[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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:36:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/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:75:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
#'   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:126:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L276) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:301:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L301) *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:308:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L308) *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:309:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:310:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:311:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L311) *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:313:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L313) *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:315:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L315) *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:316:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L316) *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:320:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L186) *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:274:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L274) *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:275:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L344) *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:345:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/plot_nLTT.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:51:28:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/plot_nLTT.R#L51) *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:51:33:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/plot_nLTT.R#L51) *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:52:28:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/plot_nLTT.R#L52) *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:94:32:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/plot_nLTT.R#L94) *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/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-abc_smc_nltt.R#L30) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-abc_smc_nltt.R:35:3:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:55:3:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-get_average_nltt.R#L10) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_average_nltt.R:41:5:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-get_average_nltt.R#L41) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mcmc_nltt.R:14:3:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```
[tests/testthat/test-mcmc_nltt.R:58:3:](https://github.com/Neves-P/nLTT/blob/fc46bdc0a5aca3da683f6e77ce77275d62ba98fd/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments reason: Unexpected token A in JSON at position 0
~~~


Successfully deployed to following URLs:

* https://cyber-security-base-19-4jr1spkzd.now.sh
* https://cybersecuritybase.mooc.fi
* https://cyber-security-base-19.mooc.now.sh
* https://cyber-security-base-19-git-master.mooc.now.sh


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?forceNew=1 reason: Unexpected token A in JSON at position 0
~~~


I wonder if we should take for account situation where `decimals()` is 0 and allow the minimum of 1 token transfer.


所处的时代


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_hzuqV6vdNAfV7ta4XaUI6HSH reason: Unexpected token A in JSON at position 0
~~~


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_2p5rIhVqKRQrDrj1AEggz8vt reason: Unexpected token A in JSON at position 0
~~~


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/64cef359-6977-4ece-b9d9-3f28e3e7b37f?env_id=ibm%3Ayp%3Aus-south "cloud-native-toolchain-tutorial-20190930160951797"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/93e9df02-23ba-4892-a398-4dfd5203a142 "sample-cloud-native-toolchain-tutorial-20190930160951797") deployed [sample-cloud-native-toolchain-tutorial-20190930160951797](https://github.com/viniciusaito/sample-cloud-native-toolchain-tutorial-20190930160951797/releases/tag/deploy-ibm-yp-us-south-vinicius.saito-ibm.com-dev-20191101-150332 "deploy-ibm-yp-us-south-vinicius.saito-ibm.com-dev-20191101-150332") to [dev](https://console.bluemix.net/apps/91c1ba70-f84e-4ce1-a464-377a5ca75184?env_id=ibm:yp:us-south "ibm:yp:us-south:vinicius.saito@ibm.com:dev"), including this commit


You can use the SBMLReader or SBMLWriter to do simple test quickly but try to not commit the changes to the main. In general try to commit the minimum changes for the feature or bug you work on.


Congrats on the daughter ! Mine just turned one year old so I definitely know what your going through 😊

 I also lowered my involvement in the community for the first few months to be as helpful as I could.  Now I still ask my wife for some "me" time once a week to cater to my need to relax and enjoy the game - it's still mostly the only game I play or have any interest in.

  To the issue at hand-  is it anything like this:[ visual-signals mod](https://mods.factorio.com/mod/visual-signals)


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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:36:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/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:75:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
#'   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:126:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L276) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:301:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L301) *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:308:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L308) *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:309:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:310:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:311:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L311) *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:313:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L313) *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:315:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L315) *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:316:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L316) *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:320:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/nltt_diff_exact_notnorm.R:25:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
nltt_diff_exact_notnorm <- function(
^
```
[R/nltt_diff_exact_notnorm.R:47:27:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L47) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_notnorm.R:54:25:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L54) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_notnorm.R:116:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L116) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:117:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L117) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:118:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L118) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:119:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L119) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:121:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L121) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:122:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L122) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:123:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L123) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:124:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltt_diff_exact_notnorm.R#L124) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L186) *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:274:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L274) *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:275:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L344) *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:345:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/plot_nLTT.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:51:28:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/plot_nLTT.R#L51) *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:51:33:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/plot_nLTT.R#L51) *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:52:28:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/plot_nLTT.R#L52) *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:94:32:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/plot_nLTT.R#L94) *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/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-abc_smc_nltt.R#L30) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-abc_smc_nltt.R:35:3:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:55:3:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-get_average_nltt.R#L10) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_average_nltt.R:41:5:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-get_average_nltt.R#L41) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mcmc_nltt.R:14:3:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```
[tests/testthat/test-mcmc_nltt.R:58:3:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-nltt_diff_exact_notnorm.R:52:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-nltt_diff_exact_notnorm.R#L52) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_notnorm.R:53:1:](https://github.com/Neves-P/nLTT/blob/da48f1b3795a99b09d9508defdee47e0e5157081/tests/testthat/test-nltt_diff_exact_notnorm.R#L53) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_7YuSd3mVBc7YzBJxyKW0d6Wi reason: Unexpected token A in JSON at position 0
~~~


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_pdoO475xQht6NIknC6z6ihb3 reason: Unexpected token A in JSON at position 0
~~~


соре но я захотел сделать так


Hmm.. a test should be added here ?
https://github.com/tzickel/cpython/commit/d679a0b0dee91c563436bf947a8d7915953a377c#diff-b046ab474480855fb4a01de88cfc82bb


`NULL` is misleading because it sounds like there is an absence when in fact there are `0`. Putting `address(0)` inline in the code is better.


In general, we want to avoid doing recursive things in the normal toString(). Here by putting `listOfCreators`, you will print all of the creators and we don't want that here. So like for the modified dates, only printing the size would be fine.

You can then add a different method, something like printHistory() where you can print the full history, all creators and all modified dates.


Successfully deployed to following URLs:

* https://freddieridellcom-75e28jj3c.now.sh
* https://freddieridell.com
* https://www.freddieridell.com
* https://freddieridellcom.freddieridell.now.sh
* https://freddieridellcom-git-master.freddieridell.now.sh


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v3/now/deployments reason: Unexpected token A in JSON at position 0
~~~


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments reason: Unexpected token A in JSON at position 0
~~~


Thanks Alex
I'm using observe so that whenever new notes are inserted to the database it gets uploaded underneath, so that I don't need to handle that onResume for the activity and refresh my recyclerview.
And yes setTasks calls notifyDataSetChanged.
So you want me to use notifyItemDeleted when I delete items from recycler view in order to get that nice animation, right?


Deployment failed with the following error:

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


Well, actually it does only `model_parameters(psych::fa(x, nfactors = n, rotate = rotation, ...), sort = sort, threshold = threshold)`. It does _not_ all this extra stuff that `principal_components()` does (the loadings etc.).


Finish The-Pro


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_pTF2AxpeXbsUYAf7WGhyrPaI reason: Unexpected token A in JSON at position 0
~~~


Ele nós!


<details>

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

Taskcluster-GitHub attempted to create a task for this event with the following scopes:

```
[
  "assume:repo:github.com/taskcluster/taskcluster:pull-request",
  "queue:route:checks",
  "queue:scheduler-id:taskcluster-github"
]
```

The expansion of these scopes is not sufficient to create the task, leading to the following:

Client ID static/taskcluster/github does not have sufficient scopes and is missing the following scopes:

```
{
  "AllOf": [
    "assume:project:taskcluster:tests:taskcluster",
    "docker-worker:cache:project-taskcluster-test-*",
    {
      "AnyOf": [
        {
          "AnyOf": [
            "queue:create-task:highest:aws-provisioner-v1/github-worker",
            "queue:create-task:very-high:aws-provisioner-v1/github-worker",
            "queue:create-task:high:aws-provisioner-v1/github-worker",
            "queue:create-task:medium:aws-provisioner-v1/github-worker",
            "queue:create-task:low:aws-provisioner-v1/github-worker",
            "queue:create-task:very-low:aws-provisioner-v1/github-worker",
            "queue:create-task:lowest:aws-provisioner-v1/github-worker"
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/github-worker",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/github-worker",
                "queue:task-group-id:taskcluster-github/dmztEvLaRge0IasQNJ2Cmw",
                "queue:schedule-task:taskcluster-github/dmztEvLaRge0IasQNJ2Cmw/DJDlCwB-S7iYlnr0_MCyWg"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

This request requires the client to satisfy the following scope expression:

```
{
  "AllOf": [
    "assume:project:taskcluster:tests:taskcluster",
    "docker-worker:cache:project-taskcluster-test-*",
    "queue:route:checks",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/github-worker",
                "queue:create-task:very-high:aws-provisioner-v1/github-worker",
                "queue:create-task:high:aws-provisioner-v1/github-worker",
                "queue:create-task:medium:aws-provisioner-v1/github-worker",
                "queue:create-task:low:aws-provisioner-v1/github-worker",
                "queue:create-task:very-low:aws-provisioner-v1/github-worker",
                "queue:create-task:lowest:aws-provisioner-v1/github-worker"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/github-worker",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/github-worker",
                "queue:task-group-id:taskcluster-github/dmztEvLaRge0IasQNJ2Cmw",
                "queue:schedule-task:taskcluster-github/dmztEvLaRge0IasQNJ2Cmw/DJDlCwB-S7iYlnr0_MCyWg"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-11-01T15:11:37.464Z

</details>


this solution have a problem... don't test and check the errors


removed as of [this commit (e527036)](https://github.com/semininja/short-fugues/commit/022196abff16401349ab4233b12434136e527036)


FixMinDurHrsShownAnnual-7502 (JasonGlazer) - x86_64-MacOS-10.13-clang: OK (2578 of 2579 tests passed, 0 test warnings)

Failures:\n

ZoneUnitarySysTest Test Summary
 * Passed: 9
 * Failed: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.96%25-yellow.png)


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_m88XoOH6G0F2vUpqm8VFOvxQ reason: Unexpected token A in JSON at position 0
~~~


This was meant to be #226


Support cloud file system schemes in HDFS URIs (Issue # 5988)


Seguro que Batman se escribe así?


Tha


Ij


Thanks!
Hungarian Notation is a naming convention that allows a programmer to determine the type of variable or constant just by looking at its name
For example:
float fX = 0;
int	iY = 0;
I hope you got the point Israa, for more info take a look at that:
http://www2.sys-con.com/itsg/virtualcd/java/archives/0409/farn/index.html


This looks to have been made to master in error. Removing requirements.txt file has broken scripts. Going to revert. New commits go in "development" branch.


Aliasing was ignored due to a new commit existing for this branch, which will be aliased instead.


I


168195503_Issue7477 (Unknown) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (11 of 11 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_E7DFQXOGTVLTGPzCb2tRS40h reason: Unexpected token A in JSON at position 0
~~~


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{this-is-not-json}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


> is it anything like this:[ visual-signals mod](https://mods.factorio.com/mod/visual-signals) ?

Yeah, like that, but also combined with tracking each signal's fill/empty rate; like this (it's the one on the right):
![prodmon](https://i.imgur.com/6guyabq.png).

Can be prettier, too, now that we have rich text in mod GUIs.


Deployment failed with the following error:

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


Successfully deployed to following URLs:

* https://amertav2-oft0st097.now.sh
* https://amertav2.vino0397.now.sh
* https://amertav2-git-master.vino0397.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v1-with-alias-uhenlqyhrb.now.sh
* https://z-github-e2e-tests-dev-only.now.sh


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments reason: Unexpected token A in JSON at position 0
~~~


There is no such line in `master` > https://github.com/lighttransport/nanort/blob/master/examples/nanosg/obj-loader.cc#L9


Ly


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v3/now/deployments?teamId=team_WMX7HBP10AO5sTaf2MqsH538 reason: Unexpected token A in JSON at position 0
~~~


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_U7eyXmmTMQ0A33TAjBPO3Fc9 reason: Unexpected token A in JSON at position 0
~~~


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-without-alias-r4vl82vqc.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://ccc-lp9yhi2uo.now.sh
* https://ccc.zeit-github-test-dev1.now.sh
* https://ccc-git-master.zeit-github-test-dev1.now.sh


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments?teamId=team_WMX7HBP10AO5sTaf2MqsH538 reason: Unexpected token A in JSON at position 0
~~~


B


我也是知乎上看到答主这个胡扯生成器的


@georgeclaghorn The original commit was PG only, but the reviewer mentioned that same change should apply to MySQL and Sqlite as well, so it's for all three databases.


is there a slide here from the first tutorial(last week)?


168195503_Issue7477 (Unknown) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


<details>

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

Taskcluster-GitHub attempted to create a task for this event with the following scopes:

```
[
  "assume:repo:github.com/taskcluster/docker-worker:branch:packet-net",
  "queue:route:statuses",
  "queue:scheduler-id:taskcluster-github"
]
```

The expansion of these scopes is not sufficient to create the task, leading to the following:

Client ID static/taskcluster/github does not have sufficient scopes and is missing the following scopes:

```
{
  "AllOf": [
    "secrets:get:repo:github.com/taskcluster/docker-worker:ci-creds",
    "secrets:get:repo:github.com/taskcluster/docker-worker:pulse-creds",
    {
      "AnyOf": [
        {
          "AnyOf": [
            "queue:create-task:highest:aws-provisioner-v1/worker-ci-test",
            "queue:create-task:very-high:aws-provisioner-v1/worker-ci-test",
            "queue:create-task:high:aws-provisioner-v1/worker-ci-test",
            "queue:create-task:medium:aws-provisioner-v1/worker-ci-test",
            "queue:create-task:low:aws-provisioner-v1/worker-ci-test",
            "queue:create-task:very-low:aws-provisioner-v1/worker-ci-test",
            "queue:create-task:lowest:aws-provisioner-v1/worker-ci-test"
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/worker-ci-test",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/worker-ci-test",
                "queue:task-group-id:taskcluster-github/XQWpPzh1SsKRm2o4aWTKag",
                "queue:schedule-task:taskcluster-github/XQWpPzh1SsKRm2o4aWTKag/XQWpPzh1SsKRm2o4aWTKag"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

This request requires the client to satisfy the following scope expression:

```
{
  "AllOf": [
    "docker-worker:cache:docker-worker-garbage-*",
    "docker-worker:capability:privileged",
    "docker-worker:capability:device:loopbackAudio",
    "docker-worker:capability:device:loopbackVideo",
    "secrets:get:repo:github.com/taskcluster/docker-worker:ci-creds",
    "secrets:get:repo:github.com/taskcluster/docker-worker:pulse-creds",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/worker-ci-test",
                "queue:create-task:very-high:aws-provisioner-v1/worker-ci-test",
                "queue:create-task:high:aws-provisioner-v1/worker-ci-test",
                "queue:create-task:medium:aws-provisioner-v1/worker-ci-test",
                "queue:create-task:low:aws-provisioner-v1/worker-ci-test",
                "queue:create-task:very-low:aws-provisioner-v1/worker-ci-test",
                "queue:create-task:lowest:aws-provisioner-v1/worker-ci-test"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/worker-ci-test",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/worker-ci-test",
                "queue:task-group-id:taskcluster-github/XQWpPzh1SsKRm2o4aWTKag",
                "queue:schedule-task:taskcluster-github/XQWpPzh1SsKRm2o4aWTKag/XQWpPzh1SsKRm2o4aWTKag"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-11-01T15:21:44.076Z

</details>


Whoops, that was my bad.


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v3/now/deployments?teamId=team_lH64UNI7W53f2HC1M17w9Ycn reason: Unexpected token A in JSON at position 0
~~~


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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:36:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/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:75:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
#'   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:126:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L276) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:301:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L301) *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:308:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L308) *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:309:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:310:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:311:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L311) *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:313:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L313) *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:315:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L315) *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:316:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L316) *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:320:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/nltt_diff_exact_notnorm.R:25:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
nltt_diff_exact_notnorm <- function(
^
```
[R/nltt_diff_exact_notnorm.R:47:27:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L47) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_notnorm.R:54:25:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L54) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_notnorm.R:116:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L116) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:117:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L117) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:118:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L118) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:119:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L119) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:121:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L121) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:122:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L122) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:123:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L123) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:124:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltt_diff_exact_notnorm.R#L124) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L186) *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:274:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L274) *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:275:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L344) *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:345:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/plot_nLTT.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:51:28:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/plot_nLTT.R#L51) *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:51:33:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/plot_nLTT.R#L51) *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:52:28:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/plot_nLTT.R#L52) *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:94:32:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/plot_nLTT.R#L94) *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/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-abc_smc_nltt.R#L30) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-abc_smc_nltt.R:35:3:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:55:3:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-get_average_nltt.R#L10) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_average_nltt.R:41:5:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-get_average_nltt.R#L41) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mcmc_nltt.R:14:3:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```
[tests/testthat/test-mcmc_nltt.R:58:3:](https://github.com/Neves-P/nLTT/blob/d255cc0af839400a088413bb7ccb265cc3ff2800/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```


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I think the condition should be
```cpp
#if defined(wxHAS_GENERIC_DATAVIEWCTRL) || !defined(__WXOSX__)
```
to ensure that this is compiled in for wxGTK (where native control is used).

Could you please check this and make a PR if it works for you? TIA!


There were the following issues with your Pull Request

  * Subject needs to conform to "%{type} #%{issue_number}: %{description}"

Guidelines are available at https://github.com/OpenNebula/one/blob/master/share/doc/dev/COMMIT_MESSAGES.md

---
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good


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test


TeamCity Bvcms / Build [Build 2554](https://builds.tpsdb.com/viewLog.html?buildId=9565&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 151 Build time: 00:28:31


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Deployment failed with the following error:

~~~
The chosen alias "create-react-app-redux.now.sh" is already in use by another account.
~~~


# 1.0 Instructions for Windows (.exe / Executeable File)

 - Download the ".exe" variant of the program.
 - Double click or right click -> execute the file
 - Enter the ID of a youtube livestream
 - Enter an amount of threads
 - See the viewers rise!

# 2.0 Instructions for Windows/Linux (.py / Python)

# 3.0 Whats the ID of a Livestram?

YouTube URLs look something like this => https://www.youtube.com/watch?v=hrthusdusdf <br />
Then _dsfsdefgdfdsf_ would be the ID of the video.


ImplementedvBlockchain Architecture


# 1.0 Instructions for Windows (.exe / Executeable File)

 - Download the ".exe" variant of the program.
 - Double click or right click -> execute the file
 - Enter the ID of a youtube livestream
 - Enter an amount of threads
 - See the viewers rise!

# 2.0 Instructions for Windows/Linux (.py / Python)

# 3.0 Whats the ID of a Livestram?

YouTube URLs look something like this => https://www.youtube.com/watch?v=dsfsdefgdfdsf <br />
Then _dsfsdefgdfdsf_ would be the ID of the video.


-[Macrumors.com] (https://forums.macrumors.com/threads/opencore-on-the-mac-pro.2207814/) in English


Deployment failed with the following error:

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


![](https://github.trello.services/images/mini-trello-icon.png) [Lista Query](https://trello.com/c/RCvILHB4/17-lista-query)


Thanks. Fixed in 5081817.


Rever o método, possuí falhas ainda não encontradas


ainda sem novidades 😢


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Funciona bien, hasta que haces algo prudente, seguí así


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Deployment failed with the following error:

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


Probaste esa tu mierda???? Probala y me escribís pedazo de imbécil


I tried a full build a few days back, and after removing the lifetime-dse, the compile proceeded almost to the end. Then the devdelegate change made itself all too apparent.


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Deployment failed with the following error:

~~~
You tried to create a Now 1.0 deployment. Please use Now 2.0 instead: https://zeit.co/upgrade
~~~


hiii


Оставил коммент


@JamesHarker The fix to the MongoDB test failure you are seeing in your build is in `master` branch. Sync with master and you are good!


holamhola


@Igor7086 👍


Please fix the name format to "lastname, firstname"! This is essential for the infrastructure! If there is no comma in the name, it means there is just one name part; for instance, "Aline Silveira" will be sorted under "Aline", not under "Silveira", which, I suppose, would be the desired way.


TeamCity Consultations / "Private Beta" - BuildAndPublish .NET Core 2.1 [Build 2461](https://teamcity.nice.org.uk/viewLog.html?buildId=60528&buildTypeId=Consultations_PrivateBetaBuildAndPublish21) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) (new) Build time: 00:00:32


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wchar_t형을 쓰지 않고
후면버퍼를[행][열][3] 이런식으로 2차원 문자열 행렬로 만드는 방법을 적용 시켜 봐야겠음


RemoveSynonyms-6601PartB (mjwitte) - x86_64-MacOS-10.13-clang: OK (2584 of 2584 tests passed, 0 test warnings)

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


dinhviethoa,
could you, please, create a new release.
I'm making new modules for an asterisk project based on this lib.
One of the modules uses quota. It would be better if the asterisk depends on the release version instead of patched/bundled version.
Thank you.


@Alex-Turchyn Обязательно поговорим об этом на занятии. Ты не один так сделал:) Ответ: нет, не корректно, но есть одно НО и мы об этом поговорим


Todo bien


This project is so much cleaner than the OverWolf equivalent. Well done on this. Sad to see it go! Best of luck IRL!


It might be simpler to use
`load("@npm//typescript:index.bzl", "tsc")`
and see if we can get that working. ts_library runs a custom compiler for things like tsickle but can also introduce incompatibilites


![](https://github.trello.services/images/mini-trello-icon.png) [Opzetten/automatiseren van AD Server](https://trello.com/c/h0fh0qyy/3-opzetten-automatiseren-van-ad-server)


Está dando problemas con la memoria


![](https://github.trello.services/images/mini-trello-icon.png) [Opzetten/automatiseren van SCCM Server](https://trello.com/c/Rj7xAOfq/4-opzetten-automatiseren-van-sccm-server)


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 738-IDAM-284-Validation-](https://teamcity.nice.org.uk/viewLog.html?buildId=60527&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **SUCCESS**
Summary: Running Build time: 00:05:25


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> Well, actually it does only model_parameters(psych::fa(x, nfactors = n, rotate = rotation, ...),

oops, I missed that ^^

Well then yes! good idea to have a wrapper like this. I'll look into it!


Well Ubuntu 16.04 has only available [tesseract 3.04](https://packages.ubuntu.com/search?keywords=tesseract&searchon=names) and it will not be upgraded to 4.x branch...
For 4.1 release there is [required cmake 3.6](https://github.com/tesseract-ocr/tesseract/blob/5280bbcade4e2dec5eef439a6e189504c2eadcd9/CMakeLists.txt#L11) and nobody complains yet ;-) ...
AFAIR newer cmake version (especially for version tesseract 5) is needed for c++14 and c++17 support, so compiler version could be next problem...


@ProtoDroidBot good catch, thanks! Will fix now.


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Updates


clientarea.php


@pgirskiy Я просмотрела! Я бы что-то делала не так, но ты имеешь право:)


Hello @TaciteOFF , désolé, je n'avais pas vu ton commentaire. Merci d'avoir corrigé les produits !
Je vais ajouter la facette.


> Don't we need the patched ims.apk anymore to get volte working?

no it wont be needed with oreo blobs, but i havent tested these yet


TeamCity Consultations / "Private Beta" - BuildAndPublish .NET Core 2.1 [Build 0.1.0.2462-EC-722-Export-Questi](https://teamcity.nice.org.uk/viewLog.html?buildId=60529&buildTypeId=Consultations_PrivateBetaBuildAndPublish21) outcome was **SUCCESS**
Summary: Tests passed: 473 Build time: 00:07:19


Tak se mi ty problémy asi podařilo vyřešit


also need to adapt stuff in dt for the new blobs


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@dpochernin Супер!


@dpochernin Этот момент ты хочешь обсудить?


168195503_Issue7477 (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2610 of 2620 tests passed, 0 test warnings)

Messages:\n
 * 10 tests had: EIO diffs.
 * 10 tests had: Table big diffs.
 * 5 tests had: AUD diffs.

Failures:\n

regression Test Summary
 * Passed: 679
 * Failed: 10

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.62%25-yellow.png)


@AleksandarPetrov
The module `dt-device-loader` is not completing the loading.
https://github.com/duckietown/dt-device-loader/blob/de8d4f67b2719bd08b47179b4ded03ab872a7ec5/code/code_loader/code_loader.py#L232


¿ Sabes que significa eficiencia ? quita las listas de coprimos de fi y N que no se están utilizando y busca otra forma de calcular e porque se calcula, pero no es eficiente.


I saw and read your codes


Sabés qué significa ME VALE VERGA????? PUES INVESTIGA PEDAZO DE CEROTE


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Получается серверу немножко все равно на структуру джейсона
Как по мне это не корректно
Но так как у нас нет ТЗ к серверной части, то мы и не можем нормально сформулировать тесты


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@dpochernin Не уверена, что всем твоим тестовым методам нужны эти setUp и tearDown. Стоит разделить тесты по разным классам с одинаковыми setUp и tearDown. Можно наследоваться


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We could re-interpret the demo flag as automatically setting the named values for the poll intervals and avoid interactively prompting for demo-mode conditional on whether the intervals are set (assume non-demo if at least one is set and resume the state flow from there). Same applies for serverIP/serverURL. It's a minor change in the state-machine implementation, and tbh, I like this idea better than the one currently implemented - this way you won't be annoyed by the interactive prompt when you forget to set the demo flag or mixed server-ip / server-url flags.


Could always add it to the casts variable on the Thread model to be sure. That way you're doing an explicit check instead of the implicit (does 1 equal true? vs does true equal true?)

```php
protected $casts = [
    'is_pinned' => 'boolean',
];
```


Nice job


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Yes, that's bad, I know :(


closes #4


I will!


This is not right, application name should be allowed to have &


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saya baru belajar


Noted, thank you!


I will add a relevant placeholder.


TeamCity Bvcms / Build [Build 2555](https://builds.tpsdb.com/viewLog.html?buildId=9566&buildTypeId=Bvcms_Build) outcome was **FAILURE**
Summary: Tests failed: 1, passed: 150 Build time: 00:27:48
### Failed tests
```
Webapp collection (1): IntegrationTests.Areas.Manage.AccountTests.MyData_User_ChangePassword_Test: System.NullReferenceException : Object reference not set to an instance of an object.
   at IntegrationTests.Support.AccountTestBase.Logout() in C:\TeamCity\buildAgent\work\de2c4e6ef697cb99\IntegrationTests\Support\AccountTestBase.cs:line 49
   at IntegrationTests.Areas.Manage.AccountTests.MyData_User_ChangePassword_Test() in C:\TeamCity\buildAgent\work\de2c4e6ef697cb99\IntegrationTests\Areas\Manage\AccountTests.cs:line 73

```


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