[R/calculate_frequencies.R:3:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/R/fst.R#L19) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop1[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:20:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/fst.R#L20) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop1[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:26:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/fst.R#L26) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop2[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:27:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/fst.R#L27) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop2[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/fst.R:42:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L130) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(indiv$chromosome1[1,1] != 0) {
    ^
```
[R/individual_class.R:130:26:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L130) *style:* **Commas should always have a space after.**
```r
  if(indiv$chromosome1[1,1] != 0) {
                         ^
```
[R/individual_class.R:134:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L134) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(tail(indiv$chromosome1,1)[2] != -1) {
    ^
```
[R/individual_class.R:134:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L134) *style:* **Commas should always have a space after.**
```r
  if(tail(indiv$chromosome1,1)[2] != -1) {
                            ^
```
[R/individual_class.R:139:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L139) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(max(abs(indiv$chromosome1[,2])) > 10000) {
    ^
```
[R/individual_class.R:139:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L139) *style:* **Commas should always have a space after.**
```r
  if(max(abs(indiv$chromosome1[,2])) > 10000) {
                                ^
```
[R/individual_class.R:144:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L144) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(indiv$chromosome2[1,1] != 0) {
    ^
```
[R/individual_class.R:144:26:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L144) *style:* **Commas should always have a space after.**
```r
  if(indiv$chromosome2[1,1] != 0) {
                         ^
```
[R/individual_class.R:149:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L149) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(tail(indiv$chromosome2,1)[2] != -1) {
    ^
```
[R/individual_class.R:149:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L149) *style:* **Commas should always have a space after.**
```r
  if(tail(indiv$chromosome2,1)[2] != -1) {
                            ^
```
[R/individual_class.R:154:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L154) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(max(abs(indiv$chromosome2[,2])) > 10000) {
    ^
```
[R/individual_class.R:154:33:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/individual_class.R#L154) *style:* **Commas should always have a space after.**
```r
  if(max(abs(indiv$chromosome2[,2])) > 10000) {
                                ^
```
[R/individual_class.R:164:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/R/RcppExports.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/simulate_admixture_migration.R:17:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_migration.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_1$population, "population")) {
      ^
```
[R/simulate_admixture_migration.R:32:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_migration.R#L32) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_1, "population")) {
      ^
```
[R/simulate_admixture_migration.R:33:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_migration.R#L33) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population_1 <- population_to_vector(input_population_1)
                            ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:41:5:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_migration.R#L41) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.list(input_population_2)) {
    ^
```
[R/simulate_admixture_migration.R:44:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_migration.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!is(input_population_2, "population")) {
      ^
```
[R/simulate_admixture_migration.R:46:9:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_migration.R#L46) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(sum(input_population_2 == "individual") ==
        ^
```
[R/simulate_admixture_migration.R:52:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_migration.R#L52) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is(input_population_2$population, "population")) {
      ^
```
[R/simulate_admixture_migration.R:56:7:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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$population_1)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:129:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_migration.R#L129) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_2 <- create_pop_class(selected_pop$population_2)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:139:1:](https://github.com/thijsjanzen/GenomeAdmixR/blob/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/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/da852c6bc189d88e9c03c373e170d2b667d96964/R/simulate_admixture_until.R#L68) *style:* **Commas should always have a space after.**
```r
    cat(total_generations,"\t", fst ,"\n")
                          ^
```


Add support for EGOLD


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

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

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Cool, would be awesome :1st_place_medal:


Successfully aliased the URL <https://boycott-dwvs53x1h.now.sh> to the following aliases.

* https://boycott.gabriel-wu.com
* https://boycott.lucifer1004.now.sh
* https://boycott-git-master.lucifer1004.now.sh


I searched for usages of my command globally on github :D You were one of the two (other is CBA)


Deployment failed with the following error:

~~~
You are not owner of the domain "nextjs.org"
~~~


why only apply this on the tfs-tree? The git-tree can also have alternative folder separators.

I encountered this using git-tfs v0.30 + git 2.21.0.windows.1: both git and tfs entry.FullName have forward slashes.


lägga till Eva


Ha! Well spotted :-)

I can fix it now...


In ConsoleSay,
```java
String message = "";
for (String s : args) {
	message = message + s + " ";
}
```
using this method is very memory consuming, as every words are stored separately in the string pool. Using a StringBuilder is generally a better idea:
```java
StringBuilder message = new StringBuilder();
for (String s : args) {
        message.append(s);
}
```


One further Q for you @jeroen: The explicit `ubuntugis/ppa` is no longer necessary, as far as I understand it, right? That was mostly only due to former (trusty) machines having older GDAL versions that weren't `sf`-compatible. Current xenial obviates this, as far as I understand, right  @edzer? At least, it all works smoothly for me without on [this repo](https://github.com/moveability/moveability/blob/master/.travis.yml).


'nombre' => $_POST['nombreUsuario'], //la asignacion es a 'nombre', hay que darle el mismo q en la BDD


![](https://github.trello.services/images/mini-trello-icon.png) [Versión 20190604.1 (en mantenimiento)](https://trello.com/c/QDKKGQVV/29-versi%C3%B3n-201906041-en-mantenimiento)


okej , eva är bra


you can squash/update previous commits;
no need to add fix commits in branches;


:loudspeaker: Reporting! Here's a latest version of testing map, which was extended by @jeffdoggett:
[switches3.zip](https://github.com/fabiangreffrath/crispy-doom/files/3261119/switches3.zip)


So is current_max_z_feedrate now unused? There remains the Maximum Z Speed and Maximum Speed Z settings that can be set in the GUI. Are they now redundant? Should one or both be removed?


Successfully aliased the URL <https://repl-hva68yjs1.now.sh> to the following aliases.

* https://repl.teleporthq.io
* https://repl.teleport-dev.now.sh
* https://repl-git-master.teleport-dev.now.sh


Ура!


@jkrayco  I think `morphSwapSrc` and `morphSwapDst` are treated as well.

In my opinion, rules of an access to `Globals` should be defined from the view of the access control. any components which can be accessed globally offer conveniences but could cause of making the code messed up quickly.


The studio can create files with assembler listings, where you can find out who owns this part of the code.
What does turning off the expansion option still use SSE operations?


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

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

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


You can distribute it as long as you follow the license, though I would suggest you give yourself a credit *somewhere* in the download.


![](https://github.trello.services/images/mini-trello-icon.png) [[RTM-4]: Counting 1-bits](https://trello.com/c/VEXNHFbN/4-rtm-4-counting-1-bits)


Fixed. Thanks @kroer


Successfully aliased the URL <https://repl-286whpxhr.now.sh> to the following aliases.

* https://repl.teleporthq.io
* https://repl.teleport-dev.now.sh
* https://repl-git-master.teleport-dev.now.sh


hmm, then my whole patch may be wrong. Do you like me to revert it?

BTW: I think, this is another "incomplete" feature, that leaded to addition of hundred exception checks and still keeps thousands of uncovered places.


Successfully aliased the URL <https://topics-manager-84fvfdx7l.now.sh> to the following aliases.

* https://topics-manager.now.sh
* https://topics-manager.iamstarkov.now.sh
* https://topics-manager-git-master.iamstarkov.now.sh


evaaaaaaaaaaaaaa