[R/create_next_gen_traits.R:21:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/create_next_gen_traits.R#L21) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:22:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/create_next_gen_traits.R#L22) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(nb_offspring_pop)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:23:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/create_next_gen_traits.R#L23) *warning:* **no visible global function definition for ‘testarg_not_this’**
```r
  testarg_not_this(nb_offspring_pop, Inf)
  ^~~~~~~~~~~~~~~~
```
[R/create_next_gen_traits.R:24:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/create_next_gen_traits.R#L24) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(nb_offspring_pop, length(traits_pop))
  ^~~~~~~~~~~~~~
```
[R/create_next_gen_traits.R:25:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/create_next_gen_traits.R#L25) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(mutation_sd)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:26:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/create_next_gen_traits.R#L26) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(mutation_sd)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:39:5:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/create_next_gen_traits.R#L39) *warning:* **no visible global function definition for ‘testarg_num’**
```r
    testarg_num(next_gen_traits)
    ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:40:5:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/create_next_gen_traits.R#L40) *warning:* **no visible global function definition for ‘testarg_length’**
```r
    testarg_length(next_gen_traits, sum(nb_offspring_pop))
    ^~~~~~~~~~~~~~
```
[R/draw_nb_offspring.R:12:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/draw_nb_offspring.R#L12) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(fitness)
  ^~~~~~~~~~~
```
[R/draw_nb_offspring.R:13:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/draw_nb_offspring.R#L13) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(fitness)
  ^~~~~~~~~~~
```
[R/draw_nb_offspring.R:20:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/draw_nb_offspring.R#L20) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(nb_offspring)
  ^~~~~~~~~~~
```
[R/draw_nb_offspring.R:21:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/draw_nb_offspring.R#L21) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(nb_offspring)
  ^~~~~~~~~~~
```
[R/draw_nb_offspring.R:22:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/draw_nb_offspring.R#L22) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(nb_offspring, length(fitness))
  ^~~~~~~~~~~~~~
```
[R/get_carr_cap.R:17:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L17) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_ind)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:18:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L18) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_opt)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:19:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L19) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:20:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L20) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_opt) # is a nb of ind
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:21:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L21) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_width)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:22:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L22) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_width) # is a variance
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:46:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L46) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap) # catch NAs, NaNs and NULL
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:47:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L47) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:48:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_carr_cap.R#L48) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(carr_cap, length(trait_ind))
  ^~~~~~~~~~~~~~
```
[R/get_comp_coeff.R:22:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_comp_coeff.R#L22) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_ind)
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:23:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_comp_coeff.R#L23) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(trait_ind, 1) # not vectorized!
  ^~~~~~~~~~~~~~
```
[R/get_comp_coeff.R:24:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_comp_coeff.R#L24) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:25:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_comp_coeff.R#L25) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:26:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_comp_coeff.R#L26) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width) # is a variance
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:37:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_comp_coeff.R#L37) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(coeffs, length(traits_pop))
  ^~~~~~~~~~~~~~
```
[R/get_comp_coeff.R:49:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_comp_coeff.R#L49) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(coeffs)
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:50:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_comp_coeff.R#L50) *warning:* **no visible global function definition for ‘testarg_prop’**
```r
  testarg_prop(coeffs)
  ^~~~~~~~~~~~
```
[R/get_fitness.R:30:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L30) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/get_fitness.R:31:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L31) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(growth_rate)
  ^~~~~~~~~~~
```
[R/get_fitness.R:32:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L32) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(growth_rate)
  ^~~~~~~~~~~
```
[R/get_fitness.R:33:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L33) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/get_fitness.R:34:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L34) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width)
  ^~~~~~~~~~~
```
[R/get_fitness.R:35:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L35) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_opt)
  ^~~~~~~~~~~
```
[R/get_fitness.R:36:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L36) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/get_fitness.R:37:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L37) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/get_fitness.R:38:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L38) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_width)
  ^~~~~~~~~~~
```
[R/get_fitness.R:39:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L39) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_width)
  ^~~~~~~~~~~
```
[R/get_fitness.R:61:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L61) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(fitness)
  ^~~~~~~~~~~
```
[R/get_fitness.R:62:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_fitness.R#L62) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(fitness, length(traits_pop))
  ^~~~~~~~~~~~~~
```
[R/get_n_eff.R:12:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_n_eff.R#L12) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/get_n_eff.R:13:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_n_eff.R#L13) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/get_n_eff.R:14:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_n_eff.R#L14) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width) # is a variance
  ^~~~~~~~~~~
```
[R/get_n_eff.R:29:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_n_eff.R#L29) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(n_eff)
  ^~~~~~~~~~~
```
[R/get_n_eff.R:30:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_n_eff.R#L30) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(n_eff)
  ^~~~~~~~~~~
```
[R/get_n_eff.R:31:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/get_n_eff.R#L31) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(n_eff, length(traits_pop))
  ^~~~~~~~~~~~~~
```
[R/plot_generation_traits.R:14:23:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_generation_traits.R#L14) *style:* **Put spaces around all infix operators.**
```r
plot_generation_traits<- function(path_to_file,
                     ~^
```
[R/plot_generation_traits.R:17:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_generation_traits.R#L17) *warning:* **no visible global function definition for ‘testarg_char’**
```r
  testarg_char(path_to_file)
  ^~~~~~~~~~~~
```
[R/plot_generation_traits.R:18:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_generation_traits.R#L18) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(generation)
  ^~~~~~~~~~~
```
[R/plot_generation_traits.R:19:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_generation_traits.R#L19) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(generation)
  ^~~~~~~~~~~
```
[R/plot_generation_traits.R:20:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_generation_traits.R#L20) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(binwidth)
  ^~~~~~~~~~~
```
[R/plot_generation_traits.R:21:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_generation_traits.R#L21) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(binwidth)
  ^~~~~~~~~~~
```
[R/plot_generation_traits.R:36:20:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_generation_traits.R#L36) *warning:* **no visible global function definition for ‘%>%’**
```r
  gen_data <- data %>% dplyr::filter(data$t == generation)
                   ^~~
```
[R/plot_population_size.R:13:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_size.R#L13) *warning:* **no visible global function definition for ‘testarg_char’**
```r
  testarg_char(path_to_file)
  ^~~~~~~~~~~~
```
[R/plot_population_size.R:23:5:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_size.R#L23) *style:* **Commented code should be removed.**
```r
  # xgrain <- max(data$t) / 100
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_population_size.R:30:1:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_size.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_hline(yintercept = 1000, linetype = "dashed", color = "grey60") +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:14:1:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_trait_evolution.R#L14) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_population_trait_evolution <- function(path_to_file,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:17:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_trait_evolution.R#L17) *warning:* **no visible global function definition for ‘testarg_char’**
```r
  testarg_char(path_to_file)
  ^~~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:18:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_trait_evolution.R#L18) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(xgrain)
  ^~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:19:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_trait_evolution.R#L19) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(xgrain)
  ^~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:20:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_trait_evolution.R#L20) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(ygrain)
  ^~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:21:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_trait_evolution.R#L21) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(ygrain)
  ^~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:31:5:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/plot_population_trait_evolution.R#L31) *style:* **Commented code should be removed.**
```r
  # xgrain <- max(data$t) / 100
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/run_generation_step.R:13:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L13) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:14:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L14) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(growth_rate)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:15:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L15) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(growth_rate)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:16:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L16) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:17:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L17) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:18:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L18) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_opt)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:19:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L19) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:20:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L20) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:21:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L21) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_width)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:22:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L22) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_width)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:23:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L23) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(mutation_sd)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:24:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L24) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(mutation_sd)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:36:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L36) *warning:* **no visible global function definition for ‘testarg_not_this’**
```r
  testarg_not_this(fitness_pop, Inf)
  ^~~~~~~~~~~~~~~~
```
[R/run_generation_step.R:39:23:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_generation_step.R#L39) *warning:* **no visible global function definition for ‘draw_nb_offspring’**
```r
  nb_offspring_pop <- draw_nb_offspring(fitness = fitness_pop)
                      ^~~~~~~~~~~~~~~~~
```
[R/run_simulation.R:40:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L40) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(init_pop)
  ^~~~~~~~~~~
```
[R/run_simulation.R:41:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L41) *warning:* **no visible global function definition for ‘testarg_char’**
```r
  testarg_char(output_path)
  ^~~~~~~~~~~~
```
[R/run_simulation.R:42:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L42) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(sampling_frequency)
  ^~~~~~~~~~~
```
[R/run_simulation.R:43:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L43) *warning:* **no visible global function definition for ‘testarg_int’**
```r
  testarg_int(sampling_frequency)
  ^~~~~~~~~~~
```
[R/run_simulation.R:44:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L44) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(seed)
  ^~~~~~~~~~~
```
[R/run_simulation.R:45:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L45) *warning:* **no visible global function definition for ‘testarg_int’**
```r
  testarg_int(seed)
  ^~~~~~~~~~~
```
[R/run_simulation.R:46:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L46) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(nb_generations)
  ^~~~~~~~~~~
```
[R/run_simulation.R:47:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L47) *warning:* **no visible global function definition for ‘testarg_int’**
```r
  testarg_int(nb_generations)
  ^~~~~~~~~~~
```
[R/run_simulation.R:48:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L48) *warning:* **no visible global function definition for ‘testarg_not_this’**
```r
  testarg_not_this(nb_generations, c(0, Inf))
  ^~~~~~~~~~~~~~~~
```
[R/run_simulation.R:49:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L49) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(growth_rate)
  ^~~~~~~~~~~
```
[R/run_simulation.R:50:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L50) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(growth_rate)
  ^~~~~~~~~~~
```
[R/run_simulation.R:51:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L51) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/run_simulation.R:52:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L52) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width)
  ^~~~~~~~~~~
```
[R/run_simulation.R:53:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L53) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_opt)
  ^~~~~~~~~~~
```
[R/run_simulation.R:54:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L54) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/run_simulation.R:55:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L55) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/run_simulation.R:56:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L56) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_width)
  ^~~~~~~~~~~
```
[R/run_simulation.R:57:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L57) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_width)
  ^~~~~~~~~~~
```
[R/run_simulation.R:58:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L58) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(mutation_sd)
  ^~~~~~~~~~~
```
[R/run_simulation.R:59:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/run_simulation.R#L59) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(mutation_sd)
  ^~~~~~~~~~~
```
[R/set_sampling_frequency.R:21:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/set_sampling_frequency.R#L21) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(nb_generations)
  ^~~~~~~~~~~
```
[R/set_sampling_frequency.R:22:3:](https://github.com/TheoPannetier/comrad/blob/cc69e6a79816e3a8f7615f112938fd96d7ee037f/R/set_sampling_frequency.R#L22) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(nb_generations)
  ^~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://personal-website-ts-ac6ba3dtp.now.sh
* https://danielagg.com
* https://personal-website-ts.danielagg.now.sh
* https://personal-website-ts-git-master.danielagg.now.sh


This commit has been mentioned on **Discourse Meta**. There might be relevant details there:

https://meta.discourse.org/t/revision-history-for-flagged-post-isnt-comparing-the-correct-revisions/139585/11


This will not work. In exercise 3 you ask students to create a Windows Function App. This creates a Windows App Service Plan in the same RG where you have Linux App Service plans. This is not supported.


This commit addresses some of the issues in #1 by introducing the argument `style`. This will, in time, allow for control over the appearance of the data table.

This commit also includes improvements to the `td` element. This includes adding the cell value to the data attribute `data-value`. A new  class was also rendered `column-n` (where `n` is the column number). This allows for more control over cell alignment.

```r
# in r
datatable(data = iris, id = "tbl")
```

```css
#tbl .column-1 {
   text-align: right;
}
```


Successfully deployed to following URLs:

* https://website-nhjl9mmwq.now.sh
* https://keplersj.com
* https://website.keplersj.now.sh
* https://website-git-master.keplersj.now.sh


Successfully deployed to following URLs:

* https://597w9uun3-pn2oe1ycl.now.sh
* https://johno.com
* https://git-master.johno1.now.sh


Salve a tutti, da qui in poi si ha un problema. Si da per certo che fatturapa_attachment esista, quando invece dipende da questo: https://github.com/OCA/l10n-italy/commit/93e42e904f6e914a6620e3e99f2b0d930c257ffc#diff-5fb11faea2ef6bedb3b026d3f02c689dL67
Se non dovesse essere lanciata la funzione create_fatturapa_attachment_in va in errore la funzione con:

e_invoice_received_date = fatturapa_attachment.create_date.date()
AttributeError: 'bool' object has no attribute 'date'


Beta


Successfully deployed to following URLs:

* https://nordnet-ui-5ygiojm14.now.sh
* https://nordnet-ui.nordnet1.now.sh
* https://nordnet-ui-git-master.nordnet1.now.sh


Successfully deployed to following URLs:

* https://interface-mv2tx1ran.now.sh
* https://melon.avantgarde.finance
* https://interface.avantgarde-finance.now.sh
* https://interface-git-master.avantgarde-finance.now.sh


Successfully deployed to following URLs:

* https://surname-site-kkc54eqzs.now.sh
* https://stickajones.org
* https://surname-site.keplersj.now.sh
* https://surname-site-git-master.keplersj.now.sh


Successfully deployed to following URLs:

* https://biscuit-qgfle3kq9.now.sh
* https://biscui.tech
* https://beta.biscui.tech
* https://biscuit.biscuitech.now.sh
* https://biscuit-git-master.biscuitech.now.sh


170845444_Issue7464 (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (677 of 678 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 677
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.35%25-green.png)


Deploy preview for _website_ ready!

Built with commit 55e50c69ae479858d4830dcd0b9f4ede4b524503

https://zenunu-k3qx0wqwh.now.sh


> I see your token)
It's not my token)

https://core.telegram.org/bots#6-botfather


Makes sense to still try and do morx in vertical if there is no GSUB. Test on the [Chromium bot with this change was succesful](https://chromium-review.googlesource.com/c/chromium/src/+/2020963). Thanks for fine tuning the fix. LGTM.


Successfully deployed to following URLs:

* https://derekmislercom-b4xty8len.now.sh
* https://derekmisler.com
* https://*.derekmisler.com
* https://derekmislercom.derekmisler.now.sh
* https://derekmislercom-git-master.derekmisler.now.sh


Successfully deployed to following URLs:

* https://turing-hw-2-947e90v3q.now.sh
* https://turing-hw-2.now.sh
* https://turing-hw-2.filipobsivac.now.sh
* https://turing-hw-2-git-master.filipobsivac.now.sh


Successfully deployed to following URLs:

* https://frontend-js2uexzv7.now.sh
* https://nonncov.now.sh
* https://frontend.wuhan-support.now.sh
* https://frontend-git-dev.wuhan-support.now.sh


Why?


Successfully deployed to following URLs:

* https://gatsby-forestry-iujkmh8yl.now.sh
* https://gatsby-forestry.now.sh
* https://gatsby-forestry.paulbremer.now.sh
* https://gatsby-forestry-git-master.paulbremer.now.sh


Hard times lol


so fast


Yeah sure 🙂.


Reeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee


Successfully deployed to following URLs:

* https://ursusprados-frontend-mmxqivsha.now.sh
* https://ursusprados.now.sh
* https://ursusprados-frontend.romilo903.now.sh
* https://ursusprados-frontend-git-master.romilo903.now.sh


Successfully deployed to following URLs:

* https://programming-20-elqk1qqi4.now.sh
* https://programming-20.mooc.fi
* https://java-programming.mooc.fi
* https://programming-20.mooc.now.sh
* https://programming-20-git-master.mooc.now.sh


Hi csprance, How can I install Secrets?


TeamCity Identity and Access Management / identity-hostedpages [Build 1257](https://teamcity.nice.org.uk/viewLog.html?buildId=65161&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) (new) Build time: 00:00:20


TeamCity Identity and Access Management / identity-hostedpages [Build 1258](https://teamcity.nice.org.uk/viewLog.html?buildId=65162&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) is now running


I'm getting an error from this line: aapl['log_return'] = np.log_price.diff()


Successfully deployed to following URLs:

* https://nteract-site-7tag4l0a8.now.sh
* https://nteract.io
* https://nteract-site.nteract.now.sh
* https://nteract-site-git-master.nteract.now.sh


Hi elm michael here


Successfully deployed to following URLs:

* https://crm-frontend-4iznegdx8.now.sh
* https://crm-frontend-omega-ten.now.sh
* https://crm-frontend.khansen0415.now.sh
* https://crm-frontend-git-master.khansen0415.now.sh


Successfully deployed to following URLs:

* https://jobsite-kn60p4m6h.now.sh
* https://jobsite.now.sh
* https://jobsite.dylandamsma.now.sh
* https://jobsite-git-master.dylandamsma.now.sh


Successfully deployed to following URLs:

* https://carousel-jlesydf31.now.sh
* https://carousel-beta-five.now.sh
* https://carousel.chet444.now.sh
* https://carousel-git-master.chet444.now.sh


Successfully deployed to following URLs:

* https://jobsite-6w2picuta.now.sh
* https://jobsite.now.sh
* https://jobsite.dylandamsma.now.sh
* https://jobsite-git-master.dylandamsma.now.sh


You got it!


Successfully deployed to following URLs:

* https://trendy-resume-bg5y3gv4v.now.sh
* https://trendy-resume.now.sh
* https://trendy-resume.junhoyeo.now.sh
* https://trendy-resume-git-master.junhoyeo.now.sh


comment


Successfully deployed to following URLs:

* https://jobsite-6v0ct6pw2.now.sh
* https://jobsite.now.sh
* https://jobsite.dylandamsma.now.sh
* https://jobsite-git-master.dylandamsma.now.sh


![Difference between blocks](https://raw.githubusercontent.com/jan1616/fll2020/3a27eafa545946ff876fea5dc5971ebb415e8e5b/.github/makecode/blocksdiff.png)


新規登録データのみが先頭に来るわけではなく、全てのデータを降順、すなわちデカいidから小さいidになっているだけなので結果的に新規データが先頭に来ているように見える。テストデータはあまり実感ないからね。


Names must be added once per game.
and names should be taken from msg.


Deployment failed with the following error:

~~~
Couldn't parse JSON file /tmp/eHHVEawcuUQkQkQLcnI2sKrV/repo/now.json.
~~~


На другой машине ( Ubuntu)

lizzy@vb:~$ git config --global user.name "Sayapina Liza"
lizzy@vb:~$ git config --global user.email sayapina@reg.ru
lizzy@vb:~$ git config --list
user.name=Sayapina Liza
user.email=sayapina@reg.ru
lizzy@vb:~$ git clone https://github.com/SayapinaLiza/My_Central_Repo.git
Клонирование в «My_Central_Repo»…
remote: Enumerating objects: 8, done.
remote: Counting objects: 100% (8/8), done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 8 (delta 0), reused 0 (delta 0), pack-reused 0
Распаковка объектов: 100% (8/8), готово.
lizzy@vb:~$ cd My_Central_Repo
lizzy@vb:~/My_Central_Repo$
lizzy@vb:~/My_Central_Repo$ touch fileA.txt
lizzy@vb:~/My_Central_Repo$ touch fileB.txt
izzy@vb:~/My_Central_Repo$ git status
На ветке master
Ваша ветка обновлена в соответствии с «origin/master».

Неотслеживаемые файлы:
  (используйте «git add <файл>…», чтобы добавить в то, что будет включено в коммит)

	fileA.txt
	fileB.txt

ничего не добавлено в коммит, но есть неотслеживаемые файлы (используйте «git add», чтобы отслеживать их)
lizzy@vb:~/My_Central_Repo$ git add fileA.txt
lizzy@vb:~/My_Central_Repo$ git add fileB.txt
lizzy@vb:~/My_Central_Repo$ git status
На ветке master
Ваша ветка обновлена в соответствии с «origin/master».

Изменения, которые будут включены в коммит:
  (используйте «git reset HEAD <файл>…», чтобы убрать из индекса)

	новый файл:    fileA.txt
	новый файл:    fileB.txt
lizzy@vb:~/My_Central_Repo$ git commit -m "New_Files"
[master 9a2a195] New_Files
 2 files changed, 2 insertions(+)
 create mode 100644 fileA.txt
 create mode 100644 fileB.txt
lizzy@vb:~/My_Central_Repo$ git push
Username for 'https://github.com': SayapinaLiza
Password for 'https://SayapinaLiza@github.com':
Перечисление объектов: 5, готово.
Подсчет объектов: 100% (5/5), готово.
При сжатии изменений используется до 3 потоков
Сжатие объектов: 100% (2/2), готово.
Запись объектов: 100% (4/4), 375 bytes | 187.00 KiB/s, готово.
Всего 4 (изменения 0), повторно использовано 0 (изменения 0)
To https://github.com/SayapinaLiza/My_Central_Repo.git
   1818179..9a2a195  master -> master


> names should be taken from msg
Why?


@Pixelated24 I do not see Answers 10-13, thus -20 points. Also, please add your actual name to your account as well.


Successfully deployed to following URLs:

* https://guac-web-9eolt8lv7.now.sh
* https://guac.live
* https://www.guac.live
* https://guac-web.guaclive.now.sh
* https://guac-web-git-master.guaclive.now.sh


Successfully deployed to following URLs:

* https://turing-hw-2-4rsn110c0.now.sh
* https://turing-hw-2.now.sh
* https://turing-hw-2.filipobsivac.now.sh
* https://turing-hw-2-git-master.filipobsivac.now.sh


They already are. This is a wip commit.


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/get_norm_brts.R:22:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:47:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L47) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:70:27:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L70) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:77:25:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L77) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:102:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:107:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:108:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L108) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:175:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L175) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:176:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L176) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:177:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L177) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:178:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L178) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:180:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L180) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:181:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L181) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:182:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L182) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L183) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:222:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L222) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:223:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L223) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:224:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L224) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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_brts.R:40:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_brts.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    regexp = "branching times must be negative, for example -3 time units since the present"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:66:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_brts.R#L66) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:30:16:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:95:16:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L95) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:96:16:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


You don;t need setter.


# Specs execution successful
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### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Hmm I handle for null in the receiver


UnNecessary I agree


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using `this` is unnecessary.


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Stream builder here you come right?


![Difference between blocks](https://raw.githubusercontent.com/asexto/star-fruits/69eb91ea75d592209c0cd59c7ae5b11825aa495e/.makecode/blocksdiff.png)


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Deployment failed with the following error:

~~~
Schema verification failed
~~~


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hmm, i can leave a comment but seem to not be figuring out the edit thing.


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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):
~~~


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Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v1-with-alias-harfydiuwi.now.sh
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Failed to assign a domain to your deployment due to the following error:

~~~
The domain drrhznv0bv.com is not verfied and cannot be used as an alias.
~~~

([Learn more](http://localhost:3000/zeit-github-test-dev/github-e2e-test-dev-domain-issues/1r7k0vnfj) or [visit](https://github-e2e-test-dev-domain-issues-1r7k0vnfj.now.sh) the non-aliased deployment)


Note to myself. We probably also want to do this for everything in bin. (At least) when running `cuda-gdb`, it tries to dlopen libcuda.so and cannot find it unless LD_LIBRARY_PATH or LD_PRELOAD is set. By having addOpenGLRunpath added this wouldn't be needed (given that /run/opengl-driver/lib is populated with all the cuda libs).


This better?

On 26-Jan-2020, at 1:53 PM, thelocalite <notifications@github.com<mailto:notifications@github.com>> wrote:

Don’t know some fucking config issue. Will check later.

> On 26-Jan-2020, at 1:52 PM, technologic808 <notifications@github.com<mailto:notifications@github.com>> wrote:
>
> Don't reply as the localite
> Why are you logged in as localite anyway?
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub <https://github.com/thelocalite/thelocalite-core/commit/6d1470012e4a33d86ab8bee7094e247832cb885f?email_source=notifications&email_token=AOBM37KMXJV5ZCK6N2CUGWDQ7VB3ZA5CNFSM4KLVRZGKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBDIFFO#commitcomment-36967598>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOBM37OMVO5R4J6FSWHXGFDQ7VB3ZANCNFSM4KLVRZGA>.
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@JuliaRegistrator register


Registration pull request created: [JuliaRegistries/General/8458](https://github.com/JuliaRegistries/General/pull/8458)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.25.0 -m "<description of version>" efdd2048d7e04c8cf6ce9ac9f74bb5c6cde53575
git push origin v0.25.0
```


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That's what the `empty($rebuild)` prevents.


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@ceylan12345 Was zum Teufel redest du?


Successfully deployed to following URLs:

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Registration pull request created: [JuliaRegistries/General/8459](https://github.com/JuliaRegistries/General/pull/8459)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.16.1 -m "<description of version>" e63b63ac4b5ca4215acc776faa731c3508559b35
git push origin v0.16.1
```


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/get_norm_brts.R:22:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:47:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L47) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:70:27:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L70) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:77:25:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L77) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:102:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:107:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:108:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L108) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:175:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L175) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:176:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L176) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:177:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L177) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:178:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L178) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:180:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L180) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:181:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L181) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:182:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L182) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:5:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L183) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:222:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L222) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:223:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L223) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:224:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/R/nltt_diff_exact_extinct.R#L224) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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_brts.R:40:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_brts.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    regexp = "branching times must be negative, for example -3 time units since the present"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:66:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_brts.R#L66) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:30:16:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:95:16:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L95) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:96:16:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


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no ^^


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That was #3449


@liuzfesp Please why was this changed? Is there a problem with lower output power? We want to be able to set it down to 0 dBm.


Good to know - I actually just spent 4 hours yesterday trying to get pylibmc working by following the docs but it simply wouldn't work.  Came here, saw the code update, switched to bmemcached and it magically worked!


- Change borrowBook to PROCEDURE
- borrowBook now take arguments
- Add error handling


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