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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


The whole API is about CRUD - so it worse to use generics to get a set of generified Get/Put/Post/Delete methods so you should only specify the entity and you will no need to duplicate code.


Successfully aliased the URL <https://static-fun-qe1kskvh4.zeit.sh> to the following aliases:

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


Successfully aliased the URL <https://leetcode-mk28w80jq.now.sh> to the following aliases:

* https://leetcode.katekuo.now.sh
* https://leetcode-git-master.katekuo.now.sh


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/7f81f2c1-43f2-4599-8827-de5a2dc64fc7?env_id=ibm%3Ayp%3Aeu-de "tea-bot-chain"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/88325222-5db0-4b94-9ff2-610f280f9685 "tea-bot-pipe") deployed [tea-bot](https://github.com/tea-bot-project/tea-bot/releases/tag/deploy-ibm-yp-eu-gb-fajsiexofficial-gmail.com-dev-20190910-144332 "deploy-ibm-yp-eu-gb-fajsiexofficial-gmail.com-dev-20190910-144332") to [dev](https://console.bluemix.net/apps/3b214498-c629-4d6f-a5ca-e6fe3a6981ce?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:fajsiexofficial@gmail.com:dev"), including this commit


WaterToAirHP6323 (rraustad) - x86_64-MacOS-10.13-clang: OK (2550 of 2553 tests passed, 10 test warnings)

Messages:\n
 * 6 tests had: EIO diffs.
 * 1 test had: ERR diffs.
 * 3 tests had: ESO big diffs.
 * 1 test had: MTR big diffs.
 * 1 test had: Table big diffs.
 * 7 tests had: BND diffs.
 * 3 tests had: ESO small diffs.
 * 5 tests had: MTR small diffs.
 * 4 tests had: Table small diffs.

Failures:\n

regression Test Summary
 * Passed: 665
 * Failed: 3

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.88%25-yellow.png)


I am commenting this commit now


Created multidev environment [d8-digital-stlawu#ci-505](https://dashboard.pantheon.io/sites/9f185cec-9c0b-4fcb-972f-9a5f2f6ed252#ci-505).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-505-d8-digital-stlawu.pantheonsite.io/)


So you open session each time... please think about lazy init, Singlenton/factory etc.


Why not re-throwing the exception?


Successfully aliased the URL <https://answers-server-82l8ogy5u.now.sh> to the following aliases:

* https://answers-server.lollymay.now.sh
* https://answers-server-git-master.lollymay.now.sh


Correction: The 64 bit counters are ifHCInOctets, ifHCOutOctets, etc.
HwIfInOctets and HwIfOutOctets describe the ethtool names.


[R/sdr_archive_file.R:3:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_archive_file.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' \code{sdr_archive_file} is an internal function that moves a file from a source directory to an archive directory.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_archive_file.R:25:12:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_archive_file.R#L25) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  tryCatch({file.rename(from = source_file_path, to = archive_file_path)},
           ^
```
[R/sdr_archive_file.R:27:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_archive_file.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
             message(paste0("Failed to move file from: ", source_file_path, " to: ", archive_file_path))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_archive_file.R:31:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_archive_file.R#L31) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/sdr_create_connection.R:3:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_create_connection.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' \code{sdr_create_connection} is an internal function to create and open an ODBC database connection.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_create_connection.R:21:12:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_create_connection.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  tryCatch({odbc::dbConnect(odbc::odbc(),
           ^
```
[R/sdr_create_connection.R:22:35:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_create_connection.R#L22) *style:* **Put spaces around all infix operators.**
```r
                            Driver="SQL Server",
                                 ~^~
```
[R/sdr_create_connection.R:23:47:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_create_connection.R#L23) *style:* **Put spaces around all infix operators.**
```r
                            Trusted_Connection="True",
                                             ~^~
```
[R/sdr_create_connection.R:24:37:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_create_connection.R#L24) *style:* **Put spaces around all infix operators.**
```r
                            DATABASE=database,
                                   ~^~
```
[R/sdr_create_connection.R:25:35:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_create_connection.R#L25) *style:* **Put spaces around all infix operators.**
```r
                            SERVER=server)},
                                 ~^~
```
[R/sdr_create_connection.R:27:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_create_connection.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
             message(paste0("Failed to create connection to database: ", database, " on server: ", server))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_delete_table.R:3:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_delete_table.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' \code{sdr_delete_table} opens an ODBC connection and deletes a specified table.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_delete_table.R:21:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_delete_table.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
  connection <- sdrUpload:::sdr_create_connection(database = database, server = server)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_delete_table.R:26:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_delete_table.R#L26) *style:* **Lines should not be more than 80 characters.**
```r
        message(paste0("Failed to delete table: ", table, " from database: ", database, " on server: ", server))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:3:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' \code{sdr_upload} uploads all Excel worksheets in a specified location to a specified database.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:5:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param source \code{string}. The path of the directory containing Excel files.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:6:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param archive \code{string}. The path of the directory to send processed files to.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:15:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
#' sdr_upload("C://example_source", "C://example_archive", "database_name", "server_name")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:22:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
  connection <- sdrUpload:::sdr_create_connection(database = database, server = server)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:32:28:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L32) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    worksheets <- tryCatch({readxl::excel_sheets(file_path)},
                           ^
```
[R/sdr_upload.R:34:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L34) *style:* **Lines should not be more than 80 characters.**
```r
                             message(paste0("Failed to read sheets from file: ", file_path))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:42:22:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L42) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      df <- tryCatch({readxl::read_excel(file_path, sheet = worksheet)},
                     ^
```
[R/sdr_upload.R:44:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
                       message(paste0("Failed to read worksheet: ", worksheet, " from file: ", file_path))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:49:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
      database_table_name <- gsub(" ", "_", paste0(tolower(gsub("\\..*", "", file)), "_", tolower(worksheet)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:52:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
      tryCatch({odbc::dbWriteTable(conn = connection, name = database_table_name, value = df)},
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sdr_upload.R:52:16:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L52) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      tryCatch({odbc::dbWriteTable(conn = connection, name = database_table_name, value = df)},
               ^
```
[R/sdr_upload.R:54:1:](https://github.com/thomascrines/sdrUpload/blob/e1e89a8b9b1464e5fc78493f510733472b902706/R/sdr_upload.R#L54) *style:* **Lines should not be more than 80 characters.**
```r
                 message(paste0("Failed to write worksheet: ", worksheet, " to database: ", database))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


The get* etc methods are very similar, please consider heave refactoring and usage of generics.


Default should be `remove_seen=True`


@JuliaRegistrator register


Successfully aliased the URL <https://my-website-5mj1h7kyj.now.sh> to the following aliases:

* https://my-website.lindafaithharrison.now.sh
* https://my-website-git-master.lindafaithharrison.now.sh


Registration pull request created: [JuliaRegistries/General/3430](https://github.com/JuliaRegistries/General/pull/3430)

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 v0.3.0 -m "<description of version>" ee4d4fe72f1ded12cd6fe857cd88c7c9ed8842e2
git push origin v0.3.0
```


### Keybase proof

I hereby claim:

  * I am giangino on github.
  * I am rael (https://keybase.io/rael) on keybase.
  * I have a public key ASBbmLSpgEUxNMzvGl9YPDFt8BpgUarj1HSgyiiVTm4zqwo

To claim this, I am signing this object:

```json
{
  "body": {
    "key": {
      "eldest_kid": "01205b98b4a980453134ccef1a5f583c316df01a6051aae3d474a0ca28954e6e33ab0a",
      "host": "keybase.io",
      "kid": "01205b98b4a980453134ccef1a5f583c316df01a6051aae3d474a0ca28954e6e33ab0a",
      "uid": "ca7e01c2aa809127e401f443eee8d819",
      "username": "rael"
    },
    "merkle_root": {
      "ctime": 1568125371,
      "hash": "591e5fb94951262fda612482fba0ab56f53bdfc728c2fee8fa43b0c7c75db99bbbc57456090832bfec88ca96ea740d73fa759811e9a53f0580fc6f0a14c1221a",
      "hash_meta": "e04eb96658091da1e503c0208bb3c4108f2fa550ffd98059edf8fc02cad7fc4b",
      "seqno": 6424988
    },
    "service": {
      "entropy": "nDurDXeO+YNpHuyRl6PskXX1",
      "name": "github",
      "username": "giangino"
    },
    "type": "web_service_binding",
    "version": 2
  },
  "client": {
    "name": "keybase.io go client",
    "version": "4.4.0"
  },
  "ctime": 1568125409,
  "expire_in": 504576000,
  "prev": "1d99ce97f3e14bd0c76d8f55075084386dd02995e5759b0e67ed41447098e523",
  "seqno": 5,
  "tag": "signature"
}
```

with the key [ASBbmLSpgEUxNMzvGl9YPDFt8BpgUarj1HSgyiiVTm4zqwo](https://keybase.io/rael), yielding the signature:

```
hKRib2R5hqhkZXRhY2hlZMOpaGFzaF90eXBlCqNrZXnEIwEgW5i0qYBFMTTM7xpfWDwxbfAaYFGq49R0oMoolU5uM6sKp3BheWxvYWTESpcCBcQgHZnOl/PhS9DHbY9VB1CEOG3QKZXldZsOZ+1BRHCY5SPEIIDNNcVWmZ+iX3wjpaUe/N7q/TlMGJgT+RnhngzasnUOAgHCo3NpZ8RAl9X/7vXX+NxviWhPxrq2pB4NWQDgzRa0PaqNqVGSjq9EEVagzjrLifVsK+BLXg5FmoUxUC6JkuzRhIwg/g7yAqhzaWdfdHlwZSCkaGFzaIKkdHlwZQildmFsdWXEIKnP4g/YXgxXiy3mY150PZwAsJm21/Xl7FhJ0ciGAIxvo3RhZ80CAqd2ZXJzaW9uAQ==

```

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

### My publicly-auditable identity:

https://keybase.io/rael

### From the command line:

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

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


Successfully aliased the URL <https://now-github-starter-5e7ft026o.now.sh> to the following aliases:

* https://now-github-starter.timnolet.now.sh
* https://now-github-starter-git-master.timnolet.now.sh


Successfully aliased the URL <https://react-beautiful-dnd-9u0nwcq0m.now.sh> to the following aliases:

* https://react-beautiful-dnd.mirandajignacio.now.sh
* https://react-beautiful-dnd-git-master.mirandajignacio.now.sh


TeamCity Bvcms / Build [Build 2009](https://builds.tpsdb.com/viewLog.html?buildId=8349&buildTypeId=Bvcms_Build) is now running


Lombok.


FixLCC_Escalataion_6144 (JasonGlazer) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (673 of 673 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.44%25-green.png)


Successfully aliased the URL <https://my-website-ptyxezrkx.now.sh> to the following aliases:

* https://my-website.lindafaithharrison.now.sh
* https://my-website-git-master.lindafaithharrison.now.sh


Please add messages-on-fail to your asserts for easier debuging and failures investigations.


Hello GitHub


make this field final and add to constructor.  SortNode should be immutable


Successfully aliased the URL <https://answers-server-oe1nkx5tk.now.sh> to the following aliases:

* https://answers-server.lollymay.now.sh
* https://answers-server-git-master.lollymay.now.sh


誤）カード写真のstyleをCSSに寄せました。
正）formタグをform_withに変更しました。


Thank you very much for sharing these very useful repos with us.
Concerning the commit on the Java source download location, the 206.167.181.71 address seems to be no longer accessible (while the previous "https://github.com/cgeroux/packages/raw/master" link seems fine). Would it be possible to fix this?


Successfully aliased the URL <https://next-piveqmuw7.now.sh> to the following aliases:

* https://next.julio157ramirez.now.sh
* https://next-git-master.julio157ramirez.now.sh


General question, why do you do direct pushes instead of creating pull-request and going through normal code review process?


the sort node created above is the one that should be created with isPartial set to true


I would have returned here and in the catch then returned the rejected promise instead.


Successfully aliased the URL <https://awesome-templates-3yy55bouh.now.sh> to the following aliases:

* https://awesome-templates.dev
* https://awesome-templates.pablosz.now.sh
* https://awesome-templates-git-master.pablosz.now.sh


Could this commit be included into 2.0 versions: 2.0.0-alpha, 2.0.0-beta0, 2.0.0-beta1, 2.0.0-rc0?
I experience this problem with deserialization SequenceCategoricalColumn and have seen that changes fix my issue.


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/4454daa171f7bec0c99ed181ee2bc1bda32dcd9a/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
check_pir_out <- function(
^
```
[R/create_alignment_impl.R:34:1:](https://github.com/richelbilderbeek/pirouette/blob/4454daa171f7bec0c99ed181ee2bc1bda32dcd9a/R/create_alignment_impl.R#L34) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
create_alignment_impl <- function(
^
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/4454daa171f7bec0c99ed181ee2bc1bda32dcd9a/R/create_all_experiments.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 30.**
```r
create_all_experiments <- function(
^
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/4454daa171f7bec0c99ed181ee2bc1bda32dcd9a/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 24.**
```r
est_evidences <- function(
^
```
[R/select_candidate_evidences.R:25:1:](https://github.com/richelbilderbeek/pirouette/blob/4454daa171f7bec0c99ed181ee2bc1bda32dcd9a/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```


Принято 👍
Можно лучше: Странные ограничения для доммена, в реальности, домены могут принимать очень разные названия, например сушествуют таки доменны как mobil moscow.
Также хорошо бы в названии url считать валидными числа и знаки


Make .gitignore file so that you do not need to upload machine-specific files (e.g. .idea ...)


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

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


Задание выполнено!
Удачи в дальнейшей учебе.


168195503_Issue7477 (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1217 of 1217 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.15%25-green.png)


Successfully aliased the URL <https://react-beautiful-dnd-lqbmwv3gr.now.sh> to the following aliases:

* https://react-beautiful-dnd.mirandajignacio.now.sh
* https://react-beautiful-dnd-git-master.mirandajignacio.now.sh


Successfully aliased the URL <https://now-mongo-answers-nm9lqxon2.now.sh> to the following aliases:

* https://now-mongo-answers.lollymay.now.sh
* https://now-mongo-answers-git-master.lollymay.now.sh


### Keybase proof

I hereby claim:

  * I am tommyabbey on github.
  * I am tommyabbey (https://keybase.io/tommyabbey) on keybase.
  * I have a public key ASC1ScIHbS2swQqW-rAyHakJMemM_TxZjxx-NqLdNl7Z_Ao

To claim this, I am signing this object:

```json
{
  "body": {
    "key": {
      "eldest_kid": "0120b549c2076d2dacc10a96fab0321da90931e98cfd3c598f1c7e36a2dd365ed9fc0a",
      "host": "keybase.io",
      "kid": "0120b549c2076d2dacc10a96fab0321da90931e98cfd3c598f1c7e36a2dd365ed9fc0a",
      "uid": "102ad51366796c2958e49833efbd8819",
      "username": "tommyabbey"
    },
    "merkle_root": {
      "ctime": 1568127206,
      "hash": "659a8f11067a1dba697fb766e0bd51c6d54b6708436f8330cdc103feb30b10050df7e15bf7f17736bedda78f9c1f375c567ad0b5a6c7b2c80603e58f38dc283d",
      "hash_meta": "51888d44f1066bc4d6ca7f9c6b2d38e65e86625008a2f6bd3294b25e6b641dab",
      "seqno": 6432627
    },
    "service": {
      "entropy": "46CtaXg1dLmqErriVMWNKku7",
      "name": "github",
      "username": "tommyabbey"
    },
    "type": "web_service_binding",
    "version": 2
  },
  "client": {
    "name": "keybase.io go client",
    "version": "4.4.0"
  },
  "ctime": 1568127142,
  "expire_in": 504576000,
  "prev": "a599f11f647bf3fef0e39eefaa9d482a55346c0a47625b1bb52c73ed82adc765",
  "seqno": 5,
  "tag": "signature"
}
```

with the key [ASC1ScIHbS2swQqW-rAyHakJMemM_TxZjxx-NqLdNl7Z_Ao](https://keybase.io/tommyabbey), yielding the signature:

```
hKRib2R5hqhkZXRhY2hlZMOpaGFzaF90eXBlCqNrZXnEIwEgtUnCB20trMEKlvqwMh2pCTHpjP08WY8cfjai3TZe2fwKp3BheWxvYWTESpcCBcQgpZnxH2R78/7w457vqp1IKlU0bApHYlsbtSxz7YKtx2XEIIBoYs+RSe/zf72Ic862tWpIqQt2hW6oXT9bX2m3vmcoAgHCo3NpZ8RAnkOw661eQrPZcO3c7po6QnuylcYEohMSg9c93zD0XQAxA6HJUbrfhe4lbF8O6zHPDykbj53WgJKEJi1fgj/HCqhzaWdfdHlwZSCkaGFzaIKkdHlwZQildmFsdWXEIL5T5RFFE2zco6sLlCEYgF2idDcySruQ45zSN5eNcjA3o3RhZ80CAqd2ZXJzaW9uAQ==

```

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

### My publicly-auditable identity:

https://keybase.io/tommyabbey

### From the command line:

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

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


Successfully aliased the URL <https://files-aq7kkbxuw.now.sh> to the following aliases:

* https://files.jaruesink.now.sh
* https://files-git-master.jaruesink.now.sh


Setting state to `success` where context is `VSTS: device tests (iOS-Beta)`.

No blocking issues found


Setting state to `success` where context is `continuous-integration/jenkins/branch`.

No blocking issues found


With him


Successfully aliased the URL <https://awesome-templates-hianbslxr.now.sh> to the following aliases:

* https://awesome-templates.dev
* https://awesome-templates.pablosz.now.sh
* https://awesome-templates-git-master.pablosz.now.sh


Successfully aliased the URL <https://frontend-pzzb1zpr2.now.sh> to the following aliases:

* https://niyonapp-staging.now.sh
* https://niyonapp.now.sh
* https://niyon-frontend-dev.now.sh
* https://niyonapp.com
* https://frontend.labseu2-niyon.now.sh
* https://frontend-git-master.labseu2-niyon.now.sh


why tf did you just copy my fork and not merge it????


Successfully aliased the URL <https://gw2017-7dnvziceq.now.sh> to the following alias:


Created multidev environment [d8-digital-stlawu#ci-507](https://dashboard.pantheon.io/sites/9f185cec-9c0b-4fcb-972f-9a5f2f6ed252#ci-507).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-507-d8-digital-stlawu.pantheonsite.io/)


###### :x: Test Failed: `va/deploy/1-cache`
  ```bash
  drush $DRUSH_ALIAS cr
  ```
  ```bash
  <em class="placeholder">Notice</em>: Undefined offset: 6 in <em class="placeholder">Drupal\Core\Database\Database::parseConnectionInfo()</em> (line <em class="placeholder">212</em> of <em class="placeholder">/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php</em>).<em class="placeholder">Notice</em>: Undefined index: driver in <em class="placeholder">Drupal\Core\Database\Database::openConnection()</em> (line <em class="placeholder">364</em> of <em class="placeholder">/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php</em>).<em class="placeholder">Notice</em>: Undefined index: driver in <em class="placeholder">Drupal\Core\Database\Database::openConnection()</em> (line <em class="placeholder">364</em> of <em class="placeholder">/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php</em>).
Notice: Undefined index: driver in /var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php on line 364

Notice: Undefined index: driver in /var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php on line 364

  PHP Notice:  Undefined index: driver in /var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php on line 364
PHP Notice:  Undefined index: driver in /var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php on line 364
Drupal\Core\Database\DriverNotSpecifiedException: Driver not         [error]
specified for this database connection: default in
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php:365
Stack trace:
#0
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php(166):
Drupal\Core\Database\Database::openConnection('default', 'default')
#1 [internal function]:
Drupal\Core\Database\Database::getConnection('default')
#2
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(248):
call_user_func_array(Array, Array)
#3
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(171):
Drupal\Component\DependencyInjection\Container->createService(Array,
'database')
#4
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(480):
Drupal\Component\DependencyInjection\Container->get('database', 1)
#5
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(230):
Drupal\Component\DependencyInjection\Container->resolveServicesAndParameters(Array)
#6
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(171):
Drupal\Component\DependencyInjection\Container->createService(Array,
'cache.backend.d...')
#7
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Cache/ChainedFastBackendFactory.php(82):
Drupal\Component\DependencyInjection\Container->get('cache.backend.d...')
#8
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Cache/CacheFactory.php(83):
Drupal\Core\Cache\ChainedFastBackendFactory->get('bootstrap')
#9 [internal function]:
Drupal\Core\Cache\CacheFactory->get('bootstrap')
#10
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(248):
call_user_func_array(Array, Array)
#11
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(171):
Drupal\Component\DependencyInjection\Container->createService(Array,
'cache.bootstrap')
#12
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(480):
Drupal\Component\DependencyInjection\Container->get('cache.bootstrap',
1)
#13
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(230):
Drupal\Component\DependencyInjection\Container->resolveServicesAndParameters(Array)
#14
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Component/DependencyInjection/Container.php(171):
Drupal\Component\DependencyInjection\Container->createService(Array,
'module_handler')
#15
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/DrupalKernel.php(585):
Drupal\Component\DependencyInjection\Container->get('module_handler')
#16
/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/DrupalKernel.php(746):
Drupal\Core\DrupalKernel->preHandle(Object(Symfony\Component\HttpFoundation\Request))
#17
/var/aegir/projects/cms/pr571/docroot/core/includes/utility.inc(43):
Drupal\Core\DrupalKernel->prepareLegacyRequest(Object(Symfony\Component\HttpFoundation\Request))
#18
/usr/share/devshop/vendor/drush/drush/commands/core/cache.drush.inc(302):
drupal_rebuild(Object(Composer\Autoload\ClassLoader),
Object(Symfony\Component\HttpFoundation\Request))
#19 /usr/share/devshop/vendor/drush/drush/includes/command.inc(422):
drush_cache_rebuild()
#20 /usr/share/devshop/vendor/drush/drush/includes/command.inc(231):
_drush_invoke_hooks(Array, Array)
#21 /usr/share/devshop/vendor/drush/drush/includes/command.inc(199):
drush_command()
#22
/usr/share/devshop/vendor/drush/drush/lib/Drush/Boot/BaseBoot.php(67):
drush_dispatch(Array)
#23 /usr/share/devshop/vendor/drush/drush/includes/preflight.inc(67):
Drush\Boot\BaseBoot->bootstrap_and_dispatch()
#24 /usr/share/devshop/vendor/drush/drush/drush.php(12): drush_main()
#25 {main}

  ```
*AUTOMATED COMMENT FROM provision-ops/yaml-tests, running on devshop.cms.va.gov*


###### :x: Test Failed: `va/deploy/2-update`
  ```bash
  drush $DRUSH_ALIAS updatedb --yes
  ```
  ```bash
  <em class="placeholder">Notice</em>: Undefined offset: 6 in <em class="placeholder">Drupal\Core\Database\Database::parseConnectionInfo()</em> (line <em class="placeholder">212</em> of <em class="placeholder">/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php</em>).Error: Call to undefined function drupal_get_installed_schema_version() in drupal_load_updates() (line 81 of /var/aegir/projects/cms/pr571/docroot/core/includes/install.inc).

  Error: Call to undefined function drupal_get_installed_schema_version() in /var/aegir/projects/cms/pr571/docroot/core/includes/install.inc on line 81 #0 /usr/share/devshop/vendor/drush/drush/commands/core/drupal/update.inc(135): drupal_load_updates()
#1 /usr/share/devshop/vendor/drush/drush/commands/core/core.drush.inc(466): update_main()
#2 /usr/share/devshop/vendor/drush/drush/includes/command.inc(422): drush_core_updatedb()
#3 /usr/share/devshop/vendor/drush/drush/includes/command.inc(231): _drush_invoke_hooks(Array, Array)
#4 /usr/share/devshop/vendor/drush/drush/includes/command.inc(199): drush_command()
#5 /usr/share/devshop/vendor/drush/drush/lib/Drush/Boot/BaseBoot.php(67): drush_dispatch(Array)
#6 /usr/share/devshop/vendor/drush/drush/includes/preflight.inc(67): Drush\Boot\BaseBoot->bootstrap_and_dispatch()
#7 /usr/share/devshop/vendor/drush/drush/drush.php(12): drush_main()
#8 {main}
Drush command terminated abnormally due to an unrecoverable error.   [error]

  ```
*AUTOMATED COMMENT FROM provision-ops/yaml-tests, running on devshop.cms.va.gov*


###### :x: Test Failed: `va/deploy/3-config`
  ```bash
  drush $DRUSH_ALIAS cim --yes && drush $DRUSH_ALIAS cr
  ```
  ```bash
  <em class="placeholder">Notice</em>: Undefined offset: 0 in <em class="placeholder">Drupal\Core\Database\Database::parseConnectionInfo()</em> (line <em class="placeholder">212</em> of <em class="placeholder">/var/aegir/projects/cms/pr571/docroot/core/lib/Drupal/Core/Database/Database.php</em>).
  Command config-import needs a higher bootstrap level to run - you    [error]
will need to invoke drush from a more functional Drupal environment
to run this command.
The drush command 'cim' could not be executed.                       [error]
Drush was not able to start (bootstrap) the Drupal database.         [error]
Hint: This may occur when Drush is trying to:
 * bootstrap a site that has not been installed or does not have a
configured database. In this case you can select another site with a
working database setup by specifying the URI to use with the --uri
parameter on the command line. See `drush topic docs-aliases` for
details.
 * connect the database through a socket. The socket file may be
wrong or the php-cli may have no access to it in a jailed shell. See
http://drupal.org/node/1428638 for details.
 * connect to the database through a cli command using the
--defaults-extra-file parameter to pass credentials through a tmp
file. This method can break if other credentials are specified in a
~/.my.cnf file in your home directory. You may have to delete or
rename the ~/.my.cnf file in your home directory.

Drush was attempting to connect to:
 Drupal version        :  8.6.10
 Site URI              :  pr571.ci.cms.va.gov
 PHP executable        :  /usr/bin/php
 PHP configuration     :  /etc/php.ini
 PHP OS                :  Linux
 Drush script          :  /usr/share/devshop/vendor/drush/drush/dru
                          sh.php
 Drush version         :  8.3.0
 Drush temp            :  /tmp
 directory
 Drush configuration   :  /var/aegir/projects/cms/pr571/docroot/sit
                          es/all/drush/drushrc.php
                          /var/aegir/.drush/drushrc.php
 Drush alias files     :  /var/aegir/.drush/project_aliases/cms.ali
                          ases.drushrc.php "
                          There are 55 more alias files. Run with
                          --full to see the full list."
 Drupal root           :  /var/aegir/projects/cms/pr571/docroot
 Drupal Settings       :  sites/pr571.ci.cms.va.gov/settings.php
 File
 Site path             :  sites/pr571.ci.cms.va.gov
 Sync config path      :  ../config/sync

  ```
*AUTOMATED COMMENT FROM provision-ops/yaml-tests, running on devshop.cms.va.gov*


第一个网页


Get 84 points. The mistake is in the generateY function, where Y should be `X %*% beta + sigma * rnorm(n)` instead of `X %*% beta`.