:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L69) *style:* **Commented code should be removed.**
```r
#  testit::assert(all.equal(unique(phased_data$location), selected_markers))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:71:6:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in unique(phased_data$individual)) {
     ^
```
[R/sim_phased_with_error.R:77:7:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/sim_phased_with_error.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(to_flip) > 0) {
      ^
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L22) *warning:* **no visible global function definition for ‘get_states_vector’**
```r
  return( get_states_vector(local_anc))
          ^~~~~~~~~~~~~~~~~
```
[R/util.R:26:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L26) *style:* **functions should have cyclomatic complexity of less than 15, this has 32.**
```r
get_states_vector <- function(local_anc) {
^
```
[R/util.R:46:1:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L46) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
get_states_phased <- function(local_anc_matrix) {
^
```
[R/util.R:56:42:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L108) *style:* **Variable and function name style 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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L108) *style:* **Variable and function name style 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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L146) *style:* **Variable and function name style 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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/R/util.R#L146) *style:* **Variable and function name style 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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/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/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-equations.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-equations.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
  J <- junctions::number_of_junctions(N = 100, R = 1000,
  ^
```
[tests/testthat/test-marker_dist.R:4:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-marker_dist.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-marker_dist.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-marker_dist.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-marker_dist.R#L60) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-marker_dist.R#L61) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-phased-error.R:53:31:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-phased-error.R#L53) *style:* **Put spaces around all infix operators.**
```r
  expected_heterozygosity <- 2*0.5*0.5 * (1 - 1 / (2*100) )^200
                             ~^~
```
[tests/testthat/test-phased-error.R:53:35:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-phased-error.R#L53) *style:* **Put spaces around all infix operators.**
```r
  expected_heterozygosity <- 2*0.5*0.5 * (1 - 1 / (2*100) )^200
                                 ~^~
```
[tests/testthat/test-phased-error.R:53:53:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-phased-error.R#L53) *style:* **Put spaces around all infix operators.**
```r
  expected_heterozygosity <- 2*0.5*0.5 * (1 - 1 / (2*100) )^200
                                                   ~^~
```
[tests/testthat/test-phased-error.R:53:58:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-phased-error.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  expected_heterozygosity <- 2*0.5*0.5 * (1 - 1 / (2*100) )^200
                                                         ^
```
[tests/testthat/test-phased-error.R:55:6:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-phased-error.R#L55) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in unique(true_data$individual)) {
     ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-sims.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-sims.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-sims.R#L6) *style:* **Variable and function name style should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:7:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-sims.R#L7) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-sims.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-sims.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:31:3:](https://github.com/thijsjanzen/junctions/blob/6a31ed3cc5bbf1c86eb64e3550aa7df6d3ed3bb4/tests/testthat/test-sims.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```


Looks like there are a few commits with this line on and off in different forks, so we are overwriting it from time to time when rebasing and pushing new changes from our forks. Probably the best way to fix this is to merge the final state of this line to `master` branch and notify everyone to rebase on top of latest changes and stop editing this line.


Successfully aliased the URL <https://italian-5mrl48c89.now.sh> to the following aliases:

* https://italian.kejender.now.sh
* https://italian-git-master.kejender.now.sh


No no, don't worry about it. If you release 5.4.1 now, then 5.4.53 would still be the "latest" on PyPI, but appear later in our release page.

It's not a big deal. Carry on from 53.


Successfully aliased the URL <https://surname-site-k72dyviwc.now.sh> to the following aliases:

* https://stickajones.org
* https://surname-site.keplersj.now.sh
* https://surname-site-git-master.keplersj.now.sh


this was done on purpose so we can have have interfaces under different paths like /v1.2.3 and /v1.2.4


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

InterpreterError at template.tasks[0]: unknown context value push

</details>


Okay :)


will add the @Getter @Setter in class level and all remove from variable level


I thought it was needed for enabling cache_programs command while using discovery service API


Successfully aliased the URL <https://surname-site-a6mogigzt.now.sh> to the following aliases:

* https://stickajones.org
* https://surname-site.keplersj.now.sh
* https://surname-site-git-master.keplersj.now.sh


Ok, I should review this part then because it wasn't working locally for me


Still wish this was `aegir test --💯`


Successfully aliased the URL <https://domus-nucf8z29x.now.sh> to the following aliases:

* https://domus.now.sh
* https://domus.cogito-study.now.sh
* https://domus-git-master.cogito-study.now.sh


it's good. How to export the result to csv or anyother format?


Successfully aliased the URL <https://nestjs-mongodb-q03hc28le.now.sh> to the following aliases:

* https://nestjs-mongodb.webmasterdevlin.now.sh
* https://nestjs-mongodb-git-master.webmasterdevlin.now.sh


I missed that it is nullable


The better method to fix this is to provide the height estimator with regular terrain height corrections when on ground and not moving - see https://github.com/priseborough/ecl/tree/ekfOptFlowTakeoff-wip

This may require the value of EKF2_MOVE_TEST to be increased depending on the amount of IMU noise and frame movement before takeoff. Incorporating a movement test allows the vehicle to be picked up and moved without invalidating the estimate of the terrain position wrt the NED datum.


🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3037449)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/3037449/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>15 tests failed, 98 tests passed.</summary>

## Failed tests

 * monotouch-test/iOS Unified 64-bits - device/Debug: Failed
 * [xUnit] Mono BCL tests group 4/iOS Unified 64-bits - device/Debug: TimedOut
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Failed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * monotouch-test/iOS Unified 64-bits - device/Release: Failed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Failed
 * monotouch-test/iOS Unified 64-bits - device/Debug (dynamic registrar): Failed
 * monotouch-test/iOS Unified 64-bits - device/Release (all optimizations): Failed
 * monotouch-test/iOS Unified 64-bits - device/Debug (all optimizations): Failed
 * monotouch-test/iOS Unified 64-bits - device/Debug: SGenConc: Failed
 * monotouch-test/iOS Unified 64-bits - device/Debug (interpreter): Failed
 * monotouch-test/iOS Unified 64-bits - device/Debug (interpreter -mscorlib): Failed
 * monotouch-test/iOS Unified 64-bits - device/Release (interpreter -mscorlib): Failed
</details>


✅ Device tests passed on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3037625)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/issue-6876/da602403e90fcabd0da23f2f22dfe1d619d7a295/3037625/device-tests/jenkins-results/tests/index.html) ✅

# Test results

# All 113 tests passed


@n8v8R Tomorrow!

There's a few more things I need to finish for the next release. Chrome 77 was released today so those profiles will be updated as well.

I'm working on making releases more modern and transparent by using more of Github's features, [milestones](https://github.com/sereneblue/chameleon/milestones) and [projects](https://github.com/sereneblue/chameleon/projects). I've been a bit busy with another project but once it's complete, I'll be able to put more time into Chameleon. Some exciting things to look forward to!


I thought non functional simplifications like this didn't need testing.  Has that changed?


Successfully aliased the URL <https://nuxt-express-now-hlradh7yw.now.sh> to the following alias:

* https://nuxt-express-now-git-master.msurguy.now.sh


🔥 Device tests completed (Failed) on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3037451)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/3037451/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>15 tests failed, 98 tests passed.</summary>

## Failed tests

 * monotouch-test/tvOS - device/Debug: Failed
 * monotouch-test/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * monotouch-test/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * monotouch-test/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * monotouch-test/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * monotouch-test/tvOS - device/Release: Failed
 * monotouch-test/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * monotouch-test/tvOS - device/Debug (dynamic registrar): Failed
 * monotouch-test/tvOS - device/Release (all optimizations): Failed
 * monotouch-test/tvOS - device/Debug (all optimizations): Failed
 * monotouch-test/tvOS - device/Debug: SGenConc: Failed
 * monotouch-test/tvOS - device/Debug (interpreter): Failed
 * monotouch-test/tvOS - device/Debug (interpreter -mscorlib): Failed
 * monotouch-test/tvOS - device/Release (interpreter -mscorlib): Failed
 * [NUnit] Mono BCL tests group 2/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
</details>


Successfully aliased the URL <https://cf401-finalproject-hsaidtdy1.now.sh> to the following aliases:

* https://cf401-finalproject.mcolgin.now.sh
* https://cf401-finalproject-git-master.mcolgin.now.sh


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-83-sb-buildtools-demo.pantheonsite.io/)

Created multidev environment [pr-83](https://dashboard.pantheon.io/sites/e832afc4-9cba-44f8-9341-89975d2cf194#pr-83) for sb-buildtools-demo.


Hi Susan,

I am sorry for making a mistake.

I have been traveling internationally and attempted to get my show and tell
update ready on the plane. I must have missed Heike's original email in the
shuffle of spotty WiFi this week.

I will correct my mistake as soon as possible. My computer is dead but I
will fix it as soon as I get back to my apartment later tonight.

I apologize to everyone copied on this email that you are having to wait
for me to fix this mistake.

It will not happen again.

Kiegan

On Tue, Sep 10, 2019, 11:03 AM Susan VanderPlas <notifications@github.com>
wrote:

> Kiegan -
>
> Can you please run the commands indicated in the readme? You pushed
> docs-local and _bookdown_files/, causing conflicts for everyone else who
> pulls.
>
> usethis::use_git_ignore(ignores=c("docs-local", "_bookdown_files/"))
>
> Please only commit the files you directly modify. This will save everyone
> a huge headache and a lot of future merge conflicts
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/CSAFE-ISU/this-is-us/commit/8edab07ee954855ab91ceaa7d087e2c4a7516aa2?email_source=notifications&email_token=AFJANM4M7T6CCGEYXH4OB6DQI67JZA5CNFSM4IVJRNAKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBBM3NE#commitcomment-35024292>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AFJANMYBCF5Q5G3CML3VFX3QI67JZANCNFSM4IVJRNAA>
> .
>


I believe you can use border: null or background: null.


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

end of the stream or a document separator is expected at line 12, column 1:
    -
    ^

</details>


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-172-example-wordpress-composer.pantheonsite.io/)

Created multidev environment [pr-172](https://dashboard.pantheon.io/sites/46afe9ed-ebf0-44fe-acac-229694bfd8b3#pr-172) for example-wordpress-composer.


❌ [Build was (probably) aborted](https://jenkins.internalx.com/job/macios/job/issue-6876/1/display/redirect)

🔥 [Jenkins job](https://jenkins.internalx.com/job/macios/job/issue-6876/1/display/redirect) (on internal Jenkins) failed in stage(s) 'Running XM tests on '10.10', Running XM tests on '10.12', Running XM tests on '10.11', Running XM tests on '10.9', Running XM tests on '10.13', Running XM tests on '10.13'' 🔥

✅ [Build succeeded](https://jenkins.internalx.com/job/macios/job/issue-6876/1//console)
✅ Packages:
* [xamarin.ios-12.15.0.328.pkg (Not notarized)](https://bosstoragemirror.blob.core.windows.net/wrench/jenkins/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/1/package/xamarin.ios-12.15.0.328.pkg)
* [xamarin.mac-5.15.0.328.pkg (Not notarized)](https://bosstoragemirror.blob.core.windows.net/wrench/jenkins/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/1/package/xamarin.mac-5.15.0.328.pkg)
* [xamarin.ios-12.15.0.328.pkg (Notarized)](https://bosstoragemirror.blob.core.windows.net/wrench/jenkins/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/1/package/notarized/xamarin.ios-12.15.0.328.pkg)
* [xamarin.mac-5.15.0.328.pkg (Notarized)](https://bosstoragemirror.blob.core.windows.net/wrench/jenkins/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/1/package/notarized/xamarin.mac-5.15.0.328.pkg)

✅ [API Diff (from stable)](http://xamarin-storage/jenkins/xamarin-macios/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/1/jenkins-results/api-diff/index.html)
✅ [API Diff (from PR only)](http://xamarin-storage/jenkins/xamarin-macios/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/1/jenkins-results/apicomparison/api-diff.html) (no change)
✅ [Generator Diff](http://xamarin-storage/jenkins/xamarin-macios/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/1/jenkins-results/generator-diff/index.html) (no change)
🔥 [Xamarin.Mac tests on 10.10 failed: Xamarin.Mac tests on macOS 10.10 failed (xammac_tests)](https://jenkins.internalx.com/job/macios/job/issue-6876/1/display/redirect) 🔥
🔥 [Xamarin.Mac tests on 10.12 failed: Xamarin.Mac tests on macOS 10.12 failed (xammac_tests)](https://jenkins.internalx.com/job/macios/job/issue-6876/1/display/redirect) 🔥
🔥 [Xamarin.Mac tests on 10.11 failed: Xamarin.Mac tests on macOS 10.11 failed (xammac_tests)](https://jenkins.internalx.com/job/macios/job/issue-6876/1/display/redirect) 🔥
🔥 [Xamarin.Mac tests on 10.9 failed: Xamarin.Mac tests on macOS 10.9 failed (xammac_tests)](https://jenkins.internalx.com/job/macios/job/issue-6876/1/display/redirect) 🔥
🔥 [Xamarin.Mac tests on 10.13 failed: Xamarin.Mac tests on macOS 10.13 failed (xammac_tests)](https://jenkins.internalx.com/job/macios/job/issue-6876/1/display/redirect) 🔥
🔥 [Test run failed](http://xamarin-storage/jenkins/xamarin-macios/issue-6876/bb4e8b1b66cac361bea9bcd97fe57f20bc2ba9f2/1/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>15 tests failed, 156 tests passed.</summary>

## Failed tests

 * xammac tests/Mac/Debug: Failed (Test run crashed (exit code: 134).)
 * xammac tests/Mac/Release: Failed (Test run crashed (exit code: 134).)
 * monotouch-test/iOS Unified 32-bits - simulator/Debug: Failed
 * monotouch-test/iOS Unified 32-bits - simulator/Debug (static registrar): Failed
 * monotouch-test/iOS Unified 64-bits - simulator/Debug: Failed
 * monotouch-test/iOS Unified 64-bits - simulator/Debug (static registrar): Failed
 * monotouch-test/tvOS - simulator/Debug: Failed
 * monotouch-test/tvOS - simulator/Debug (static registrar): Failed
 * monotouch-test/watchOS 32-bits - simulator/Debug: Failed
 * monotouch-test/watchOS 32-bits - simulator/Debug (LinkSdk): Failed
 * monotouch-test/watchOS 32-bits - simulator/Debug (static registrar): Failed
 * monotouch-test/watchOS 32-bits - simulator/Release (all optimizations): Failed
 * monotouch-test/watchOS 32-bits - simulator/Debug (all optimizations): Failed
 * introspection/watchOS 32-bits - simulator/Debug (watchOS 2.0): Crashed
 * MMP Regression Tests/Mac: Failed
</details>


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-147-mtcv.pantheonsite.io/)

Created multidev environment [pr-147](https://dashboard.pantheon.io/sites/ad79477c-5d06-4234-b6b8-582ebeee0e5c#pr-147) for mtcv.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-162-topperstation.pantheonsite.io/)

Created multidev environment [pr-162](https://dashboard.pantheon.io/sites/db5fb5e4-3225-46f0-b0a9-1cc803600c48#pr-162) for topperstation.


Successfully aliased the URL <https://cf401-finalproject-8xj5v4noe.now.sh> to the following aliases:

* https://cf401-finalproject.mcolgin.now.sh
* https://cf401-finalproject-git-master.mcolgin.now.sh


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-3-zk02.pantheonsite.io/)

Created multidev environment [pr-3](https://dashboard.pantheon.io/sites/604d5166-1deb-47e8-ba51-6aa183f12d17#pr-3) for zk02.


all tests pass:
success: https://travis-ci.org/stellar/stellar-core/builds/583419592?utm_source=github_status&utm_medium=notification


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-1-notterrible-d8-composer-demo.pantheonsite.io/)

Created multidev environment [pr-1](https://dashboard.pantheon.io/sites/f8c9b990-1a2e-4527-bcaa-18b045b80d8f#pr-1) for notterrible-d8-composer-demo.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-12-build-tools-2805.pantheonsite.io/)

Created multidev environment [pr-12](https://dashboard.pantheon.io/sites/de28c483-8c8a-4ef5-ae7b-2dc529ebc499#pr-12) for build-tools-2805.


I needed to change the CSS padding for the image because the bounding box was too big. The padding of the image was affecting the box over the face in the image. Also, I had to set the div wrapping the img element to absolute so the box and image would be as we wanted to.


data-center-docs (XuanLuoLBL) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1219 of 1219 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.13%25-green.png)


i don't think this works yet.


TESTE NOVO


See #40114


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-277-ci-example-d8-composer.pantheonsite.io/)

Created multidev environment [pr-277](https://dashboard.pantheon.io/sites/c401fd14-f745-4e51-9af2-f30b45146a0c#pr-277) for ci-example-d8-composer.


No big deal. I was honestly surprised someone was working on a Tuesday. 😂

I didn't so much want to call you out specifically as emphasize that this
format only works if we all observe certain conventions. I know you missed
last week, but we had a terrible time getting stuff compiled and a lot of
people's work wasn't visible because of similar issues.

Anyways, you were the first one to do it after the meeting, so you
triggered the warning email, but you also have a much better excuse than
one of the other worst offenders😁.

Get some sleep!

On Tue, Sep 10, 2019, 19:06 Kiegan Rice <notifications@github.com> wrote:

> Hi Susan,
>
> I am sorry for making a mistake.
>
> I have been traveling internationally and attempted to get my show and tell
> update ready on the plane. I must have missed Heike's original email in the
> shuffle of spotty WiFi this week.
>
> I will correct my mistake as soon as possible. My computer is dead but I
> will fix it as soon as I get back to my apartment later tonight.
>
> I apologize to everyone copied on this email that you are having to wait
> for me to fix this mistake.
>
> It will not happen again.
>
> Kiegan
>
>
>
>
>
> On Tue, Sep 10, 2019, 11:03 AM Susan VanderPlas <notifications@github.com>
> wrote:
>
> > Kiegan -
> >
> > Can you please run the commands indicated in the readme? You pushed
> > docs-local and _bookdown_files/, causing conflicts for everyone else who
> > pulls.
> >
> > usethis::use_git_ignore(ignores=c("docs-local", "_bookdown_files/"))
> >
> > Please only commit the files you directly modify. This will save everyone
> > a huge headache and a lot of future merge conflicts
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub
> > <
> https://github.com/CSAFE-ISU/this-is-us/commit/8edab07ee954855ab91ceaa7d087e2c4a7516aa2?email_source=notifications&email_token=AFJANM4M7T6CCGEYXH4OB6DQI67JZA5CNFSM4IVJRNAKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBBM3NE#commitcomment-35024292
> >,
> > or mute the thread
> > <
> https://github.com/notifications/unsubscribe-auth/AFJANMYBCF5Q5G3CML3VFX3QI67JZANCNFSM4IVJRNAA
> >
> > .
> >
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/CSAFE-ISU/this-is-us/commit/8edab07ee954855ab91ceaa7d087e2c4a7516aa2?email_source=notifications&email_token=AAQHKFMM2UXKYRP3ONFCBZDQJAZBFA5CNFSM4IVJRNAKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBBNBNJ#commitcomment-35030441>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAQHKFKSAWAXSH2EQELNVALQJAZBFANCNFSM4IVJRNAA>
> .
>


Successfully aliased the URL <https://codeforgsogithubio-c8jbz5f4d.now.sh> to the following aliases:

* https://codeforgsogithubio.codeforgso.now.sh
* https://codeforgsogithubio-git-dev.codeforgso.now.sh


fast-forwarding master to auto = 07b049e0


Successfully aliased the URL <https://codeforgsogithubio-i13bc34i4.now.sh> to the following aliases:

* https://codeforgsogithubio.codeforgso.now.sh
* https://codeforgsogithubio-git-dev.codeforgso.now.sh


Reverted due to #40114


dont put the same data in there


@matdehaast any thoughts on this? I share the same sentiment as dj here.


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:eab22129-8002-0109-7d36-684dc6000000
Time:2019-09-11T00:20:04.4527029Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:368183ee-6002-002e-7d36-6891da000000
Time:2019-09-11T00:20:04.4514335Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:a87887cb-6002-0108-3836-684c3b000000
Time:2019-09-11T00:20:04.4543520Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:57479503-8002-00e3-1d36-68f492000000
Time:2019-09-11T00:20:04.4531197Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:92df7e17-d002-00fb-5936-68d907000000
Time:2019-09-11T00:20:04.7092116Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:31e99c2e-3002-0097-0d36-6872d4000000
Time:2019-09-11T00:20:09.4445805Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:1352c717-9002-007f-4f36-688f2f000000
Time:2019-09-11T00:20:09.4456388Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:eab223d7-8002-0109-5c36-684dc6000000
Time:2019-09-11T00:20:09.4423942Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:a9a2efdd-f002-0020-5a36-687dd1000000
Time:2019-09-11T00:20:09.4434472Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

The specified entity already exists.
RequestId:a87889fe-6002-0108-4436-684c3b000000
Time:2019-09-11T00:20:09.4421194Z

</details>


The credits file is automatically generated through `git log`, but I do think we need to have a way to let authors/contributors defined their own name should they want it.

You can freely edit the file to change the name displayed here (as some contributors have done). I'll try to keep track of the changes when I do another roundd of credits update.


Now could not deploy this pull request since it contains the following references to invalid secrets in the `env` sections of the `now.json` file:

* `franz-statickit-id` (in env: `STATICKIT_ID)`
* `franz-authentication-service` (in env: `AUTHENTICATION_SERVICE)`

Add those secrets or remove them from the `env` maps in the `now.json` file.


Thanks a lot, I will learn it.


Just tried it on another device and I think the new add podcast screen is a big enough feature to make this 1.8.