The whole point here was to choose a non-first software product to demonstrate that the server-driven preselection works ok with Polymer binding.

The above change most probably hides the problem instead of fixing it.

I think that the above line should be even more explicit:

```cs
this.SelectedProduct.Data = Db.SQL("SELECT p FROM KitchenSink.SoftwareProduct p WHERE p.Name = ?", "Starcounter Database").First;
```


[R/RLearner_oneclass_h2oautoencoder.R:257:5:](https://github.com/mlr-org/mlr/blob/e1254f4f2585d59a69b90cf24c737751b48521c4/R/RLearner_oneclass_h2oautoencoder.R#L257) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(.learner$predict.type == "response"){
    ^
```
[R/RLearner_oneclass_h2oautoencoder.R:260:57:](https://github.com/mlr-org/mlr/blob/e1254f4f2585d59a69b90cf24c737751b48521c4/R/RLearner_oneclass_h2oautoencoder.R#L260) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
      indices.threshold = order(p.df)[round(length(p.df)*0.95)]  #mse reconstruction error in [0,inf[
                                                       ~^~
```
[R/StackedLearner.R:556:50:](https://github.com/mlr-org/mlr/blob/e1254f4f2585d59a69b90cf24c737751b48521c4/R/StackedLearner.R#L556) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      m = makeLearner("regr.nnet", predict.type = )
                                                 ^
```
[R/performance.R:52:7:](https://github.com/mlr-org/mlr/blob/e1254f4f2585d59a69b90cf24c737751b48521c4/R/performance.R#L52) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(levels(pred$data$response)) == 1) {
      ^
```
[R/performance.R:71:11:](https://github.com/mlr-org/mlr/blob/e1254f4f2585d59a69b90cf24c737751b48521c4/R/performance.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(length(levels(pred$data$truth)) == 1) {
          ^
```
[tests/testthat/test_base_learnerArgsToControl.R:15:21:](https://github.com/mlr-org/mlr/blob/e1254f4f2585d59a69b90cf24c737751b48521c4/tests/testthat/test_base_learnerArgsToControl.R#L15) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  arg1 = quote(expr =)
                    ^~
```
[tests/testthat/test_base_learnerArgsToControl.R:16:21:](https://github.com/mlr-org/mlr/blob/e1254f4f2585d59a69b90cf24c737751b48521c4/tests/testthat/test_base_learnerArgsToControl.R#L16) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  arg2 = quote(expr =)
                    ^~
```
[tests/testthat/test_base_learnerArgsToControl.R:41:23:](https://github.com/mlr-org/mlr/blob/e1254f4f2585d59a69b90cf24c737751b48521c4/tests/testthat/test_base_learnerArgsToControl.R#L41) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  devmax = quote(expr =)
                      ^~
```


@DU-jdto
Yes, thus the reason why I stopped it.


Whurt the hell?


Yes! Hail yes. Finally different values. This whole commit comes in so handy regarding to fishing \*dreams\*


then we have no choice but to move the file back ;)

fwiw, I always recommend /etc/rc.conf and now /etc/rc.conf.local works as well.


Created multidev environment [knowledger#pr-update](https://dashboard.pantheon.io/sites/329e9b0f-8280-4fa6-ac4c-2201516511a4#pr-update).

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


using System.Data;
using System.Configuration;
using System.Data.SqlClient;
using System.Windows.Forms;

namespace tamrin.dataaccess
{
    class Classdel
    {
        SqlConnection con = new SqlConnection(ConfigurationManager.ConnectionStrings["con"].ConnectionString);

        public  void   del( string family)
    {

       try
            {
               SqlParameter _family =new SqlParameter();
               _family.ParameterName = "family";
               _family.SqlDbType = SqlDbType.NVarChar;
               _family.Value = family;

                con.Open();
                SqlCommand cmd = new SqlCommand();
                cmd.CommandText = "storedprocedure2";
                cmd.CommandType = CommandType.StoredProcedure;
                cmd.Connection = con;

                cmd.Parameters.Add(_family);

                cmd.ExecuteNonQuery();
                con.Close();

            }
            catch (Exception e)
            {
                con.Close();
                MessageBox.Show(e.Message);}}}}

using System.Linq;
using System.Text;

namespace tamrin.bussiness
{
    class Classbussinessdel
    {
        string K_family;

      dataaccess .Classdel _classdel =new dataaccess.Classdel();

        public Classbussinessdel(string family)
        {
            K_family = family;

        }
        public void  dell()
        {

            _classdel.del(K_family);

        }

    }

}

        private void button2_Click(object sender, EventArgs e)
        {
            bussiness.Classbussinessdel classdelete = new bussiness.Classbussinessdel(txtfa.Text);
            classdelete.dell();
        }


Add delete


Muchas gracias , me da error de conexión y me marca en System la línea 125 de DB_driver.php me falta ajustar algún parámetro?

Enviado desde mi iPhone

> El 4 may. 2017, a las 21:25, Héctor Espinoza <notifications@github.com> escribió:
>
> Subi una base de datos https://github.com/hespinoza/inventario/blob/master/inventario123.sql
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub, or mute the thread.
>


found many other errors after removing these ports. Are you sure all other references were converted from localhost:port to container:port already?
maybe some missing files on this commit?
thanks


What about "shearing" sheeps?


It checks for an empty value to avoid turning uncontrolled input into controlled one.


... which brings us back where it all started, rc.freebsd fails on this (also in your version)


switch to using long ids


remove test print statment.


feel free to revert this change, I'm out of ideas here and too busy with other things.


Indent


replace with a proper check


any idea how to use it with Markup??


Microsoft face Testing


It works with 1.0.5 sorry.


Can we move this script to this repo?


The script was not considering mixed-use schedules correctly. so it was fixed. The schedules per every occupancy type remained the same. please let me know if this helps


comment from


Add del


The Romanian language should be updated.


@thebigsmileXD https://github.com/pmmp/PocketMine-MP/blob/fe4322bea957b422ea8596712ccaf022a388c9b7/src/pocketmine/item/Shears.php#L49


do we have strong reason to increase the sleep time?


@thg303 what sort of markup


[R/RLearner_oneclass_svm.R:39:6:](https://github.com/mlr-org/mlr/blob/5eb947ac3441ab46ea6489b6af86df2c2f7a2c60/R/RLearner_oneclass_svm.R#L39) *style:* **Place a space before left parenthesis, except in a function call.**
```r
   if(.learner$predict.type == "response"){
     ^
```
[R/StackedLearner.R:556:50:](https://github.com/mlr-org/mlr/blob/5eb947ac3441ab46ea6489b6af86df2c2f7a2c60/R/StackedLearner.R#L556) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      m = makeLearner("regr.nnet", predict.type = )
                                                 ^
```
[tests/testthat/test_base_learnerArgsToControl.R:15:21:](https://github.com/mlr-org/mlr/blob/5eb947ac3441ab46ea6489b6af86df2c2f7a2c60/tests/testthat/test_base_learnerArgsToControl.R#L15) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  arg1 = quote(expr =)
                    ^~
```
[tests/testthat/test_base_learnerArgsToControl.R:16:21:](https://github.com/mlr-org/mlr/blob/5eb947ac3441ab46ea6489b6af86df2c2f7a2c60/tests/testthat/test_base_learnerArgsToControl.R#L16) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  arg2 = quote(expr =)
                    ^~
```
[tests/testthat/test_base_learnerArgsToControl.R:41:23:](https://github.com/mlr-org/mlr/blob/5eb947ac3441ab46ea6489b6af86df2c2f7a2c60/tests/testthat/test_base_learnerArgsToControl.R#L41) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  devmax = quote(expr =)
                      ^~
```


Why the port of single-port can't be used for multi-tenancy? What's the obstacle here? Technical?

How do you expect people to configure things if using both features? Different ports?


Could you give me your imports ?

Each components should import only one file : `@import '../[until root]/scss/variables.scss'`and this file should contains no css selectors at all (or you'll result in unecessary duplicates). `variables.scss` can import `colors.scss`, `fonts.scss`, etc... and of course contains your own variables which define your components : `$header-height: 50px`

If you need some global css, you can create a `main.scss` file into the `scss/` folder which import your variables and contains global style:

```scss
@import 'variables';
@import 'fonts';
@import 'icons';

//... some style
```
Then into the `css/` folder, create a `main.scss` file with `@import '../scss/main';` only.
Playing with import and with the help of cache + progeny helps a lot in compilation time removing unecessary re-compilation.

In this context, the script only select the @import AND the files which changes. You should not import anything else than variables, mixins or abstract selectors on your `app.component.scss`. If you import `header.component.scss` and this last one doesn't changes, it's normal it won't recompile...


Thank you very much (we can contact by hangouts or email) ;)
I send fixes to you for review when I done with it ;)


I see, its quite inconsistent. Looks like only Sheers has it.


replace with a `when`


The first clause of this check is superfluous, because if `carved_mesh_idx == carving_mesh_idx` then the second check is equal to `carving_mesh.getSettingBoolean("cutting_mesh")` and you checked that at the beginning of this function.


ok


just a stylistic note - putting the star up against the variable name is a throwover from old C code, it's better ot keep the star adjacent to the type. e.g. `auto* pMutex`


Hi Rhamille. I appreciate this message as it alerted me that I had mistakenly committed the "payment.PaymentInstrumentType" line of code on Friday in my haste to get this in the project.

The story on this parameter is that it is part of the Commerce-update1 product but not in the initial release (which we unfortunately need to keep using). We received a hotfix from the Commerce team to fix Paypal checkout in the initial release of the product which this line of code was a part of (but you need a supporting new assembly which is not on the public Nuget feed yet). I have removed the offending line of code and will test everything again this morning.

Please let me know if you see any more issues like this.

Thanks!


@dorimanx This seems to be happening only in LA.HB Kernel. It doesn't come back on screen wake, my dmesg outputs the same result on the Le Pro3.


Init commit


That creates a child of the current environment rather than a child of the empty environment by the way. This should be `child_env(NULL)`, I'll fix it with the other changes.


I don't understand this point. Since when can a router depend on another router? Documentation on multi-tenancy does not explain this possibility (see [here](http://infinispan.org/docs/stable/server_guide/server_guide.html#multi_tenant_router)).

My understanding is that if you have a single port entry, all defined routers would be accessed through this port. Each router should really be independent.


Created multidev environment [knowledger#pr-update](https://dashboard.pantheon.io/sites/329e9b0f-8280-4fa6-ac4c-2201516511a4#pr-update).

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


Can we have a release of this package to fix Plone 5.0 deployments?


Sorry, this whole thing is fried. Why would one allow and use dashes in the service name, but then not support pulling from the same configuration file? I'll fix this, don't worry.


app.component.ts wurde nicht verändert


thanks!


Since we don't do callback handling in webidl2js this may meee more coercion on returnValue. The new WPTs are pretty exhaustive.


@kyuwankim 이 placeholder 왜 지웠어요??


Fixed a bug where the deckdes player would always be `tp` in `DMBox.DecktopToManaOperation(p,d)`.


测试


Whenever changes occur in the coverity_scan branch, coverity run a new analysis for the code in that branch. As soon as you have a some code that you want tested, simply overwrite the coverity_scan branch.


I'm not sure what this include is for.  If it's to support the implementation, I would put it in the `.cpp` file to keep implementation details out of the headers.


*blushes* thanks


Mooi! Dit is wat ik in gedachten had


TeamCity Xbim :: Xbim Geometry :: XbimGeometry [Build 358](http://xbimbuilds.cloudapp.net/viewLog.html?buildId=1575&buildTypeId=Xbim_XbimGeometry_XbimGeometry) is now running


A fix for the readme


hai anche tolto tutti gli accento sulle lettere e hai messo questo �


[R/Prediction.R:217:53:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/R/Prediction.R#L217) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
        indices.threshold = order(y)[round(length(y)*0.95)]  #mse reconstruction error in [0,inf[
                                                   ~^~
```
[R/RLearner_oneclass_h2oautoencoder.R:257:5:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/R/RLearner_oneclass_h2oautoencoder.R#L257) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(.learner$predict.type == "response"){
    ^
```
[R/RLearner_oneclass_h2oautoencoder.R:260:57:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/R/RLearner_oneclass_h2oautoencoder.R#L260) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
      indices.threshold = order(p.df)[round(length(p.df)*0.95)]  #mse reconstruction error in [0,inf[
                                                       ~^~
```
[R/RLearner_oneclass_svm.R:39:6:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/R/RLearner_oneclass_svm.R#L39) *style:* **Place a space before left parenthesis, except in a function call.**
```r
   if(.learner$predict.type == "response"){
     ^
```
[R/StackedLearner.R:556:50:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/R/StackedLearner.R#L556) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      m = makeLearner("regr.nnet", predict.type = )
                                                 ^
```
[R/performance.R:52:7:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/R/performance.R#L52) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(levels(pred$data$response)) == 1) {
      ^
```
[R/performance.R:71:11:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/R/performance.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(length(levels(pred$data$truth)) == 1) {
          ^
```
[tests/testthat/test_base_learnerArgsToControl.R:15:21:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/tests/testthat/test_base_learnerArgsToControl.R#L15) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  arg1 = quote(expr =)
                    ^~
```
[tests/testthat/test_base_learnerArgsToControl.R:16:21:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/tests/testthat/test_base_learnerArgsToControl.R#L16) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  arg2 = quote(expr =)
                    ^~
```
[tests/testthat/test_base_learnerArgsToControl.R:41:23:](https://github.com/mlr-org/mlr/blob/e6b601eec94a32fe375edb1961f0fe247f86266e/tests/testthat/test_base_learnerArgsToControl.R#L41) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  devmax = quote(expr =)
                      ^~
```


here we go


I have an error .. When I import project to android studio
Its "time out connection"


-fpic uses short offsets while -fPIC uses large offsets.


HTML shouldn't appear in the email subject.


Yes, we need to define a variable that can be used all along as part of  the 'plumed- ...'
string


it's not pretty, but I think it's a decent way of indicating what we mean.


you're right, this is easier.


yes. ok. Again with a variable so that we can easily replace all strings.


nice!


그게 이미지가 꽉 맞게 설정이안되서 플레이스홀더를 없애야 그게되더라구


The container on cloud.docker is build automatically at every push on github,
you just need to define the hook


@tiennes : do you really mean paired end or simply multiple files? Have a look at the examples at http://bioinf.wehi.edu.au/featureCounts/:
- Summarize paired-end reads and count fragments (instead of reads)
- Summarize multiple paired-end datasets


Go it now, I've created #426


Why not make this also accept an reference?


Read it!


Hehe, die komplizierten URLs waren deshalb drin, damit man den Abschnitt einfach mit copy paste ins Readme vom main repo tun kann: er taucht [hier](https://github.com/theislab/scanpy/blob/master/README.md) ab l. 26 nochmal auf. Die Idee ist, im main repo nur ein paar "top tutorials und beispiele" zu zeigen, in "scanpy_usage" dagegen alles. Da sich dieser Text wohl nicht mehr aendern wird und hoechstens aus dem main repo rausgenommen wird, passt das aber so. ;)


Event wat uitleg over de `parentNode` omdat je dat maar half verstond.

In JS/HTML is een `node` is gelijk aan een HTML tag, bijvoorbeeld : `<td>`,`<tr>`, `<table>`, `<div>`, `span`, `body`, etc ...

Waneer jij dus `deleteRow(this)` oproept, zal `this` verwijzen naar de `node` of `HTML` element waarvan de `deleteRow(this)` is opgeroepen.

Dus laten we dan eens even zien naar het volgende :
```
var deleteRow = function (link) {
   var button = this; // Verwijst naar <button> waar je functie aan hangt via de onclick
   var tdNode = link.parentNode; // Verwijst naar de parent <td> waarin je button zich bevind
   var trNode = tdCell.parentNode; // Verwijst naar de <tr> waarin je <td> zich bevind, deze lijn kan je ook schrijven als:  var trNode = link.parentNode.parentNode
    var row = link.parentNode.parentNode; // Dit is hetzelfde als wat er in trCell zit
    var table = row.parentNode; // De parent node van je <tr> is <tbody>
    table.removeChild(row);
}```

Dus zoals je kan zien in het voorbeeld hier boven, de `.parentNode` is dus het `parent html tag` dat je opvraagt.


Nice. If the username is `bauer` we could also add `--prompt="I suck. >"`


What happen!? the files on weblate are fine!
How pt_PT ends in pt-rPT?


This is necessary for building the correct jar, otherwise you just have an empty jar.

The ns `log4-clj-layout.layout` needs to be AOTed because it lives in the log4j loading cycle which is before clojure is loaded.


I guess this is a _very_ strong hint that such repetitive code should be done by the caller, i.e. the pixelpipe.


Created multidev environment [knowledger#pr-update](https://dashboard.pantheon.io/sites/329e9b0f-8280-4fa6-ac4c-2201516511a4#pr-update).

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


We're passing an unescaped arbitrary key through a regular expression, and we know this key will contain dots.  This probably should be a set of fixed string replacements instead.


Tema cambiado para Pages Github


The first one:
Summarize paired-end reads and count fragments (instead of reads)


Still trying to understand the "JAR" use case. When could it happen that we might have a test touching a "business class" in the JAR?


Madre mia la has jodido cabrón


I'm curious — why was `aot` removed?


i will try to not boost the 624000.ufshc
as this is the main fail before kernel crash on null pointer.


[inst/doc/trees_with_root_edge.R:8:7:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/trees_with_root_edge.R#L8) *style:* **Variable or function name should be snake_case.**
```r
tree1$edge.length <- tree1$edge.length / tree1$edge.length[1]
      ^~~~~~~~~~~
```
[inst/doc/trees_with_root_edge.R:12:7:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/trees_with_root_edge.R#L12) *style:* **Variable or function name should be snake_case.**
```r
tree2$root.edge <- 1
      ^~~~~~~~~
```
[inst/doc/walkthrough.R:53:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L53) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return (t)
           ^
```
[inst/doc/walkthrough.R:58:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L58) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( rexp(n = 1, rate = 10) )
           ^
```
[inst/doc/walkthrough.R:58:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( rexp(n = 1, rate = 10) )
            ^
```
[inst/doc/walkthrough.R:58:36:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( rexp(n = 1, rate = 10) )
                                   ^
```
[inst/doc/walkthrough.R:62:11:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L62) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
   return( dexp( val[1], rate = 10) )
          ^
```
[inst/doc/walkthrough.R:62:17:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L62) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
   return( dexp( val[1], rate = 10) )
                ^
```
[inst/doc/walkthrough.R:62:36:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L62) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
   return( dexp( val[1], rate = 10) )
                                   ^
```
[inst/doc/walkthrough.R:74:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L74) *style:* **Variable or function name should be snake_case.**
```r
A <- abc_smc_nltt(
^
```
[inst/doc/walkthrough.R:85:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L85) *style:* **Variable or function name should be snake_case.**
```r
LL_B <- function(params, phy) {
^~~~
```
[inst/doc/walkthrough.R:97:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L97) *style:* **Variable or function name should be snake_case.**
```r
  ML <- stats::optimize(f = fun, interval = c(0, 1))
  ^~
```
[inst/doc/walkthrough.R:108:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L108) *style:* **Variable or function name should be snake_case.**
```r
B <- mcmc_nltt(obs, LL_B, parameters = c(0.5),
^
```
[inst/doc/walkthrough.R:114:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/inst/doc/walkthrough.R#L114) *style:* **Variable or function name should be snake_case.**
```r
B.mcmc <- coda::as.mcmc(B)
^~~~~~
```
[R/ABC_SMC.R:11:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
# @param    current                 vector       Current parameter combination for which we are determining the weight
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:12:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                   scalar       standard deviation of the perturbation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:13:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function  function     Function to calculate the prior probability of a set of parameters
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:21:8:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along( particles)) {
       ^
```
[R/ABC_SMC.R:21:24:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for ( i in seq_along( particles)) {
                       ^
```
[R/ABC_SMC.R:23:25:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L23) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    for (j in seq_along( current)) {
                        ^
```
[R/ABC_SMC.R:31:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L31) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (numerator / sum( vals))
         ^
```
[R/ABC_SMC.R:31:27:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return (numerator / sum( vals))
                          ^
```
[R/ABC_SMC.R:36:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
# @brief apply the ABC routine used in our Methods in Ecology and Evolution Paper
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:43:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
# @param    statistics                    vector      A vector containing functions that take a tree as an argument and return a single scalar value (the statistic).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:44:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
# @param    simulation_function           vector      A function that implements the diversification model and returns an object of class phylo
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:45:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
# @param    init_epsilon_values           vector      A vector containing the initial threshold values for the summary statistics from the vector statistics.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:46:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_generating_function     function    Function to generate parameters from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:47:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function        function    Function to calculate the prior probability of a set of parameters (should match prior_generating_function in shape)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:48:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
# @param    number_of_particles           scalar      Number of particles to be used per iteration of the ABC-SMC algorithm.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:49:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                         scalar      Standard deviation of the perturbance distribution (perturbance distribution is a gaussian with mean 0).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:50:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
# @param    stop_rate                     scalar      If the acceptance rate drops below \code{stopRate}, stop the ABC-SMC algorithm  and assume convergence.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:51:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
# @return                                 matrix      A matrix with n columns, where n is the number of parameters you are trying to estimate.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:54:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L54) *style:* **Lines should not be more than 80 characters.**
```r
#' A function to perform Approximate Bayesian Computation within an Sequential Markov Chain (ABC-SMC), for diversification analysis of phylogenetic trees.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:55:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L55) *style:* **Lines should not be more than 80 characters.**
```r
#' @description This function performs ABC-SMC as described in Toni 2009 for given diversification model, provided a phylogenetic tree. ABC-SMC is not limited to only using the normalized LTT as statistic.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:62:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L62) *style:* **Lines should not be more than 80 characters.**
```r
#' @param tree an object of class \code{"phylo"}; the tree upon which we want to fit our diversification model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:63:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
#' @param statistics A vector containing functions that take a tree as an argument and return a single scalar value (the statistic).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:64:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
#' @param simulation_function A function that implements the diversification model and returns an object of class \code{"phylo"}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:65:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
#' @param init_epsilon_values A vector containing the initial threshold values for the summary statistics from the vector \code{statistics}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:66:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
#' @param prior_generating_function Function to generate parameters from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:67:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L67) *style:* **Lines should not be more than 80 characters.**
```r
#' @param prior_density_function Function to calculate the prior probability of a set of parameters.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:68:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_particles Number of particles to be used per iteration of the ABC-SMC algorithm.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:69:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sigma Standard deviation of the perturbance distribution (perturbance distribution is a gaussian with mean 0).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:70:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
#' @param stop_rate   If the acceptance rate drops below \code{stopRate}, stop the ABC-SMC algorithm  and assume convergence.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:71:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A matrix with \code{n} columns, where \code{n} is the number of parameters you are trying to estimate.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:72:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L72) *style:* **Lines should not be more than 80 characters.**
```r
#' @references  Toni, T., Welch, D., Strelkowa, N., Ipsen, A., & Stumpf, M.P.H. (2009). Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of the Royal Society Interface, 6(31), 187-202.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:161:22:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L161) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  new_params <- list( c( seq_along(parameters)))
                     ^
```
[R/ABC_SMC.R:161:25:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L161) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  new_params <- list( c( seq_along(parameters)))
                        ^
```
[R/ABC_SMC.R:163:28:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L163) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  previous_params  <- list( c( seq_along(parameters)))
                           ^
```
[R/ABC_SMC.R:163:31:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L163) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  previous_params  <- list( c( seq_along(parameters)))
                              ^
```
[R/ABC_SMC.R:168:17:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L168) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  for (i in 1:50 ) {
                ^
```
[R/ABC_SMC.R:184:26:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L184) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      new_params <- list( c( seq_along(parameters))) #clear new params
                         ^
```
[R/ABC_SMC.R:184:29:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L184) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      new_params <- list( c( seq_along(parameters))) #clear new params
                            ^
```
[R/ABC_SMC.R:228:15:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L228) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
          if ( abs(stats[k] - obs_statistics[k]) > epsilon[i, k] ) {
              ^
```
[R/ABC_SMC.R:228:65:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L228) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
          if ( abs(stats[k] - obs_statistics[k]) > epsilon[i, k] ) {
                                                                ^
```
[R/ABC_SMC.R:236:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L236) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( accept ) {
            ^
```
[R/ABC_SMC.R:236:20:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L236) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( accept ) {
                   ^
```
[R/ABC_SMC.R:248:15:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L248) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
          if ( (number_accepted) %%
              ^
```
[R/ABC_SMC.R:259:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L259) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:274:25:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L274) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    for (m in seq_along( parameters)) {
                        ^
```
[R/ABC_SMC.R:275:16:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      add <- c( add, previous_params[[k]][m])
               ^
```
[R/ABC_SMC.R:279:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L279) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (output)
         ^
```
[R/ABC_SMC.R:284:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L284) *style:* **Lines should not be more than 80 characters.**
```r
# @brief Estimate the likelihood of a given tree, provided a likelihood function, using a Monte Carlo Markov Chain
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:291:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L291) *style:* **Lines should not be more than 80 characters.**
```r
# @param    likelihood_function   function    Function that calculates the likelihood of our diversification model, given the tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:292:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L292) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:293:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L293) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:294:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L294) *style:* **Lines should not be more than 80 characters.**
```r
# @param    logtransforms         scalar      Whether to perform jumps on logtransformed parameters (TRUE) or not (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:296:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L296) *style:* **Lines should not be more than 80 characters.**
```r
# @param    burnin                scalar      Length of the burnin, default is 30% of iterations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:298:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L298) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                 scalar      Standard deviation of the jumping distribution, which is N(0, sigma).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:299:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L299) *style:* **Lines should not be more than 80 characters.**
```r
# @return                         mcmc        An MCMC object, as used by the package "coda".
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:316:26:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L316) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  chain <- array(dim = c( floor( iterations / thinning) + 1,
                         ^
```
[R/ABC_SMC.R:316:33:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L316) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  chain <- array(dim = c( floor( iterations / thinning) + 1,
                                ^
```
[R/ABC_SMC.R:338:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L338) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    for ( j in seq_along(parameters) ) {
         ^
```
[R/ABC_SMC.R:338:37:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L338) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    for ( j in seq_along(parameters) ) {
                                    ^
```
[R/ABC_SMC.R:339:11:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L339) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if ( logtransforms[j] == TRUE ) {
          ^
```
[R/ABC_SMC.R:339:36:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L339) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if ( logtransforms[j] == TRUE ) {
                                   ^
```
[R/ABC_SMC.R:340:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L340) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( parameters[j] == 0) {
            ^
```
[R/ABC_SMC.R:353:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L353) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( is.finite(new_pp) &&
            ^
```
[R/ABC_SMC.R:355:59:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L355) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
             new_pp - pp + hr > log(stats::runif(1, 0, 1)) ) {
                                                          ^
```
[R/ABC_SMC.R:372:15:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L372) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
          if ( is.finite(new_pp) &&
              ^
```
[R/ABC_SMC.R:374:61:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L374) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
               new_pp - pp + hr > log(stats::runif(1, 0, 1)) ) {
                                                            ^
```
[R/ABC_SMC.R:387:11:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L387) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if ( (i) %% ( (iterations - burnin) / print_frequency) == 0) {
          ^
```
[R/ABC_SMC.R:387:20:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L387) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if ( (i) %% ( (iterations - burnin) / print_frequency) == 0) {
                   ^
```
[R/ABC_SMC.R:391:11:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L391) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if ( (i - burnin) %% thinning == 0 ) {
          ^
```
[R/ABC_SMC.R:391:41:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L391) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if ( (i - burnin) %% thinning == 0 ) {
                                        ^
```
[R/ABC_SMC.R:392:15:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L392) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        chain[ (i - burnin) / thinning + 1, ] <- parameters
              ^
```
[R/ABC_SMC.R:398:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L398) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( coda::as.mcmc(chain) )
         ^
```
[R/ABC_SMC.R:398:31:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/ABC_SMC.R#L398) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( coda::as.mcmc(chain) )
                              ^
```
[R/get_average_nltt_matrix.R:3:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_average_nltt_matrix.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param phylogenies the phylogenies, supplied as either a list or a multiPhylo object, where the phylogenies are of type 'phylo'
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_average_nltt_matrix.R:4:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_average_nltt_matrix.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param dt The timestep resolution, where 1/dt is the number of points evaluated
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_average_nltt_matrix.R:5:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_average_nltt_matrix.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A matrix of timepoints with the average number of (normalized) lineages through (normalized) time
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_braching_times.R:15:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_braching_times.R#L15) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return (c(brts[1] + phylogeny$root.edge, brts))
           ^
```
[R/get_braching_times.R:17:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_braching_times.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (brts)
         ^
```
[R/get_n_lineages.R:17:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_n_lineages.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return (1:length(phylogeny$tip.label))
           ^
```
[R/get_n_lineages.R:19:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_n_lineages.R#L19) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (2:length(phylogeny$tip.label))
         ^
```
[R/get_nltt_values.R:3:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_nltt_values.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param phylogenies the phylogenies, supplied as either a list or a multiPhylo object, where the phylogenies are of type 'phylo'
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_nltt_values.R:4:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_nltt_values.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param dt The timestep resolution, where 1/dt is the number of points evaluated
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_nltt_values.R:5:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_nltt_values.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A dataframe of timepoints with the nLTT value of each phylogeny in time
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_norm_brts.R:20:9:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_norm_brts.R#L20) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
 return (brts)
        ^
```
[R/get_norm_n.R:20:9:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/get_norm_n.R#L20) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
 return (ns)
        ^
```
[R/nLTTDiff.R:8:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @return (scalar) normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:16:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L16) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (nLTT::nltt_diff( tree1, tree2, distance_method, ignore_stem))
         ^
```
[R/nLTTDiff.R:16:27:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return (nLTT::nltt_diff( tree1, tree2, distance_method, ignore_stem))
                          ^
```
[R/nLTTDiff.R:25:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lineages2 the number of lineages, usually one to the number of lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:33:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
#'  \item{"ago: "}{the branching times are postive, as these are in time units ago}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:34:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L34) *style:* **Lines should not be more than 80 characters.**
```r
#'  \item{"since: "}{the branching times are negative, as these are in time units since present}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:48:32:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testit::assert(length(b_times ) == length(lineages ))
                               ^
```
[R/nLTTDiff.R:48:53:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testit::assert(length(b_times ) == length(lineages ))
                                                    ^
```
[R/nLTTDiff.R:71:32:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L71) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testit::assert(length(b_times ) == length(lineages ))
                               ^
```
[R/nLTTDiff.R:71:53:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L71) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  testit::assert(length(b_times ) == length(lineages ))
                                                    ^
```
[R/nLTTDiff.R:80:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L80) *style:* **Variable or function name should be snake_case.**
```r
  b_times_N <- 1.0 - b_times / min(b_times) #normalize branching times
  ^~~~~~~~~
```
[R/nLTTDiff.R:81:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L81) *style:* **Variable or function name should be snake_case.**
```r
  lineages_N <- lineages / max(lineages)  #normalize lineages
  ^~~~~~~~~~
```
[R/nLTTDiff.R:86:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L86) *style:* **Variable or function name should be snake_case.**
```r
  b_times2_N <- 1 - b_times2 / min(b_times2) #normalize branching times
  ^~~~~~~~~~
```
[R/nLTTDiff.R:87:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L87) *style:* **Variable or function name should be snake_case.**
```r
  lineages2_N <- lineages2 / max(lineages2)  #normalize lineages
  ^~~~~~~~~~~
```
[R/nLTTDiff.R:90:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L90) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (nltt_diff_exact_norm_brts(
         ^
```
[R/nLTTDiff.R:105:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L105) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lineages_N the number of lineages, usually one to the number of lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:107:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lineages2_N the number of lineages, usually one to the number of lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:111:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L111) *style:* **Variable or function name should be snake_case.**
```r
  b_times_N,
  ^~~~~~~~~
```
[R/nLTTDiff.R:112:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L112) *style:* **Variable or function name should be snake_case.**
```r
  lineages_N,
  ^~~~~~~~~~
```
[R/nLTTDiff.R:113:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L113) *style:* **Variable or function name should be snake_case.**
```r
  b_times2_N,
  ^~~~~~~~~~
```
[R/nLTTDiff.R:114:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L114) *style:* **Variable or function name should be snake_case.**
```r
  lineages2_N,
  ^~~~~~~~~~~
```
[R/nLTTDiff.R:167:33:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L167) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        diff <- diff + dt * abs( lins1 - lins2)     #update the difference
                                ^
```
[R/nLTTDiff.R:170:30:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L170) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        diff <- diff + dt * ( lins1 - lins2) * ( lins1 - lins2)
                             ^
```
[R/nLTTDiff.R:170:49:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L170) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        diff <- diff + dt * ( lins1 - lins2) * ( lins1 - lins2)
                                                ^
```
[R/nLTTDiff.R:173:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L173) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return ( diff)
         ^
```
[R/nLTTDiff.R:173:11:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L173) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return ( diff)
          ^
```
[R/nLTTDiff.R:176:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L176) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:182:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L182) *style:* **Lines should not be more than 80 characters.**
```r
#' @return (scalar) normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:228:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L228) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (
         ^
```
[R/nLTTDiff.R:249:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L249) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:250:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L250) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:253:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L253) *style:* **Lines should not be more than 80 characters.**
```r
#' This function takes two ultrametric phylogenetic trees, calculates the normalized Lineage-Through-Time statistic for both trees and then calculates the difference between the two statistics.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:254:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L254) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Calculate the difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:258:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L258) *style:* **Lines should not be more than 80 characters.**
```r
#' @param distance_method Chosen measurement of distance between the two nLTT curves, options are (case sensitive):\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:291:7:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L291) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( distance_method != "abs" && distance_method != "squ") {
      ^
```
[R/nLTTDiff.R:299:27:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L299) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diff <- nLTT::nltt_diff( tree1, tree2, distance_method, ignore_stem)
                          ^
```
[R/nLTTDiff.R:300:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L300) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (diff)
         ^
```
[R/nLTTDiff.R:313:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L313) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:314:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L314) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:315:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L315) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:318:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L318) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the exact difference between two normalized Lineage-Through-Time curves, given two phylogenetic trees.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:319:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L319) *style:* **Lines should not be more than 80 characters.**
```r
#' @description This function takes two ultrametric phylogenetic trees, calculates the normalized Lineage-Through-Time statistic for both trees and then calculates the exact difference between the two statistics. Whereas the function \code{nLTTstat} uses an approximation to calculate the difference (which is faster for large trees), the function \code{nLTTstat_exact} calculates the exact difference, and should generally be preferred. Although the estimates are highly similar, \code{nLTTstat_exact} tends to return slightly higher values.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:325:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L325) *style:* **Lines should not be more than 80 characters.**
```r
#'   Chosen measurement of distance between the two nLTT curves, options are (case sensitive):\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:364:33:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L364) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diff <- nLTT::nltt_diff_exact( tree1, tree2, distance_method, ignore_stem)
                                ^
```
[R/nLTTDiff.R:365:10:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nLTTDiff.R#L365) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  return (diff)
         ^
```
[R/nltts_plot.R:4:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nltts_plot.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param dt The timestep resolution, where 1/dt is the number of points evaluated
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:8:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/nltts_plot.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param replot If false, start a clean plot. If true, plot the new data over the current
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_nLTT.R:15:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
#' This function uses a modified version of the ltt.plot function from \code{"ape"} to plot the normalized number of lineages through normalized time, where the number of lineages is normalized by dividing by the number of tips of the tree, and the time is normalized by the total time between the most common recent ancestor and the present, such that t(MRCA) = 0 & t(present) = 1.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_nLTT.R:17:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nltt_plot(phy, xlab = "Normalized Time", ylab = "Normalized Lineages", ...)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_nLTT.R:29:23:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L29) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:40:30:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L40) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy <- ape::ltt.plot.coords( phy, backward = TRUE, tol = 1e-6)
                             ^
```
[R/plot_nLTT.R:43:28:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                           ^
```
[R/plot_nLTT.R:43:33:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                                ^
```
[R/plot_nLTT.R:44:28:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] / max( xy[, 1])      #normalize time
                           ^
```
[R/plot_nLTT.R:61:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
#' This is a modified version of the \code{ape} function ltt.lines: add the normalized Lineage-Through-Time statistic of a phylogenetic tree to an already existing plot
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_nLTT.R:80:30:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L80) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy <- ape::ltt.plot.coords( phy, backward = TRUE, tol = 1e-6)
                             ^
```
[R/plot_nLTT.R:81:28:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 2] <- xy[, 2] / max( xy[, 2]) #normalize number lineages
                           ^
```
[R/plot_nLTT.R:83:28:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L83) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                           ^
```
[R/plot_nLTT.R:83:33:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L83) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                                ^
```
[R/plot_nLTT.R:84:28:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/plot_nLTT.R#L84) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] / max( xy[, 1])      #normalize time
                           ^
```
[R/stretch_nltt_matrix.R:4:1:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/stretch_nltt_matrix.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param dt The resultion, a value e [0.0001, 1]. If 'dt' is set to a very small value, this function will stop
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/stretch_nltt_matrix.R:47:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/stretch_nltt_matrix.R#L47) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    m <- m[ -rows_to_delete, ]
           ^
```
[R/stretch_nltt_matrix.R:65:15:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/R/stretch_nltt_matrix.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  n <- matrix( c(n_ts, n_ns), ncol = 2, nrow = n_nrow)
              ^
```
[tests/testthat/test-abc_smc_nltt.R:6:50:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L6) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
   Sys.getenv("HOME") == "/home/p230198") return ()
                                                 ^
```
[tests/testthat/test-abc_smc_nltt.R:13:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L13) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return (t)
           ^
```
[tests/testthat/test-abc_smc_nltt.R:17:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( rexp(n = 1, rate = 10) )
           ^
```
[tests/testthat/test-abc_smc_nltt.R:17:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( rexp(n = 1, rate = 10) )
            ^
```
[tests/testthat/test-abc_smc_nltt.R:17:36:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( rexp(n = 1, rate = 10) )
                                   ^
```
[tests/testthat/test-abc_smc_nltt.R:21:11:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
   return( dexp( val[1], rate = 10) )
          ^
```
[tests/testthat/test-abc_smc_nltt.R:21:17:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
   return( dexp( val[1], rate = 10) )
                ^
```
[tests/testthat/test-abc_smc_nltt.R:21:36:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
   return( dexp( val[1], rate = 10) )
                                   ^
```
[tests/testthat/test-abc_smc_nltt.R:27:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L27) *style:* **Variable or function name should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:41:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L41) *style:* **Variable or function name should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:47:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L47) *style:* **Variable or function name should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-abc_smc_nltt.R:66:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L66) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return (t)
           ^
```
[tests/testthat/test-abc_smc_nltt.R:70:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L70) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( rexp(n = 2, rate = 1) )
           ^
```
[tests/testthat/test-abc_smc_nltt.R:70:34:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L70) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( rexp(n = 2, rate = 1) )
                                 ^
```
[tests/testthat/test-abc_smc_nltt.R:77:12:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L77) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( dexp( val[1], rate = 1) *
           ^
```
[tests/testthat/test-abc_smc_nltt.R:77:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L77) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( dexp( val[1], rate = 1) *
            ^
```
[tests/testthat/test-abc_smc_nltt.R:77:19:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L77) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( dexp( val[1], rate = 1) *
                  ^
```
[tests/testthat/test-abc_smc_nltt.R:78:21:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L78) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
               dexp( val[2], rate = 1) )
                    ^
```
[tests/testthat/test-abc_smc_nltt.R:78:39:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-abc_smc_nltt.R#L78) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
               dexp( val[2], rate = 1) )
                                      ^
```
[tests/testthat/test-get_branching_times.R:17:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-get_branching_times.R#L17) *style:* **Variable or function name should be snake_case.**
```r
  phylogeny$root.edge <- 2
            ^~~~~~~~~
```
[tests/testthat/test-get_n_lineages.R:7:13:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-get_n_lineages.R#L7) *style:* **Variable or function name should be snake_case.**
```r
  phylogeny$root.edge <- 2
            ^~~~~~~~~
```
[tests/testthat/test-mcmc_nltt.R:6:51:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-mcmc_nltt.R#L6) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    Sys.getenv("HOME") == "/home/p230198") return ()
                                                  ^
```
[tests/testthat/test-mcmc_nltt.R:13:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-mcmc_nltt.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:27:37:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-mcmc_nltt.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return(-1 * LL_BD(params, tree1) )
                                    ^
```
[tests/testthat/test-mcmc_nltt.R:30:3:](https://github.com/richelbilderbeek/nLTT/blob/a7da011bed820e57b63a2bb52cb4f4a812a8dbdd/tests/testthat/test-mcmc_nltt.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```


Btw the '#' char at the front of the line will achieve the same thing and is a bit easier to manage - https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet#headers. I've never got round to converting the markdown to something a bit cleaner.


Perhaps something like:
```
foreach (array('href','src','action','data') as $attr) {
	$targetString = str_replace(' '.$attr.'="{$'.$key.'}"', ' '.$attr.'="'.htmlspecialchars($value).'"', $targetString);
	$targetString = str_replace(' '.$attr."='{$".$key."}'", ' '.$attr."='".htmlspecialchars($value)."'", $targetString);
}
```


Index.js should be at root. And the use pointing tl wwwroot like you used to have


`using System;
using System.Collections.Generic;
using System.ComponentModel;
using System.Data;
using System.Data.SqlClient;
using System.Drawing;
using System.Linq;
using System.Text;
using System.Windows.Forms;
using System.Configuration;

namespace HW2.DATAACCESS
{
    class Addform
    {
   SqlConnection connection=new SqlConnection(ConfigurationManager.ConnectionStrings["conn"].ConnectionString);

        public void funcaddform(string Course_id)

      {
          try
          {
              //parameter1
              SqlParameter _Courseid = new SqlParameter();
              _Courseid.ParameterName = "@Course_id";
              _Courseid.SqlDbType = SqlDbType.NChar;
              _Courseid.Value = Course_id;

              //conection
              connection.Open();
              SqlCommand cmd = new SqlCommand();
              cmd.Connection = connection;
              cmd.CommandType = CommandType.StoredProcedure;
              cmd.CommandText = "addtoform";

              //addparameter
              cmd.Parameters.Add(_Courseid);

              //exe
              cmd.ExecuteNonQuery();
              //
              connection.Close();
          }
          catch (Exception e)
          {
              connection.Close();
              MessageBox.Show(e.Message);

          }
      }

    }
}`


The goal of this branch is to introduce a distinct "Customisation Layer" to simplify maintenance of local customisations of XTF, including migrating those customisations forward to new versions of XTF over time. I hope this structural addition will make it easier to manage customisations, and to package and share them.

The commit splits all the XSLT files into two layers:

- A base layer which consists of the core XSLT stylesheets in the `style` folder,
- A "local" customisation layer, which consists of a matching set of stylesheets which do nothing except defer to the corresponding core stylesheets.

The `local` XSLT stylesheets simply defer all processing the original stylesheet using `xsl:import` but otherwise they are empty and therefore they behave exactly as the original stylesheets did. However, if XTF users insert new templates into these files, they will take precedence over templates in the imported files. This means that the contents of the `local` XSLT files could consist only of additions and changes to XTF's "built-in" behaviour.


Updated Swedish translation
[gc_sv.txt](https://github.com/GoldenCheetah/GoldenCheetah/files/983438/gc_sv.txt)


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/ab1ebf2d-8da3-4b75-9d89-74e9f182bb82 "catalog-api-toolchain-demo-20170508120735934"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/906f8623-24b6-4b5a-9077-925d20a792a2 "catalog-api-toolchain-demo-20170508120735934") deployed [catalog-api-toolchain-demo-20170505112009013](https://github.com/zivondai/catalog-api-toolchain-demo-20170505112009013/releases/tag/deploy-ibm-yp-us-south-user_1-dev-20170508-122812 "deploy-ibm-yp-us-south-user_1-dev-20170508-122812") to [dev](https://console.ng.bluemix.net/apps/aeab418d-e707-40d4-b1f9-d8aed76bcb12 "ibm:yp:us-south:user_1:dev"), including this commit


ScreenShot


plz fix editor need newline at end of file


合并


第9页最后一段第三行的“和”字应去掉


Hi @ncopa! Looks like the related pull request https://github.com/eclipse/mosquitto/pull/281 is stuck on the request for you to sign a contributor agreement. Is there something ongoing, would be great to have this fix in the main track.


The second link is my article and the first link seems a mirror of my article, and I am also the author of the FishHook project.
If you are interested in the project, here is some more articles about the internals of FishHook. (In Chinese)
http://blog.csdn.net/myjisgreat/article/details/53262932
http://blog.csdn.net/myjisgreat/article/details/46478303
http://blog.csdn.net/myjisgreat/article/category/5585727

I paid much attention in hooking APIs under UAC environments. Hooking explorer.exe seems working, since I have tested this before.


Thanks @mseaton 👍


TeamCity Xbim :: Xbim Geometry :: XbimGeometry [Build 358](http://xbimbuilds.cloudapp.net/viewLog.html?buildId=1575&buildTypeId=Xbim_XbimGeometry_XbimGeometry) outcome was **FAILURE**
Summary: Compilation error: Xbim.ModelGeometry.Scene\Xbim.ModelGeometry.Scene.csproj (new) Build time: 00:32:25


In reference to point 1, here's some additional info.  It's useful to look at the result of each tracker.  Below, values are shown for (tracker.mean, tracker.variance, tracker.count) for L = 0,1,2,3,4.

for d(log S)
```
(0.1029617290759855, 0.022368004542547983, 10000)
(3.801876511613867e-18, 2.517614914452706e-33, 10000)
(3.3372027157499495e-18, 4.350355646040273e-33, 10000)
(-2.1797425333252837e-17, 9.050100482824169e-33, 10000)
(1.0391795798411237e-17, 1.9520444217590393e-32, 10000)
```

for d(S)
```
(0.10139506762148065, 0.016737322363272085, 10000)
(0.0022427354629029127, 0.00048040377466578347, 10000)
(0.0004726862252449845, 0.00011199879147652713, 10000)
(0, 1.8134466447527934e-05, 2.8862875525094009e-05, 10000)
(2.9654107249644601e-05, 7.1203945531969153e-06, 10000)
```

What's interesting is that they both converge on the same answer (aka sum(t.mean) ~ .10) but, for the variable change the accuracy is obtained almost entirely at the first level (aka L = 0).  The corrections obtained at finer grid levels are all minuscule.  Recall that at L=0, we're simulating a solution to the SDE with only a single step!  The fact that the variable change method converged instantly to the solution of the SDE seemed consistent with an exact solution (as opposed to an iterative / numerical solution)


Welcome, if it's regular homework links etc you can just add it directly. If you make changes in the existing curriculum please make a PR. But since the module you are teaching is extra don't worry about it at the moment.


libmei/atts_shared.h is generated file and should not be edited by hand.


thank you Ed !


This commit seems to have gotten lost?


Hallo das ist ein testkommentar


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/f1c6b92c-7783-4e94-b800-67b13b50af53 "parkingbot"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/b043f627-3a3b-4dc2-a359-421e1a4e548b "parkingbot") deployed [parkingbot](https://github.com/aliuspetraska/parkingbot/releases/tag/deploy-ibm-yp-us-south-alius.petraska-ibm.com-parkingbot-20170508-124000 "deploy-ibm-yp-us-south-alius.petraska-ibm.com-parkingbot-20170508-124000") to [parkingbot](https://console.ng.bluemix.net/apps/b7800fe2-7e0f-4791-bb11-72adbed9c5e3 "ibm:yp:us-south:alius.petraska@ibm.com:parkingbot"), including this commit


Or if alternate extra wall is enabled.


Fixed in e014158291d39f1093683dcf670e29d59f520cb7


Great job! Way more consistency now :)


Removed `foldLeft` entirely -- it was only used in 1 place.


This is intentionally blank.  The function in the while does all the work and returns 0 when there is no more to do (ending the loop).


TeamCity OTA+ :: rvi_sota_server :: ci [Build 2477](http://teamcity.prod01.internal.advancedtelematic.com:8111/viewLog.html?buildId=31214&buildTypeId=ota_plus_RviSotaServer_Ci) is now running


es waren aber doch auch andere relative links drin


The penny dropped - much better. (029c89a65fb44b2a198a1add553ada5f9d7065a9) also covers point on staying in integers. Thanks for this


I left this as-is for now -- `toChunk` is the same implementation as the now-removed `toList`. We can replace implementation whenever though.


Only if top or bottom layer counts are more than 0 or fill small gaps is enabled.


Where is `x` coming from here?


Correction: that author was asked, he just didn't reply.


Sidebar should have a variable by itself even if it's a copy from the code one so people can change that color, what do you think @sapegin?


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/d51663fd-b462-4b43-9633-93f842e276e6 "nodeexemplu"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/6fb5be88-9ecf-4e03-b842-53fb23d8ba7c "nodeexemplu") deployed [nodeexemplu](https://github.com/Ammonaton01/nodeexemplu/releases/tag/deploy-ibm-yp-us-south-catalin.neagoe-ro.ibm.com-dev-20170508-124452 "deploy-ibm-yp-us-south-catalin.neagoe-ro.ibm.com-dev-20170508-124452") to [dev](https://console.ng.bluemix.net/apps/f42f519e-bc3b-4b0a-875b-e56485ff32a3 "ibm:yp:us-south:catalin.neagoe@ro.ibm.com:dev"), including this commit


Also, we do need to constrain it to 128 bits (perhaps that is still happening?


Or spiralize or wireframe is enabled.


sorry I mean markdown


Hi
Thanks for this lovely tutorial. I am facing one issue in this code.
_api.fetchPopularRepos is not a function_
I am still new to React so I couldn't make it work. Could you help me please?


Yeah, I’ll do that.


Approved fixes.


I'm not sure we can do this in guaranteed small enough amount of gas.  We may need to expose a helper method to fix users with too many events, assuming we can't do any sort of memzero.


600 ms seems like an awfully long time to make a user wait. 180ms is generally when the brain perceives changes. What do carousel-like controls typically do here? I imagine there is an Easing function that controls both animations.


The stack trace will never be displayed since there is only one '{}' in the message.


Looks great!  Yeah, a mockup with descriptions of where there are interactive pieces would be great, for instance how does `. session--details` get revealed? Click on the enclosing `div.session`?


TeamCity Xbim :: Xbim Geometry :: XbimGeometry [Build 359](http://xbimbuilds.cloudapp.net/viewLog.html?buildId=1576&buildTypeId=Xbim_XbimGeometry_XbimGeometry) is now running


@Inifield Latest release updated now with latest commits
https://github.com/sidsukana/QSpellWork/releases/download/v2.0.0/QSW_2.0.0_Win32.7z


@chelmuth: please add to staging


[R/Prediction.R:217:53:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/R/Prediction.R#L217) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
        indices.threshold = order(y)[round(length(y)*0.95)]  #mse reconstruction error in [0,inf[
                                                   ~^~
```
[R/RLearner_oneclass_h2oautoencoder.R:257:5:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/R/RLearner_oneclass_h2oautoencoder.R#L257) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(.learner$predict.type == "response"){
    ^
```
[R/RLearner_oneclass_h2oautoencoder.R:260:57:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/R/RLearner_oneclass_h2oautoencoder.R#L260) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
      indices.threshold = order(p.df)[round(length(p.df)*0.95)]  #mse reconstruction error in [0,inf[
                                                       ~^~
```
[R/StackedLearner.R:556:50:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/R/StackedLearner.R#L556) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      m = makeLearner("regr.nnet", predict.type = )
                                                 ^
```
[R/performance.R:52:7:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/R/performance.R#L52) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(levels(pred$data$response)) == 1) {
      ^
```
[R/performance.R:71:11:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/R/performance.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(length(levels(pred$data$truth)) == 1) {
          ^
```
[tests/testthat/test_base_learnerArgsToControl.R:15:21:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/tests/testthat/test_base_learnerArgsToControl.R#L15) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  arg1 = quote(expr =)
                    ^~
```
[tests/testthat/test_base_learnerArgsToControl.R:16:21:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/tests/testthat/test_base_learnerArgsToControl.R#L16) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  arg2 = quote(expr =)
                    ^~
```
[tests/testthat/test_base_learnerArgsToControl.R:41:23:](https://github.com/mlr-org/mlr/blob/186272fc81a77a5d686c2b34fef0ccdf6716b6ca/tests/testthat/test_base_learnerArgsToControl.R#L41) *style:* **Put spaces around all infix operators (except exponentiation).**
```r
  devmax = quote(expr =)
                      ^~
```


Or alternate extra wall is enabled.