[R/calculate_frequencies.R:3:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_frequencies.R#L3) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_frequencies.R:12:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_frequencies.R#L12) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(dim(vv)[1] > 0) {
      ^
```
[R/calculate_frequencies.R:24:6:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_frequencies.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq_along(all_types)) {
     ^
```
[R/calculate_frequencies.R:27:21:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_frequencies.R#L27) *style:* **Commas should always have a space after.**
```r
  output <- output[,c("location","ancestor","frequency")]
                    ^
```
[R/calculate_frequencies.R:27:34:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_frequencies.R#L27) *style:* **Commas should always have a space after.**
```r
  output <- output[,c("location","ancestor","frequency")]
                                 ^
```
[R/calculate_frequencies.R:27:45:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_frequencies.R#L27) *style:* **Commas should always have a space after.**
```r
  output <- output[,c("location","ancestor","frequency")]
                                            ^
```
[R/calculate_frequencies.R:37:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_frequencies.R#L37) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/calculate_frequencies.R:39:18:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_frequencies.R#L39) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
  pop_for_cpp <- population_to_vector(source_pop)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:2:51:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L2) *style:* **Commas should always have a space after.**
```r
                               markers = seq(1e-6,1-1e-6,length.out = 100),
                                                  ^
```
[R/calculate_tajima_d.R:2:52:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L2) *style:* **Put spaces around all infix operators.**
```r
                               markers = seq(1e-6,1-1e-6,length.out = 100),
                                                  ~^~
```
[R/calculate_tajima_d.R:2:58:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L2) *style:* **Commas should always have a space after.**
```r
                               markers = seq(1e-6,1-1e-6,length.out = 100),
                                                         ^
```
[R/calculate_tajima_d.R:5:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L5) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:13:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L13) *style:* **Put spaces around all infix operators.**
```r
                        nrow = 2*number_of_sampled_individuals)
                               ~^~
```
[R/calculate_tajima_d.R:15:6:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L15) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(m in seq_along(markers)) {
     ^
```
[R/calculate_tajima_d.R:16:8:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(indiv in seq_along(indices_sampled_individuals)) {
       ^
```
[R/calculate_tajima_d.R:18:28:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L18) *style:* **Put spaces around all infix operators.**
```r
      indiv_start <- (indiv*2)-1
                          ~^~
```
[R/calculate_tajima_d.R:18:31:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L18) *style:* **Put spaces around all infix operators.**
```r
      indiv_start <- (indiv*2)-1
                             ~^~
```
[R/calculate_tajima_d.R:30:3:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L30) *warning:* **local variable ‘expected_theta’ assigned but may not be used**
```r
  expected_theta <- 4*pop_size * mutation_rate
  ^~~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:30:22:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L30) *style:* **Put spaces around all infix operators.**
```r
  expected_theta <- 4*pop_size * mutation_rate
                    ~^~
```
[R/calculate_tajima_d.R:32:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L32) *style:* **Put spaces around all infix operators.**
```r
  n <- 2*number_of_sampled_individuals
       ~^~
```
[R/calculate_tajima_d.R:34:14:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L34) *style:* **Put spaces around all infix operators.**
```r
  a1 <- sum(1/tmp)
            ~^~
```
[R/calculate_tajima_d.R:35:14:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L35) *style:* **Put spaces around all infix operators.**
```r
  a2 <- sum(1/tmp^2)
            ~^~
```
[R/calculate_tajima_d.R:36:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L36) *style:* **Put spaces around all infix operators.**
```r
  b1 <- (n + 1)/(3 * (n - 1))
              ~^~
```
[R/calculate_tajima_d.R:36:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  b1 <- (n + 1)/(3 * (n - 1))
                ^
```
[R/calculate_tajima_d.R:37:26:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L37) *style:* **Put spaces around all infix operators.**
```r
  b2 <- 2 * (n^2 + n + 3)/(9 * n * (n - 1))
                        ~^~
```
[R/calculate_tajima_d.R:37:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L37) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  b2 <- 2 * (n^2 + n + 3)/(9 * n * (n - 1))
                          ^
```
[R/calculate_tajima_d.R:38:15:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L38) *style:* **Put spaces around all infix operators.**
```r
  c1 <- b1 - 1/a1
             ~^~
```
[R/calculate_tajima_d.R:39:21:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L39) *style:* **Put spaces around all infix operators.**
```r
  c2 <- b2 - (n + 2)/(a1 * n) + a2/a1^2
                   ~^~
```
[R/calculate_tajima_d.R:39:22:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L39) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  c2 <- b2 - (n + 2)/(a1 * n) + a2/a1^2
                     ^
```
[R/calculate_tajima_d.R:39:35:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L39) *style:* **Put spaces around all infix operators.**
```r
  c2 <- b2 - (n + 2)/(a1 * n) + a2/a1^2
                                 ~^~
```
[R/calculate_tajima_d.R:40:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L40) *style:* **Put spaces around all infix operators.**
```r
  e1 <- c1/a1
         ~^~
```
[R/calculate_tajima_d.R:41:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L41) *style:* **Put spaces around all infix operators.**
```r
  e2 <- c2/(a1^2 + a2)
         ~^~
```
[R/calculate_tajima_d.R:41:12:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L41) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  e2 <- c2/(a1^2 + a2)
           ^
```
[R/calculate_tajima_d.R:45:6:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L45) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq_along(loci_matrix[,1])) {
     ^
```
[R/calculate_tajima_d.R:45:35:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L45) *style:* **Commas should always have a space after.**
```r
  for(i in seq_along(loci_matrix[,1])) {
                                  ^
```
[R/calculate_tajima_d.R:46:8:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L46) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(j in 1:i) {
       ^
```
[R/calculate_tajima_d.R:47:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L47) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(i != j) {
        ^
```
[R/calculate_tajima_d.R:48:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L48) *style:* **Commas should always have a space after.**
```r
        loci_1 <- loci_matrix[i,]
                                ^
```
[R/calculate_tajima_d.R:49:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L49) *style:* **Commas should always have a space after.**
```r
        loci_2 <- loci_matrix[j,]
                                ^
```
[R/calculate_tajima_d.R:54:14:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L54) *style:* **Commented code should be removed.**
```r
        #    cat(i,j,"\n")
             ^~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:59:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L59) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(choose(2*number_of_sampled_individuals, 2) != cnt) {
    ^
```
[R/calculate_tajima_d.R:59:14:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L59) *style:* **Put spaces around all infix operators.**
```r
  if(choose(2*number_of_sampled_individuals, 2) != cnt) {
            ~^~
```
[R/calculate_tajima_d.R:63:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L63) *style:* **Put spaces around all infix operators.**
```r
  pi <- pi * 1.0 / (choose(2*number_of_sampled_individuals, 2))
                           ~^~
```
[R/calculate_tajima_d.R:65:3:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L65) *style:* **Variable or function name should be snake_case.**
```r
  S <- 0 # number of segregating sites
  ^
```
[R/calculate_tajima_d.R:66:6:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L66) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq_along(loci_matrix[1,])) {
     ^
```
[R/calculate_tajima_d.R:66:36:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L66) *style:* **Commas should always have a space after.**
```r
  for(i in seq_along(loci_matrix[1,])) {
                                   ^
```
[R/calculate_tajima_d.R:67:34:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L67) *style:* **Commas should always have a space after.**
```r
    a <- as.numeric(loci_matrix[,i])
                                 ^
```
[R/calculate_tajima_d.R:68:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(unique(a)) > 1) {
      ^
```
[R/calculate_tajima_d.R:69:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L69) *style:* **Variable or function name should be snake_case.**
```r
      S <- S + 1
      ^
```
[R/calculate_tajima_d.R:73:31:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L73) *style:* **Put spaces around all infix operators.**
```r
  D <- (pi - S / a1) / sqrt(e1*S + e2 * S * (S - 1))
                             ~^~
```
[R/calculate_tajima_d.R:75:3:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L75) *style:* **Variable or function name should be snake_case.**
```r
  Dmin <- (2/n - 1/a1)/sqrt(e2)
  ^~~~
```
[R/calculate_tajima_d.R:75:13:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L75) *style:* **Put spaces around all infix operators.**
```r
  Dmin <- (2/n - 1/a1)/sqrt(e2)
           ~^~
```
[R/calculate_tajima_d.R:75:19:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L75) *style:* **Put spaces around all infix operators.**
```r
  Dmin <- (2/n - 1/a1)/sqrt(e2)
                 ~^~
```
[R/calculate_tajima_d.R:75:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L75) *style:* **Put spaces around all infix operators.**
```r
  Dmin <- (2/n - 1/a1)/sqrt(e2)
                     ~^~
```
[R/calculate_tajima_d.R:76:3:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L76) *style:* **Variable or function name should be snake_case.**
```r
  Dmax <- ((n + 1)/(2 * n) - 1/a1)/sqrt(e2)
  ^~~~
```
[R/calculate_tajima_d.R:76:19:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L76) *style:* **Put spaces around all infix operators.**
```r
  Dmax <- ((n + 1)/(2 * n) - 1/a1)/sqrt(e2)
                 ~^~
```
[R/calculate_tajima_d.R:76:20:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L76) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  Dmax <- ((n + 1)/(2 * n) - 1/a1)/sqrt(e2)
                   ^
```
[R/calculate_tajima_d.R:76:31:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L76) *style:* **Put spaces around all infix operators.**
```r
  Dmax <- ((n + 1)/(2 * n) - 1/a1)/sqrt(e2)
                             ~^~
```
[R/calculate_tajima_d.R:76:35:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L76) *style:* **Put spaces around all infix operators.**
```r
  Dmax <- ((n + 1)/(2 * n) - 1/a1)/sqrt(e2)
                                 ~^~
```
[R/calculate_tajima_d.R:79:20:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L79) *style:* **Put spaces around all infix operators.**
```r
  a <- -tmp1 * Dmax/tmp2
                  ~^~
```
[R/calculate_tajima_d.R:80:19:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L80) *style:* **Put spaces around all infix operators.**
```r
  b <- tmp1 * Dmin/tmp2
                 ~^~
```
[R/calculate_tajima_d.R:81:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L81) *style:* **Put spaces around all infix operators.**
```r
  p <- pbeta((D - Dmin)/tmp2, b, a)
                      ~^~
```
[R/calculate_tajima_d.R:82:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L82) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.nan(p)) {
    ^
```
[R/calculate_tajima_d.R:84:13:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L84) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      2 * p } else {2 * (1 - p)}
            ^
```
[R/calculate_tajima_d.R:84:20:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L84) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      2 * p } else {2 * (1 - p)}
                   ^
```
[R/calculate_tajima_d.R:84:32:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/calculate_tajima_d.R#L84) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      2 * p } else {2 * (1 - p)}
                               ^
```
[R/fst.R:13:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/fst.R#L13) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/fst.R:19:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/fst.R#L19) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop1[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:20:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/fst.R#L20) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop1[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:26:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/fst.R#L26) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop2[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:27:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/fst.R#L27) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop2[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:42:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/fst.R#L42) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop1 <- check_input_pop(pop1)
          ^~~~~~~~~~~~~~~
```
[R/fst.R:44:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/fst.R#L44) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop2 <- check_input_pop(pop2)
          ^~~~~~~~~~~~~~~
```
[R/individual_class.R:24:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L24) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(num_colors > 20) num_colors <- 20
    ^
```
[R/individual_class.R:85:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L85) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(num_colors > 20) num_colors <- 20
    ^
```
[R/individual_class.R:128:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L128) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is(indiv, "individual")) return(FALSE)
    ^
```
[R/individual_class.R:130:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L130) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(indiv$chromosome1[1,1] != 0) {
    ^
```
[R/individual_class.R:130:26:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L130) *style:* **Commas should always have a space after.**
```r
  if(indiv$chromosome1[1,1] != 0) {
                         ^
```
[R/individual_class.R:134:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L134) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(tail(indiv$chromosome1,1)[2] != -1) {
    ^
```
[R/individual_class.R:134:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L134) *style:* **Commas should always have a space after.**
```r
  if(tail(indiv$chromosome1,1)[2] != -1) {
                            ^
```
[R/individual_class.R:139:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L139) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(max(abs(indiv$chromosome1[,2])) > 10000) {
    ^
```
[R/individual_class.R:139:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L139) *style:* **Commas should always have a space after.**
```r
  if(max(abs(indiv$chromosome1[,2])) > 10000) {
                                ^
```
[R/individual_class.R:144:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L144) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(indiv$chromosome2[1,1] != 0) {
    ^
```
[R/individual_class.R:144:26:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L144) *style:* **Commas should always have a space after.**
```r
  if(indiv$chromosome2[1,1] != 0) {
                         ^
```
[R/individual_class.R:149:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L149) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(tail(indiv$chromosome2,1)[2] != -1) {
    ^
```
[R/individual_class.R:149:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L149) *style:* **Commas should always have a space after.**
```r
  if(tail(indiv$chromosome2,1)[2] != -1) {
                            ^
```
[R/individual_class.R:154:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L154) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(max(abs(indiv$chromosome2[,2])) > 10000) {
    ^
```
[R/individual_class.R:154:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L154) *style:* **Commas should always have a space after.**
```r
  if(max(abs(indiv$chromosome2[,2])) > 10000) {
                                ^
```
[R/individual_class.R:164:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L164) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is(pop, "population"))  {
    ^
```
[R/individual_class.R:165:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L165) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!is(pop$population, "population")) {
      ^
```
[R/individual_class.R:171:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L171) *warning:* **no visible binding for global variable ‘verify_individual’**
```r
  v <- unlist(lapply(pop, verify_individual))
                          ^~~~~~~~~~~~~~~~~
```
[R/individual_class.R:172:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/individual_class.R#L172) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(sum(v) != length(v)) return(FALSE)
    ^
```
[R/iso_female.R:9:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/iso_female.R#L9) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/ld.R:1:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L1) *style:* **Variable or function name should be snake_case.**
```r
calculate_average_LD <- function(alleles_pos_1, alleles_pos_2) {
^~~~~~~~~~~~~~~~~~~~
```
[R/ld.R:3:20:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L3) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  all_alleles <- c( as.vector(alleles_pos_1), as.vector(alleles_pos_2))
                   ^
```
[R/ld.R:6:3:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L6) *style:* **Variable or function name should be snake_case.**
```r
  LD <- 0
  ^~
```
[R/ld.R:10:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L10) *style:* **Variable or function name should be snake_case.**
```r
      p_A_i <- length(which(alleles_pos_1 == i)) / length(alleles_pos_1)
      ^~~~~
```
[R/ld.R:11:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L11) *style:* **Variable or function name should be snake_case.**
```r
      p_B_j <- length(which(alleles_pos_2 == j)) / length(alleles_pos_2)
      ^~~~~
```
[R/ld.R:13:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L13) *style:* **Variable or function name should be snake_case.**
```r
      countAB <- 0
      ^~~~~~~
```
[R/ld.R:15:13:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L15) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (alleles_pos_1[a, 1]) == i && (alleles_pos_2[a, 1] == j)) {
            ^
```
[R/ld.R:16:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L16) *style:* **Variable or function name should be snake_case.**
```r
          countAB <- countAB + 1
          ^~~~~~~
```
[R/ld.R:19:13:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (alleles_pos_1[a, 2]) == i && (alleles_pos_2[a, 2] == j)) {
            ^
```
[R/ld.R:20:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L20) *style:* **Variable or function name should be snake_case.**
```r
          countAB <- countAB + 1
          ^~~~~~~
```
[R/ld.R:24:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L24) *style:* **Variable or function name should be snake_case.**
```r
      p_A_i_B_j <- countAB / (length(alleles_pos_1[, 1]) +
      ^~~~~~~~~
```
[R/ld.R:27:30:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L27) *style:* **Variable or function name should be snake_case.**
```r
      if (is.nan(p_A_i_B_j)) p_A_i_B_j <- 0
                             ^~~~~~~~~
```
[R/ld.R:29:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L29) *style:* **Variable or function name should be snake_case.**
```r
      D_i_j <- p_A_i_B_j - p_A_i * p_B_j
      ^~~~~
```
[R/ld.R:31:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L31) *style:* **Variable or function name should be snake_case.**
```r
      D_i_j_max <- 1
      ^~~~~~~~~
```
[R/ld.R:34:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L34) *style:* **Variable or function name should be snake_case.**
```r
        D_i_j_max <- min(p_A_i * p_B_j, (1 - p_A_i) * (1 - p_B_j))
        ^~~~~~~~~
```
[R/ld.R:36:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L36) *style:* **Variable or function name should be snake_case.**
```r
        D_i_j_max <- min(p_A_i * (1 - p_B_j), (1 - p_A_i) * p_B_j)
        ^~~~~~~~~
```
[R/ld.R:40:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L40) *style:* **Variable or function name should be snake_case.**
```r
        LD <- LD + p_A_i * p_B_j * abs(D_i_j / D_i_j_max)
        ^~
```
[R/ld.R:52:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L52) *style:* **Variable or function name should be snake_case.**
```r
calculate_LD <- function(pop,
^~~~~~~~~~~~
```
[R/ld.R:57:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L57) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/ld.R:63:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L63) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/ld.R:69:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L69) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 1 + findtype(pop[[i]]$chromosome1, focal_marker)
                      ^~~~~~~~
```
[R/ld.R:70:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L70) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 1 + findtype(pop[[i]]$chromosome2, focal_marker)
                      ^~~~~~~~
```
[R/ld.R:79:3:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L79) *style:* **Variable or function name should be snake_case.**
```r
  LD_matrix   <- matrix(nrow = length(markers), ncol = length(markers), NA)
  ^~~~~~~~~
```
[R/ld.R:86:21:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L86) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        index1 <- c( (x - 1) * 2 + 1, (x - 1) * 2 + 2)
                    ^
```
[R/ld.R:87:21:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L87) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        index2 <- c( (y - 1) * 2 + 1, (y - 1) * 2 + 2)
                    ^
```
[R/ld.R:91:15:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/ld.R#L91) *warning:* **no visible global function definition for ‘calculate_average_LD’**
```r
        ld <- calculate_average_LD(g1, g2)
              ^~~~~~~~~~~~~~~~~~~~
```
[R/plot.R:6:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L6) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/plot.R:7:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L7) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if("population" %in% colnames(frequencies)) {
    ^
```
[R/plot.R:18:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L18) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(picked_ancestor == "ALL") {
    ^
```
[R/plot.R:46:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L46) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if("population" %in% colnames(a1)) {
    ^
```
[R/plot.R:58:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L58) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(picked_ancestor[[1]] == "ALL") {
    ^
```
[R/plot.R:96:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L96) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if("population" %in% colnames(a1)) {
    ^
```
[R/plot.R:103:36:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L103) *style:* **Commas should always have a space after.**
```r
  a1 <- dplyr::select(a1, c("time","location","ancestor","frequency"))
                                   ^
```
[R/plot.R:103:47:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L103) *style:* **Commas should always have a space after.**
```r
  a1 <- dplyr::select(a1, c("time","location","ancestor","frequency"))
                                              ^
```
[R/plot.R:103:58:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L103) *style:* **Commas should always have a space after.**
```r
  a1 <- dplyr::select(a1, c("time","location","ancestor","frequency"))
                                                         ^
```
[R/plot.R:104:36:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L104) *style:* **Commas should always have a space after.**
```r
  a2 <- dplyr::select(a2, c("time","location","ancestor","frequency"))
                                   ^
```
[R/plot.R:104:47:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L104) *style:* **Commas should always have a space after.**
```r
  a2 <- dplyr::select(a2, c("time","location","ancestor","frequency"))
                                              ^
```
[R/plot.R:104:58:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L104) *style:* **Commas should always have a space after.**
```r
  a2 <- dplyr::select(a2, c("time","location","ancestor","frequency"))
                                                         ^
```
[R/plot.R:106:31:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L106) *style:* **Commas should never have a space before.**
```r
  colnames(a1) <- c("time"    ,  "location" , "ancestor" , "frequency_before")
                          ~~~~^
```
[R/plot.R:106:45:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L106) *style:* **Commas should never have a space before.**
```r
  colnames(a1) <- c("time"    ,  "location" , "ancestor" , "frequency_before")
                                           ~^
```
[R/plot.R:106:58:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L106) *style:* **Commas should never have a space before.**
```r
  colnames(a1) <- c("time"    ,  "location" , "ancestor" , "frequency_before")
                                                        ~^
```
[R/plot.R:107:31:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L107) *style:* **Commas should never have a space before.**
```r
  colnames(a2) <- c("time"    ,  "location" , "ancestor" , "frequency_after")
                          ~~~~^
```
[R/plot.R:107:45:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L107) *style:* **Commas should never have a space before.**
```r
  colnames(a2) <- c("time"    ,  "location" , "ancestor" , "frequency_after")
                                           ~^
```
[R/plot.R:107:58:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L107) *style:* **Commas should never have a space before.**
```r
  colnames(a2) <- c("time"    ,  "location" , "ancestor" , "frequency_after")
                                                        ~^
```
[R/plot.R:109:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L109) *style:* **Commas should always have a space after.**
```r
  ax <- dplyr::full_join(a1,a2, by = c("location", "ancestor"))
                            ^
```
[R/plot.R:115:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L115) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(picked_ancestor[[1]] == "ALL") {
    ^
```
[R/plot.R:170:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L170) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(to_plot$time) == 0) {
    ^
```
[R/plot.R:175:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L175) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if("population" %in% colnames(frequencies)) {
    ^
```
[R/plot.R:211:12:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/plot.R#L211) *warning:* **no visible global function definition for ‘calculate_dist_junctions’**
```r
  junct <- calculate_dist_junctions(pop)
           ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:4:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
calculate_allele_spectrum_cpp <- function(input_population, markers, progress_bar) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_GenomeAdmixR_calculate_allele_spectrum_cpp', PACKAGE = 'GenomeAdmixR', input_population, markers, progress_bar)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L5) *style:* **Only use double-quotes.**
```r
    .Call('_GenomeAdmixR_calculate_allele_spectrum_cpp', PACKAGE = 'GenomeAdmixR', input_population, markers, progress_bar)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:5:68:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L5) *style:* **Only use double-quotes.**
```r
    .Call('_GenomeAdmixR_calculate_allele_spectrum_cpp', PACKAGE = 'GenomeAdmixR', input_population, markers, progress_bar)
                                                                   ^~~~~~~~~~~~~~
```
[R/RcppExports.R:8:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
simulate_cpp <- function(input_population, select, pop_size, number_of_founders, starting_proportions, total_runtime, morgan, progress_bar, track_frequency, track_markers, track_junctions, multiplicative_selection) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:9:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_GenomeAdmixR_simulate_cpp', PACKAGE = 'GenomeAdmixR', input_population, select, pop_size, number_of_founders, starting_proportions, total_runtime, morgan, progress_bar, track_frequency, track_markers, track_junctions, multiplicative_selection)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:9:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L9) *style:* **Only use double-quotes.**
```r
    .Call('_GenomeAdmixR_simulate_cpp', PACKAGE = 'GenomeAdmixR', input_population, select, pop_size, number_of_founders, starting_proportions, total_runtime, morgan, progress_bar, track_frequency, track_markers, track_junctions, multiplicative_selection)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:9:51:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L9) *style:* **Only use double-quotes.**
```r
    .Call('_GenomeAdmixR_simulate_cpp', PACKAGE = 'GenomeAdmixR', input_population, select, pop_size, number_of_founders, starting_proportions, total_runtime, morgan, progress_bar, track_frequency, track_markers, track_junctions, multiplicative_selection)
                                                  ^~~~~~~~~~~~~~
```
[R/RcppExports.R:13:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
    invisible(.Call('_GenomeAdmixR_test_fish_functions', PACKAGE = 'GenomeAdmixR'))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:13:21:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L13) *style:* **Only use double-quotes.**
```r
    invisible(.Call('_GenomeAdmixR_test_fish_functions', PACKAGE = 'GenomeAdmixR'))
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:13:68:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L13) *style:* **Only use double-quotes.**
```r
    invisible(.Call('_GenomeAdmixR_test_fish_functions', PACKAGE = 'GenomeAdmixR'))
                                                                   ^~~~~~~~~~~~~~
```
[R/RcppExports.R:16:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
simulate_migration_cpp <- function(input_population_1, input_population_2, select, pop_size, starting_frequencies, total_runtime, morgan, progress_bar, track_frequency, track_markers, track_junctions, multiplicative_selection, migration_rate) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:17:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
    .Call('_GenomeAdmixR_simulate_migration_cpp', PACKAGE = 'GenomeAdmixR', input_population_1, input_population_2, select, pop_size, starting_frequencies, total_runtime, morgan, progress_bar, track_frequency, track_markers, track_junctions, multiplicative_selection, migration_rate)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:17:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L17) *style:* **Only use double-quotes.**
```r
    .Call('_GenomeAdmixR_simulate_migration_cpp', PACKAGE = 'GenomeAdmixR', input_population_1, input_population_2, select, pop_size, starting_frequencies, total_runtime, morgan, progress_bar, track_frequency, track_markers, track_junctions, multiplicative_selection, migration_rate)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RcppExports.R:17:61:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L17) *style:* **Only use double-quotes.**
```r
    .Call('_GenomeAdmixR_simulate_migration_cpp', PACKAGE = 'GenomeAdmixR', input_population_1, input_population_2, select, pop_size, starting_frequencies, total_runtime, morgan, progress_bar, track_frequency, track_markers, track_junctions, multiplicative_selection, migration_rate)
                                                            ^~~~~~~~~~~~~~
```
[R/RcppExports.R:19:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/RcppExports.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/simulate_admixture_migration.R:17:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L17) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.list(input_population_1)) {
    ^
```
[R/simulate_admixture_migration.R:20:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!is(input_population_1, "population")) {
      ^
```
[R/simulate_admixture_migration.R:21:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L21) *warning:* **local variable ‘all_are_individuals’ assigned but may not be used**
```r
      all_are_individuals <- sapply(input_population_1, class)
      ^~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:22:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(sum(input_population_1 == "individual") ==
        ^
```
[R/simulate_admixture_migration.R:28:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_1$population, "population")) {
      ^
```
[R/simulate_admixture_migration.R:32:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L32) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_1, "population")) {
      ^
```
[R/simulate_admixture_migration.R:33:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L33) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_1 <- population_to_vector(input_population_1)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:41:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L41) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.list(input_population_2)) {
    ^
```
[R/simulate_admixture_migration.R:44:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!is(input_population_2, "population")) {
      ^
```
[R/simulate_admixture_migration.R:46:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L46) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(sum(input_population_2 == "individual") ==
        ^
```
[R/simulate_admixture_migration.R:52:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L52) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_2$population, "population")) {
      ^
```
[R/simulate_admixture_migration.R:56:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L56) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_2, "population")) {
      ^
```
[R/simulate_admixture_migration.R:57:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L57) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_2 <- population_to_vector(input_population_2)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:65:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L65) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(sum(initial_frequencies[[1]]) != 1) {
    ^
```
[R/simulate_admixture_migration.R:66:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    initial_frequencies[[1]] <- initial_frequencies[[1]] / sum(initial_frequencies[[1]])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:69:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(sum(initial_frequencies[[2]]) != 1) {
    ^
```
[R/simulate_admixture_migration.R:70:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
    initial_frequencies[[2]] <- initial_frequencies[[2]] / sum(initial_frequencies[[2]])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:75:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L75) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.matrix(select_matrix)) {
    ^
```
[R/simulate_admixture_migration.R:87:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L87) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(is.na(select_matrix)) {
        ^
```
[R/simulate_admixture_migration.R:88:41:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L88) *style:* **Put spaces around all infix operators.**
```r
        select_matrix <- matrix(-1, nrow=2,ncol=2)
                                       ~^~
```
[R/simulate_admixture_migration.R:88:44:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L88) *style:* **Commas should always have a space after.**
```r
        select_matrix <- matrix(-1, nrow=2,ncol=2)
                                           ^
```
[R/simulate_admixture_migration.R:88:48:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L88) *style:* **Put spaces around all infix operators.**
```r
        select_matrix <- matrix(-1, nrow=2,ncol=2)
                                              ~^~
```
[R/simulate_admixture_migration.R:92:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L92) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(markers) == 1) {
    ^
```
[R/simulate_admixture_migration.R:93:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L93) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.na(markers))  {
      ^
```
[R/simulate_admixture_migration.R:108:6:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L108) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in 1:length(initial_frequencies)) {
     ^
```
[R/simulate_admixture_migration.R:109:8:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L109) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(j in 1:length(initial_frequencies[[i]])) {
       ^
```
[R/simulate_admixture_migration.R:114:42:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  selected_pop <- simulate_migration_cpp( input_population_1,
                                         ^
```
[R/simulate_admixture_migration.R:128:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L128) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_1 <- create_pop_class(selected_pop$population_1)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:129:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L129) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_2 <- create_pop_class(selected_pop$population_2)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:139:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L139) *style:* **Lines should not be more than 80 characters.**
```r
  colnames(final_freq_tibble) <- c("time", "location", "ancestor", "frequency", "population")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:143:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L143) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(track_frequency == FALSE && track_junctions == FALSE) {
    ^
```
[R/simulate_admixture_migration.R:148:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L148) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(track_frequency == FALSE && track_junctions == TRUE) {
    ^
```
[R/simulate_admixture_migration.R:154:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L154) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(track_frequency == TRUE && track_junctions == FALSE) {
    ^
```
[R/simulate_admixture_migration.R:156:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L156) *style:* **Lines should not be more than 80 characters.**
```r
    colnames(frequencies_tibble) <- c("time","location","ancestor","frequency", "population")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:156:46:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L156) *style:* **Commas should always have a space after.**
```r
    colnames(frequencies_tibble) <- c("time","location","ancestor","frequency", "population")
                                             ^
```
[R/simulate_admixture_migration.R:156:57:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L156) *style:* **Commas should always have a space after.**
```r
    colnames(frequencies_tibble) <- c("time","location","ancestor","frequency", "population")
                                                        ^
```
[R/simulate_admixture_migration.R:156:68:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L156) *style:* **Commas should always have a space after.**
```r
    colnames(frequencies_tibble) <- c("time","location","ancestor","frequency", "population")
                                                                   ^
```
[R/simulate_admixture_migration.R:165:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L165) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(track_frequency == TRUE && track_junctions == TRUE) {
    ^
```
[R/simulate_admixture_migration.R:167:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L167) *style:* **Lines should not be more than 80 characters.**
```r
    colnames(frequencies_tibble) <- c("time","location","ancestor","frequency", "population")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:167:46:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L167) *style:* **Commas should always have a space after.**
```r
    colnames(frequencies_tibble) <- c("time","location","ancestor","frequency", "population")
                                             ^
```
[R/simulate_admixture_migration.R:167:57:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L167) *style:* **Commas should always have a space after.**
```r
    colnames(frequencies_tibble) <- c("time","location","ancestor","frequency", "population")
                                                        ^
```
[R/simulate_admixture_migration.R:167:68:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_migration.R#L167) *style:* **Commas should always have a space after.**
```r
    colnames(frequencies_tibble) <- c("time","location","ancestor","frequency", "population")
                                                                   ^
```
[R/simulate_admixture_until.R:24:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_until.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
                                       initial_frequencies = initial_frequencies,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_until.R:25:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_until.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
                                       total_runtime = generations_between_update,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_until.R:32:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_until.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
                                       multiplicative_selection = multiplicative_selection,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_until.R:46:8:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_until.R#L46) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  while(fst < critical_fst && total_generations < total_runtime) {
       ^
```
[R/simulate_admixture_until.R:50:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_until.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
                                         initial_frequencies = initial_frequencies,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_until.R:51:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_until.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
                                         total_runtime = generations_between_update,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_until.R:58:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_until.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
                                         multiplicative_selection = multiplicative_selection,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_until.R:68:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/c616131dd5821a1fc9afea03c7b7555c15b4965e/R/simulate_admixture_until.R#L68) *style:* **Commas should always have a space after.**
```r
    cat(total_generations,"\t", fst ,"\n")
                          ^
```


But one message has the overhead of adding a message type. Therefore this is faster and easier to read


problem with HTML tag in a custom error message


good point, I'll change it


> If you found any regression in Django 2.2 please add a [new ticket](https://code.djangoproject.com/newticket) and describe it.
>
> This change will appear in Django 3.0.

I got it.
Thanks, felixxm


Successfully aliased the URL <https://pikbet-pzrvmnn1l.now.sh> to the following aliases.

* https://pikbet.now.sh
* https://pikbet.shimanskiy1.now.sh
* https://pikbet-git-master.shimanskiy1.now.sh


Collaborator: Review for this commit was created. [Link to review](http://217.170.125.19:40101/ui#review:id=24)


$hoge
がどれも条件付きのselectを実行するSQL結果を入れていたので
$find_resultとしました


![ToDolist project](https://user-images.githubusercontent.com/44446425/59022043-01e18f00-8888-11e9-90fd-23dbad4184ae.png)


TeamCity Consultations / "Private Beta" - BuildAndPublish .NET Core 2.1 [Build 0.1.0.2145-EC-781-GlobalNav](https://teamcity.nice.org.uk/viewLog.html?buildId=54530&buildTypeId=Consultations_PrivateBetaBuildAndPublish21) outcome was **FAILURE**
Summary: Tests passed: 208;
       "C:\BuildAgent\work\fbec5a364d953ddb\Consultations.sln" (default target) (1) ->
       (Restore target) ->
         C:\Program Files\dotnet\sdk\2.2.104\NuGet.targets(114,5): error : A task was canceled.
 (new); exit code 1 ... Build time: 00:03:44


![techno tech lab landing page](https://user-images.githubusercontent.com/44446425/59022083-16258c00-8888-11e9-8a7d-754f69854e78.png)


Collaborator: Review for this commit was created. [Link to review](http://217.170.125.19:40101/ui#review:id=26)


There's no need to downvote this. The whole point of status icons is to add a new layer to the perk item system. It isn't a new system, it's still the same. It makes no sense to split this. It's the same like splitting the main hud into two since the role is independant of the health ...


Alarms are implemented as notifications with sounds. Not sure if that is possible given the constraints of notifications


Additionally the code becomes ugly by adding multiple ifs and checks how many parameters have been transmitted.


its not faster but its not such a big issue, so let that be as it is for now.


Successfully aliased the URL <https://com-redirect-2f16f4ww7.now.sh> to the following aliases.

* https://www.andykenward.com
* https://com-redirect.andykenward.now.sh
* https://com-redirect-git-master.andykenward.now.sh


うっす！


ok


df


106行目の
$debug を $kouho_implode
に変更しました


transmitting another value and adding multiple ifs is always slower


Szybciej


Successfully aliased the URL <https://ohjelmointi-19-hlexv1xp7.now.sh> to the following aliases.

* https://ohjelmointi-19.mooc.fi
* https://ohjelmointi-19.mooc.now.sh
* https://ohjelmointi-19-git-master.mooc.now.sh


Done


ですね・・・


削除しました


Haha, what is this sorcery? 🌬


Just want to give a option for same native client, which have not ability to connet to websocket but still can work with your mediasoup, It just a planing work, but still not on going.


Done. I searched through the file object and used the proper method... Say hi to inputPath and outputPath. I could/should use the new object to simplify the rest of the script later.


Unified/rejector.py --clone pdmvserv_task_PPD-RunIISummer19UL17wmLHEGEN-00002__v1_T_190530_185009_8702 --short_task --comment "internal issue with long task name"

Unified/injector.py task_PPD-RunIISummer19UL17wmLHEGEN-00002

Unified/assignor.py task_PPD-RunIISummer19UL17wmLHEGEN-00002


Successfully aliased the URL <https://jeremyswinnen-95jatxmii.now.sh> to the following aliases.

* https://www.jeremyswinnen.com
* https://jeremyswinnen.com
* https://jeremyswinnen.jereswinnen.now.sh
* https://jeremyswinnen-git-master.jereswinnen.now.sh


TeamCity Consultations / "Private Beta" - BuildAndPublish .NET Core 2.1 [Build 0.1.0.2146-EC-781-GlobalNav](https://teamcity.nice.org.uk/viewLog.html?buildId=54531&buildTypeId=Consultations_PrivateBetaBuildAndPublish21) outcome was **SUCCESS**
Summary: Tests passed: 430 Build time: 00:09:54


noted.


This change introduces a type mismatch:
```
  We've found a bug for you!
  /home/chris/Projects/fidap/frontend/node_modules/reason-apollo/src/graphql-types/ReasonApolloMutation.re 138:55-61

  136 ┆     ~children: (apolloMutation, renderPropObj) => React.element,
  137 ┆   ) =>
  138 ┆ <JsMutation mutation=graphqlMutationAST variables onError onCompleted
        >
  139 ┆   {(mutation, apolloData) =>
  140 ┆      children(

  This has type:
    option(ReasonApolloTypes.apolloError => unit)
  But somewhere wanted:
    option(unit => unit)

  The incompatible parts:
    ReasonApolloTypes.apolloError (defined as
      {. "graphQLErrors": Js.Nullable.t(array(ReasonApolloTypes.graphqlError)),
        "message": string, "networkError": Js.Nullable.t(string)})
    vs
    unit
```
`apolloError => unit` clashes with [ReasonApolloMutation.re:119](https://github.com/apollographql/reason-apollo/blob/ff68a9b4a53ae86694a431c67db72555b202a682/src/graphql-types/ReasonApolloMutation.re#L119) `unit => unit`


looks so much better than mine


it is not, they are two independent systems and should not be mixed, they aren't even displayed together (statuses are displayed with a margin). That alone indicates a difference, which is better expressed as a standalone element, that is attached to the items element. Statuses != Items and this element is specifically named to represent items.  Even if the function to draw them is the same, that does not mean they belong to the same element, this is where our inheritance comes into use. Having them split up (also see mini-scoreboard and teamindicator, gives you much more options, as at least being able to disable the status effects visually and so on...


thanks


Collaborator: Review for this commit was created. [Link to review](https://gmail133.smartbeartrial.com/ui#review:id=549)


I could add a child element for this. But I don't think it's worth it since they both share most of the codebase anyways


foreachを消去しました。
確かに全く必要ないループでした。。。


Wish my work looked this well


nothing to attach


> Is it reasonable to make this type more expressive? Or rustdoc must cover the bytes are from abi
> ![Screenshot_20190606-180946](https://user-images.githubusercontent.com/4891004/59021259-77e4f680-8886-11e9-94bb-444f3fecca18.jpg)

Yes I wanna clean types and document.
https://github.com/cryptoeconomicslab/plasma-rust-framework/issues/60


Successfully aliased the URL <https://pikbet-6ulhlestg.now.sh> to the following aliases.

* https://pikbet.vitaliks1.now.sh
* https://pikbet-git-master.vitaliks1.now.sh


Please look at our HUD system again and reconsider, otherwise let me know if there is anything about it, that you did not understand.


I think it should read something like:

`* AdoptOpenJDK 11 or Oracle JDK 11 (the former is installed automatically as of [Mendix 8.0.0 Beta 3](/releasenotes/studio-pro/8.0#803) if you do not have any JDK 11 installed)
`
We support both AdoptOpenJDK and Oracle's JDK, both in version 11. And if you don't have either of them on your system, we will install the AdoptOpenJDK one.


Code review passed


It re-enables sound clipping for map which obviously should never have their sound clipping disabled.

Sound clipping was intentionally disabled for E1M8, E2M8 and E3M8, which only had single boss monsters (well, two in the case of E1M8). It was also - most probably by accident - applied to E4M8 and Doom2's MAP08, so we fixed that.


Improved speed by 30 to 40%


could you update msm8909 to external codec C47L24 DSP codec full linux stack using dts.


OK I will thinking how we can abstract it. PredicatePlugin's methods are strictly defined by spec I think. So, make another trait.


@prusnak This `Set screen rotation via user setting` should be `Set screen rotation via trezorctl`


Oh, I thought we decided we were going to specify such dependencies here instead of the app, as those are the core of our actual stack.