[R/block.R:2:32:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
block_class <- R6Class("Block",
                               ^
```
[R/block.R:8:29:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      assert_that(all(border[ , 1] < border[ , 2]))
                            ^
```
[R/block.R:9:31:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L9) *style:* **Commas should never have a space before.**
```r
      assert_that(all(border[ , 1] < border[ , 2]))
                             ~^
```
[R/block.R:9:46:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L9) *style:* **Commas should never have a space before.**
```r
      assert_that(all(border[ , 1] < border[ , 2]))
                                            ~^
```
[R/block.R:20:42:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      upper <- denormalize(private$border[ , 2], jaatha)
                                         ^
```
[R/block.R:20:44:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L20) *style:* **Commas should never have a space before.**
```r
      lower <- denormalize(private$border[ , 1], jaatha)
                                          ~^
```
[R/block.R:21:44:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L21) *style:* **Commas should never have a space before.**
```r
      upper <- denormalize(private$border[ , 2], jaatha)
                                          ~^
```
[R/block.R:25:27:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L25) *style:* **Commas should never have a space before.**
```r
      all(private$border[ , 1] - 1e-15 <= point &
                         ~^
```
[R/block.R:25:50:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L25) *style:* **Trailing whitespace is superfluous.**
```r
      all(private$border[ , 1] - 1e-15 <= point &
                                                 ^
```
[R/block.R:26:38:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L26) *style:* **Commas should never have a space before.**
```r
            point <= private$border[ , 2] + 1e-15)
                                    ~^
```
[R/block.R:28:27:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L28) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      m <- (private$border[ , 2] - private$border[ , 1]) / 2 +
                          ^
```
[R/block.R:29:29:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L29) *style:* **Commas should never have a space before.**
```r
      m <- (private$border[ , 2] - private$border[ , 1]) / 2 +
                           ~^
```
[R/block.R:29:52:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L29) *style:* **Commas should never have a space before.**
```r
      m <- (private$border[ , 2] - private$border[ , 1]) / 2 +
                                                  ~^
```
[R/block.R:29:63:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L29) *style:* **Trailing whitespace is superfluous.**
```r
      m <- (private$border[ , 2] - private$border[ , 1]) / 2 +
                                                              ^
```
[R/block.R:30:25:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L30) *style:* **Commas should never have a space before.**
```r
        private$border[ , 1]
                       ~^
```
[R/block.R:36:26:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L36) *style:* **Commas should never have a space before.**
```r
        private$border[i , , drop = FALSE]
                        ~^
```
[R/block.R:36:28:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L36) *style:* **Commas should never have a space before.**
```r
        private$border[i , , drop = FALSE]
                          ~^
```
[R/block.R:37:7:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L37) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      }), KEEP.OUT.ATTRS = FALSE)
      ^
```
[R/block.R:45:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L45) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/block.R:49:58:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L49) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                  max = self$get_border()[ , 2]),
                                                         ^
```
[R/block.R:49:60:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L49) *style:* **Commas should never have a space before.**
```r
                                  min = self$get_border()[ , 1],
                                                          ~^
```
[R/block.R:50:60:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L50) *style:* **Commas should never have a space before.**
```r
                                  max = self$get_border()[ , 2]),
                                                          ~^
```
[R/block.R:52:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/block.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/boot_jaatha.R:24:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L24) *warning:* **no visible global function definition for ‘require_package’**
```r
  require_package("boot")
  ^~~~~~~~~~~~~~~
```
[R/boot_jaatha.R:28:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L28) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/boot_jaatha.R:33:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L33) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/boot_jaatha.R:38:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L38) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/boot_jaatha.R:41:76:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L41) *style:* **Trailing whitespace is superfluous.**
```r
                   file = tempfile(paste0("boot_log_", Sys.getpid(), "_")),
                                                                           ^
```
[R/boot_jaatha.R:43:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/boot_jaatha.R:46:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L46) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/boot_jaatha.R:49:5:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L49) *warning:* **no visible global function definition for ‘create_jaatha_data.default’**
```r
    create_jaatha_data.default(sim_data, model)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/boot_jaatha.R:51:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L51) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/boot_jaatha.R:52:39:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L52) *style:* **Trailing whitespace is superfluous.**
```r
  boot::boot(data, jaatha_stat, R = R,
                                      ^
```
[R/boot_jaatha.R:53:33:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L53) *style:* **Trailing whitespace is superfluous.**
```r
             sim = "parametric",
                                ^
```
[R/boot_jaatha.R:54:38:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/boot_jaatha.R#L54) *style:* **Trailing whitespace is superfluous.**
```r
             ran.gen = simulate_data,
                                     ^
```
[R/coala_interface.R:33:45:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L33) *style:* **Trailing whitespace is superfluous.**
```r
create_jaatha_model.coalmodel <- function(x,
                                            ^
```
[R/coala_interface.R:44:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L44) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:45:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L45) *warning:* **no visible global function definition for ‘require_package’**
```r
  require_package("coala")
  ^~~~~~~~~~~~~~~
```
[R/coala_interface.R:48:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L48) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:50:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:53:38:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L53) *style:* **Commas should always have a space after.**
```r
  par_ranges <- as.matrix(par_table[,-1])
                                     ^
```
[R/coala_interface.R:60:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:61:64:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L61) *style:* **Trailing whitespace is superfluous.**
```r
  create_jaatha_model.function(sim_func, par_ranges, sum_stats,
                                                               ^
```
[R/coala_interface.R:69:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L69) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:70:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L70) *warning:* **no visible global function definition for ‘require_package’**
```r
  require_package("coala")
  ^~~~~~~~~~~~~~~
```
[R/coala_interface.R:71:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L71) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.string(jsfs_summary))
  ^~~~~~~~~~~
```
[R/coala_interface.R:71:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L71) *warning:* **no visible global function definition for ‘is.string’**
```r
  assert_that(is.string(jsfs_summary))
              ^~~~~~~~~
```
[R/coala_interface.R:72:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L72) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:75:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L75) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/coala_interface.R:80:11:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L80) *warning:* **no visible global function definition for ‘coarsen_jsfs’**
```r
          coarsen_jsfs(x[[name]], jsfs_part, jsfs_part_hi)
          ^~~~~~~~~~~~
```
[R/coala_interface.R:90:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L90) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/coala_interface.R:93:14:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L93) *warning:* **no visible global function definition for ‘create_jaatha_stat’**
```r
      return(create_jaatha_stat(name, function(x, opts) x[[name]]))
             ^~~~~~~~~~~~~~~~~~
```
[R/coala_interface.R:95:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L95) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/coala_interface.R:99:20:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L99) *style:* **Commas should never have a space before.**
```r
        x[[name]][ , c(1, 2, 6), drop = FALSE]
                  ~^
```
[R/coala_interface.R:100:7:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L100) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      }, poisson = FALSE, breaks = four_gamete_breaks))
      ^
```
[R/coala_interface.R:102:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L102) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/coala_interface.R:106:49:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L106) *style:* **Trailing whitespace is superfluous.**
```r
                                poisson = FALSE,
                                                ^
```
[R/coala_interface.R:109:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/coala_interface.R:119:4:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L119) *style:* **Commented code should be removed.**
```r
  ## A[p[1,1]:p[1:2],p[2,1]:p[2:2],...] consists of the same values as A[v],
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/coala_interface.R:122:12:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L122) *style:* **Commas should always have a space after.**
```r
  v <- p[N,1]:p[N,2]
           ^
```
[R/coala_interface.R:122:19:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L122) *style:* **Commas should always have a space after.**
```r
  v <- p[N,1]:p[N,2]
                  ^
```
[R/coala_interface.R:125:28:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L125) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      v <- as.vector(outer((v - 1)*d[n], p[n, 1]:p[n, 2], "+"))
                           ^
```
[R/coala_interface.R:125:35:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L125) *style:* **Put spaces around all infix operators.**
```r
      v <- as.vector(outer((v - 1)*d[n], p[n, 1]:p[n, 2], "+"))
                                 ~^~
```
[R/coala_interface.R:128:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L128) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:177:26:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L177) *style:* **Commas should always have a space after.**
```r
      if (tail(part[[i]],1) >= upper[1]) {
                         ^
```
[R/coala_interface.R:183:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L183) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:187:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L187) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:189:18:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L189) *style:* **Trailing whitespace is superfluous.**
```r
  combinations <-
                 ^
```
[R/coala_interface.R:191:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L191) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:199:20:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L199) *warning:* **no visible global function definition for ‘multi_index_range’**
```r
    z[i] <- sum(ja[multi_index_range(d, p)])
                   ^~~~~~~~~~~~~~~~~
```
[R/coala_interface.R:201:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L201) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/coala_interface.R:204:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/coala_interface.R#L204) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/fit_glm.R:8:52:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L8) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
fit_glm.jaatha_model <- function(x, sim_data, ...) {
                                                   ^
```
[R/fit_glm.R:8:53:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
fit_glm.jaatha_model <- function(x, sim_data, ...) {
                                                    ^
```
[R/fit_glm.R:10:29:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L10) *warning:* **no visible binding for global variable ‘fit_glm’**
```r
  lapply(x$get_sum_stats(), fit_glm, sim_data, ...)
                            ^~~~~~~
```
[R/fit_glm.R:19:16:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L19) *style:* **Trailing whitespace is superfluous.**
```r
  X <- cbind(1,
               ^
```
[R/fit_glm.R:21:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L21) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/fit_glm.R:24:21:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L24) *style:* **Commas should never have a space before.**
```r
      glm.fit(X, Y[ , i], family = poisson("log"),
                   ~^
```
[R/fit_glm.R:24:51:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L24) *style:* **Trailing whitespace is superfluous.**
```r
      glm.fit(X, Y[ , i], family = poisson("log"),
                                                  ^
```
[R/fit_glm.R:28:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L28) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/fit_glm.R:42:5:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L42) *style:* **Commented code should be removed.**
```r
#   par_names <- names(sim_data[[1]]$pars)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/fit_glm.R:50:7:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L50) *style:* **Commented code should be removed.**
```r
#     colnames(pars) <- names(sim_result$pars.normal)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/fit_glm.R:51:7:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L51) *style:* **Commented code should be removed.**
```r
#     data.frame(pars, sim_result[[sum_stat$get_name()]])
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/fit_glm.R:57:5:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L57) *style:* **Commented code should be removed.**
```r
#   if (!smooth_glm$converged) stop("GLM did not converge")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/fit_glm.R:59:5:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/fit_glm.R#L59) *style:* **Commented code should be removed.**
```r
#   list(smooth=smooth_glm)
    ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/initialization.R:1:70:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L1) *style:* **Trailing whitespace is superfluous.**
```r
get_start_pos <- function(model, data, reps, sim, init_method, cores,
                                                                     ^
```
[R/initialization.R:3:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L3) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/initialization.R:6:18:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L6) *warning:* **no visible global function definition for ‘do_zoom_in_search’**
```r
    start_pos <- do_zoom_in_search(model, data, reps, sim, cores, sim_cache)
                 ^~~~~~~~~~~~~~~~~
```
[R/initialization.R:8:18:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L8) *warning:* **no visible global function definition for ‘do_initial_search’**
```r
    start_pos <- do_initial_search(model, data, reps, sim, cores, sim_cache)
                 ^~~~~~~~~~~~~~~~~
```
[R/initialization.R:12:62:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
    start_pos <- matrix(runif(reps * model$get_par_number()),
                                                             ^
```
[R/initialization.R:17:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L17) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/initialization.R:18:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L18) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.matrix(start_pos))
  ^~~~~~~~~~~
```
[R/initialization.R:19:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L19) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(all((dim(start_pos) == c(reps, model$get_par_number()))))
  ^~~~~~~~~~~
```
[R/initialization.R:19:19:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L19) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  assert_that(all((dim(start_pos) == c(reps, model$get_par_number()))))
                  ^
```
[R/initialization.R:27:21:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L27) *warning:* **no visible global function definition for ‘determine_bpp’**
```r
  blocks_per_par <- determine_bpp(par_number, reps)
                    ^~~~~~~~~~~~~
```
[R/initialization.R:28:13:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L28) *warning:* **no visible global function definition for ‘create_initial_blocks’**
```r
  blocks <- create_initial_blocks(model$get_par_ranges(), blocks_per_par)
            ^~~~~~~~~~~~~~~~~~~~~
```
[R/initialization.R:29:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L29) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/initialization.R:31:62:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
  estimates <- lapply(blocks, estimate_local_ml, model, data,
                                                             ^
```
[R/initialization.R:37:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L37) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/initialization.R:39:76:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L39) *style:* **Trailing whitespace is superfluous.**
```r
  best_indexes <- order(vapply(estimates, function(x) x$value, numeric(1)),
                                                                           ^
```
[R/initialization.R:41:55:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L41) *style:* **Trailing whitespace is superfluous.**
```r
  t(vapply(estimates[best_indexes], function(x) x$par,
                                                      ^
```
[R/initialization.R:62:17:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L62) *warning:* **no visible global function definition for ‘create_block’**
```r
    return(list(create_block(basic_block)))
                ^~~~~~~~~~~~
```
[R/initialization.R:64:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L64) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/initialization.R:72:45:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L72) *warning:* **no visible global function definition for ‘create_block’**
```r
      blocks[[(j - 1) * par_number + i]] <- create_block(new_block)
                                            ^~~~~~~~~~~~
```
[R/initialization.R:75:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L75) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/initialization.R:86:17:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L86) *warning:* **no visible global function definition for ‘estimate_local_ml’**
```r
      middle <- estimate_local_ml(block, model, data, sim, cores, sim_cache)$par
                ^~~~~~~~~~~~~~~~~
```
[R/initialization.R:90:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/initialization.R#L90) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  }, numeric(model$get_par_number())))
  ^
```
[R/jaatha_data.R:2:44:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_data.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
jaatha_data_class <- R6Class("jaatha_data",
                                           ^
```
[R/jaatha_data.R:16:57:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_data.R#L16) *style:* **Trailing whitespace is superfluous.**
```r
          stop("Data has missing values for statistic ",
                                                        ^
```
[R/jaatha_data.R:26:9:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_data.R#L26) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
        }, numeric(1))
        ^
```
[R/jaatha_data.R:84:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_data.R#L84) *warning:* **no visible binding for global variable ‘jaatha_data_class’**
```r
  jaatha_data_class$new(data, model)
  ^~~~~~~~~~~~~~~~~
```
[R/jaatha_data.R:90:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_data.R#L90) *warning:* **no visible global function definition for ‘create_jaatha_data’**
```r
  create_jaatha_data(test_data, model)
  ^~~~~~~~~~~~~~~~~~
```
[R/jaatha_log.R:1:42:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L1) *style:* **Trailing whitespace is superfluous.**
```r
jaatha_log_class <- R6Class("jaatha_log",
                                         ^
```
[R/jaatha_log.R:18:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L18) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha_log.R:26:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L26) *style:* **lines should not be more than 80 characters.**
```r
      private$final_estimates <- private$estimates[[1]][rep(1, 5 * par_number), ]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/jaatha_log.R:44:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L44) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha_log.R:47:76:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L47) *style:* **Trailing whitespace is superfluous.**
```r
        message(" Step ", step, ": Loglikelihood ", format(estimate$value),
                                                                           ^
```
[R/jaatha_log.R:50:66:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L50) *style:* **Trailing whitespace is superfluous.**
```r
        message(" Parameter: ", private$format_par(estimate$par),
                                                                 ^
```
[R/jaatha_log.R:51:53:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L51) *style:* **Trailing whitespace is superfluous.**
```r
                ", Loglikelihood ", format(old_llh),
                                                    ^
```
[R/jaatha_log.R:57:36:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L57) *style:* **Trailing whitespace is superfluous.**
```r
        message("Repetition ", rep,
                                   ^
```
[R/jaatha_log.R:63:31:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L63) *style:* **Use <-, not =, for assignment.**
```r
      private$converged[step] = TRUE
                              ^
```
[R/jaatha_log.R:67:60:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L67) *style:* **Trailing whitespace is superfluous.**
```r
      message("Determining starting positions using the '",
                                                           ^
```
[R/jaatha_log.R:88:45:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_log.R#L88) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      param <- as.numeric(best_estimate[1, -(1:3)])
                                            ^
```
[R/jaatha_model.R:4:46:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L4) *style:* **Trailing whitespace is superfluous.**
```r
jaatha_model_class <- R6Class("jaatha_model",
                                             ^
```
[R/jaatha_model.R:13:71:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L13) *style:* **Trailing whitespace is superfluous.**
```r
        stop("There already is a summary statistic with name '", name,
                                                                      ^
```
[R/jaatha_model.R:21:59:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
    initialize = function(sim_func, par_ranges, sum_stats,
                                                          ^
```
[R/jaatha_model.R:43:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha_model.R:46:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L46) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha_model.R:51:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L51) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/jaatha_model.R:55:9:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L55) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
        }, error = function(e) {
        ^
```
[R/jaatha_model.R:56:22:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L56) *style:* **Use <-, not =, for assignment.**
```r
          error_dump = tempfile("jaatha_frame_dump_", fileext = ".Rda")
                     ^
```
[R/jaatha_model.R:59:76:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
          stop(paste(e$message, "[Frame dump written to", error_dump, "]"),
                                                                           ^
```
[R/jaatha_model.R:62:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L62) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/jaatha_model.R:63:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L63) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/jaatha_model.R:68:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L68) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/jaatha_model.R:72:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L72) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/jaatha_model.R:74:7:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L74) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      }, mc.preschedule = !private$slow_sim, mc.cores = cores)
      ^
```
[R/jaatha_model.R:75:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L75) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha_model.R:83:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L83) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/jaatha_model.R:93:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L93) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha_model.R:97:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L97) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/jaatha_model.R:100:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L100) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/jaatha_model.R:103:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L103) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha_model.R:134:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L134) *style:* **lines should not be more than 80 characters.**
```r
create_jaatha_model.default <- function(x, ..., scaling_factor = 1, test = TRUE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/jaatha_model.R:167:61:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L167) *style:* **Trailing whitespace is superfluous.**
```r
                                         scaling_factor = 1,
                                                            ^
```
[R/jaatha_model.R:169:51:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha_model.R#L169) *style:* **Trailing whitespace is superfluous.**
```r
  jaatha_model_class$new(x, par_ranges, sum_stats,
                                                  ^
```
[R/jaatha.R:64:32:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L64) *style:* **Trailing whitespace is superfluous.**
```r
jaatha <- function(model, data,
                               ^
```
[R/jaatha.R:65:36:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L65) *style:* **Trailing whitespace is superfluous.**
```r
                   repetitions = 3,
                                   ^
```
[R/jaatha.R:66:54:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L66) *style:* **Trailing whitespace is superfluous.**
```r
                   sim = model$get_par_number() * 25,
                                                     ^
```
[R/jaatha.R:67:36:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L67) *style:* **Trailing whitespace is superfluous.**
```r
                   max_steps = 100,
                                   ^
```
[R/jaatha.R:68:64:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L68) *style:* **Trailing whitespace is superfluous.**
```r
                   init_method = c("zoom-in", "initial-search",
                                                               ^
```
[R/jaatha.R:74:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L74) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/jaatha.R:76:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L76) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is_jaatha_model(model))
  ^~~~~~~~~~~
```
[R/jaatha.R:76:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L76) *warning:* **no visible global function definition for ‘is_jaatha_model’**
```r
  assert_that(is_jaatha_model(model))
              ^~~~~~~~~~~~~~~
```
[R/jaatha.R:77:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L77) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is_jaatha_data(data))
  ^~~~~~~~~~~
```
[R/jaatha.R:77:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L77) *warning:* **no visible global function definition for ‘is_jaatha_data’**
```r
  assert_that(is_jaatha_data(data))
              ^~~~~~~~~~~~~~
```
[R/jaatha.R:78:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L78) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.count(repetitions))
  ^~~~~~~~~~~
```
[R/jaatha.R:78:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L78) *warning:* **no visible global function definition for ‘is.count’**
```r
  assert_that(is.count(repetitions))
              ^~~~~~~~
```
[R/jaatha.R:79:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L79) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.count(sim))
  ^~~~~~~~~~~
```
[R/jaatha.R:79:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L79) *warning:* **no visible global function definition for ‘is.count’**
```r
  assert_that(is.count(sim))
              ^~~~~~~~
```
[R/jaatha.R:80:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L80) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.count(cores))
  ^~~~~~~~~~~
```
[R/jaatha.R:80:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L80) *warning:* **no visible global function definition for ‘is.count’**
```r
  assert_that(is.count(cores))
              ^~~~~~~~
```
[R/jaatha.R:81:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L81) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.numeric(block_width) && length(block_width) == 1)
  ^~~~~~~~~~~
```
[R/jaatha.R:82:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L82) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(block_width > 0 && block_width < 1)
  ^~~~~~~~~~~
```
[R/jaatha.R:83:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L83) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/jaatha.R:85:10:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L85) *warning:* **no visible global function definition for ‘create_jaatha_log’**
```r
  log <- create_jaatha_log(model, data, repetitions, max_steps, verbose = TRUE)
         ^~~~~~~~~~~~~~~~~
```
[R/jaatha.R:87:16:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L87) *warning:* **no visible global function definition for ‘create_sim_cache’**
```r
  sim_cache <- create_sim_cache(sim_cache_limit)
               ^~~~~~~~~~~~~~~~
```
[R/jaatha.R:89:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L89) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/jaatha.R:94:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L94) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/jaatha.R:100:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L100) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/jaatha.R:103:64:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L103) *style:* **Trailing whitespace is superfluous.**
```r
                                  estimate + block_width * .5),
                                                               ^
```
[R/jaatha.R:105:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L105) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha.R:106:19:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L106) *warning:* **no visible global function definition for ‘estimate_local_ml’**
```r
      local_ml <- estimate_local_ml(block, model, data, sim, cores, sim_cache)
                  ^~~~~~~~~~~~~~~~~
```
[R/jaatha.R:113:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L113) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha.R:118:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L118) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/jaatha.R:125:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L125) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/jaatha.R:131:65:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L131) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llh <- estimate_llh(model, data, as.numeric(best_values[i, -(1:3)]),
                                                                ^
```
[R/jaatha.R:131:73:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L131) *style:* **Trailing whitespace is superfluous.**
```r
    llh <- estimate_llh(model, data, as.numeric(best_values[i, -(1:3)]),
                                                                        ^
```
[R/jaatha.R:135:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/jaatha.R#L135) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:1:52:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L1) *style:* **Trailing whitespace is superfluous.**
```r
calc_poisson_llh <- function(data, stat, loglambda,
                                                   ^
```
[R/likelihood.R:3:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L3) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:7:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L7) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:10:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L10) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:11:49:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L11) *style:* **Trailing whitespace is superfluous.**
```r
  llh <- sum(data$get_values(stat) * loglambda -
                                                ^
```
[R/likelihood.R:13:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L13) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:14:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L14) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.finite(llh))
  ^~~~~~~~~~~
```
[R/likelihood.R:25:75:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L25) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
approximate_llh.default <- function(x, data, param, glm_fitted, sim, ...) {
                                                                          ^
```
[R/likelihood.R:25:76:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L25) *style:* **Trailing whitespace is superfluous.**
```r
approximate_llh.default <- function(x, data, param, glm_fitted, sim, ...) {
                                                                           ^
```
[R/likelihood.R:32:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L32) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is_jaatha_data(data))
  ^~~~~~~~~~~
```
[R/likelihood.R:32:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L32) *warning:* **no visible global function definition for ‘is_jaatha_data’**
```r
  assert_that(is_jaatha_data(data))
              ^~~~~~~~~~~~~~
```
[R/likelihood.R:33:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L33) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.numeric(param))
  ^~~~~~~~~~~
```
[R/likelihood.R:34:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L34) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.list(glm_fitted))
  ^~~~~~~~~~~
```
[R/likelihood.R:42:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L42) *style:* **Variable and function names should not be longer than 30 characters.**
```r
approximate_llh.jaatha_stat_basic  <- function(x, data, param, glm_fitted,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/likelihood.R:42:75:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L42) *style:* **Trailing whitespace is superfluous.**
```r
approximate_llh.jaatha_stat_basic  <- function(x, data, param, glm_fitted,
                                                                          ^
```
[R/likelihood.R:44:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L44) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:48:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L48) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:50:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L50) *warning:* **no visible global function definition for ‘calc_poisson_llh’**
```r
  calc_poisson_llh(data, x, loglambda, sim, scaling_factor)
  ^~~~~~~~~~~~~~~~
```
[R/likelihood.R:59:25:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L59) *warning:* **no visible global function definition for ‘approximate_llh’**
```r
                        approximate_llh(model, data, param, glms, sim)
                        ^~~~~~~~~~~~~~~
```
[R/likelihood.R:61:41:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L61) *style:* **Commas should never have a space before.**
```r
                      lower = boundary[ , 1, drop = FALSE],
                                       ~^
```
[R/likelihood.R:61:60:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L61) *style:* **Trailing whitespace is superfluous.**
```r
                      lower = boundary[ , 1, drop = FALSE],
                                                           ^
```
[R/likelihood.R:62:41:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L62) *style:* **Commas should never have a space before.**
```r
                      upper = boundary[ , 2, drop = FALSE],
                                       ~^
```
[R/likelihood.R:63:43:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L63) *style:* **Trailing whitespace is superfluous.**
```r
                      method = "L-BFGS-B",
                                          ^
```
[R/likelihood.R:65:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L65) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:66:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L66) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(block$includes(best_value$par))
  ^~~~~~~~~~~
```
[R/likelihood.R:73:68:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L73) *style:* **Trailing whitespace is superfluous.**
```r
    sim_data <- model$simulate(pars = block$sample_pars(sim, TRUE),
                                                                   ^
```
[R/likelihood.R:75:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L75) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:79:5:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L79) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(length(sim_data) >= sim)
    ^~~~~~~~~~~
```
[R/likelihood.R:80:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L80) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/likelihood.R:82:22:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L82) *warning:* **no visible global function definition for ‘fit_glm’**
```r
    glms <- tryCatch(fit_glm(model, sim_data), error = identity)
                     ^~~~~~~
```
[R/likelihood.R:83:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L83) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:87:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L87) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/likelihood.R:91:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L91) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:92:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L92) *warning:* **no visible global function definition for ‘optimize_llh’**
```r
  optimize_llh(block, model, data, glms, length(sim_data))
  ^~~~~~~~~~~~
```
[R/likelihood.R:115:60:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L115) *style:* **Trailing whitespace is superfluous.**
```r
estimate_llh <- function(model, data, parameter, sim = 100,
                                                           ^
```
[R/likelihood.R:117:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L117) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:118:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L118) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is_jaatha_model(model))
  ^~~~~~~~~~~
```
[R/likelihood.R:118:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L118) *warning:* **no visible global function definition for ‘is_jaatha_model’**
```r
  assert_that(is_jaatha_model(model))
              ^~~~~~~~~~~~~~~
```
[R/likelihood.R:119:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L119) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is_jaatha_data(data))
  ^~~~~~~~~~~
```
[R/likelihood.R:119:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L119) *warning:* **no visible global function definition for ‘is_jaatha_data’**
```r
  assert_that(is_jaatha_data(data))
              ^~~~~~~~~~~~~~
```
[R/likelihood.R:120:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L120) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.numeric(parameter))
  ^~~~~~~~~~~
```
[R/likelihood.R:121:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L121) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.count(sim))
  ^~~~~~~~~~~
```
[R/likelihood.R:121:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L121) *warning:* **no visible global function definition for ‘is.count’**
```r
  assert_that(is.count(sim))
              ^~~~~~~~
```
[R/likelihood.R:122:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L122) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.count(cores))
  ^~~~~~~~~~~
```
[R/likelihood.R:122:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L122) *warning:* **no visible global function definition for ‘is.count’**
```r
  assert_that(is.count(cores))
              ^~~~~~~~
```
[R/likelihood.R:123:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L123) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is_single_logical(normalized))
  ^~~~~~~~~~~
```
[R/likelihood.R:123:15:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L123) *warning:* **no visible global function definition for ‘is_single_logical’**
```r
  assert_that(is_single_logical(normalized))
              ^~~~~~~~~~~~~~~~~
```
[R/likelihood.R:124:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L124) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:135:5:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L135) *warning:* **no visible global function definition for ‘calc_poisson_llh’**
```r
    calc_poisson_llh(data, stat, log_means, sim, model$get_scaling_factor())
    ^~~~~~~~~~~~~~~~
```
[R/likelihood.R:136:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L136) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  }, numeric(1)))
  ^
```
[R/likelihood.R:137:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L137) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/likelihood.R:138:3:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/likelihood.R#L138) *warning:* **no visible global function definition for ‘assert_that’**
```r
  assert_that(is.finite(llh))
  ^~~~~~~~~~~
```
[R/par_ranges.R:2:42:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
par_ranges_class <- R6Class("par_ranges",
                                         ^
```
[R/par_ranges.R:13:32:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      assert_that(all(par_range[ , 1] < par_range[ , 2]))
                               ^
```
[R/par_ranges.R:14:34:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L14) *style:* **Commas should never have a space before.**
```r
      assert_that(all(par_range[ , 1] < par_range[ , 2]))
                                ~^
```
[R/par_ranges.R:14:52:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L14) *style:* **Commas should never have a space before.**
```r
      assert_that(all(par_range[ , 1] < par_range[ , 2]))
                                                  ~^
```
[R/par_ranges.R:21:53:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L21) *style:* **Commas should never have a space before.**
```r
      private$log_range_width <- private$log_range[ , 2] -
                                                   ~^
```
[R/par_ranges.R:21:59:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
      private$log_range_width <- private$log_range[ , 2] -
                                                          ^
```
[R/par_ranges.R:22:55:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L22) *style:* **Commas should never have a space before.**
```r
                                   private$log_range[ , 1]
                                                     ~^
```
[R/par_ranges.R:26:39:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L26) *style:* **Commas should never have a space before.**
```r
      (log_value - private$log_range[ , 1]) / private$log_range_width
                                     ~^
```
[R/par_ranges.R:29:64:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L29) *style:* **Commas should never have a space before.**
```r
      exp(value * private$log_range_width + private$log_range[ , 1]) +
                                                              ~^
```
[R/par_ranges.R:29:71:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L29) *style:* **Trailing whitespace is superfluous.**
```r
      exp(value * private$log_range_width + private$log_range[ , 1]) +
                                                                      ^
```
[R/par_ranges.R:36:23:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L36) *style:* **Commas should never have a space before.**
```r
      (private$range[ , 2] - private$range[ , 1]) / 2 + private$range[ , 1]
                     ~^
```
[R/par_ranges.R:36:45:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L36) *style:* **Commas should never have a space before.**
```r
      (private$range[ , 2] - private$range[ , 1]) / 2 + private$range[ , 1]
                                           ~^
```
[R/par_ranges.R:36:72:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/par_ranges.R#L36) *style:* **Commas should never have a space before.**
```r
      (private$range[ , 2] - private$range[ , 1]) / 2 + private$range[ , 1]
                                                                      ~^
```
[R/simulation_cache.R:22:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/simulation_cache.R#L22) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/simulation_cache.R:27:7:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/simulation_cache.R#L27) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      }, logical(1))
      ^
```
[R/simulation_cache.R:29:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/simulation_cache.R#L29) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/simulation_cache.R:37:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/simulation_cache.R#L37) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/simulation_cache.R:40:7:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/simulation_cache.R#L40) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      }, logical(1))
      ^
```
[R/stat_basic.R:8:1:](https://github.com/statgenlmu/jaatha/blob/cfe6e52205afd66de8ff7acd5dd44c0b9486c890/R/stat_basic.R#L8) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```


I would expect it to be called `read_register`. Does `reg` refer to multiple registers?


Can you update this commit to just remove the copy associated with the `?test` parameter altogether? I plan on rewriting this template anyway. It's ugly and outdated.


Right here you could use Bluebird's [`promisifyAll`](http://bluebirdjs.com/docs/api/promise.promisifyall.html) API, which conveniently auto-promise-wraps apis and functions for you. See its example:

``` js
var fs = Promise.promisifyAll(require("fs"));

fs.readFileAsync("myfile.js", "utf8").then(function(contents) {
    console.log(contents);
}).catch(function(e) {
    console.error(e.stack);
});
```

This means you'd have "promise-wrapped" variants of these fs functions you're using, as `fs.statAsync` and `fs.mkdirAsync`. You could then neatly chain them as you would any other promise:

``` js
var userDir = path.join('assets', 'profiles', steamid);

return fs.statAsync(userDir)
  .then(function(stat) {
    // stat() yields a `stat` object. you don't need/use it here, but
    // I'm including it to make things more explicit
    return fs.mkdirAsync(userDir);
  })
  .then(function() {
    // mkdir doesn't yield any value, but you can still chain on it
    return userDir;
  });
```


It looks like the 'troubleshooting' section went away a while back, so we need to either recreate that section, or remove these links entirely.


One of the main reasons for using `path.join` is that you don't have to worry about a given platform's path separator, so if you're gonna use it, you might as well go all the way. Change this to:

``` js
var userDir = path.join('assets', 'profiles', steamid);
```


Same for next test cases


http://homeworktips.about.com/od/improvingyourgrammar/qt/its.htm

;) Always a confusing one, but `its` is correct in this context.


yup... but line 788 does the same thing outside of block-based conditionalization :-P


Mathworks prefer to see it written MATLAB rather than Matlab.


Same again. Don't wrap promises in promises. So this becomes:

``` js
return validateSteamID(key, input)
  .then(function(steamid) {
    return steamid;
  }
```

which is just:

``` js
return validateSteamID(key, input);
```

which means that this `exports.steamid` is simply acting as an alias for `validateSteamID`, so is it really necessary? Perhaps I'm overlooking something.


``` js
path.join('assets', 'profiles', profileID);
```


Add:
```go
if len(parms) != 3 {
  // handle error
}
```


There is something called GPL :3 WTF you are doing? kanging others work.. and you are making kernel with just renaming local version 9d7337d7d54a0e4da82188d6c14b267c28868818
I will @mazda-- here


Please never check versions using Regex.


This needs to be annotated with `@XmlTransient` as well as `@JsonIgnore` to make sure it doesn't show up in XML as well as JSON.