NOTE:  This commit also changes the endpoint to `commons.wikimedia.org`


Can you add unit-test for this commit?


@JuliaRegistrator register


Please only refrence Github Issues and not internal issue number, either create a descriptive commt message only, or better create an issue describing the problem first in girhub and then reference it in the commit.


Registration pull request created: [JuliaRegistries/General/6923](https://github.com/JuliaRegistries/General/pull/6923)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.4.2 -m "<description of version>" 8547e8ccba72748c7c3488139a1afafcccaef22e
git push origin v0.4.2
```


> Can you add unit-test for this commit?

Ahh, You writed unit-test in other commit.


The actual compiling for release is done automatically on a Linux server, the Windows builds being cross-compiled, so changing the Visual Studio version will make no difference to what platforms are supported by the compiled builds.


![](https://github.trello.services/images/mini-trello-icon.png) [#1.14 Add a dropdown of apponitment types to clinic listing page](https://trello.com/c/ncbGC6La/211-114-add-a-dropdown-of-apponitment-types-to-clinic-listing-page)


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I will continue to review tomorrow


No it cannot be overwritten, I already checked. prettier is very opinionated and they generally refuse to add any options, that's why I'm not using it.


This needs to be in the first `require_modules` because the second one is ignored.


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Same as the previous comment. Is encode required here?


Thanks for the heads up, I've removed `benchmark` from `hydra`.


Please read my comment elsewhere again. I am pretty sure I said that `password.length > 0` is always true.

Keyword: `.length`...


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@sindresorhus Any estimates on when version with this fix will be released?


# Specs execution successful
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[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

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Typo: turorial -> tutorial


:thinking:


would it be more visual to use strings for client types?


Hei hei,

`markovian-nlp@7.0.0` was just released with a [significantly smaller file size](https://bundlephobia.com/result?p=markovian-nlp@7.0.0) than `markovian-nlp@5.0.1`. It's now 23.73% smaller than what you're using!

To upgrade to the latest version, run `npm i markovian-nlp@latest` from this package's command line.

Lykke til!


gay


第二句可以修改为：不属于 Java 虚拟机规范的实现细节不会限制实现者的创造力。


revert


@JuliaRegistrator register

Release notes:
- Approximately 50% performance improvement.
- Exported function AudzeEglaisObjective! in favor of AudzeEglaisObjective.
- Fixed typo in documentation where the equation for AudzeEglaisObjective was wrong


Registration pull request created: [JuliaRegistries/General/6924](https://github.com/JuliaRegistries/General/pull/6924)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v1.4.0 -m "<description of version>" f4d855be990649162a7dd9afcf4134b0159536e0
git push origin v1.4.0
```


Non, ça n'est pas le bon test car ta clé est totalement fausse. Prends plutôt la clé privée de test suivante ici :
`80219e4d24caf16cb4755c1ae85bad02b6a3efb1e3233379af6f2cc1a18442c4`


padding jābūt 50 0 0 0


Collaborator: Review for this commit was created. [Link to review](http://0e0d4cf9.eu.ngrok.io/ui#review:id=812)


Collaborator cannot find remote user mapping for user that pushed commits, review created by system administrator


yes because i'm not done from the emoji check


![](https://github.trello.services/images/mini-trello-icon.png) [#2.7 can remove an existing appointment type](https://trello.com/c/auedmd5r/207-27-can-remove-an-existing-appointment-type)


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Ce ai facut Sorine aici?


aaf


![](https://github.trello.services/images/mini-trello-icon.png) [Leetcode Problem # 230](https://trello.com/c/O06TCyVw/91-leetcode-problem-230)


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[VPP] Fix MFX status for RGB565 and RGBP color formats

Fixes: fcca4c ("Reallocate frame (system memory or vaapi surface) for VP9 DRC decoding.")

sample_vpp returns correct status for RGB565->* and NV12->RGBP color conversions.


js-классы не нужны в текущей реализации


Build flag:
`-DREGION_EU868="ON"`


第一句：运行在 Java 虚拟机上的已编译代码表示为一种与硬件及操作系统无关的二进制格式。
最后一句疑问？是细节被采纳还是字节顺序被采纳？


Текст через константы


Simple test case added"


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Нужен ли нам сейчас data-id?


one more update to add HTTP proxy: https://github.com/ehorohorin/openhab2-addons/commit/ecd3ab7a7b36a03693d28f769c5bc7674878c0b6


You can use [Slf4j Android](http://www.slf4j.org/android/) instead


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Both proxies on the same LAN work well (HTTP and SOCKS5) sending images to telegram


Это должно быть в отдельном классе по добавлению


Нужно ли это теперь?


[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/fcf1c19edcac32782ccd8dfd9a4d2782876ea7fd/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
est_evidences <- function(
^
```
[R/get_sim_twal_with_same_n_mutation_fun.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/fcf1c19edcac32782ccd8dfd9a4d2782876ea7fd/R/get_sim_twal_with_same_n_mutation_fun.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twal_with_same_n_mutation_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


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第一句：与 Java 编程语言一样，Java 虚拟机可进行两种类型的操作。


Yet to pull patient Visit details on the page


df


using Parcelable with `Parcelize` in Kotlin for safer and better performance


The main function starts from here.


`{ IEEE_OUI, 0x00, 0x00, 0x00, 0x00, 0x00 }`


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit e6c5230e87db7e8620a4355afb974a90401e1cb8.

You can try again later or [upgrade](https://zeit.co/account/plan) your plan.


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ok you said

> "Anyway, .length == 32 always with a bytes32. Useless check."

I understood:

> "its not possible to send empty/zero values to a bytes32"

So what is the correct way to validate the input?


1.0.x: `LORAWAN_APP_EUI`
1.1.x: `LORAWAN_JOIN_EUI`

`{ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00 }`


[R/clock_model_to_xml_prior_distr.R:14:23:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/clock_model_to_xml_prior_distr.R#L14) *warning:* **no visible global function definition for ‘rln_clock_model_to_xml_mean_rate_prior’**
```r
      text <- c(text, rln_clock_model_to_xml_mean_rate_prior(clock_model)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_state.R:32:23:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/clock_models_to_xml_state.R#L32) *warning:* **no visible global function definition for ‘clock_model_to_xml_state’**
```r
    line_to_remove <- clock_model_to_xml_state(clock_models[[1]]) # nolint
                      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:9:19:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_beast2_input_distr.R#L9) *warning:* **no visible global function definition for ‘tree_priors_to_xml_prior_distr’**
```r
  text <- c(text, tree_priors_to_xml_prior_distr(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:10:19:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_beast2_input_distr.R#L10) *warning:* **no visible global function definition for ‘gamma_site_models_to_xml_prior_distr’**
```r
  text <- c(text, gamma_site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:11:19:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_beast2_input_distr.R#L11) *warning:* **no visible global function definition for ‘site_models_to_xml_prior_distr’**
```r
  text <- c(text, site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:27:19:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_beast2_input_operators.R#L27) *warning:* **no visible global function definition for ‘site_models_to_xml_operators’**
```r
  text <- c(text, site_models_to_xml_operators(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_run.R:23:11:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_beast2_input_run.R#L23) *warning:* **no visible global function definition for ‘mcmc_to_xml_run’**
```r
  text <- mcmc_to_xml_run(mcmc) # nolint beautier function
          ^~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:24:19:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_beast2_input_state.R#L24) *warning:* **no visible global function definition for ‘site_models_to_xml_state’**
```r
  text <- c(text, site_models_to_xml_state(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:33:19:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_beast2_input_state.R#L33) *warning:* **no visible global function definition for ‘tree_priors_to_xml_state’**
```r
  text <- c(text, tree_priors_to_xml_state(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_clock_models_from_names.R:5:26:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_clock_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_clock_model_from_name’**
```r
    clock_models[[i]] <- create_clock_model_from_name(clock_model_name) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_site_models_from_names.R:5:25:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_site_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_site_model_from_name’**
```r
    site_models[[i]] <- create_site_model_from_name(site_model_name) # nolint beautier function
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:17:19:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_tracelog_xml.R#L17) *warning:* **no visible global function definition for ‘tree_models_to_xml_tracelog’**
```r
  text <- c(text, tree_models_to_xml_tracelog(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:32:19:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/create_tracelog_xml.R#L32) *warning:* **no visible global function definition for ‘tree_priors_to_xml_tracelog’**
```r
  text <- c(text, tree_priors_to_xml_tracelog(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_section_from_lines.R:7:12:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/extract_xml_section_from_lines.R#L7) *warning:* **no visible global function definition for ‘extract_xml_operators_from_lines’**
```r
    return(extract_xml_operators_from_lines(lines)) # nolint beautier function
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_last_xml_closing_tag_line.R:6:3:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/find_last_xml_closing_tag_line.R#L6) *warning:* **no visible global function definition for ‘find_last_regex_line’**
```r
  find_last_regex_line(lines, paste0("</", section, ">")) # nolint beautier function
  ^~~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:11:12:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/has_xml_opening_tag.R#L11) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
    tag <- get_xml_opening_tag(lines) # nolint
           ^~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:14:24:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/has_xml_opening_tag.R#L14) *warning:* **no visible global function definition for ‘find_first_xml_opening_tag_line’**
```r
  !beautier::is_one_na(find_first_xml_opening_tag_line(lines, section))
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:10:10:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/init_clock_models.R#L10) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames) # nolint beautier function
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_distr.R:9:1:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/init_distr.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
init_distr <- function(
^
```
[R/init_inference_model.R:39:22:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/init_inference_model.R#L39) *warning:* **no visible global function definition for ‘init_mrca_prior’**
```r
  inference_model <- init_mrca_prior(input_filename, inference_model)
                     ^~~~~~~~~~~~~~~
```
[R/is_distr.R:37:1:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_distr.R#L37) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
is_distr <- function(
^
```
[R/is_init_site_model.R:36:1:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_init_site_model.R#L36) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
is_init_gtr_site_model <- function(
^
```
[R/is_mrca_align_ids_in_fastas.R:6:10:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_mrca_align_ids_in_fastas.R#L6) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:55:1:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_site_model.R#L55) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
is_gtr_site_model <- function(
^
```
[R/is_site_model.R:171:1:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_site_model.R#L171) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
is_tn93_site_model <- function(
^
```
[R/is_tree_prior.R:5:8:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_tree_prior.R#L5) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:3:8:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_xml.R#L3) *warning:* **no visible global function definition for ‘has_xml_opening_tag’**
```r
  if (!has_xml_opening_tag(text)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:4:7:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_xml.R#L4) *warning:* **no visible global function definition for ‘has_xml_short_closing_tag’**
```r
  if (has_xml_short_closing_tag(text)) return(TRUE) # nolint beautier function
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:5:18:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_xml.R#L5) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
  opening_tag <- get_xml_opening_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:6:18:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/is_xml.R#L6) *warning:* **no visible global function definition for ‘get_xml_closing_tag’**
```r
  closing_tag <- get_xml_closing_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_state.R:22:23:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/site_model_to_xml_state.R#L22) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ac_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:25:23:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/site_model_to_xml_state.R#L25) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ag_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:47:23:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/site_model_to_xml_state.R#L47) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_1_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:51:23:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/site_model_to_xml_state.R#L51) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_2_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_models_to_xml_operators.R:4:18:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/site_models_to_xml_operators.R#L4) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_tracelog.R:6:21:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/site_models_to_xml_tracelog.R#L6) *warning:* **no visible global function definition for ‘site_model_to_xml_tracelog’**
```r
    text <- c(text, site_model_to_xml_tracelog(site_model)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_operators.R:10:22:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/tree_prior_to_xml_operators.R#L10) *warning:* **no visible global function definition for ‘get_operator_id_pre’**
```r
  operator_id_pre <- get_operator_id_pre(tree_prior) # nolint beautier function
                     ^~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:7:21:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/tree_prior_to_xml_prior_distr.R#L7) *warning:* **no visible global function definition for ‘bd_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, bd_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:9:21:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/tree_prior_to_xml_prior_distr.R#L9) *warning:* **no visible global function definition for ‘cbs_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cbs_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:11:21:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/tree_prior_to_xml_prior_distr.R#L11) *warning:* **no visible global function definition for ‘ccp_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, ccp_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:13:21:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/tree_prior_to_xml_prior_distr.R#L13) *warning:* **no visible global function definition for ‘cep_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cep_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:16:21:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/tree_prior_to_xml_prior_distr.R#L16) *warning:* **no visible global function definition for ‘yule_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, yule_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_distr.R:8:21:](https://github.com/ropensci/beautier/blob/3788ead218290535957249da70cfff9f8bfa1af8/R/tree_priors_to_xml_distr.R#L8) *warning:* **no visible global function definition for ‘tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

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* https://sui-components-git-master.schibstedspain.now.sh


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Successfully deployed to following URLs:

* https://thomas-e7xrpcf2r.now.sh
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* https://hom.as
* https://thomas.thomaslindstr-m.now.sh
* https://thomas-git-master.thomaslindstr-m.now.sh


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


Good work! and good luck!


Yeah, I solved it by hand and now I'm way too lazy to solve it generically. :(


Don't you need `b_start += temp_a.size();` here?


changes made to second draft. Please check


What about map like this

```
....
.##.
....
```

There's no need for C and thus you'd never reach this code.


Good work so far! Realy love the index ^^


@chhex , @apgsga-stb
Actually, we already load the EMUN directly, look at repos JsonProperty within RepoNamesBean. But the loop here will fill the repositories Map available within ReposImpl. Or am I understanding something wrong?


require(passwordHash > 0) without length?


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

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

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

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

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