[R/create_test_simulation_output.R:4:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/create_test_simulation_output.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param island_ontogeny Boolean indicating if an ontogeny or no ontogeny scenario
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_test_simulation_output.R:14:20:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/create_test_simulation_output.R#L14) *warning:* **no visible global function definition for ‘is_island_ontogeny_input’**
```r
    testit::assert(is_island_ontogeny_input(island_ontogeny))
                   ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_area_params.R:16:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_area_params.R#L16) *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:34:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_area_params.R#L34) *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:39:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_area_params.R#L39) *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:6:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L6) *style:* **functions should have cyclomatic complexity of less than 15, this has 35.**
```r
are_rates <- function(x) {
^
```
[R/DAISIE_check_format.R:33:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L33) *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:46:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L46) *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:68:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L68) *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:70:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L70) *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:73:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L73) *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:75:7:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L75) *style:* **Commented code should be removed.**
```r
    # if (!"branching_times" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:76:7:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L76) *style:* **Commented code should be removed.**
```r
    # if (!"stac" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:77:7:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_check_format.R#L77) *style:* **Commented code should be removed.**
```r
    # if (!"missing_species" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:5:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_create_island.R#L84) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_data.R:2:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_data.R#L165) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{$island_age} - the island age\cr
                                         ^
```
[R/DAISIE_data.R:197:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_data.R#L197) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:247:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_data.R#L247) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:256:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_data.R#L256) *style:* **Lines should not be more than 80 characters.**
```r
#' The following elements of the list each contains information on a single colonist lineage
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:270:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_data.R#L270) *style:* **Lines should not be more than 80 characters.**
```r
#' #' \code{$missing_species} - number of island species that were not sampled for
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:286:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:7:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:10:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:86:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/DAISIE_dataprep.R:87:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:88:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L88) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:89:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L89) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:90:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:98:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L98) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:100:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L104) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:113:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L113) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:114:80:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L118) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:128:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L128) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:130:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L135) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_dataprep.R:136:5:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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:154:13:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L154) *warning:* **Avoid 1:nrow(...) expressions, use seq_len.**
```r
  for (i in 1:nrow(datatable))
            ^
```
[R/DAISIE_dataprep.R:155:3:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L158) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_dataprep.R:159:1:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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:159:32:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L159) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L160) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_dataprep.R:161:7:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L163) *style:* **Lines should not be more than 80 characters.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,min(the_brts,island_age - epss))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:163:41:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L163) *style:* **Use <-, not =, for assignment.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,min(the_brts,island_age - epss))
                                        ^
```
[R/DAISIE_dataprep.R:163:56:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L163) *style:* **Commas should always have a space after.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,min(the_brts,island_age - epss))
                                                       ^
```
[R/DAISIE_dataprep.R:163:69:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L163) *style:* **Commas should always have a space after.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,min(the_brts,island_age - epss))
                                                                    ^
```
[R/DAISIE_dataprep.R:165:7:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/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/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L167) *style:* **Use <-, not =, for assignment.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,the_brts)
                                        ^
```
[R/DAISIE_dataprep.R:167:56:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L167) *style:* **Commas should always have a space after.**
```r
      datalist[[i + 1]]$branching_times = c(island_age,the_brts)
                                                       ^
```
[R/DAISIE_dataprep.R:169:7:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/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")
      ^
```
[R/DAISIE_dataprep.R:169:20:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L169) *style:* **Commas should always have a space after.**
```r
    if(datatable[i,"Status"] == "Non_endemic_MaxAge")
                   ^
```
[R/DAISIE_dataprep.R:170:5:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L170) *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:171:30:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L171) *style:* **Use <-, not =, for assignment.**
```r
      datalist[[i + 1]]$stac = 1
                             ^
```
[R/DAISIE_dataprep.R:173:7:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L173) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(datatable[i,"Status"] == "Endemic")
      ^
```
[R/DAISIE_dataprep.R:173:20:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L173) *style:* **Commas should always have a space after.**
```r
    if(datatable[i,"Status"] == "Endemic")
                   ^
```
[R/DAISIE_dataprep.R:174:5:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L174) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/DAISIE_dataprep.R:175:30:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L175) *style:* **Use <-, not =, for assignment.**
```r
      datalist[[i + 1]]$stac = 2
                             ^
```
[R/DAISIE_dataprep.R:176:9:](https://github.com/rsetienne/DAISIE/blob/a76b7928f1d25a796fb5f68118f197dc375f3578/R/DAISIE_dataprep.R#L176) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(max(the_brts)>island_age){
        ^
```


Tested it, it's working. Thank you!


Successfully deployed to following URLs:

* https://hysequa-offline-liy9obigl.now.sh
* https://hysequa-offline.now.sh
* https://hysequa.info53.now.sh
* https://hysequa-offline.info53.now.sh
* https://hysequa-offline-git-master.info53.now.sh


@JuliaRegistrator `register()`


Registration pull request created: [JuliaRegistries/General/6179](https://github.com/JuliaRegistries/General/pull/6179)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.6.6 -m "<description of version>" 13854058f29c6d7a7f845a7358dcce4dfeef3682
git push origin v0.6.6
```


The most important result for charged Higgs contribution.


Dépend de ta réponse au-dessus mais du coup pour l'équation du mouvement je suis pas certain de la deuxième composante dans les accélérations avec les vitesses relatives


Successfully deployed to following URLs:

* https://mood-fy9am7lm6.now.sh
* https://mood.rgrannell2.now.sh
* https://mood-git-master.rgrannell2.now.sh


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/c6e9d6b2-cca1-4149-aa40-ca9cc42c3182?env_id=ibm%3Ayp%3Aus-south "devops-syn-toolchain"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/730fa3f4-d5b7-440e-bd58-63da47e05777 "devops-demo-repository") deployed [devops-demo-repository](https://github.com/Jagannath73/devops-demo-repository/releases/tag/deploy-sv-syn-demo-bala-20191203-113550 "deploy-sv-syn-demo-bala-20191203-113550") to [sv-syn-demo-bala](https://console.bluemix.net/kubernetes/clusters/bneirv7d0ov1taum1rug/overview "There was a problem retrieving the space name"), including this commit


아직 미완성(name)


Successfully deployed to following URLs:

* https://gatsby-functions-bgdzxt3z5.now.sh
* https://gatsby-functions-three-khaki.now.sh
* https://gatsby-functions.dam6pl.now.sh
* https://gatsby-functions-git-master.dam6pl.now.sh


The name of the method must begin start with a small letter


mc scale has 4 active flavours and hadron scale (1 GeV) has 2 active flavours;
mb scale has 5 active flavours and mc scale has 4 active flavours


On l'utilise où par la suite ? Ne serait-ce pas mieux de définir une fonction annexe calculant les variations de masse pour l'implémenter directement dans l'équation du mouvement ?


./jok3r.py db

         ____.       __    ________              `Combine the best of...
        |    | ____ |  | __\_____  \______           ...open-source Hacking Tools`
        |    |/  _ \|  |/ /  _(__  <_  __ \
    /\__|    (  (_) )    <  /       \  | \/
    \________|\____/|__|_ \/______  /__|      v3.0
                         \/       \/

          ~ Network & Web Pentest Automation Framework ~
   [ Manage Toolbox | Automate Attacks | Chain Hacking Tools ]

[!] Unexpected error occured: do_load
Traceback (most recent call last):
  File "./jok3r.py", line 44, in __init__
    controller.run()
  File "/media/master/New Volume/jok3r-master/lib/controller/MainController.py", line 23, in run
    }.get(self.arguments.mode)(self.arguments, self.settings, self.sqlsess).run()
  File "/media/master/New Volume/jok3r-master/lib/controller/DbController.py", line 65, in __init__
    del cmd2.Cmd.do_load
AttributeError: do_load
please solve this issuse


Chrome did not allow the access of Absolute_Path of the file. Apparently it's due to security measures and most of the recent browsers don't give out the full path of the files. Leave a solution if you know your way around this issue. Cheers!


<!-- PMABOT:SPACE -->
This commit contains trailing whitespace, what is prohibited in phpMyAdmin. Please check our [Developer guidelines](https://github.com/phpmyadmin/phpmyadmin/wiki/Developer_guidelines#Indentation) for more information.

Offending files: libraries/classes/UserPassword.php


Hi. How i can use thes files


test


same here


Successfully deployed to following URLs:

* https://gatsby-functions-c05z5aofu.now.sh
* https://gatsby-functions-three-khaki.now.sh
* https://gatsby-functions.dam6pl.now.sh
* https://gatsby-functions-git-master.dam6pl.now.sh


Great Job Israel, keep it up


what is len?


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
check_pir_out <- function(
^
```
[R/create_alignment_with_std_site_model.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/create_alignment_with_std_site_model.R#L5) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/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/create_copy_twin_tree_from_true_fun.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/create_copy_twin_tree_from_true_fun.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_copy_twin_tree_from_true_fun <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
est_evidences <- function(
^
```
[R/get_sim_true_alignment_with_lns_site_model_fun.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_true_alignment_with_lns_site_model_fun.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_lns_site_model_fun <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_std_site_model_fun.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_true_alignment_with_std_site_model_fun.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_std_site_model_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_uns_site_model_fun.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_true_alignment_with_uns_site_model_fun.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_uns_site_model_fun <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_fun.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_twin_alignment_with_same_n_mutation_fun.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_std_site_model_fun.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/get_sim_twin_alignment_with_std_site_model_fun.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_std_site_model_fun <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/select_candidate_evidences.R:25:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```
[R/sim_alignment_with_std_site_model.R:15:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_alignment_with_std_site_model.R#L15) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_lns_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_true_alignment_with_lns_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_lns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_std_site_model.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_true_alignment_with_std_site_model.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_uns_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_true_alignment_with_uns_site_model.R#L13) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_uns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_lns_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_lns_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_lns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_same_n_mutation.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_std_site_model_raw.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_std_site_model_raw.R#L5) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_std_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_std_site_model.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_std_site_model.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_uns_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/0c545fd66e20f857af17ff8fcc7fa7e4767ee8c9/R/sim_twin_alignment_with_uns_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_uns_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Just Testing For the Create This project


Selenium IDE можно так же некоторые проверки записать. Они появляются в контекстном меню


Rather than patching this, you can just use an option `-o Class=mintty-debug`.


[R/clock_model_to_xml_prior_distr.R:14:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/clock_model_to_xml_prior_distr.R#L14) *warning:* **no visible global function definition for ‘rln_clock_model_to_xml_mean_rate_prior’**
```r
      text <- c(text, rln_clock_model_to_xml_mean_rate_prior(clock_model)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_state.R:32:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/clock_models_to_xml_state.R#L32) *warning:* **no visible global function definition for ‘clock_model_to_xml_state’**
```r
    line_to_remove <- clock_model_to_xml_state(clock_models[[1]]) # nolint
                      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:9:19:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_beast2_input_distr.R#L9) *warning:* **no visible global function definition for ‘tree_priors_to_xml_prior_distr’**
```r
  text <- c(text, tree_priors_to_xml_prior_distr(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:10:19:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_beast2_input_distr.R#L10) *warning:* **no visible global function definition for ‘gamma_site_models_to_xml_prior_distr’**
```r
  text <- c(text, gamma_site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:11:19:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_beast2_input_distr.R#L11) *warning:* **no visible global function definition for ‘site_models_to_xml_prior_distr’**
```r
  text <- c(text, site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:27:19:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_beast2_input_operators.R#L27) *warning:* **no visible global function definition for ‘site_models_to_xml_operators’**
```r
  text <- c(text, site_models_to_xml_operators(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_run.R:23:11:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_beast2_input_run.R#L23) *warning:* **no visible global function definition for ‘mcmc_to_xml_run’**
```r
  text <- mcmc_to_xml_run(mcmc) # nolint beautier function
          ^~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:24:19:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_beast2_input_state.R#L24) *warning:* **no visible global function definition for ‘site_models_to_xml_state’**
```r
  text <- c(text, site_models_to_xml_state(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:33:19:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_beast2_input_state.R#L33) *warning:* **no visible global function definition for ‘tree_priors_to_xml_state’**
```r
  text <- c(text, tree_priors_to_xml_state(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_clock_models_from_names.R:5:26:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_clock_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_clock_model_from_name’**
```r
    clock_models[[i]] <- create_clock_model_from_name(clock_model_name) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_site_models_from_names.R:5:25:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_site_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_site_model_from_name’**
```r
    site_models[[i]] <- create_site_model_from_name(site_model_name) # nolint beautier function
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:17:19:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_tracelog_xml.R#L17) *warning:* **no visible global function definition for ‘tree_models_to_xml_tracelog’**
```r
  text <- c(text, tree_models_to_xml_tracelog(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:32:19:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/create_tracelog_xml.R#L32) *warning:* **no visible global function definition for ‘tree_priors_to_xml_tracelog’**
```r
  text <- c(text, tree_priors_to_xml_tracelog(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_section_from_lines.R:7:12:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/extract_xml_section_from_lines.R#L7) *warning:* **no visible global function definition for ‘extract_xml_operators_from_lines’**
```r
    return(extract_xml_operators_from_lines(lines)) # nolint beautier function
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_last_xml_closing_tag_line.R:6:3:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/find_last_xml_closing_tag_line.R#L6) *warning:* **no visible global function definition for ‘find_last_regex_line’**
```r
  find_last_regex_line(lines, paste0("</", section, ">")) # nolint beautier function
  ^~~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:11:12:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/has_xml_opening_tag.R#L11) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
    tag <- get_xml_opening_tag(lines) # nolint
           ^~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:14:24:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/has_xml_opening_tag.R#L14) *warning:* **no visible global function definition for ‘find_first_xml_opening_tag_line’**
```r
  !beautier::is_one_na(find_first_xml_opening_tag_line(lines, section))
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:10:10:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/init_clock_models.R#L10) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames) # nolint beautier function
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_distr.R:9:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/init_distr.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
init_distr <- function(
^
```
[R/init_inference_model.R:39:22:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/init_inference_model.R#L39) *warning:* **no visible global function definition for ‘init_mrca_prior’**
```r
  inference_model <- init_mrca_prior(input_filename, inference_model)
                     ^~~~~~~~~~~~~~~
```
[R/is_distr.R:37:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_distr.R#L37) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
is_distr <- function(
^
```
[R/is_init_site_model.R:36:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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_mrca_align_ids_in_fastas.R:6:10:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_mrca_align_ids_in_fastas.R#L6) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:55:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/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/is_tree_prior.R:5:8:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_tree_prior.R#L5) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:3:8:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_xml.R#L3) *warning:* **no visible global function definition for ‘has_xml_opening_tag’**
```r
  if (!has_xml_opening_tag(text)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:4:7:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_xml.R#L4) *warning:* **no visible global function definition for ‘has_xml_short_closing_tag’**
```r
  if (has_xml_short_closing_tag(text)) return(TRUE) # nolint beautier function
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:5:18:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_xml.R#L5) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
  opening_tag <- get_xml_opening_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:6:18:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/is_xml.R#L6) *warning:* **no visible global function definition for ‘get_xml_closing_tag’**
```r
  closing_tag <- get_xml_closing_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_state.R:22:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/site_model_to_xml_state.R#L22) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ac_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:25:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/site_model_to_xml_state.R#L25) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ag_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:47:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/site_model_to_xml_state.R#L47) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_1_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:51:23:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/site_model_to_xml_state.R#L51) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_2_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_models_to_xml_operators.R:4:18:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/site_models_to_xml_operators.R#L4) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_tracelog.R:6:21:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/site_models_to_xml_tracelog.R#L6) *warning:* **no visible global function definition for ‘site_model_to_xml_tracelog’**
```r
    text <- c(text, site_model_to_xml_tracelog(site_model)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_operators.R:10:22:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/tree_prior_to_xml_operators.R#L10) *warning:* **no visible global function definition for ‘get_operator_id_pre’**
```r
  operator_id_pre <- get_operator_id_pre(tree_prior) # nolint beautier function
                     ^~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:7:21:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/tree_prior_to_xml_prior_distr.R#L7) *warning:* **no visible global function definition for ‘bd_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, bd_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:9:21:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/tree_prior_to_xml_prior_distr.R#L9) *warning:* **no visible global function definition for ‘cbs_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cbs_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:11:21:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/tree_prior_to_xml_prior_distr.R#L11) *warning:* **no visible global function definition for ‘ccp_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, ccp_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:13:21:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/tree_prior_to_xml_prior_distr.R#L13) *warning:* **no visible global function definition for ‘cep_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cep_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:16:21:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/tree_prior_to_xml_prior_distr.R#L16) *warning:* **no visible global function definition for ‘yule_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, yule_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_distr.R:8:21:](https://github.com/ropensci/beautier/blob/c913055d2b08c3bae4a2afa6d4a990c4dd80ead1/R/tree_priors_to_xml_distr.R#L8) *warning:* **no visible global function definition for ‘tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://curso-platzi-react-avanzado-bth3lersf.now.sh
* https://curso-platzi-react-avanzado-sigma-ten.now.sh
* https://curso-platzi-react-avanzado.enricvelascog.now.sh
* https://curso-platzi-react-avanzado-git-master.enricvelascog.now.sh


one more space missing?


Successfully deployed to following URLs:

* https://imputationbot-lwz6jcgwo.now.sh
* https://imputationbot.now.sh
* https://install.now.sh
* https://imputationbot.lukfor.now.sh
* https://imputationbot-git-master.lukfor.now.sh


what is  :array1[],len1,array2[],len2,array[].


Successfully deployed to following URLs:

* https://paulkinlanme-cbn0v9r2j.now.sh
* https://paul.kinlan.me
* https://paulkinlanme.kinlan.now.sh
* https://paulkinlanme-git-main.kinlan.now.sh


Successfully deployed to following URLs:

* https://daim-et2kznxmr.now.sh
* https://daim.now.sh
* https://daim.damienrobinson.now.sh
* https://daim-git-master.damienrobinson.now.sh


Should I move this into a separate module?


Successfully deployed to following URLs:

* https://gatsby-functions-lqdf9g3fq.now.sh
* https://gatsby-functions-three-khaki.now.sh
* https://gatsby-functions.dam6pl.now.sh
* https://gatsby-functions-git-master.dam6pl.now.sh


Successfully deployed to following URLs:

* https://afrotech-events-api-8x9m7re3c.now.sh
* https://afrotech-events-api.now.sh
* https://api.afrotech.events
* https://afrotech-events-api.ezeikel.now.sh
* https://afrotech-events-api-git-master.ezeikel.now.sh


@nanosoldier `runtests(ALL, isdaily = true)`


-不中


These are just good defaults. Since we're not in the framework repo, none of this really matters.


On doit pas la faire découpler via une boucle qui vérifie quand il n'y a plus de carburant dans le dernier étage ?


阿萨德


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

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

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

### Deployments updated

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

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


增加了一句
system.out.println("实验结束");


Yes, it should be there...


Good Job! I've tried same to reduce the load! Thank you very much for this Commit!!!


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/c6e9d6b2-cca1-4149-aa40-ca9cc42c3182?env_id=ibm%3Ayp%3Aus-south "devops-syn-toolchain"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/730fa3f4-d5b7-440e-bd58-63da47e05777 "devops-demo-repository") deployed [devops-demo-repository](https://github.com/Jagannath73/devops-demo-repository/releases/tag/deploy-sv-syn-demo-bala-20191203-114802 "deploy-sv-syn-demo-bala-20191203-114802") to [sv-syn-demo-bala](https://console.bluemix.net/kubernetes/clusters/bneirv7d0ov1taum1rug/overview "There was a problem retrieving the space name"), including this commit


Just my 2 cents...

You can improve this putting your logic into a `try-catch` block.

You must have to close the database connection by calling `close()` method to prevent memory leaks and release database resources that are maybe holding on to.


@zayatnik, Ваша почта не указана в профиле, поэтому пишу сюда. Вы зачем создали pull request в репозиторий к А.В. Сысоеву? Вот он удивился, наверное. Закройте его там, пока никто (надеюсь) не видел, и сделайте pull request к себе в репозиторий.


cái này hàm của tui đừng xóa nữa nhá bạn


Contato do site


Deployment failed with the following error:

~~~
Schema verification failed
~~~


Successfully deployed to following URLs:

* https://imputationbot-gmzp9444q.now.sh
* https://imputationbot.now.sh
* https://install.now.sh
* https://imputationbot.lukfor.now.sh
* https://imputationbot-git-master.lukfor.now.sh


> [0872f7d#diff-04c6e90faac2675aa89e2176d2eec7d8](https://github.com/zixun/GodEye/commit/0872f7d09f11fe991ae781c4b67eed81d189bce0#diff-04c6e90faac2675aa89e2176d2eec7d8)

@liotoon


LGTM


That's true. I will incorporate that...


Successfully deployed to following URLs:

* https://mood-b3ackupw6.now.sh
* https://mood.rgrannell2.now.sh
* https://mood-git-master.rgrannell2.now.sh


Ok, I was missing an explicit completion confirmation in my settings (`inoremap <expr> <cr> pumvisible() ? "\<C-y>" : "\<C-g>u\<CR>"`). Thanks for the help.


"webpack-bundle-analyzer": "^3.6.0",


*NLP not NPL (natural language processing)


Successfully deployed to following URLs:

* https://nuxt-typescript-vuetify-mf8k1jnun.now.sh
* https://nuxt-typescript-vuetify.justhannes.now.sh
* https://nuxt-typescript-vuetify-git-master.justhannes.now.sh


Successfully deployed to following URLs:

* https://quartz-a2ejqnfnn.now.sh
* https://quartz.connctd.now.sh
* https://quartz-git-master.connctd.now.sh


Missing space before `(`. Missing error check.


Diez çıkartıldı.


Please use `xfclose` for the error check.


Please use `xfopen`.


test


Likewise `xfopen`.


Successfully deployed to following URLs:

* https://zvekovcom-ngpfjxr34.now.sh
* https://zvekov.com
* https://zvekovcom.zvekov.now.sh
* https://zvekovcom-git-master.zvekov.now.sh


Thank you for feedbacking me! As soon as possible i Will make a new commit with the changes!

Obter o Outlook para Android<https://aka.ms/ghei36>

________________________________
From: Wellington Costa <notifications@github.com>
Sent: Tuesday, December 3, 2019 8:48:08 AM
To: henri1996x/connection-class-singleton-pattern <connection-class-singleton-pattern@noreply.github.com>
Cc: Henrique Braga <henriqueprof@outlook.com>; Author <author@noreply.github.com>
Subject: Re: [henri1996x/connection-class-singleton-pattern] First Commit (bd29c26)

Just my 2 cents...

You can improve this putting your logic into a try-catch block.

You must have to close the database connection by calling close() method to prevent memory leaks and release database resources that are maybe holding on to.

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/henri1996x/connection-class-singleton-pattern/commit/bd29c26342a4494cb6b9b2f10c1932b2092f0d9f?email_source=notifications&email_token=AMYBF7ASQJLOEGEFEIKKUJDQWZBPRA5CNFSM4JUWS272YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBCSB2G#commitcomment-36243270>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMYBF7ELS57SJHVVH7APVLTQWZBPRANCNFSM4JUWS27Q>.


`xfclose`, please.


Successfully deployed to following URLs:

* https://andrezzoidgithubio-gnyfz1qoe.now.sh
* https://andrejonas.com
* https://www.andrejonas.com
* https://andrezzoidgithubio.andrezzoid.now.sh
* https://andrezzoidgithubio-git-master.andrezzoid.now.sh


Deployment failed with the following error:

~~~
The property `builds` is only allowed on Now 2.0 — please upgrade: https://zeit.co/upgrade
~~~


Missing space before `(DSO_DIR` (twice).


Successfully deployed to following URLs:

* https://quartz-f0g6v6itu.now.sh
* https://quartz.connctd.now.sh
* https://quartz-git-master.connctd.now.sh


Missing space.


Because the caller is SkautIS, not the caller of `/finish`


Successfully deployed to following URLs:

* https://imputationbot-m8xuygs1o.now.sh
* https://imputationbot.now.sh
* https://install.now.sh
* https://imputationbot.lukfor.now.sh
* https://imputationbot-git-master.lukfor.now.sh