[R/calculate_frequencies.R:3:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/fst.R#L19) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop1[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:20:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/fst.R#L20) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop1[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:26:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/fst.R#L26) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop2[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:27:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/fst.R#L27) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop2[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:42:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L130) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(indiv$chromosome1[1,1] != 0) {
    ^
```
[R/individual_class.R:130:26:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L130) *style:* **Commas should always have a space after.**
```r
  if(indiv$chromosome1[1,1] != 0) {
                         ^
```
[R/individual_class.R:134:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L134) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(tail(indiv$chromosome1,1)[2] != -1) {
    ^
```
[R/individual_class.R:134:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L134) *style:* **Commas should always have a space after.**
```r
  if(tail(indiv$chromosome1,1)[2] != -1) {
                            ^
```
[R/individual_class.R:139:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L139) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(max(abs(indiv$chromosome1[,2])) > 10000) {
    ^
```
[R/individual_class.R:139:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L139) *style:* **Commas should always have a space after.**
```r
  if(max(abs(indiv$chromosome1[,2])) > 10000) {
                                ^
```
[R/individual_class.R:144:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L144) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(indiv$chromosome2[1,1] != 0) {
    ^
```
[R/individual_class.R:144:26:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L144) *style:* **Commas should always have a space after.**
```r
  if(indiv$chromosome2[1,1] != 0) {
                         ^
```
[R/individual_class.R:149:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L149) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(tail(indiv$chromosome2,1)[2] != -1) {
    ^
```
[R/individual_class.R:149:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L149) *style:* **Commas should always have a space after.**
```r
  if(tail(indiv$chromosome2,1)[2] != -1) {
                            ^
```
[R/individual_class.R:154:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L154) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(max(abs(indiv$chromosome2[,2])) > 10000) {
    ^
```
[R/individual_class.R:154:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/individual_class.R#L154) *style:* **Commas should always have a space after.**
```r
  if(max(abs(indiv$chromosome2[,2])) > 10000) {
                                ^
```
[R/individual_class.R:164:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/RcppExports.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/simulate_admixture_migration.R:17:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_migration.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_1$population, "population")) {
      ^
```
[R/simulate_admixture_migration.R:32:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_migration.R#L32) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_1, "population")) {
      ^
```
[R/simulate_admixture_migration.R:33:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_migration.R#L33) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_1 <- population_to_vector(input_population_1)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:41:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_migration.R#L41) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.list(input_population_2)) {
    ^
```
[R/simulate_admixture_migration.R:44:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_migration.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!is(input_population_2, "population")) {
      ^
```
[R/simulate_admixture_migration.R:46:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_migration.R#L46) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(sum(input_population_2 == "individual") ==
        ^
```
[R/simulate_admixture_migration.R:52:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_migration.R#L52) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_2$population, "population")) {
      ^
```
[R/simulate_admixture_migration.R:56:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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$population_1)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:129:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_migration.R#L129) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_2 <- create_pop_class(selected_pop$population_2)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:139:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/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/1003bef4cd454495bc94b944e2e9e44bbc4d9bdc/R/simulate_admixture_until.R#L68) *style:* **Commas should always have a space after.**
```r
    cat(total_generations,"\t", fst ,"\n")
                          ^
```


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I noticed the `subset` parameter heritaged from base `embed` class and in all `process_*_dataset` method of its offsprings. I guess it is used to shorten sentences input by given a consistent subset index. Am I right?

If so, I wonder what the scenario is for this process and I doubt if `target_maxlen` should be less than the maxim of sequence_lengths, or this kind of shrinking would be meaningless after padding.


gets error:
	"message": "Property 'map' does not exist on type 'Observable<Object>'.",


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@rakanalh Is this used for both serializing to SQLite and to JSON? If it is, doesn't this change the JSON message format by providing chain_ids and channel_ids as strings?


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afarin


`subset` is for getting batches while training. Check here https://github.com/BrikerMan/Kashgari/blob/966e53dbe1d68c8fe313ce8f049f8fdb5a30056e/kashgari/tasks/base_model.py#L122


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