[R/create_figure_acceptance_mcmc_operators.R:7:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_acceptance_mcmc_operators.R#L7) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_acceptance_mcmc_operators <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_alignment_qualities.R:2:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_alignment_qualities.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @param alignments data frame with alignments, as returned by 'read_collected_alignments'
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_alignment_qualities.R:7:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_alignment_qualities.R#L7) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_alignment_qualities <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_mean.R:8:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_mean.R#L8) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_alignment_length_mean <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_mean.R:24:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_mean.R#L24) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_alignment_length_mean.R:33:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_mean.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
  df_means <- merge(x = parameters, y = nltt_stat_means, by = "filename", all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_mean.R:41:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_mean.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::aes(x = as.factor(scr), y = mean, fill = as.factor(sequence_length))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_mean.R:45:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_mean.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
      ggplot2::ylab(latex2exp::TeX("Mean nLTT statistics, $\\bar{\\Delta_{nLTT}}$")) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_mean.R:48:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_mean.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
        title = "The effect of alignment length on mean nLTT statistic for\ndifferent speciation completion rates (x axis boxplot),\nspeciation initiation rates (columns)\nand extinction rates (rows)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_median.R:8:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_median.R#L8) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_alignment_length_median <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_median.R:25:37:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_median.R#L25) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_medians <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                  ~~^
```
[R/create_figure_error_alignment_length_median.R:34:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_median.R#L34) *style:* **Lines should not be more than 80 characters.**
```r
  df_medians <- merge(x = parameters, y = nltt_stat_medians, by = "filename", all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_median.R:37:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_median.R#L37) *style:* **Lines should not be more than 80 characters.**
```r
  df_medians <- merge(x = df_medians, y = esses, by = c("filename", "sti", "ai", "pi"), all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_median.R:42:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_median.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::aes(x = as.factor(scr), y = median, fill = as.factor(sequence_length))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_median.R:46:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_median.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
      ggplot2::ylab(latex2exp::TeX("Median nLTT statistics, $\\widetilde{\\Delta_{nLTT}}$")) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length_median.R:49:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length_median.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
        title = "The effect of alignment length on median nLTT statistic for\ndifferent speciation completion rates (x axis boxplot),\nspeciation initiation rates (columns)\nand extinction rates (rows)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length.R:9:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_alignment_length <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length.R:23:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
  parameters <- dplyr::select(parameters, c(sirg, scr, erg, sequence_length, filename))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length.R:39:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::aes(x = as.factor(scr), y = nltt_stat, fill = as.factor(sequence_length))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_alignment_length.R:42:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_alignment_length.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
      ggplot2::xlab("Speciation completion rate (probability per lineage per million years)") +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd_mean.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd_mean.R:17:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L17) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_bd_mean.R:22:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L22) *style:* **Commented code should be removed.**
```r
  # print("Connect the mean nLTT stats and parameters")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd_mean.R:27:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L27) *style:* **Commented code should be removed.**
```r
  # print("Only keep rows with the highest SCR (as those are a BD model)")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd_mean.R:28:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L28) *style:* **Commented code should be removed.**
```r
  # print(paste0("Rows before: ", nrow(df)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd_mean.R:31:12:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  df <- df[ df$scr == scr_bd, ]
           ^
```
[R/create_figure_error_bd_mean.R:32:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L32) *style:* **Commented code should be removed.**
```r
  # print(paste0("Rows after: ", nrow(df)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd_mean.R:34:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L34) *style:* **Commented code should be removed.**
```r
  # print("Creating figure")
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd_mean.R:45:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd_mean.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
    title = "Mean nLTT statistics\nfor different extinction (columns)\nand speciation inition rates (rows)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd.R:20:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd.R#L20) *style:* **Commented code should be removed.**
```r
  # print("Only keep rows with the highest SCR (as those are a BD model)")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd.R:21:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd.R#L21) *style:* **Commented code should be removed.**
```r
  # print(paste0("Rows before: ", nrow(df)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd.R:22:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd.R#L22) *style:* **Commented code should be removed.**
```r
  # dplyr::count(df, scr)
    ^~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd.R:24:12:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  df <- df[ df$scr == scr_bd, ]
           ^
```
[R/create_figure_error_bd.R:25:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd.R#L25) *style:* **Commented code should be removed.**
```r
  # print(paste0("Rows after: ", nrow(df)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_bd.R:35:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_bd.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
        "nLTT statistics\nfor different extinction (columns)\nand speciation inition rates (rows)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_for_scr.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_for_scr.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_for_scr.R:25:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_for_scr.R#L25) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_for_scr.R:40:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_for_scr.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
  ggplot2::xlab("Speciation completion rate (probability per lineage per million years)") +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_for_scr.R:43:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_for_scr.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
    title = "Mean nLTT statistic for\ndifferent speciation completion rates (x axis boxplot),\nspeciation initiation rates (columns)\nand extinction rates (rows)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:9:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_low_high_ess_mean <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:26:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L26) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_low_high_ess_mean.R:31:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L31) *style:* **Commented code should be removed.**
```r
  # print("Add mean duration of speciation to parameters")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:48:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
  df_mean <- merge(x = parameters, y = nltt_stat_means, by = "filename", all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:55:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L55) *style:* **Commented code should be removed.**
```r
  # Convert: TRUE -> OK
    ^~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:56:18:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  esses$ess_type[ esses$ess_type == TRUE ] <- "High"
                 ^
```
[R/create_figure_error_low_high_ess_mean.R:56:41:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  esses$ess_type[ esses$ess_type == TRUE ] <- "High"
                                        ^
```
[R/create_figure_error_low_high_ess_mean.R:57:18:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L57) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  esses$ess_type[ esses$ess_type == FALSE ] <- "Low"
                 ^
```
[R/create_figure_error_low_high_ess_mean.R:57:42:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L57) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  esses$ess_type[ esses$ess_type == FALSE ] <- "Low"
                                         ^
```
[R/create_figure_error_low_high_ess_mean.R:61:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
  df <- merge(x = df, y = esses, by = c("filename", "sti", "ai", "pi"), all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:62:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L62) *style:* **Lines should not be more than 80 characters.**
```r
  df_mean <- merge(x = df_mean, y = esses, by = c("filename", "sti", "ai", "pi"), all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:70:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
      ggplot2::xlab(latex2exp::TeX("$\\lambda$ (probability per lineage per million years)")) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:73:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
        title = "The effect of a low and high ESS of tree likelihood on mean nLTT statistic for\ndifferent speciation completion rates (x axis boxplot),\nspeciation initiation rates (columns)\nand extinction rates (rows)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:84:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L84) *style:* **Commented code should be removed.**
```r
#   grDevices::svg("~/figure_error_expected_mean_dur_spec_low_high_ess.svg")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:85:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L85) *style:* **Commented code should be removed.**
```r
#   set.seed(42)
    ^~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:86:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L86) *style:* **Commented code should be removed.**
```r
#   n_sampled <- 5000
    ^~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:87:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L87) *style:* **Commented code should be removed.**
```r
#   n_data_points <- nrow(stats::na.omit(df))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:88:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L88) *style:* **Commented code should be removed.**
```r
#   nltt_stat_cutoff <- 0.12
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:90:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L90) *style:* **Commented code should be removed.**
```r
#   options(warn = 1) # Allow points not to be plotted
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:93:7:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L93) *style:* **Commented code should be removed.**
```r
#     ggplot2::aes(x = mean_durspec, y = nltt_stat, color = ess_type)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:100:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
#       ggplot2::aes(label = paste(..eq.label.., ..adj.rr.label.., sep = "~~~~")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:103:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
#     ggplot2::scale_y_continuous(limits = c(0, nltt_stat_cutoff)) + # Will have some outliers unplotted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:107:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
#       title = "nLTT statistic\nfor different expected mean duration of speciation,\nfor ESSes",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:108:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L108) *style:* **Lines should not be more than 80 characters.**
```r
#       caption  = paste0("n = ", n_sampled, " / ", n_data_points, ", figure_error_expected_mean_dur_spec_ess_low_high")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:108:9:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L108) *style:* **Commented code should be removed.**
```r
#       caption  = paste0("n = ", n_sampled, " / ", n_data_points, ", figure_error_expected_mean_dur_spec_ess_low_high")
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:111:7:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L111) *style:* **Commented code should be removed.**
```r
#     ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:113:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L113) *style:* **Commented code should be removed.**
```r
#   options(warn = 2) # Be strict
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:115:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L115) *style:* **Commented code should be removed.**
```r
#   grDevices::dev.off()
    ^~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:117:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
#   grDevices::svg("~/figure_error_expected_mean_dur_spec_mean_low_high_ess.svg")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:117:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L117) *style:* **Commented code should be removed.**
```r
#   grDevices::svg("~/figure_error_expected_mean_dur_spec_mean_low_high_ess.svg")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:118:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L118) *style:* **Commented code should be removed.**
```r
#   options(warn = 1) # Allow points to fall off plot range
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:122:7:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L122) *style:* **Commented code should be removed.**
```r
#     ggplot2::aes(x = mean_durspec, y = mean, color = ess_type)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:130:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L130) *style:* **Lines should not be more than 80 characters.**
```r
#       ggplot2::aes(label = paste(..eq.label.., ..adj.rr.label.., sep = "~~~~")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:132:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L132) *style:* **Lines should not be more than 80 characters.**
```r
#     #ggplot2::scale_y_continuous(limits = c(0, nltt_stat_cutoff)) + # Will have some outliers unplotted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:132:7:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L132) *style:* **Commented code should be removed.**
```r
#     #ggplot2::scale_y_continuous(limits = c(0, nltt_stat_cutoff)) + # Will have some outliers unplotted
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:137:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
#       title = "Mean nLTT statistic\nfor different expected mean duration of speciation,\nfor tree likelihood ESSes aboven and below median",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:138:9:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L138) *style:* **Commented code should be removed.**
```r
#       caption  = "figure_error_expected_mean_dur_spec_mean_low_high_ess"
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:141:7:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L141) *style:* **Commented code should be removed.**
```r
#     ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:144:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L144) *style:* **Commented code should be removed.**
```r
#   options(warn = 2) # Be strict
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess_mean.R:146:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess_mean.R#L146) *style:* **Commented code should be removed.**
```r
#   ggplot2::ggsave(file = filename, width = 7, height = 7)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess.R:9:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_low_high_ess <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess.R:26:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L26) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_low_high_ess.R:31:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L31) *style:* **Commented code should be removed.**
```r
  # print("Add mean duration of speciation to parameters")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess.R:44:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
  df <- merge(x = parameters, y = dplyr::sample_n(nltt_stats, size = sample_size), by = "filename", all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess.R:51:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L51) *style:* **Commented code should be removed.**
```r
  # Convert: TRUE -> OK
    ^~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess.R:52:18:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  esses$ess_type[ esses$ess_type == TRUE ] <- "High"
                 ^
```
[R/create_figure_error_low_high_ess.R:52:41:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  esses$ess_type[ esses$ess_type == TRUE ] <- "High"
                                        ^
```
[R/create_figure_error_low_high_ess.R:53:18:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  esses$ess_type[ esses$ess_type == FALSE ] <- "Low"
                 ^
```
[R/create_figure_error_low_high_ess.R:53:42:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  esses$ess_type[ esses$ess_type == FALSE ] <- "Low"
                                         ^
```
[R/create_figure_error_low_high_ess.R:57:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
  df <- merge(x = df, y = esses, by = c("filename", "sti", "ai", "pi"), all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess.R:64:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
      ggplot2::xlab(latex2exp::TeX("$\\lambda$ (probability per lineage per million years)")) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_low_high_ess.R:67:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_low_high_ess.R#L67) *style:* **Lines should not be more than 80 characters.**
```r
        title = "The effect of a low and high ESS of tree likelihood on nLTT statistic for\ndifferent speciation completion rates (x axis boxplot),\nspeciation initiation rates (columns)\nand extinction rates (rows)",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_max.R:24:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_max.R#L24) *style:* **Commented code should be removed.**
```r
  # print("Add mean duration of speciation to parameters")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_max.R:32:70:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_max.R#L32) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  parameters <- subset(parameters, select = c(filename, mean_durspec) )
                                                                     ^
```
[R/create_figure_error_max.R:39:5:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_max.R#L39) *style:* **Commented code should be removed.**
```r
  # print("Order by nltt_stat, highest value first")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_max.R:40:24:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_max.R#L40) *warning:* **no visible binding for global variable ‘nltt_stat’, Did you mean 'nltt_stats'?**
```r
  df <- stats::na.omit(nltt_stats[with(nltt_stats, order(-nltt_stat)), ])
                       ^~~~~~~~~
```
[R/create_figure_error_max.R:41:3:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_max.R#L41) *warning:* **local variable ‘filenames’ assigned but may not be used**
```r
  filenames <- unique(utils::head(df, 1000)$filename)
  ^~~~~~~~~
```
[R/create_figure_error_max.R:62:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_max.R#L62) *style:* **Lines should not be more than 80 characters.**
```r
  ape::plot.phylo(main = "posterior tree", posterior_stree, show.tip.label = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_max.R:67:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_max.R#L67) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:9:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_mean_dur_spec_alignment_length <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:33:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L33) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:39:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
  parameters <- dplyr::select(parameters, c(filename, scr, mean_durspec, sequence_length))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:56:8:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    df[ df$scr == scr_bd & df$sequence_length == 1000 , ]$nltt_stat)
       ^
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:56:55:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L56) *style:* **Commas should never have a space before.**
```r
    df[ df$scr == scr_bd & df$sequence_length == 1000 , ]$nltt_stat)
                                                     ~^
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:58:8:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    df[ df$scr == scr_bd & df$sequence_length == 10000, ]$nltt_stat)
       ^
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:73:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::aes(x = mean_durspec, y = nltt_stat, color = as.factor(sequence_length))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:83:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_hline(yintercept = mean_bd_error_1000, linetype = "dotted", color = scales::hue_pal()(2)[1]) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:84:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L84) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_hline(yintercept = mean_bd_error_10000, linetype = "dotted", color = scales::hue_pal()(2)[2]) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:85:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L85) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::scale_y_continuous(limits = c(0, nltt_stat_cutoff)) + # Will have some outliers unplotted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:89:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L89) *style:* **Lines should not be more than 80 characters.**
```r
      title = "nLTT statistic\nfor different expected mean duration of speciation,\nfor different DNA alignment lengths",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_alignment_length.R:90:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_alignment_length.R#L90) *style:* **Lines should not be more than 80 characters.**
```r
      caption  = paste0("n = ", sample_size, " / ", n_data_points, ", ", filename)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:7:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L7) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_mean_dur_spec_mean_alignment_length <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:29:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L29) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:35:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
  parameters <- dplyr::select(parameters, c(filename, scr, mean_durspec, sequence_length))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:44:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
  df_mean <- merge(x = parameters, y = nltt_stat_means, by = "filename", all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:48:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
  mean_bd_error_1000  <- mean(stats::na.omit(df[ df$scr == scr_bd & df$sequence_length == 1000 , ]$nltt_stat))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:48:49:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  mean_bd_error_1000  <- mean(stats::na.omit(df[ df$scr == scr_bd & df$sequence_length == 1000 , ]$nltt_stat))
                                                ^
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:48:96:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L48) *style:* **Commas should never have a space before.**
```r
  mean_bd_error_1000  <- mean(stats::na.omit(df[ df$scr == scr_bd & df$sequence_length == 1000 , ]$nltt_stat))
                                                                                ~^
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:49:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
  mean_bd_error_10000 <- mean(stats::na.omit(df[ df$scr == scr_bd & df$sequence_length == 10000, ]$nltt_stat))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:49:49:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L49) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  mean_bd_error_10000 <- mean(stats::na.omit(df[ df$scr == scr_bd & df$sequence_length == 10000, ]$nltt_stat))
                                                ^
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:66:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::scale_y_continuous(limits = c(0, nltt_stat_cutoff)) + # Will have some outliers unplotted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:68:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_hline(yintercept = mean_bd_error_1000, linetype = "dotted", color = scales::hue_pal()(2)[1]) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:69:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_hline(yintercept = mean_bd_error_10000, linetype = "dotted", color = scales::hue_pal()(2)[2]) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_alignment_length.R:73:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_alignment_length.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
      title = "Mean nLTT statistic\nfor different expected mean duration of speciation,\nfor different DNA alignment lengths",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_sampling.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_sampling.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_sampling.R:7:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_sampling.R#L7) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_mean_dur_spec_mean_sampling <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_sampling.R:30:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_sampling.R#L30) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_mean_dur_spec_mean_sampling.R:59:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_sampling.R#L59) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::scale_y_continuous(limits = c(0, 0.05)) + # Will have some outliers unplotted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean_sampling.R:64:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean_sampling.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
      title = "Mean nLTT statistic for different duration of speciations\nfor different sampling methods",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:1:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Create 'figure_error_expected_mean_dur_spec_mean' (tailing mean: use the mean nLTT statistic)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:7:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L7) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_mean_dur_spec_mean <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:30:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L30) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_mean_dur_spec_mean.R:32:37:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L32) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_medians <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                  ~~^
```
[R/create_figure_error_mean_dur_spec_mean.R:42:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
  df_means <- merge(x = parameters, y = nltt_stat_means, by = "filename", all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:43:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
  df_medians <- merge(x = parameters, y = nltt_stat_medians, by = "filename", all = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:46:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(max(stats::na.omit(df_means$scr)) == max(stats::na.omit(df_medians$scr)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:49:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
  mean_bd_error <- mean(stats::na.omit(df_means[ df_means$scr == scr_bd, ]$mean))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:49:49:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L49) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  mean_bd_error <- mean(stats::na.omit(df_means[ df_means$scr == scr_bd, ]$mean))
                                                ^
```
[R/create_figure_error_mean_dur_spec_mean.R:50:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
  median_bd_error <- mean(stats::na.omit(df_medians[ df_medians$scr == scr_bd, ]$median))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:50:3:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L50) *warning:* **local variable ‘median_bd_error’ assigned but may not be used**
```r
  median_bd_error <- mean(stats::na.omit(df_medians[ df_medians$scr == scr_bd, ]$median))
  ^~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:50:53:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L50) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  median_bd_error <- mean(stats::na.omit(df_medians[ df_medians$scr == scr_bd, ]$median))
                                                    ^
```
[R/create_figure_error_mean_dur_spec_mean.R:58:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_smooth(method = "lm", color = "blue", size = 0.5, alpha = 0.25) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:66:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_smooth(method = "loess", color = "red", size = 0.5, alpha = 0.25) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:68:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::scale_y_continuous(limits = c(0, 0.05)) + # Will have some outliers unplotted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_mean.R:70:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_mean.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::ylab(latex2exp::TeX("Mean nLTT statistic $\\bar{\\Delta_{nLTT}}$")) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_median.R:1:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_median.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Create 'figure_error_expected_mean_dur_spec_median' (tailing median: use the median nLTT statistic)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_median.R:3:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_median.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param nltt_stats the nLTT statistics, as returned from read_collected_nltt_stats
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_median.R:7:1:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_median.R#L7) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_figure_error_mean_dur_spec_median <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_figure_error_mean_dur_spec_median.R:30:35:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_median.R#L30) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_means <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                ~~^
```
[R/create_figure_error_mean_dur_spec_median.R:32:37:](https://github.com/richelbilderbeek/wiritttea/blob/b01b773d263342de83a946f7b108eca6ecf91a11/R/create_figure_error_mean_dur_spec_median.R#L32) *style:* **`%>%` should always have a space before it and a new line after it, unless the full pipeline fits on one line.**
```r
  nltt_stat_medians <- nltt_stats %>% dplyr::group_by(filename, sti, ai, pi) %>%
                                  ~~^
```


New-Feature---Account-for-fan-heat-is-zone-cooling-coils (rraustad) - i386-Windows-7-VisualStudio-14: OK (2995 of 2995 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)


Is MyDashboardUI the same as DashboardUI?


Why nb_samples is increased by 3?


Thought you were on holiday? :)


Well done... That's a lot of work in a few hours, damn. I wish I had the knowledge to help you develop this.


 const snapAndClick = async (selector = ".inmplayer-popover-button-next") => {
  ...
}
the default click is on the inline-manual "next" button.


Dao


Maybe we should proxy the actual error from the app somehow?


Hello @Jermolene
I can understand that this is just for human purposes only. But this leads to us to a new situation where it's possible to end with several drafts of the same tiddler. Would't that be a problem ? Which one will be used when you edit a tiddler ? The most recent ? Alphabetical order ?
That can be equally confusing


comment here


Nej det är värdelöst. Håller med. Men det fungerade i vart fall inte som favicon!


> Shouldn't these changes be made in a different PR?

Yes, but I'm too lazy :wink:


create new instance for each page is not good.


I think it woild make sense to add the calling app-id to the platform data.


Dangit, yes, they have all been flagged and deleted. I sent them out to only the top-starred 85 out of 950 projects depending on FastClasspathScanner. It took a day or two though for the bug reports to disappear though, so maybe somebody reported their issue as spam, and someone at GitHub went through and manually deleted them all.


WebDriver is set up from DriverSetting.java, so we don't need it here. You may need to clone the latest code from master to your branch first.


Wrong input for commit.

Added functionality and basic csv writing capabilities.


感觉也会被喷,单独其实做search就行了, lru放外面...


@fichtner with the colouring it's not that noticeable, but we can always add something similar there.


Automated Test Suite Message


Hi @danielo515

Right now, the following can happen:

1. UserA edits HelloThere to create a draft
2. Before that tiddler has synced back to the server, UserB also edits HelloThere to create a second draft
3. While UserA and UserB are working on their respective drafts, the sync mechanism will make one of them overwrite the other

This change avoids that situation.


好像以下都没有free?


Message related to leantrx is not displayed on scrren when using SoapyRemote button.
Last quote missing on line 10:
`echo "<BR>You can also now use LeanTRX <a href="/leantrx/">here</a>"`


@Voronenko stepped up and continues the maintenance.


@TomasTomecek unfortunately I am not able to release on pypi - no access to pypi package maintainers.
Do you know if Joshua is available? He was expecting to commit few hours a week.


请问想使用谷歌翻译插件，编译时有哪些要注意的嘛。。
最开始提示 `警告：编码 GBK 的不可映射字符` ，通过

> 在项目下的build.gradle下添加`tasks.withType(JavaCompile) {
    options.encoding = "UTF-8"
}`

解决。现在又出现，`错误: 程序包org.omegat.core.machinetranslators不存在` ` 错误: 找不到符号
public class GoogleTranslatorX extends BaseTranslate {
                                       ^
  符号: 类 BaseTranslate` `错误: 方法不会覆盖或实现超类型的方法
    @Override
    ^` `符号:   变量 JsonParser
  位置: 类 GoogleTranslatorX
D:\baiduyun\Downloads\omegat-4cb9dd1973c41c328c95307f584a80908fcf49a7\plugin_GoogleTranslatorX\src\main\java\com\pingfangx\omegat\plugin\GoogleTranslatorX.java:126: 警告: [cast] 出现冗余的到List<Object>的转换
            List<Object> translationList = (List<Object>) JsonParser.parse(result);`
等等错误。。


Change intersecting logic to `if skynetView.frame.intersects(ballView.frame)`


#6750-Crash-when-no-control-zone-name-is-specified-for-Load-control-in-AirloopHVACUnitarySystem (mjwitte) - x86_64-Linux-Ubuntu-14.04-gcc-4.8: OK (3035 of 3035 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)


Yes, you are correct!


Никакой магии, это обычный хэш, ключ-значение:
hash  = { a: '1', b: '2' }
теперь если запросить ключ, то существующие ключи вернут нам значения
`hash[:a]` => '1'
`hash[:b]` => '1'
а несуществующий вернет nil:
`hash[:c]` => nil
Ну и последним вычислением будет `|| Car`
то есть, если nil то значение по умолчанию


fan test


Can you cut a patch release with this?


You're shadowing `sentryHook` here due to the use of `:=`


Yeah this feature doesn't work, please don't turn it on :)


code style, you need have add more blank space


lets discuss today I am having issues still just wanted to get my code onto Git so I can work on my computer today :)


Since you're dereferencing here, you should add a nil check on `sentry`, or handle the nil case before the `if`.


I do not know how to change in roxygen2, Which file do you modify?


Thank you!!
I will try again!


Could we have a filename here? e.g.
```
                echo "$f: unsupported interpreter directive \"$oldInterpreterLine\" (set dontPatchShebangs=1 and handle shebang patching yourself)"
```
It would help debugging errors a lot. I'm trying to build node package with hue number of scripts under `node_modules` and it's really hard to find the cause of this error. It's a small change but will need a mass rebuild so I start with the question here instead of a PR.

CC: @peti, @bjornfor


Thank you !

@Rocky640 : with the proposed code, all probcut will be skipped in case of an excluded move. We can imagine that in some cases probcut is still useful if we remove the excluded move.

@miguel-l : I think that if there is only one forced move, the probcut will exit immediatly because the only possible move is excluded. If your question is about the main loop, It seems to me that "movecount" will be zero and the search will return alpha.

     if (!moveCount)
        bestValue = excludedMove ? alpha
                   :     inCheck ? mated_in(ss->ply) : VALUE_DRAW;


#6750-Crash-when-no-control-zone-name-is-specified-for-Load-control-in-AirloopHVACUnitarySystem (mjwitte) - x86_64-Linux-Ubuntu-14.04-cppcheck-1.61: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


`$settings` with an "s" ;)


Yes - we discussed this. I do not think writes to variable are transactional. Shrutika can confirm the behavior in Ruby. However, assuming that writes are not transactional, we still thought it is okay to not use mutex here. First, reesource move itself is an edge case. And we are talking about a small probability of bad read happening. And even if it happens, ONLY one data push to ODS is impacted.


Ok, thanks


"than" ;)


first release


Thanks for the help @lionslair


@BringerxD don't comment, open new issue


Yes, why not.  BTW, for now I believe you can grep in the paths left behind by `--keep-failed`.


Hello brother, does this framework available on Android?


the package's README actually suggests using lower cases:

https://github.com/spf13/jWalterWeatherman/blob/master/README.md

```
jww "github.com/spf13/jwalterweatherman"
```


efjsbdfbsbfsbf


函数名字不太对..不止干了search


must+infinitive, "implement"


Ah, ok. ;)


使用两个listener，对list的数据rpop时形成竞争关系，使用两个线程，加快保存速度


Is this required for ReplacingUpdate? If it's not specified, is there a sensible default that we can use?


it is also used in `hugo` with all lower cases.

https://github.com/gohugoio/hugo/search?q=jWalterWeatherman&unscoped_q=jWalterWeatherman

Using the capital case version will cause build failures when trying to go get both hugo and this package:

https://gopkgs.io/builds/20180828-074824-e4e0ab4a


I will commit a fix. Thanks for the feedback.


# Specs execution successful
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### Plans updated

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[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

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

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----|
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Very good solution GitHub thank you


please close your eyes!


this is object having attributes day,meeting ,meeting done so we can


Would probably work better as a constant somewhere in the code? Bonus points if `ImVec4` is constexpr.


_a comment test._


Ah yeah, good point, forgot to add a `@default` marker.

Going by the CloudFormation docs, when not supplied the default is `100`.


Thank you get her very well solution


New-Feature---Account-for-fan-heat-is-zone-cooling-coils (rraustad) - Win64-Windows-7-VisualStudio-14: OK (2806 of 2995 tests passed, 35 test warnings)

Messages:

 * 34 tests had: Table small diffs.
 * 188 tests had: Table big diffs.
 * 62 tests had: EIO diffs.
 * 15 tests had: ESO small diffs.
 * 45 tests had: ESO big diffs.
 * 16 tests had: MTR big diffs.
 * 8 tests had: ERR diffs.
 * 2 tests had: MTR small diffs.

Failures:

regression Test Summary
 * Passed: 442
 * Failed: 189

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-93.69%25-yellow.png)


@vlakoff Thank you, eagle eyes 🦅 :wink:
See 22f5e94acc5df7290158e43afb8579db93b4665b