[R/check_pff_beast2_options.R:12:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_beast2_options.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'beast2_options$output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_beast2_options.R:15:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_beast2_options.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'beast2_options$output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_beast2_options.R:18:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_beast2_options.R#L18) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'beast2_options$output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_beast2_options.R:21:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_beast2_options.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'beast2_options$beast2_working_dir'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_experiment.R:5:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_experiment.R#L5) *warning:* **no visible global function definition for ‘check_pff_beast2_options’**
```r
  check_pff_beast2_options(experiment$beast2_options)
  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_experiments.R:6:5:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_experiments.R#L6) *warning:* **no visible global function definition for ‘check_pff_experiment’**
```r
    check_pff_experiment(experiments[[i]])
    ^~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_pir_params.R:16:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_pir_params.R#L16) *warning:* **no visible global function definition for ‘check_pff_twinning_params’**
```r
  check_pff_twinning_params(pir_params$twinning_params)
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_pir_params.R:17:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_pir_params.R#L17) *warning:* **no visible global function definition for ‘check_pff_alignment_params’**
```r
  check_pff_alignment_params(pir_params$alignment_params)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_pir_params.R:18:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_pir_params.R#L18) *warning:* **no visible global function definition for ‘check_pff_experiments’**
```r
  check_pff_experiments(pir_params$experiments)
  ^~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_twinning_params.R:6:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_twinning_params.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'twinning_params$twin_tree_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_twinning_params.R:9:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_twinning_params.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'twinning_params$twin_alignment_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_twinning_params.R:12:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/check_pff_twinning_params.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'twinning_params$twin_evidence_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_pff_experiments.R:20:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/create_all_pff_experiments.R#L20) *warning:* **no visible global function definition for ‘to_pff_experiments’**
```r
  to_pff_experiments(experiments)
  ^~~~~~~~~~~~~~~~~~
```
[R/create_pff_alignment_params.R:19:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/create_pff_alignment_params.R#L19) *warning:* **no visible global function definition for ‘check_pff_alignment_params’**
```r
  check_pff_alignment_params(alignment_params)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_twinning_params.R:9:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/create_pff_twinning_params.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
  twin_tree_filename = get_pff_tempfile(pattern = "tree_twin_", fileext = ".newick"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_twinning_params.R:10:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/create_pff_twinning_params.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
  twin_alignment_filename = get_pff_tempfile(pattern = "alignment_twin_", fileext = ".fasta"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_twinning_params.R:11:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/create_pff_twinning_params.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
  twin_evidence_filename = get_pff_tempfile(pattern = "evidence_twin_",  fileext = ".csv")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_twinning_params.R:22:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/create_pff_twinning_params.R#L22) *warning:* **no visible global function definition for ‘check_pff_twinning_params’**
```r
  check_pff_twinning_params(twinning_params)
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:11:38:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_beast2_options.R#L11) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    beast2_options$input_filename <- get_pff_tempfile()
                                     ^~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:14:43:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_beast2_options.R#L14) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    beast2_options$output_log_filename <- get_pff_tempfile()
                                          ^~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:17:46:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_beast2_options.R#L17) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    beast2_options$output_trees_filenames <- get_pff_tempfile()
                                             ^~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:20:45:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_beast2_options.R#L20) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    beast2_options$output_state_filename <- get_pff_tempfile()
                                            ^~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:23:42:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_beast2_options.R#L23) *warning:* **no visible global function definition for ‘get_pff_tempdir’**
```r
    beast2_options$beast2_working_dir <- get_pff_tempdir()
                                         ^~~~~~~~~~~~~~~
```
[R/to_pff_experiment.R:7:32:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_experiment.R#L7) *warning:* **no visible global function definition for ‘to_pff_beast2_options’**
```r
  experiment$beast2_options <- to_pff_beast2_options(experiment$beast2_options)
                               ^~~~~~~~~~~~~~~~~~~~~
```
[R/to_pff_experiment.R:10:35:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_experiment.R#L10) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    experiment$errors_filename <- get_pff_tempfile(fileext = ".csv")
                                  ^~~~~~~~~~~~~~~~
```
[R/to_pff_experiment.R:13:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_experiment.R#L13) *warning:* **no visible global function definition for ‘check_pff_experiment’**
```r
  check_pff_experiment(experiment)
  ^~~~~~~~~~~~~~~~~~~~
```
[R/to_pff_experiments.R:10:25:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_experiments.R#L10) *warning:* **no visible global function definition for ‘to_pff_experiment’**
```r
    experiments[[i]] <- to_pff_experiment(experiments[[i]])
                        ^~~~~~~~~~~~~~~~~
```
[R/to_pff_experiments.R:13:3:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/R/to_pff_experiments.R#L13) *warning:* **no visible global function definition for ‘check_pff_experiments’**
```r
  check_pff_experiments(experiments)
  ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_pff_experiment.R:2:1:](https://github.com/richelbilderbeek/peregrine/blob/5dbd462465c94bada7491528eb2843d11dbb4d47/tests/testthat/test-check_pff_experiment.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
  expect_silent(check_pff_experiment(peregrine::create_test_pff_gen_experiment()))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Quand on aboutit sur la page finale "Vous devez publier vos données", le lien n'est pas cliquable directement. On obtient ça comme visuel : [data.gouv.fr](https://www.data.gouv.fr). C'est normal ?


Nice! As you are not joining any table you can have used `SELECT title...` instead of `SELECT task.title`, but it is not wrong, at all :)


All counts are for terminal debugging - remember to comment them out or remove them, if you want to use the files yourself


Ej, bobek...


@dg read rfc2822


Successfully aliased the URL <https://react-pure-loaders-ds7ywvbce.now.sh> to the following aliases.

* https://reactpureloaders.io
* https://www.reactpureloaders.io
* https://react-pure-loaders.jameswlane.now.sh
* https://react-pure-loaders-git-master.jameswlane.now.sh


> restartwindow

>
![FB_IMG_1557415327486](https://user-images.githubusercontent.com/51970574/60264007-030a4880-9897-11e9-9039-615508a8c41c.jpg)


Successfully aliased the URL <https://colorado-6qjil9gal.now.sh> to the following aliases.

* https://colorado.rustx.now.sh
* https://colorado-git-master.rustx.now.sh


I will change that


请问这里转义的作用是什么呀？
更新到最新版本，发现后续 `99_content` 文件中的 `$("figure.highlight").addClass("hljs");` 无法执行成功。导致代码高亮无法生效。
因为该方法把 `<figure>` 标签转成了 `<!--�12-->` `<!--�11-->` 这样的字符

This function make figure tag invaliad. And then the highlight is useless.


Shouldn't this be a float rather than a string?


this is quite a lot of issues. I would suggest that the corrections to this and all other manuscripts which might have this errors, are submitted in the form of a Pull Request to be reviewed by @eu-genia or @thea-m and not directly to the system. I am glad to help in getting this fixed and we can use the occasion to make sure the guidelines are not ambiguous on these points and do not lead to these errors


Successfully aliased the URL <https://sendmail-tofsp-dvei4t5zm.now.sh> to the following aliases.

* https://sendmail-tofsp.abhimmit.now.sh
* https://sendmail-tofsp-git-master.abhimmit.now.sh


The benchmark job for this commit is finished.

The report is committed in this commit: TuringLang/TuringBenchmarks#67cbdf9af7470bb089224d3d2ba8dd861bc47333.

You can see the report at https://github.com/TuringLang/TuringBenchmarks/blob/report/jobs/BMCI-0-8969e19-201906271150.report.md.


I think this example worked fine... :)
As you are counting tasks, you could also have used ` COUNT(task.id)`


oo_plant_load_profile (drewyh) - x86_64-MacOS-10.13-clang: OK (2411 of 2414 tests passed, 9 test warnings)

Messages:\n
 * 3 tests had: EIO diffs.
 * 3 tests had: ESO big diffs.
 * 3 tests had: Table big diffs.
 * 2 tests had: MTR small diffs.
 * 9 tests had: ESO small diffs.

Failures:\n

regression Test Summary
 * Passed: 652
 * Failed: 3

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.88%25-yellow.png)


kenapa ngga dibikin repo lagi jo ?
Biar keliatan rapih,


>I am considering something as evil as this. Should we just try it out?

Why not?
And should we ask @JNechaevsky make a test WAD for that?


did you really encounter form fields, which didn't have attribute `disabled`? What kind of field type are these?


@tomoliveri

https://groups.google.com/forum/#!topic/awx-project/kRLrbhL4Y5o


命名需要更加规范，如 setTodo 或 saveTodo


You rock!!


可以直接传值，不必非要放到payload中


Sek gue buru buru td


命名需要更加规范


fixed in f0a6cb1


What is going on here?! Why not use `0` (rather that `2`) when calling `number_format`?


Successfully aliased the URL <https://jwlcloud-gn301ep9n.now.sh> to the following aliases.

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


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


Typo:
"Documetnation" -> "Documentation"


Successfully aliased the URL <https://laneconsultingco-bi82ugqi3.now.sh> to the following aliases.

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


Successfully aliased the URL <https://experimentwithcom-3n2gsyncx.now.sh> to the following aliases.

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


It is right! You could also have used `COUNT(id)` as you are working only with one table :)


Successfully aliased the URL <https://jestexpress-noo8tiv61.now.sh> to the following aliases.

* https://jest.express
* https://www.jest.express
* https://jestexpress.jameswlane.now.sh
* https://jestexpress-git-master.jameswlane.now.sh


Successfully aliased the URL <https://cantyoujust-72zvcj90l.now.sh> to the following aliases.

* https://cantyouju.st
* https://www.cantyouju.st
* https://cantyoujust.jameswlane.now.sh
* https://cantyoujust-git-master.jameswlane.now.sh


Successfully aliased the URL <https://jameswlanecom-men741owe.now.sh> to the following aliases.

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


Same here! It is right... you would be fine writing `WHERE due_date IS NULL` as well :)


@JuliaRegistrator register()


Kindly explain where those commands are to be written?


[R/check_pff_beast2_options.R:12:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_beast2_options.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'beast2_options$output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_beast2_options.R:15:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_beast2_options.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'beast2_options$output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_beast2_options.R:18:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_beast2_options.R#L18) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'beast2_options$output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_beast2_options.R:21:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_beast2_options.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'beast2_options$beast2_working_dir'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_experiment.R:5:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_experiment.R#L5) *warning:* **no visible global function definition for ‘check_pff_beast2_options’**
```r
  check_pff_beast2_options(experiment$beast2_options)
  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_experiments.R:6:5:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_experiments.R#L6) *warning:* **no visible global function definition for ‘check_pff_experiment’**
```r
    check_pff_experiment(experiments[[i]])
    ^~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_pir_params.R:16:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_pir_params.R#L16) *warning:* **no visible global function definition for ‘check_pff_twinning_params’**
```r
  check_pff_twinning_params(pir_params$twinning_params)
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_pir_params.R:17:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_pir_params.R#L17) *warning:* **no visible global function definition for ‘check_pff_alignment_params’**
```r
  check_pff_alignment_params(pir_params$alignment_params)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_pir_params.R:18:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_pir_params.R#L18) *warning:* **no visible global function definition for ‘check_pff_experiments’**
```r
  check_pff_experiments(pir_params$experiments)
  ^~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_twinning_params.R:6:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_twinning_params.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'twinning_params$twin_tree_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_twinning_params.R:9:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_twinning_params.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'twinning_params$twin_alignment_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_twinning_params.R:12:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/check_pff_twinning_params.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    stop("Peregrine-unfriendly filename for 'twinning_params$twin_evidence_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_pff_experiments.R:20:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/create_all_pff_experiments.R#L20) *warning:* **no visible global function definition for ‘to_pff_experiments’**
```r
  to_pff_experiments(experiments)
  ^~~~~~~~~~~~~~~~~~
```
[R/create_pff_alignment_params.R:10:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/create_pff_alignment_params.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
#'   fasta_filename = get_pff_tempfile(pattern = "alignment_", fileext = ".fasta")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_alignment_params.R:29:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/create_pff_alignment_params.R#L29) *warning:* **no visible global function definition for ‘check_pff_alignment_params’**
```r
  check_pff_alignment_params(alignment_params)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_twinning_params.R:9:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/create_pff_twinning_params.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
  twin_tree_filename = get_pff_tempfile(pattern = "tree_twin_", fileext = ".newick"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_twinning_params.R:10:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/create_pff_twinning_params.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
  twin_alignment_filename = get_pff_tempfile(pattern = "alignment_twin_", fileext = ".fasta"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_twinning_params.R:11:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/create_pff_twinning_params.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
  twin_evidence_filename = get_pff_tempfile(pattern = "evidence_twin_",  fileext = ".csv")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_twinning_params.R:22:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/create_pff_twinning_params.R#L22) *warning:* **no visible global function definition for ‘check_pff_twinning_params’**
```r
  check_pff_twinning_params(twinning_params)
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:11:38:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_beast2_options.R#L11) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    beast2_options$input_filename <- get_pff_tempfile()
                                     ^~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:14:43:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_beast2_options.R#L14) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    beast2_options$output_log_filename <- get_pff_tempfile()
                                          ^~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:17:46:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_beast2_options.R#L17) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    beast2_options$output_trees_filenames <- get_pff_tempfile()
                                             ^~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:20:45:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_beast2_options.R#L20) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    beast2_options$output_state_filename <- get_pff_tempfile()
                                            ^~~~~~~~~~~~~~~~
```
[R/to_pff_beast2_options.R:23:42:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_beast2_options.R#L23) *warning:* **no visible global function definition for ‘get_pff_tempdir’**
```r
    beast2_options$beast2_working_dir <- get_pff_tempdir()
                                         ^~~~~~~~~~~~~~~
```
[R/to_pff_experiment.R:7:32:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_experiment.R#L7) *warning:* **no visible global function definition for ‘to_pff_beast2_options’**
```r
  experiment$beast2_options <- to_pff_beast2_options(experiment$beast2_options)
                               ^~~~~~~~~~~~~~~~~~~~~
```
[R/to_pff_experiment.R:10:35:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_experiment.R#L10) *warning:* **no visible global function definition for ‘get_pff_tempfile’**
```r
    experiment$errors_filename <- get_pff_tempfile(fileext = ".csv")
                                  ^~~~~~~~~~~~~~~~
```
[R/to_pff_experiment.R:13:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_experiment.R#L13) *warning:* **no visible global function definition for ‘check_pff_experiment’**
```r
  check_pff_experiment(experiment)
  ^~~~~~~~~~~~~~~~~~~~
```
[R/to_pff_experiments.R:10:25:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_experiments.R#L10) *warning:* **no visible global function definition for ‘to_pff_experiment’**
```r
    experiments[[i]] <- to_pff_experiment(experiments[[i]])
                        ^~~~~~~~~~~~~~~~~
```
[R/to_pff_experiments.R:13:3:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/R/to_pff_experiments.R#L13) *warning:* **no visible global function definition for ‘check_pff_experiments’**
```r
  check_pff_experiments(experiments)
  ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_pff_experiment.R:2:1:](https://github.com/richelbilderbeek/peregrine/blob/6d96621716b51337fa9ef5d1f94cf9a802b32e38/tests/testthat/test-check_pff_experiment.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
  expect_silent(check_pff_experiment(peregrine::create_test_pff_gen_experiment()))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Test WAD would be MAP02 :wink:


Registration pull request created: [JuliaRegistries/General/1602](https://github.com/JuliaRegistries/General/pull/1602)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.0 -m "<description of version>" 179483e66e89d6b341ed474fce51b6909a649f8e
git push origin v0.1.0
```


This query run fine. WHERE NOT status.name ='Done' gives same answer  as  Where status.name != 'Done'


![](https://github.trello.services/images/mini-trello-icon.png) [featured screen](https://trello.com/c/h1BOBYG5/109-featured)


Successfully aliased the URL <https://effector-3ymuhmere.now.sh> to the following aliases.

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


Cool!


Okay! it's useless `if hasattr(kwargs['form'].base_fields[field_name], 'disabled' )`, that was the problem:
setting.py
```
CMSPLUGIN_CASCADE = {
...
#   'TextLinkPlugin': ('link', 'target',),
...
}
```


Successfully aliased the URL <https://react-pure-loaders-chfl4ske6.now.sh> to the following aliases.

* https://reactpureloaders.io
* https://www.reactpureloaders.io
* https://react-pure-loaders.jameswlane.now.sh
* https://react-pure-loaders-git-master.jameswlane.now.sh


Successfully aliased the URL <https://cantyoujust-ajzm3l76p.now.sh> to the following aliases.

* https://cantyouju.st
* https://www.cantyouju.st
* https://cantyoujust.jameswlane.now.sh
* https://cantyoujust-git-master.jameswlane.now.sh