[R/create_test_simulation_output.R:8:31:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/create_test_simulation_output.R#L8) *style:* **Commas should always have a space after.**
```r
  pars_equal <- c(2.550687345,2.683454548,Inf,0.00933207,1.010073119)
                              ^
```
[R/create_test_simulation_output.R:8:43:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/create_test_simulation_output.R#L8) *style:* **Commas should always have a space after.**
```r
  pars_equal <- c(2.550687345,2.683454548,Inf,0.00933207,1.010073119)
                                          ^
```
[R/create_test_simulation_output.R:8:47:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/create_test_simulation_output.R#L8) *style:* **Commas should always have a space after.**
```r
  pars_equal <- c(2.550687345,2.683454548,Inf,0.00933207,1.010073119)
                                              ^
```
[R/create_test_simulation_output.R:8:58:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/create_test_simulation_output.R#L8) *style:* **Commas should always have a space after.**
```r
  pars_equal <- c(2.550687345,2.683454548,Inf,0.00933207,1.010073119)
                                                         ^
```
[R/DAISIE_area_params.R:15:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_area_params.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
are_area_params <- function(area_params) {
^
```
[R/DAISIE_area_params.R:32:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_area_params.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
#' @param proportional_peak_t value from 0 to 1 indicating where in the island's history the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_area_params.R:37:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_area_params.R#L37) *style:* **Lines should not be more than 80 characters.**
```r
#' @return list of numerical values containing area parameters for island ontogeny
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:4:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L4) *style:* **functions should have cyclomatic complexity of less than 15, this has 35.**
```r
are_rates <- function(x) {
^
```
[R/DAISIE_check_format.R:31:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L31) *style:* **Lines should not be more than 80 characters.**
```r
  if (island_ontogeny != "const" && island_ontogeny != "linear" && island_ontogeny != "beta") return(FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:44:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
  if (island_ontogeny != 0 && island_ontogeny != 1 && island_ontogeny != 2) return(FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:50:76:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L50) *style:* **Trailing whitespace is superfluous.**
```r
#' @param simulation_outputs A list with matrices and vectors of simulation
                                                                           ^
```
[R/DAISIE_check_format.R:51:27:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L51) *style:* **Trailing whitespace is superfluous.**
```r
#' produced by DAISIE_sim.
                          ^~
```
[R/DAISIE_check_format.R:57:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L57) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/DAISIE_check_format.R:58:51:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L58) *style:* **Trailing whitespace is superfluous.**
```r
#' expect_false(is_simulation_outputs("nonsense"))
                                                  ^
```
[R/DAISIE_check_format.R:59:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_check_format.R:60:58:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L60) *style:* **Trailing whitespace is superfluous.**
```r
#' simulation_outputs <- create_test_simulation_outputs()
                                                         ^
```
[R/DAISIE_check_format.R:65:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L65) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_check_format.R:66:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    if (!"island_age" %in% names(simulation_outputs[[n_replicate]][[1]])) return(FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:68:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
        !"not_present_type1" %in% names(simulation_outputs[[n_replicate]][[1]]))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:71:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
    if (!"stt_all" %in% names(simulation_outputs[[n_replicate]][[1]])) return(FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:73:7:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L73) *style:* **Commented code should be removed.**
```r
    # if (!"branching_times" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:74:7:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L74) *style:* **Commented code should be removed.**
```r
    # if (!"stac" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:75:7:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L75) *style:* **Commented code should be removed.**
```r
    # if (!"missing_species" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:80:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_check_format.R#L80) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_create_island.R:5:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param island_spec matrix with species on island (state of system at each time point)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:7:75:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#' @param keep_final_state logical indicating if final state of simulation
                                                                          ^
```
[R/DAISIE_create_island.R:10:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
#' @return list with the island information, composed stt table, branching times of extant
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:12:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_create_island <- function(stt_table,
^~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:12:44:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
DAISIE_create_island <- function(stt_table,
                                           ^
```
[R/DAISIE_create_island.R:13:44:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L13) *style:* **Trailing whitespace is superfluous.**
```r
                                 totaltime,
                                           ^
```
[R/DAISIE_create_island.R:14:46:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L14) *style:* **Trailing whitespace is superfluous.**
```r
                                 island_spec,
                                             ^
```
[R/DAISIE_create_island.R:17:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L17) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_create_island.R:18:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L18) *style:* **Lines should not be more than 80 characters.**
```r
  ### if there are no species on the island branching_times = island_age, stac = 0, missing_species = 0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:18:104:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L18) *style:* **Trailing whitespace is superfluous.**
```r
  ### if there are no species on the island branching_times = island_age, stac = 0, missing_species = 0
                                                                                ^
```
[R/DAISIE_create_island.R:19:27:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L19) *style:* **Commas should always have a space after.**
```r
  if (length(island_spec[,1]) == 0) {
                          ^
```
[R/DAISIE_create_island.R:20:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L20) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_create_island.R:21:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L21) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_create_island.R:41:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L41) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_create_island.R:43:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_create_island.R:45:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
    island_spec[, "branching time (BP)"] <- totaltime - as.numeric(island_spec[, "branching time (BP)"])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:46:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
    island_spec[, "Colonisation time (BP)"] <- totaltime - as.numeric(island_spec[, "Colonisation time (BP)"])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:47:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L47) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_create_island.R:54:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L54) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/DAISIE_create_island.R:56:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
      colonists_present <- sort(as.numeric(unique(island_spec[, 'Mainland Ancestor'])))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:56:65:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L56) *style:* **Only use double-quotes.**
```r
      colonists_present <- sort(as.numeric(unique(island_spec[, 'Mainland Ancestor'])))
                                                                ^~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:57:60:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L57) *style:* **Trailing whitespace is superfluous.**
```r
      number_colonists_present <- length(colonists_present)
                                                           ^
```
[R/DAISIE_create_island.R:58:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L58) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/DAISIE_create_island.R:59:35:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
      island_clades_info <- list()
                                  ^~
```
[R/DAISIE_create_island.R:61:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
        subset_island <- island_spec[which(island_spec[, 'Mainland Ancestor'] == colonists_present[i]),]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:61:58:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L61) *style:* **Only use double-quotes.**
```r
        subset_island <- island_spec[which(island_spec[, 'Mainland Ancestor'] == colonists_present[i]),]
                                                         ^~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:61:104:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L61) *style:* **Commas should always have a space after.**
```r
        subset_island <- island_spec[which(island_spec[, 'Mainland Ancestor'] == colonists_present[i]),]
                                                                                ^
```
[R/DAISIE_create_island.R:61:105:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L61) *style:* **Trailing whitespace is superfluous.**
```r
        subset_island <- island_spec[which(island_spec[, 'Mainland Ancestor'] == colonists_present[i]),]
                                                                                ^
```
[R/DAISIE_create_island.R:62:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L62) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/DAISIE_create_island.R:63:37:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L63) *style:* **Only use double-quotes.**
```r
        if (class(subset_island) != 'matrix') {
                                    ^~~~~~~~
```
[R/DAISIE_create_island.R:67:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L67) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/DAISIE_create_island.R:69:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
                                                      island_spec = subset_island,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:71:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
                                                      keep_final_state = keep_final_state)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:77:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L77) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/DAISIE_create_island.R:80:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L80) *style:* **Lines should not be more than 80 characters.**
```r
                       taxon_list = island_clades_info, island_spec = island_spec)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:84:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_create_island.R#L84) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_data.R:2:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:7:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' #' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:12:34:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
#' the following elements.\cr \cr
                                 ^
```
[R/DAISIE_data.R:47:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:52:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:92:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L92) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Colonization and branching times of 8 terrestrial avifaunal clades in table
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:96:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A table containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:103:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
#' * Non_endemic: for cases where both island and non-island populations of the species have been sampled) \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:104:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L104) *style:* **Lines should not be more than 80 characters.**
```r
#' * Non_endemic_MaxAge: for cases where island population of the species has not
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:124:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L124) *style:* **Lines should not be more than 80 characters.**
```r
#' @title 1000 islands in RAW format simulated with the ML parameters of the CR model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:125:27:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L125) *style:* **Trailing whitespace is superfluous.**
```r
#' for the Galapagos data.
                          ^
```
[R/DAISIE_data.R:127:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L127) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:158:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L158) *style:* **Lines should not be more than 80 characters.**
```r
#' @title 1000 islands in DAISIE format simulated with the ML parameters of the CR
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:161:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L161) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:165:42:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L165) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{$island_age} - the island age\cr
                                         ^
```
[R/DAISIE_data.R:197:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L197) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:247:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L247) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:256:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L256) *style:* **Lines should not be more than 80 characters.**
```r
#' The following elements of the list each contains information on a single colonist lineage
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:270:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L270) *style:* **Lines should not be more than 80 characters.**
```r
#' #' \code{$missing_species} - number of island species that were not sampled for
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:286:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L286) *style:* **Lines should not be more than 80 characters.**
```r
#' format, accepted by DAISIE_ML, DAISIE_SR_ML, DAISIE_loglik_all and DAISIE_SR_loglik_all
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:290:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L290) *style:* **Lines should not be more than 80 characters.**
```r
#' #' @description A list containing the colonization and branching times of the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:290:81:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L290) *style:* **Trailing whitespace is superfluous.**
```r
#' #' @description A list containing the colonization and branching times of the
                                                                                ^
```
[R/DAISIE_data.R:295:34:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L295) *style:* **Trailing whitespace is superfluous.**
```r
#' the following elements.\cr \cr
                                 ^
```
[R/DAISIE_data.R:321:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L321) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:322:77:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_data.R#L322) *style:* **Trailing whitespace is superfluous.**
```r
#' @source Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (submitted).
                                                                            ^
```
[R/DAISIE_dataprep.R:2:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:7:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:10:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:86:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/DAISIE_dataprep.R:87:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:88:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L88) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:89:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L89) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:90:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L90) *style:* **Lines should not be more than 80 characters.**
```r
#' ### Create Galapagos data object where all taxa have the same macroevolutionary process
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:91:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:98:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L98) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:100:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:100:82:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L100) *style:* **Trailing whitespace is superfluous.**
```r
#' # for the Darwin's finches. One process applies to type 1 species (all species
                                                                                ^
```
[R/DAISIE_dataprep.R:101:79:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L101) *style:* **Trailing whitespace is superfluous.**
```r
#' # except for Darwin's finches) and the other applies only to type 2 species
                                                                              ^
```
[R/DAISIE_dataprep.R:104:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L104) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:113:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L113) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:114:80:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L114) *style:* **Trailing whitespace is superfluous.**
```r
#' ### Create Galapagos data object with a distinct macroevolutionary processes
                                                                               ^
```
[R/DAISIE_dataprep.R:115:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L115) *style:* **Lines should not be more than 80 characters.**
```r
#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:116:79:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L116) *style:* **Trailing whitespace is superfluous.**
```r
#' # except for Darwin's finches) and the other applies only to type 2 species
                                                                              ^
```
[R/DAISIE_dataprep.R:117:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
#' # (Darwin's finches). Set fraction of potential colonists of type 2 to be 0.163.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:118:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L118) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:128:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L128) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:130:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
^
```
[R/DAISIE_dataprep.R:130:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Lines should not be more than 80 characters.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:130:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
^~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:130:17:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Use <-, not =, for assignment.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
                ^
```
[R/DAISIE_dataprep.R:130:38:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Commas should always have a space after.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
                                     ^
```
[R/DAISIE_dataprep.R:130:49:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Commas should always have a space after.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
                                                ^
```
[R/DAISIE_dataprep.R:130:49:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
                                                ^
```
[R/DAISIE_dataprep.R:130:51:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Commas should always have a space after.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
                                                  ^
```
[R/DAISIE_dataprep.R:130:74:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Commas should always have a space after.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
                                                                         ^
```
[R/DAISIE_dataprep.R:130:131:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L130) *style:* **Commas should always have a space after.**
```r
DAISIE_dataprep = function(datatable,island_age,M,number_clade_types = 1,list_type2_clades = NA, prop_type2_pool = "proportional",epss = 1E-5)
                                                                                ^
```
[R/DAISIE_dataprep.R:131:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L131) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/DAISIE_dataprep.R:132:24:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L132) *style:* **Use <-, not =, for assignment.**
```r
  number_colonisations = nrow(datatable)
                       ^
```
[R/DAISIE_dataprep.R:133:12:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L133) *style:* **Use <-, not =, for assignment.**
```r
  datalist = list()
           ^
```
[R/DAISIE_dataprep.R:134:13:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L134) *style:* **Variable and function name style should be snake_case.**
```r
  datatable$Missing_species<-as.numeric(as.character(datatable$Missing_species))
            ^~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:134:28:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L134) *style:* **Put spaces around all infix operators.**
```r
  datatable$Missing_species<-as.numeric(as.character(datatable$Missing_species))
                          ~^~~
```
[R/DAISIE_dataprep.R:135:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L135) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_dataprep.R:136:5:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L136) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(number_clade_types == 1)
    ^
```
[R/DAISIE_dataprep.R:137:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L137) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/DAISIE_dataprep.R:138:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L138) *style:* **Lines should not be more than 80 characters.**
```r
    datalist[[1]] = list(island_age=island_age,not_present=(M - number_colonisations))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:138:19:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L138) *style:* **Use <-, not =, for assignment.**
```r
    datalist[[1]] = list(island_age=island_age,not_present=(M - number_colonisations))
                  ^
```
[R/DAISIE_dataprep.R:138:36:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L138) *style:* **Put spaces around all infix operators.**
```r
    datalist[[1]] = list(island_age=island_age,not_present=(M - number_colonisations))
                                  ~^~
```
[R/DAISIE_dataprep.R:138:48:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L138) *style:* **Commas should always have a space after.**
```r
    datalist[[1]] = list(island_age=island_age,not_present=(M - number_colonisations))
                                               ^
```
[R/DAISIE_dataprep.R:138:59:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L138) *style:* **Put spaces around all infix operators.**
```r
    datalist[[1]] = list(island_age=island_age,not_present=(M - number_colonisations))
                                                         ~^~
```
[R/DAISIE_dataprep.R:138:60:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L138) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    datalist[[1]] = list(island_age=island_age,not_present=(M - number_colonisations))
                                                           ^
```
[R/DAISIE_dataprep.R:140:5:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L140) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(number_clade_types == 2)
    ^
```
[R/DAISIE_dataprep.R:141:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L141) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/DAISIE_dataprep.R:142:32:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L142) *style:* **Use <-, not =, for assignment.**
```r
    number_type2_colonisations = length(list_type2_clades)
                               ^
```
[R/DAISIE_dataprep.R:143:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L143) *style:* **Lines should not be more than 80 characters.**
```r
    number_type1_colonisations = number_colonisations - number_type2_colonisations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:143:32:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L143) *style:* **Use <-, not =, for assignment.**
```r
    number_type1_colonisations = number_colonisations - number_type2_colonisations
                               ^
```
[R/DAISIE_dataprep.R:145:5:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L145) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/DAISIE_dataprep.R:146:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
      not_present_type1 = DDD::roundn((M/number_colonisations) * number_type1_colonisations) - number_type1_colonisations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:146:25:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L146) *style:* **Use <-, not =, for assignment.**
```r
      not_present_type1 = DDD::roundn((M/number_colonisations) * number_type1_colonisations) - number_type1_colonisations
                        ^
```
[R/DAISIE_dataprep.R:146:41:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L146) *style:* **Put spaces around all infix operators.**
```r
      not_present_type1 = DDD::roundn((M/number_colonisations) * number_type1_colonisations) - number_type1_colonisations
                                       ~^~
```
[R/DAISIE_dataprep.R:147:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
      not_present_type2 = DDD::roundn((M/number_colonisations) * number_type2_colonisations) - number_type2_colonisations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:147:25:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L147) *style:* **Use <-, not =, for assignment.**
```r
      not_present_type2 = DDD::roundn((M/number_colonisations) * number_type2_colonisations) - number_type2_colonisations
                        ^
```
[R/DAISIE_dataprep.R:147:41:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L147) *style:* **Put spaces around all infix operators.**
```r
      not_present_type2 = DDD::roundn((M/number_colonisations) * number_type2_colonisations) - number_type2_colonisations
                                       ~^~
```
[R/DAISIE_dataprep.R:149:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L149) *style:* **Lines should not be more than 80 characters.**
```r
      not_present_type1 = DDD::roundn(M * (1 - prop_type2_pool)) - number_type1_colonisations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:149:25:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L149) *style:* **Use <-, not =, for assignment.**
```r
      not_present_type1 = DDD::roundn(M * (1 - prop_type2_pool)) - number_type1_colonisations
                        ^
```
[R/DAISIE_dataprep.R:150:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L150) *style:* **Lines should not be more than 80 characters.**
```r
      not_present_type2 = DDD::roundn(M * prop_type2_pool) - number_type2_colonisations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:150:25:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L150) *style:* **Use <-, not =, for assignment.**
```r
      not_present_type2 = DDD::roundn(M * prop_type2_pool) - number_type2_colonisations
                        ^
```
[R/DAISIE_dataprep.R:152:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L152) *style:* **Lines should not be more than 80 characters.**
```r
    datalist[[1]] = list(island_age = island_age, not_present_type1 = not_present_type1, not_present_type2 = not_present_type2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:152:19:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L152) *style:* **Use <-, not =, for assignment.**
```r
    datalist[[1]] = list(island_age = island_age, not_present_type1 = not_present_type1, not_present_type2 = not_present_type2)
                  ^
```
[R/DAISIE_dataprep.R:155:3:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L155) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/DAISIE_dataprep.R:156:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L156) *style:* **Lines should not be more than 80 characters.**
```r
    datalist[[i + 1]] = list(colonist_name = as.character(datatable[i,"Clade_name"]),branching_times = NA,stac = NA,missing_species = datatable[i,"Missing_species"], type1or2 = 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:156:23:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L156) *style:* **Use <-, not =, for assignment.**
```r
    datalist[[i + 1]] = list(colonist_name = as.character(datatable[i,"Clade_name"]),branching_times = NA,stac = NA,missing_species = datatable[i,"Missing_species"], type1or2 = 1)
                      ^
```
[R/DAISIE_dataprep.R:156:71:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L156) *style:* **Commas should always have a space after.**
```r
    datalist[[i + 1]] = list(colonist_name = as.character(datatable[i,"Clade_name"]),branching_times = NA,stac = NA,missing_species = datatable[i,"Missing_species"], type1or2 = 1)
                                                                      ^
```
[R/DAISIE_dataprep.R:156:86:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L156) *style:* **Commas should always have a space after.**
```r
    datalist[[i + 1]] = list(colonist_name = as.character(datatable[i,"Clade_name"]),branching_times = NA,stac = NA,missing_species = datatable[i,"Missing_species"], type1or2 = 1)
                                                                                ^
```
[R/DAISIE_dataprep.R:156:107:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L156) *style:* **Commas should always have a space after.**
```r
    datalist[[i + 1]] = list(colonist_name = as.character(datatable[i,"Clade_name"]),branching_times = NA,stac = NA,missing_species = datatable[i,"Missing_species"], type1or2 = 1)
                                                                                ^
```
[R/DAISIE_dataprep.R:156:117:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L156) *style:* **Commas should always have a space after.**
```r
    datalist[[i + 1]] = list(colonist_name = as.character(datatable[i,"Clade_name"]),branching_times = NA,stac = NA,missing_species = datatable[i,"Missing_species"], type1or2 = 1)
                                                                                ^
```
[R/DAISIE_dataprep.R:156:147:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L156) *style:* **Commas should always have a space after.**
```r
    datalist[[i + 1]] = list(colonist_name = as.character(datatable[i,"Clade_name"]),branching_times = NA,stac = NA,missing_species = datatable[i,"Missing_species"], type1or2 = 1)
                                                                                ^
```
[R/DAISIE_dataprep.R:157:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L157) *style:* **Lines should not be more than 80 characters.**
```r
    the_brts = rev(sort(as.numeric(unlist(strsplit(as.character(datatable[i,"Branching_times"]),split = ",")))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:157:14:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L157) *style:* **Use <-, not =, for assignment.**
```r
    the_brts = rev(sort(as.numeric(unlist(strsplit(as.character(datatable[i,"Branching_times"]),split = ",")))))
             ^
```
[R/DAISIE_dataprep.R:157:77:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L157) *style:* **Commas should always have a space after.**
```r
    the_brts = rev(sort(as.numeric(unlist(strsplit(as.character(datatable[i,"Branching_times"]),split = ",")))))
                                                                            ^
```
[R/DAISIE_dataprep.R:157:97:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L157) *style:* **Commas should always have a space after.**
```r
    the_brts = rev(sort(as.numeric(unlist(strsplit(as.character(datatable[i,"Branching_times"]),split = ",")))))
                                                                                ^
```
[R/DAISIE_dataprep.R:158:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L158) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_dataprep.R:159:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:159:7:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
      ^
```
[R/DAISIE_dataprep.R:159:21:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Put spaces around all infix operators.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                   ~^~
```
[R/DAISIE_dataprep.R:159:33:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                ^
```
[R/DAISIE_dataprep.R:159:46:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Only use double-quotes.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                             ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:159:70:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Commas should always have a space after.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                     ^
```
[R/DAISIE_dataprep.R:159:84:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Commas should always have a space after.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^
```
[R/DAISIE_dataprep.R:159:84:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Only use double-quotes.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^~~~~~~
```
[R/DAISIE_dataprep.R:159:92:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Commas should always have a space after.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^
```
[R/DAISIE_dataprep.R:159:117:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Commas should always have a space after.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^
```
[R/DAISIE_dataprep.R:159:132:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Commas should always have a space after.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^
```
[R/DAISIE_dataprep.R:159:132:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Only use double-quotes.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:159:160:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Commas should always have a space after.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^
```
[R/DAISIE_dataprep.R:159:163:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Put spaces around all infix operators.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ~^~
```
[R/DAISIE_dataprep.R:159:164:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Only use double-quotes.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^~
```
[R/DAISIE_dataprep.R:159:168:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L159) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                                                                                ^
```
[R/DAISIE_dataprep.R:160:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L160) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_dataprep.R:161:7:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L161) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(the_brts) == 1)
      ^
```
[R/DAISIE_dataprep.R:161:30:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L161) *style:* **Trailing whitespace is superfluous.**
```r
    if(length(the_brts) == 1)
                             ^
```
[R/DAISIE_dataprep.R:162:5:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L162) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/DAISIE_dataprep.R:163:1:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L163) *style:* **Lines should not be more than 80 characters.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,min(the_brts,island_age - epss))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:163:41:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L163) *style:* **Use <-, not =, for assignment.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,min(the_brts,island_age - epss))
                                        ^
```
[R/DAISIE_dataprep.R:163:56:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L163) *style:* **Commas should always have a space after.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,min(the_brts,island_age - epss))
                                                       ^
```
[R/DAISIE_dataprep.R:163:69:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L163) *style:* **Commas should always have a space after.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,min(the_brts,island_age - epss))
                                                                    ^
```
[R/DAISIE_dataprep.R:165:7:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L165) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(the_brts) > 1)
      ^
```
[R/DAISIE_dataprep.R:165:29:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L165) *style:* **Trailing whitespace is superfluous.**
```r
    if(length(the_brts) > 1)
                            ^~
```
[R/DAISIE_dataprep.R:166:5:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L166) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/DAISIE_dataprep.R:167:41:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L167) *style:* **Use <-, not =, for assignment.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,the_brts)
                                        ^
```
[R/DAISIE_dataprep.R:167:56:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L167) *style:* **Commas should always have a space after.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,the_brts)
                                                       ^
```
[R/DAISIE_dataprep.R:169:7:](https://github.com/rsetienne/DAISIE/blob/17929de4d166aba1b62bd7cc07b9f18c67ee3713/R/DAISIE_dataprep.R#L169) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(datatable[i,"Status"] == "Non_endemic_MaxAge")
      ^
```


Successfully aliased the URL <https://boboidreamgithubio-rnnmt4afa.now.sh> to the following aliases:

* https://www.wenboz.com
* https://wenboz.com
* https://boboidreamgithubio.wenboz.now.sh
* https://boboidreamgithubio-git-master.wenboz.now.sh


Hi, @YumeMichi . I actually tries that, but it required non-trivial changes to `mm/` dir in kernel sources, and backporting seals made my device kernel not bootable. But I only needed to have `memfd_create()` working and not seals, so I decided to not invest my time into such an old, outdated and insecure kernel anyway, so I decided to skip that. Read more details at https://gitlab.com/postmarketOS/pmaports/merge_requests/479


[R/are_mrca_taxa_names_in_fastas.R:7:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/are_mrca_taxa_names_in_fastas.R#L7) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
are_mrca_taxa_names_in_fastas <- function(
^
```
[R/are_mrca_taxa_non_intersecting.R:13:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/are_mrca_taxa_non_intersecting.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
are_mrca_taxa_non_intersecting <- function(mrca_priors) {
^
```
[R/check_mrca_prior.R:27:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/check_mrca_prior.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 31.**
```r
check_mrca_prior <- function(mrca_prior) {
^
```
[R/create_beast2_input.R:18:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/create_beast2_input.R#L18) *style:* **functions should have cyclomatic complexity of less than 15, this has 36.**
```r
create_beast2_input <- function(
^
```
[R/create_beast2_input.R:223:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/create_beast2_input.R#L223) *style:* **Lines should not be more than 80 characters.**
```r
    ids = get_alignment_ids_from_fasta_filenames(fasta_filenames = input_filenames),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input.R:235:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/create_beast2_input.R#L235) *style:* **Lines should not be more than 80 characters.**
```r
    ids = get_alignment_ids_from_fasta_filenames(fasta_filenames = input_filenames),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_ids.R:53:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/get_alignment_ids.R#L53) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_alignment_ids_from_fasta_filenames <- function(fasta_filenames) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_ids.R:58:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/get_alignment_ids.R#L58) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/init_distr.R:9:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/init_distr.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
init_distr <- function(
^
```
[R/is_distr.R:37:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/is_distr.R#L37) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
is_distr <- function(
^
```
[R/is_inference_model.R:8:5:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/is_inference_model.R#L8) *warning:* **no visible global function definition for ‘check_inference_model’**
```r
    check_inference_model(x)
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_init_site_model.R:36:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/is_init_site_model.R#L36) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
is_init_gtr_site_model <- function(
^
```
[R/is_mcmc.R:11:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/is_mcmc.R#L11) *style:* **functions should have cyclomatic complexity of less than 15, this has 19.**
```r
is_mcmc <- function(
^
```
[R/is_site_model.R:55:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/is_site_model.R#L55) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
is_gtr_site_model <- function(
^
```
[R/is_site_model.R:171:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/is_site_model.R#L171) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
is_tn93_site_model <- function(
^
```
[R/parameter_to_xml.R:11:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/parameter_to_xml.R#L11) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_subst_model.R:7:1:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/R/site_model_to_xml_subst_model.R#L7) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
site_model_to_xml_subst_model <- function(
^
```
[tests/testthat/test-create_nested_sampling_mcmc.R:44:71:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/tests/testthat/test-create_nested_sampling_mcmc.R#L44) *style:* **Commas should always have a space after.**
```r
  nss_line <- na.omit(stringr::str_match(text, ".*beast.gss.NS.*"))[1,1 ]
                                                                      ^
```
[tests/testthat/test-create_nested_sampling_mcmc.R:44:72:](https://github.com/ropensci/beautier/blob/2847caf71c959e02f411233cf474e84a2bd8ebc6/tests/testthat/test-create_nested_sampling_mcmc.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  nss_line <- na.omit(stringr::str_match(text, ".*beast.gss.NS.*"))[1,1 ]
                                                                       ^
```


Successfully aliased the URL <https://java-programming-fall-19-34xakz16c.now.sh> to the following aliases:

* https://programming-f19.mooc.fi
* https://java-programming-fall-19.mooc.now.sh
* https://java-programming-fall-19-git-master.mooc.now.sh


@czue ,

This fix might break during different cases of which one will be when the alert banner is active. The reason being when Alert is active we increase top css of header and side nav to push them below the alert banner. This cause the content to be hidden again.


FixLCC_Escalataion_6144 (JasonGlazer) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1218 of 1218 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.16%25-green.png)


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/d7bf3c192fb8edd37c263ff5e27c848adba09a78/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
check_pir_out <- function(
^
```
[R/create_alignment_impl.R:34:1:](https://github.com/richelbilderbeek/pirouette/blob/d7bf3c192fb8edd37c263ff5e27c848adba09a78/R/create_alignment_impl.R#L34) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
create_alignment_impl <- function(
^
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/d7bf3c192fb8edd37c263ff5e27c848adba09a78/R/create_all_experiments.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 30.**
```r
create_all_experiments <- function(
^
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/d7bf3c192fb8edd37c263ff5e27c848adba09a78/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 24.**
```r
est_evidences <- function(
^
```
[R/select_candidate_evidences.R:25:1:](https://github.com/richelbilderbeek/pirouette/blob/d7bf3c192fb8edd37c263ff5e27c848adba09a78/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```


Successfully aliased the URL <https://nordnet-ui-1ry7mrqje.now.sh> to the following aliases:

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


Видимо ты тоже пыталась повторить картинку. Не нужно. Заголок тут весь " Welcom to gargeous Sedona", потом скорее все он просто будет картинкой. Текст-картинка. Сейчас нас не интересует размещение его на странице. Только содержание и суть.


Leave a comment NOW! Slapp like


@ashmaroli Not sure if there are other fixes required to make the plugin compatible with Jekyll v4, but I'm getting errors as well even with the relaxed spec.

The plugin seems to have problems writing out pagination pages and then crashes the whole build.

```
E:/Ruby24-x64/lib/ruby/2.4.0/fileutils.rb:230:in `mkdir': File exists @ dir_s_mkdir - E:/Users/Michael.Rose/Documents/Repositories/test-repo/_site/tag/foo/index.html (Errno::EEXIST)
        from E:/Ruby24-x64/lib/ruby/2.4.0/fileutils.rb:230:in `fu_mkdir'
        from E:/Ruby24-x64/lib/ruby/2.4.0/fileutils.rb:208:in `block (2 levels) in mkdir_p'
        from E:/Ruby24-x64/lib/ruby/2.4.0/fileutils.rb:206:in `reverse_each'
        from E:/Ruby24-x64/lib/ruby/2.4.0/fileutils.rb:206:in `block in mkdir_p'
        from E:/Ruby24-x64/lib/ruby/2.4.0/fileutils.rb:191:in `each'
        from E:/Ruby24-x64/lib/ruby/2.4.0/fileutils.rb:191:in `mkdir_p'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/convertible.rb:225:in `write'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/site.rb:219:in `block in write'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/site.rb:344:in `block (2 levels) in each_site_file'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/site.rb:343:in `each'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/site.rb:343:in `block in each_site_file'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/site.rb:342:in `each'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/site.rb:342:in `each_site_file'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/site.rb:218:in `write'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/site.rb:78:in `process'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/command.rb:28:in `process_site'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/commands/build.rb:65:in `build'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/commands/build.rb:36:in `process'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/command.rb:89:in `block in process_with_graceful_fail'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/command.rb:89:in `each'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/command.rb:89:in `process_with_graceful_fail'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/lib/jekyll/commands/build.rb:18:in `block (2 levels) in init_with_program'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/mercenary-0.3.6/lib/mercenary/command.rb:220:in `block in execute'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/mercenary-0.3.6/lib/mercenary/command.rb:220:in `each'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/mercenary-0.3.6/lib/mercenary/command.rb:220:in `execute'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/mercenary-0.3.6/lib/mercenary/program.rb:42:in `go'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/mercenary-0.3.6/lib/mercenary.rb:19:in `program'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/gems/jekyll-4.0.0/exe/jekyll:15:in `<top (required)>'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/bin/jekyll:23:in `load'
        from E:/Ruby24-x64/lib/ruby/gems/2.4.0/bin/jekyll:23:in `<main>'
```


Don't need this anymore


Oh, thanks for the heads up. When you say alert banner you mean the site-wide notification? And can you show me where the logic that manages that is so I can review?


[R/check_beast2_options.R:67:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L67) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:110:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L110) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:151:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L151) *style:* **Lines should not be more than 80 characters.**
```r
    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:154:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:157:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L157) *style:* **Lines should not be more than 80 characters.**
```r
    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:160:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L160) *style:* **Lines should not be more than 80 characters.**
```r
    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_ids.R:12:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_alignment_ids.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_ids.R:17:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_alignment_ids.R#L17) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_beast2_version.R:27:11:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L27) *warning:* **no visible global function definition for ‘create_beast2_version_cmd’**
```r
  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_beast2_version.R:32:5:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L32) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/get_beast2_version.R:69:5:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L69) *style:* **Commented code should be removed.**
```r
  # ./beast -version
    ^~~~~~~~~~~~~~~~
```
[R/get_beast2_version.R:74:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_beast2_version.R:76:24:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  last_lines <- output[ length(output) ]
                       ^
```
[R/get_beast2_version.R:76:39:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  last_lines <- output[ length(output) ]
                                      ^
```
[R/run_beast2.R:34:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/run_beast2.R#L34) *style:* **functions should have cyclomatic complexity of less than 15, this has 26.**
```r
run_beast2 <- function(
^
```
[R/upgrade_beast2.R:29:3:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/upgrade_beast2.R#L29) *warning:* **no visible global function definition for ‘uninstall_beast2’**
```r
  uninstall_beast2()
  ^~~~~~~~~~~~~~~~
```
[R/upgrade_beast2.R:30:3:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/upgrade_beast2.R#L30) *warning:* **no visible global function definition for ‘install_beast2’**
```r
  install_beast2()
  ^~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_options.R:48:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/tests/testthat/test-create_beast2_options.R#L48) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-create_beast2_options.R:49:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/tests/testthat/test-create_beast2_options.R#L49) *style:* **Trailing blank lines are superfluous.**
```r

^
```


if we fix all the tests that depend on output (which is wrong) we can use echo.wrap to print these.
However, I still feel we should stick to longer explanations in links as these can change over time.


h1 лучше оставить одни на странице, а это можно просто p и перенос на другую сторку тэгом стараются не делать, потому что при других видах сайта - мобильного или планшетного текст может иметь другую ориентацию. Здесь мы стилями это поправим в будущем, задав ширину подходящую.


Here is the change I made to the `RESTClient.php` (PHP is not my strong suit by the way if that is not evident yet)

From reading the HTTP Basic Auth spec, I believe the bare minimum requirement for an encoded `Basic` header is a `:`, so this would imply both username and password could be empty.

```
  public function basicAuthorization($username, $password)
  {
    if (!is_null($username) && !is_null($password)) {
      ...
    }

    return $this;
  }
```


цифры - это span. Заголовки только для осмылсенного текста


Successfully aliased the URL <https://static-fun-h1yaw1phi.zeit.sh> to the following aliases:

* https://static.fun
* https://*.static.fun
* https://www.static.fun
* https://static-fun.zeit.sh
* https://static-fun-git-master.zeit.sh


You are correct. Will fix.


@ianstanton guess this is where we need to get `{{ component_name }}` patched though?


pushed again, see e9f09c2ae7689c74081c2d2b520ce7c6ec9cf0d9 see what you think.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-1-build-tools-2742.pantheonsite.io/)

Created multidev environment [pr-1](https://dashboard.pantheon.io/sites/034e9f78-338e-41ff-a321-89893a0ff485#pr-1) for build-tools-2742.


Franky is "Independent Education Consultant"


Anotação necessária para que o framework reconheça o método como um teste de unidade.


Successfully aliased the URL <https://effector-pvxa8oyqa.now.sh> to the following aliases:

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


I think we might use different npm version or something and our locks are being regenerated constantly when we install stuff. I'm pretty sure that after my last installs I've left locks in a proper state, but seems like you had to regenerate them.

Not sure what's the correct, automatic, solution for this... nvm? Anyway - for starters would be good to check what node/npm are we both using right now.
```
$ node -v
v12.7.0
$ npm -v
6.10.0
```


Successfully aliased the URL <https://marp-cli-example-6lj13td9y.now.sh> to the following aliases:

* https://marp-cli-example.yhatt.now.sh
* https://marp-cli-example-git-master.yhatt.now.sh


A classe de testes deve ser pública.


Oui c'est ce que j'ai fais, clone or téléchargement et zip manuellement dans Arduino ...
https://github.com/derrgis/ESPJQ6500/issues/3


[tests/testthat/test-est_marg_lik.R:42:1:](https://github.com/richelbilderbeek/mcbette/blob/878df64f4de73afcc731152a10ccce93ca19b3a0/tests/testthat/test-est_marg_lik.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
      fasta_filename = system.file("extdata", "simple.fas", package = "mcbette"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-est_marg_lik.R:62:1:](https://github.com/richelbilderbeek/mcbette/blob/878df64f4de73afcc731152a10ccce93ca19b3a0/tests/testthat/test-est_marg_lik.R#L62) *style:* **Lines should not be more than 80 characters.**
```r
      fasta_filename = system.file("extdata", "simple.fas", package = "mcbette"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-est_marg_lik.R:123:21:](https://github.com/richelbilderbeek/mcbette/blob/878df64f4de73afcc731152a10ccce93ca19b3a0/tests/testthat/test-est_marg_lik.R#L123) *style:* **Use <-, not =, for assignment.**
```r
  inference_model_1 = create_test_ns_inference_model(
                    ^
```
[tests/testthat/test-est_marg_lik.R:128:22:](https://github.com/richelbilderbeek/mcbette/blob/878df64f4de73afcc731152a10ccce93ca19b3a0/tests/testthat/test-est_marg_lik.R#L128) *style:* **Use <-, not =, for assignment.**
```r
  inference_model_10 = create_test_ns_inference_model(
                     ^
```


Woohoo, now it works out of the box! Great stuff, thanks again! 🎉


regform


Test


Successfully aliased the URL <https://ant-design-plus-dywmhhxrm.now.sh> to the following aliases:

* https://ant-design-plus.alita.now.sh
* https://ant-design-plus-git-master.alita.now.sh


@ianstanton do we want `max()` here or something like `container_fs_usage_bytes{pod_name=~".*(scheduler|webserver|worker).*", deployment=~"$deployment"} > 1.5GB`?

I think 1.5GB will need to be in `bytes` but you get the idea. I'm also wondering if there is a way to actually remove the hard-coding of our limit here. If a user changes this via helm or we do later, we/they have to also update it here.

I wonder if there is a `container_fs_capacity_bytes`, or something similar that we can use to calculate the percentage of usage instead.

I think I wired something similar up for the "Platform Components" dashboard. Those are using PVCs, which have both metrics though. This is a little different since these metrics come from cadvisor, not kube-state.


Yes that would be the proper assertion wouldn't it! Sorry been a while since writing some assertions


### Keybase proof

I hereby claim:

  * I am adul69 on github.
  * I am adul69 (https://keybase.io/adul69) on keybase.
  * I have a public key ASDhWFn7HOgBPuTETwSGahaNaoUOctHJ0GCteEWXPA21jwo

To claim this, I am signing this object:

```json
{
  "body": {
    "key": {
      "eldest_kid": "0120e15859fb1ce8013ee4c44f04866a168d6a850e72d1c9d060ad7845973c0db58f0a",
      "host": "keybase.io",
      "kid": "0120e15859fb1ce8013ee4c44f04866a168d6a850e72d1c9d060ad7845973c0db58f0a",
      "uid": "4e0300d9a93d1a714356313faf57e019",
      "username": "adul69"
    },
    "merkle_root": {
      "ctime": 1568123151,
      "hash": "340d44728b36978552cdb598f6c67bcc69b389ba09fee0542bcdfdebeacb85af3049cf8206f4c09e2007a1fd55f8e140fe2a5bf42cb58595209bac38702f7db4",
      "hash_meta": "3bec2e11330295bfa3dd3d995eae9baed94b42b4e50790561b436e87756b0977",
      "seqno": 6417355
    },
    "service": {
      "entropy": "z0iQ1c7as2zXfjOmS/uQpwce",
      "name": "github",
      "username": "adul69"
    },
    "type": "web_service_binding",
    "version": 2
  },
  "client": {
    "name": "keybase.io go client",
    "version": "4.3.0"
  },
  "ctime": 1568123156,
  "expire_in": 504576000,
  "prev": "c9cccb19bb8cf4590f4f438b5ed54461c0ccee747dbf21cdb1264ef88c515cae",
  "seqno": 9,
  "tag": "signature"
}
```

with the key [ASDhWFn7HOgBPuTETwSGahaNaoUOctHJ0GCteEWXPA21jwo](https://keybase.io/adul69), yielding the signature:

```
hKRib2R5hqhkZXRhY2hlZMOpaGFzaF90eXBlCqNrZXnEIwEg4VhZ+xzoAT7kxE8EhmoWjWqFDnLRydBgrXhFlzwNtY8Kp3BheWxvYWTESpcCCcQgyczLGbuM9FkPT0OLXtVEYcDM7nR9vyHNsSZO+IxRXK7EIO4OQ8lEahTh+P5xOhWLSk34Pt8NlsWzr0py/rtBChrqAgHCo3NpZ8RAiX/6sNmBRoFXg0pfY5EljUpyRtB38+M9Efm1NHBrpSpFPSbZ7rlILDoXPteLbSln2LjprsNxYmwFRnaJS5kmAqhzaWdfdHlwZSCkaGFzaIKkdHlwZQildmFsdWXEIE9c2PK/ln9jrg0lzlWl1+Z16tuqR7KZcDx1LAvjpj/wo3RhZ80CAqd2ZXJzaW9uAQ==

```

And finally, I am proving ownership of the github account by posting this as a gist.

### My publicly-auditable identity:

https://keybase.io/adul69

### From the command line:

Consider the [keybase command line program](https://keybase.io/download).

```bash
# look me up
keybase id adul69
```


[R/check_beast2_options.R:67:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L67) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:110:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L110) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:151:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L151) *style:* **Lines should not be more than 80 characters.**
```r
    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:154:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:157:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L157) *style:* **Lines should not be more than 80 characters.**
```r
    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_beast2_options.R:160:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/check_beast2_options.R#L160) *style:* **Lines should not be more than 80 characters.**
```r
    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_ids.R:12:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_alignment_ids.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_ids.R:17:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_alignment_ids.R#L17) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_beast2_version.R:27:11:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L27) *warning:* **no visible global function definition for ‘create_beast2_version_cmd’**
```r
  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_beast2_version.R:32:5:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L32) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/get_beast2_version.R:69:5:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L69) *style:* **Commented code should be removed.**
```r
  # ./beast -version
    ^~~~~~~~~~~~~~~~
```
[R/get_beast2_version.R:74:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_beast2_version.R:76:24:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  last_lines <- output[ length(output) ]
                       ^
```
[R/get_beast2_version.R:76:39:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/get_beast2_version.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  last_lines <- output[ length(output) ]
                                      ^
```
[R/run_beast2.R:34:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/run_beast2.R#L34) *style:* **functions should have cyclomatic complexity of less than 15, this has 26.**
```r
run_beast2 <- function(
^
```
[R/upgrade_beast2.R:29:3:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/upgrade_beast2.R#L29) *warning:* **no visible global function definition for ‘uninstall_beast2’**
```r
  uninstall_beast2()
  ^~~~~~~~~~~~~~~~
```
[R/upgrade_beast2.R:30:3:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/R/upgrade_beast2.R#L30) *warning:* **no visible global function definition for ‘install_beast2’**
```r
  install_beast2()
  ^~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_options.R:48:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/tests/testthat/test-create_beast2_options.R#L48) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-create_beast2_options.R:49:1:](https://github.com/ropensci/beastier/blob/09d9ad3f1fc57182e0d55eb0e5c47c28b1ecad12/tests/testthat/test-create_beast2_options.R#L49) *style:* **Trailing blank lines are superfluous.**
```r

^
```


> Hi
> With this commit **[b052d61](https://github.com/glpi-project/glpi/commit/b052d61bcaf02a192363d35c89b2c07d96523459)** applied on search.class.php part of a 9.4.3
> **If a profile don't have the "see private tasks option checked"** the user that use this profile can't see tickets list on the tickets page (/front/ticket.php).
> Just no results at all on the page.
> Without this commit, all is fine again.

Hi,

Could you open a new issue for this ? Commit comments are not something that can be easilly listed nor followed.

Regards


Successfully aliased the URL <https://next-eek2nm0ta.now.sh> to the following aliases:

* https://oacore.now.sh
* https://next.oacore.now.sh
* https://next-git-content.oacore.now.sh


тут тогда h3 по логике для отелей


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/7f81f2c1-43f2-4599-8827-de5a2dc64fc7?env_id=ibm%3Ayp%3Aeu-de "tea-bot-chain"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/88325222-5db0-4b94-9ff2-610f280f9685 "tea-bot-pipe") deployed [tea-bot](https://github.com/tea-bot-project/tea-bot/releases/tag/deploy-ibm-yp-eu-gb-fajsiexofficial-gmail.com-dev-20190910-140700 "deploy-ibm-yp-eu-gb-fajsiexofficial-gmail.com-dev-20190910-140700") to [dev](https://console.bluemix.net/apps/3b214498-c629-4d6f-a5ca-e6fe3a6981ce?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:fajsiexofficial@gmail.com:dev"), including this commit


```py
our, err = process.communicate()
```