[inst/doc/demo_optimize.R:18:26:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L18) *style:* **Trailing whitespace is superfluous.**
```r
data(Galapagos_datatable)
                         ^
```
[inst/doc/demo_optimize.R:20:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
Galapagos_datalist <- DAISIE_dataprep(
^~~~~~~~~~~~~~~~~~
```
[inst/doc/demo_optimize.R:20:39:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
Galapagos_datalist <- DAISIE_dataprep(
                                      ^
```
[inst/doc/demo_optimize.R:20:39:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L20) *style:* **Trailing whitespace is superfluous.**
```r
Galapagos_datalist <- DAISIE_dataprep(
                                      ^
```
[inst/doc/demo_optimize.R:21:35:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
  datatable = Galapagos_datatable,
                                  ^
```
[inst/doc/demo_optimize.R:22:18:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
  island_age = 4,
                 ^
```
[inst/doc/demo_optimize.R:27:26:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
data(Galapagos_datatable)
                         ^
```
[inst/doc/demo_optimize.R:29:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
Galapagos_datalist_2types <- DAISIE_dataprep(
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/doc/demo_optimize.R:29:46:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L29) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
Galapagos_datalist_2types <- DAISIE_dataprep(
                                             ^
```
[inst/doc/demo_optimize.R:29:46:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L29) *style:* **Trailing whitespace is superfluous.**
```r
Galapagos_datalist_2types <- DAISIE_dataprep(
                                             ^
```
[inst/doc/demo_optimize.R:30:35:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L30) *style:* **Trailing whitespace is superfluous.**
```r
  datatable = Galapagos_datatable,
                                  ^
```
[inst/doc/demo_optimize.R:31:18:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
  island_age = 4,
                 ^
```
[inst/doc/demo_optimize.R:32:12:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
  M = 1000,
           ^
```
[inst/doc/demo_optimize.R:33:26:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L33) *style:* **Trailing whitespace is superfluous.**
```r
  number_clade_types = 2,
                         ^
```
[inst/doc/demo_optimize.R:34:33:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L34) *style:* **Trailing whitespace is superfluous.**
```r
  list_type2_clades = "Finches",
                                ^
```
[inst/doc/demo_optimize.R:37:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_optimize.R#L37) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[inst/doc/demo_sim.R:27:33:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
island_replicates <- DAISIE_sim(
                                ^
```
[inst/doc/demo_sim.R:27:33:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
island_replicates <- DAISIE_sim(
                                ^
```
[inst/doc/demo_sim.R:29:26:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L29) *style:* **Trailing whitespace is superfluous.**
```r
  M = n_mainland_species,
                         ^
```
[inst/doc/demo_sim.R:45:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
island_replicates_K <- DAISIE_sim(
^~~~~~~~~~~~~~~~~~~
```
[inst/doc/demo_sim.R:45:35:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
island_replicates_K <- DAISIE_sim(
                                  ^
```
[inst/doc/demo_sim.R:45:35:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L45) *style:* **Trailing whitespace is superfluous.**
```r
island_replicates_K <- DAISIE_sim(
                                  ^
```
[inst/doc/demo_sim.R:46:21:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L46) *style:* **Trailing whitespace is superfluous.**
```r
  time = island_age,
                    ^
```
[inst/doc/demo_sim.R:47:26:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L47) *style:* **Trailing whitespace is superfluous.**
```r
  M = n_mainland_species,
                         ^
```
[inst/doc/demo_sim.R:52:2:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L52) *style:* **Trailing whitespace is superfluous.**
```r
)
 ^
```
[inst/doc/demo_sim.R:68:40:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L68) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
island_replicates_2types <- DAISIE_sim(
                                       ^
```
[inst/doc/demo_sim.R:68:40:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L68) *style:* **Trailing whitespace is superfluous.**
```r
island_replicates_2types <- DAISIE_sim(
                                       ^
```
[inst/doc/demo_sim.R:70:26:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L70) *style:* **Trailing whitespace is superfluous.**
```r
  M = n_mainland_species,
                         ^
```
[inst/doc/demo_sim.R:75:29:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L75) *style:* **Trailing whitespace is superfluous.**
```r
  replicates = n_replicates,
                            ^
```
[inst/doc/demo_sim.R:81:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/inst/doc/demo_sim.R#L81) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_test_simulation_output.R:8:31:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/create_test_simulation_output.R#L8) *style:* **Commas should always have a space after.**
```r
  pars_equal <- c(2.550687345,2.683454548,Inf,0.00933207,1.010073119)
                              ^
```
[R/create_test_simulation_output.R:8:43:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/create_test_simulation_output.R#L8) *style:* **Commas should always have a space after.**
```r
  pars_equal <- c(2.550687345,2.683454548,Inf,0.00933207,1.010073119)
                                          ^
```
[R/create_test_simulation_output.R:8:47:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/create_test_simulation_output.R#L8) *style:* **Commas should always have a space after.**
```r
  pars_equal <- c(2.550687345,2.683454548,Inf,0.00933207,1.010073119)
                                              ^
```
[R/create_test_simulation_output.R:8:58:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/create_test_simulation_output.R#L8) *style:* **Commas should always have a space after.**
```r
  pars_equal <- c(2.550687345,2.683454548,Inf,0.00933207,1.010073119)
                                                         ^
```
[R/DAISIE_area_params.R:15:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_area_params.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
are_area_params <- function(area_params) {
^
```
[R/DAISIE_area_params.R:32:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_area_params.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
#' @param proportional_peak_t value from 0 to 1 indicating where in the island's history the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_area_params.R:32:93:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_area_params.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
#' @param proportional_peak_t value from 0 to 1 indicating where in the island's history the
                                                                                ^
```
[R/DAISIE_area_params.R:37:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_area_params.R#L37) *style:* **Lines should not be more than 80 characters.**
```r
#' @return list of numerical values containing area parameters for island ontogeny
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_area_params.R:37:83:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_area_params.R#L37) *style:* **Trailing whitespace is superfluous.**
```r
#' @return list of numerical values containing area parameters for island ontogeny
                                                                                ^
```
[R/DAISIE_area_params.R:41:13:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_area_params.R#L41) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/DAISIE_area_params.R:60:28:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_area_params.R#L60) *style:* **Trailing whitespace is superfluous.**
```r
  list(max_area = max_area,
                           ^
```
[R/DAISIE_check_format.R:4:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L4) *style:* **functions should have cyclomatic complexity of less than 15, this has 35.**
```r
are_rates <- function(x) {
^
```
[R/DAISIE_check_format.R:31:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L31) *style:* **Lines should not be more than 80 characters.**
```r
  if (island_ontogeny != "const" && island_ontogeny != "linear" && island_ontogeny != "beta") return(FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:44:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
  if (island_ontogeny != 0 && island_ontogeny != 1 && island_ontogeny != 2) return(FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:50:76:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L50) *style:* **Trailing whitespace is superfluous.**
```r
#' @param simulation_outputs A list with matrices and vectors of simulation
                                                                           ^
```
[R/DAISIE_check_format.R:51:27:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L51) *style:* **Trailing whitespace is superfluous.**
```r
#' produced by DAISIE_sim.
                          ^~
```
[R/DAISIE_check_format.R:57:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L57) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/DAISIE_check_format.R:58:51:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L58) *style:* **Trailing whitespace is superfluous.**
```r
#' expect_false(is_simulation_outputs("nonsense"))
                                                  ^
```
[R/DAISIE_check_format.R:59:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_check_format.R:60:58:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L60) *style:* **Trailing whitespace is superfluous.**
```r
#' simulation_outputs <- create_test_simulation_outputs()
                                                         ^
```
[R/DAISIE_check_format.R:65:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L65) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_check_format.R:66:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    if (!"island_age" %in% names(simulation_outputs[[n_replicate]][[1]])) return(FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:68:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
        !"not_present_type1" %in% names(simulation_outputs[[n_replicate]][[1]]))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:71:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
    if (!"stt_all" %in% names(simulation_outputs[[n_replicate]][[1]])) return(FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:73:7:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L73) *style:* **Commented code should be removed.**
```r
    # if (!"branching_times" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:74:7:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L74) *style:* **Commented code should be removed.**
```r
    # if (!"stac" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:75:7:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L75) *style:* **Commented code should be removed.**
```r
    # if (!"missing_species" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:80:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_check_format.R#L80) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_create_island.R:5:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_create_island.R#L84) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_data.R:2:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_data.R#L165) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{$island_age} - the island age\cr
                                         ^
```
[R/DAISIE_data.R:197:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_data.R#L197) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:247:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_data.R#L247) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:256:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_data.R#L256) *style:* **Lines should not be more than 80 characters.**
```r
#' The following elements of the list each contains information on a single colonist lineage
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:270:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_data.R#L270) *style:* **Lines should not be more than 80 characters.**
```r
#' #' \code{$missing_species} - number of island species that were not sampled for
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:286:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:7:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:10:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:86:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/DAISIE_dataprep.R:87:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:88:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L88) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:89:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L89) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:90:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:98:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L98) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:100:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L104) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:113:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L113) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:114:80:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L118) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:128:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L128) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:130:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L135) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_dataprep.R:136:5:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L152) *style:* **Use <-, not =, for assignment.**
```r
    datalist[[1]] = list(island_age = island_age, not_present_type1 = not_present_type1, not_present_type2 = not_present_type2)
                  ^
```
[R/DAISIE_dataprep.R:155:3:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L158) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_dataprep.R:159:1:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/R/DAISIE_dataprep.R#L159) *style:* **Put spaces around all infix operators.**
```r
    if(max(the_brts)>island_age){print(paste('Colonisation time of ',max(the_brts),' for ',as.character(datatable[i,"Clade_name"]),' is older than island age',sep=''))}
                   ~^~
```
[R/DAISIE_dataprep.R:159:33:](https://github.com/rsetienne/DAISIE/blob/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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/5644dcf41acd5bed5b1cd5c748c0c99f498a4730/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=''))}
                                                                     ^
```


Ah! I didn't assign zero to wager. Will be done.


Deployment failed with the following error:

~~~
The chosen alias "boris.now.sh" is already in use by another account.
~~~


Hi there Keesbos, is their anyway of contacting yourself through email about this repository that uses python with Zerto ?


I would not use this kind of solution to align an image.
use the `Typography` align props to align the text below and wrap the image into a felxbox.


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Collaborator: Review for this commit was created. [Link to review](/ui#review:id=21)


Starting on that now.


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I'm making a 1.3, could you pull the 1.2.1 version from the index and Jazzband site?


that informs the `EndpointRunner` to use the Prepare->Start flow instead of the classic flow. I contemplated adding a new Runner but it would require to add a whole bunch of new infrastructure like Runner, Behavior, EndpointBuilder etc.


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Title means it is a fix on top of the previous... not Issue `#2`.


It was for the heading, removed.


Done.


ZEIT Now cannot deploy this project to production due to following domain related issues:

 * alias `https://relay-dashboard-api.now.sh/` is an invalid domain. Correct it.


ZÉ RAMALHO


Done, they're now separated.


Renamed.


myCoin の数が1ずつカウントダウンする等の単純な処理ではなくなっているため、この場合はwhile等のほうがふさわしいかと思います（処理が間違っているわけではないです）。


Cn't because of ESlint.


Länkade css dokumentet


Yeah, @yetty would you please make jazzband-bot an owner of the django-embed-video project on PyPI? I currently can't delete the accidental release.


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Använder div för att ändra backgrunden i en sektion


Should be an automatic thing you do.
Think in terms of invariants, or communicating vases if you want. `plays[hashValue].wager -> balances[playerOneAddress]`.


Ah, got it, perhaps change the name of they key to say that?
EndpointRunner.UseBlah

On Fri, 30 Aug 2019 at 13:02, Szymon Pobiega <notifications@github.com>
wrote:

> that informs the EndpointRunner to use the Prepare->Start flow instead of
> the classic flow. I contemplated adding a new Runner but it would require
> to add a whole bunch of new infrastructure like Runner, Behavior,
> EndpointBuilder etc.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/Particular/NServiceBus/commit/f7a2b808c98f2784e304ba4e146d840ed434f0fc?email_source=notifications&email_token=AAA6QZBUUH5MI5PORQW5NP3QHD45ZA5CNFSM4ISMBYV2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBBI44J#commitcomment-34894729>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAA6QZAZ2Z46CXLZLHT7743QHD45ZANCNFSM4ISMBYVQ>
> .
>


sub1()の処理を説明するヘッダがほしいです。


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* https://react-relay-dashboard-api-git-master.borisp.now.sh


makes one boid loop across the screen


dwsdw


@aleksihakli I know it's easy to make quick releases, please take the impact releases have on users when deciding which version to use. It's critical to do this before pushing the release to PyPI since it gets complicated quickly and will increase the amount of work when not done properly. Your efforts not withstanding of course!


I can't import or use it.


https://github.com/remedcu/RockPaperScissors/commit/477f7defcfd0c421d08d2cf7f97015ed4810e125 :smiley:


Collaborator: Review for this commit was created. [Link to review](/ui#review:id=27)


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Wouldn't 320x288px be better dimensions for Game Boy screenshots? Right now they are quite blurry.

Also, `image-rendering: pixelated;` is not supported by Firefox. MDN suggests the following:

> In practical use, the pixelated and crisp-edges rules can be combined to provide some fallback for each other. (Just prepend the actual rules with the fallback.)

If I understand correctly, this would look like this:

```
image-rendering: crisp-edges;
image-rendering: pixelated;
```

Unsupported values will be ignored, and `pixelated` will be preferred.


Ramar in den


Done.


Renamed.


Because it doesn’t work.


ändrar den vanliga texten


ändrar titeln


weasdf


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ändrar den andra titeln


ändrar huvud backgrunden


gazdsfasfasf


Removed.


git commit --amend -m "message"


sqsqsqs


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cl /W4 main.c ap_isalpha.c /link /out:alpha.exe

alpha


return TRUE or FALSE


Wow! I didn't know this is possible!


range alphabetic symbols of ascii table


@jezdez Yeah I agree wholeheartedly and agree that things should be done as cleanly as possible. I'll pay more attention to the semver in the future. I removed the 1.2.1 tag from the repo and made a 1.3 tag instead, can you handle the Jazzband registry and PyPI side of things so we can get this cleaned up?


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doesn't seem like the right fix, there's actually already a similar logic in `explode`, can you check if without your fix it's indeed raising an error when creating a manufacturing order for a cycle bom? if so, then it's working as expected and maybe we could adapt only the bom structure report (either by getting bom and sub boms via explode or calling a dummy explode when starting the report and make it raise if necessary)


It would be better to make commits of more digestible sizes.


Hi, just jumping in here because it popped up in my github timeline. The `2to3` tool is overcorrecting in cases like this: Python 3's `dict.items()` is equivalent to `dict.iteritems()` in Python 2, which is actually what we should use here. Basically whenever `items()`/`keys()`/`values()` is used in a `for` loop, we can leave it as it is, we only need to wrap it in `list` if it will be accessed with `[...]` syntax or e.g. when you use `np.array(...)` to convert it into a numpy array.


What can you tell me about this function?
**Very important**. Answer below.


This contract is meant to be inherited from. So are you inviting the developer of the smart contract to overwrite this `owner` field at will?


Hight -> Height


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It is good practice to help the reader understand what these unnamed parameters represent.
Reduce the mental load of your code auditor.


j'ai l'impression que les lignes 83 à 85 ne sont plus valable, non ?


this shouldn't be 2 callbacks, it should just tell the Activity `onIpAddressValid` and the activity will decide what to do with that information. The Service shouldn't know about it's listener having a progressDialog or what action it will take


@aleksihakli I can handle the Jazzband side, but not the PyPI release until @yetty has granted the owner permissions to `jazzband-bot`. I think in the future we should ask new repos to provide that permission to the `jazzband-bot` instead of just maintainer.


Why choose to name the parameter as `owner`, when `owner` is already used in `Ownable`. Is it to tell users to use the real owner? If so, why ask it in the parameters at all?


equally this should not tell the activity to dismiss it's dialog because it shouldn't know about it


Updated from upstream master, was conflict in overlays.js.


Who is the real owner? This one or the one found in `Ownable`, via `Stoppable`?


Смотри: тебе не нужен второй конструктор с передаваемым в него displayName, это не удобно и не кошерно.
Тебе достаточно чуть-чуть изменить определение DisplayName свойства, сделав его следующим образом:
`public abstract string DisplayName { get; }`
Это обяжет всех наследников явно определять это значение. Т.е. в каком-нибудь `Dog` у тебя будет уже такая строчка:
`public override string DisplayName { get { return "Пёсель"} }`

Студия может предложит тебе даже более простую, но идентичную по смыслу, запись этой конструкции:
`public override string DisplayName => "Пёсель"`


hight -> height


permission granted


**Recursion**


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This is re-entrance vulnerable because the transfers are actually handing over flow control to the receiving contracts. Their callbacks will fire (if they are contracts) and this appoach is hoping that control will be returned as expected. What if the attacker has other ideas? The issue is that flow control might not come back right away and that could lead to a situation in which the money is sent and the accounting is not taken care of.

A solution to this problem is to do "optimistic" account first. Then try the transfer, and if necessary, revert the accounting. The transfer method will actually revert for you if something goes wrong. Keep the idea in mind for cases where a failed communication could result in a false response and/or you want processing to continue for some reason.