[inst/doc/demo_optimize.R:18:26:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_area_params.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
#' @param proportional_peak_t value from 0 to 1 indicating where in the island's history the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_area_params.R:37:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_area_params.R#L37) *style:* **Lines should not be more than 80 characters.**
```r
#' @return list of numerical values containing area parameters for island ontogeny
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:4:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_create_island.R#L84) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_data.R:2:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_data.R#L165) *style:* **Trailing whitespace is superfluous.**
```r
#' \code{$island_age} - the island age\cr
                                         ^
```
[R/DAISIE_data.R:197:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_data.R#L197) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:247:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_data.R#L247) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:256:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_data.R#L256) *style:* **Lines should not be more than 80 characters.**
```r
#' The following elements of the list each contains information on a single colonist lineage
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:270:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_data.R#L270) *style:* **Lines should not be more than 80 characters.**
```r
#' #' \code{$missing_species} - number of island species that were not sampled for
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:286:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:7:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:10:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:86:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/DAISIE_dataprep.R:87:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:88:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L88) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:89:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L89) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:90:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:98:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L98) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:100:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L104) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:113:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L113) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:114:80:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L118) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:128:3:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L128) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_dataprep.R:130:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L135) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/DAISIE_dataprep.R:136:5:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/R/DAISIE_dataprep.R#L158) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/DAISIE_dataprep.R:159:1:](https://github.com/rsetienne/DAISIE/blob/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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/d8d7ec382ac426786512395dfd231c9f1ed0f622/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=''))}
                                                                                ^
```


You may want to include the [whole game](https://r-pkgs.org/whole-game.html) chapter of the upcoming revision to the R packages book as well.


@mjyaqubi
Done!


int id, может не id а position
И в чем измеряется позиция?


In  HTML there is already a tag under the hood


笑死我了 @BingLingGroup


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Did you forget to release react-reconciler with this version update?


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может пул потоков, а не создавать каждый раз?


re-added
https://github.com/uBlockOrigin/uAssets/commit/6f86a47e160c22d02ee70ae24cb95921ee74be26


It is necessary to write the full name of the classes for more readable code.


done


зачем делать атрибутом объекта?
Если так оставить, то стоит дать понятное имя, что делает этот Runnable


This all can be for the most part can be placed in one background


我来看看，大佬们不要介意


牛批啊老铁 [@BingLingGroup](https://github.com/BingLingGroup)


so not worth to do


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@JuliaRegistrator `register()`


Registration pull request created: [JuliaRegistries/General/3078](https://github.com/JuliaRegistries/General/pull/3078)

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 v2.1.9 -m "<description of version>" dc9cd902beec7d238667f23b04680811701076bb
git push origin v2.1.9
```


@JuliaRegistrator register()


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Registration pull request created: [JuliaRegistries/General/3079](https://github.com/JuliaRegistries/General/pull/3079)

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 v0.1.1 -m "<description of version>" dbea81e1f376d359c42d79497894ca526f4f3f34
git push origin v0.1.1
```


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추가로 iamport 결제 부분 연동 / naver map api 연동 구현


Is this comment still relevant?


It is better to store all images in separate folders intended for them. And it is necessary to correct the code ( marked by commits )


cl /W4 main.c ap_isdigit.c /link /out:digit.exe


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Hi @Neves-P: what does this line do? Up until now, I've never seen it.

As far as I can see [lintr will report the folders created by unpacking this tarball](https://travis-ci.org/rsetienne/DAISIE/builds/578805973#L1006), which is a disadvantage. Could you share what the advantage is?

Thanks!


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NullTime is true if assertion is failed: for example Scan(int64(42))
error is "unsupported Scan, storing driver.Value type int64 into type *time.Time", but time is already true.
Is this good?


No without your change one of my work document break complelty.

I could not share due to confidential reason but it break (unknow command)

At least normalfont need to be proetected, but it is not sufficient.

So any idea ?

On Fri, Aug 30, 2019 at 2:50 PM Jürgen Spitzmüller
<notifications@github.com> wrote:
>
> Yes it does. You can see it when compiling the polyglossia manual. After 6.1. arabic, the arabic font leaks into the following text. You can see it in the dot which changes in the subsection headers, and particularly in sec. 6.9 french, where "frenchfootnote" is typeset as "frencfhootnote".
>
> Obviously, the normalfont needs to be defined globally.
>
> So please revert this.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or mute the thread.


害怕.jpg，我本来以为我没有写权限，直接就release了


What is Message Compiler? Is it an internal tool?


Well, that was fast @borisschapira! 😅


@barclayn this update altered the format of the table causing AI and Machine Learning to display as a column on the right and makes the headers of the table confusing.


That’s a great question.

To be honest I think service factories should be pure. Actions being updated are enough, as that’s the only part that will actually contain impure code.


If it's an internal tool, perhaps we should remove this comment? External contributors do not need to know about it.


thanks
https://github.com/uBlockOrigin/uAssets/commit/d7ff8332c4eb34d5562882e72f05360d70c9fef0


I encountered the problem that my appendices section started with an additional empty "Appendix A".


Вот это меню только лишнее. Это было только для учебных целей.
Если, что - можно удалить.


>  User Deprecated: Passing a command as string when creating a "Symfony\Component\Process\Process" instance is deprecated since Symfony 4.2, pass it as an array of its arguments instead, or use the "Process::fromShellCommandline()" constructor if you need features provided by the shell. exception="[object] (ErrorException(code: 0): User Deprecated: Passing a command as string when creating a \"Symfony\\Component\\Process\\Process\" instance is deprecated since Symfony 4.2, pass it as an array of its arguments instead, or use the \"Process::fromShellCommandline()\" constructor if you need features provided by the shell. at \\vendor\\symfony\\process\\Process.php:147)"


И коментарии тоже лучше не оставлять в коде.


Optional isn't really supported by the metadata. Have you tried to auto-complete those properties in an IDE?