[R/calculate_allele_frequencies.R:34:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_allele_frequencies.R#L34) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/calculate_allele_frequencies.R:36:18:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_allele_frequencies.R#L36) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
  pop_for_cpp <- population_to_vector(source_pop)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_fst.R:41:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L41) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop1 <- check_input_pop(pop1)
          ^~~~~~~~~~~~~~~
```
[R/calculate_fst.R:43:11:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L43) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop2 <- check_input_pop(pop2)
          ^~~~~~~~~~~~~~~
```
[R/calculate_fst.R:72:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L72) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_fst.R:78:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L78) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop1[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:79:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L79) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop1[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:85:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L85) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 10 + findtype(pop2[[i]]$chromosome1, focal_marker)
                       ^~~~~~~~
```
[R/calculate_fst.R:86:24:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_fst.R#L86) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 10 + findtype(pop2[[i]]$chromosome2, focal_marker)
                       ^~~~~~~~
```
[R/calculate_ld.R:39:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L39) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_ld.R:45:16:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L45) *warning:* **no visible global function definition for ‘create_random_markers’**
```r
    markers <- create_random_markers(number_of_markers)
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_ld.R:51:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L51) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_1 <- 1 + findtype(pop[[i]]$chromosome1, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:52:23:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L52) *warning:* **no visible global function definition for ‘findtype’**
```r
      allele_2 <- 1 + findtype(pop[[i]]$chromosome2, focal_marker)
                      ^~~~~~~~
```
[R/calculate_ld.R:73:15:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_ld.R#L73) *warning:* **no visible global function definition for ‘calculate_average_ld’**
```r
        ld <- calculate_average_ld(g1, g2)
              ^~~~~~~~~~~~~~~~~~~~
```
[R/calculate_marker_frequency.R:31:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_marker_frequency.R#L31) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/calculate_tajima_d.R:28:10:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/calculate_tajima_d.R#L28) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  pop <- check_input_pop(pop)
         ^~~~~~~~~~~~~~~
```
[R/iso_female.R:44:17:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/iso_female.R#L44) *warning:* **no visible global function definition for ‘check_input_pop’**
```r
  source_pop <- check_input_pop(source_pop)
                ^~~~~~~~~~~~~~~
```
[R/junctions.R:25:12:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/junctions.R#L25) *warning:* **no visible global function definition for ‘calculate_dist_junctions’**
```r
  junct <- calculate_dist_junctions(pop)
           ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:105:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L105) *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:130:29:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L130) *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:202:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L202) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_1 <- create_pop_class(selected_pop$population_1)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture_migration.R:203:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture_migration.R#L203) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct_2 <- create_pop_class(selected_pop$population_2)
                          ^~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:81:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture.R#L81) *warning:* **no visible global function definition for ‘population_to_vector’**
```r
      input_population <- population_to_vector(input_population)
                          ^~~~~~~~~~~~~~~~~~~~
```
[R/simulate_admixture.R:142:25:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/simulate_admixture.R#L142) *warning:* **no visible global function definition for ‘create_pop_class’**
```r
  selected_popstruct <- create_pop_class(selected_pop$population)
                        ^~~~~~~~~~~~~~~~
```
[R/utilities.R:275:27:](https://github.com/thijsjanzen/GenomeAdmixR/blob/6b99a8965d6cbefa3383d482e6564286c2f3bea9/R/utilities.R#L275) *warning:* **no visible binding for global variable ‘verify_individual’**
```r
  v <- unlist(lapply(pop, verify_individual))
                          ^~~~~~~~~~~~~~~~~
```


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 325](https://teamcity.nice.org.uk/viewLog.html?buildId=56836&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) (new) Build time: 00:00:35


[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after an infinite number of generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:11:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L11) *style:* **Variable or function name should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L12) *style:* **Variable or function name should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  K <- H_0 * C * 2 * N * R / (2 * N * C + R)
  ^
```
[R/calc_K.R:19:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L19) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L23) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L27) *style:* **Variable or function name should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the error in the estimate of the onset of hybridisation, following Equations 3 & 4 in the Supplementary information of Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param relative Boolean flag, if TRUE: return the relative error, if FALSE: return error in generations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:15:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L15) *style:* **Variable or function name should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L17) *style:* **Variable or function name should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L18) *style:* **Variable or function name should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_error.R:30:7:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
      ^
```
[R/calculate_error.R:30:25:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
                        ^
```
[R/calculate_MAT.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Function that calculates the maximum time after hybridization after which the number of junctions can still be reliably used to estimate the onset of hybridization. This is following equation 15 in Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:12:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L12) *style:* **Variable or function name should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_time.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the number of junctions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 14 in Janzen et al. 2018
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' estimate_time(J = J, N = 100, R = 1000, H_0 = 0.5, C = 1)  # should be 200 again
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:13:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L13) *style:* **Variable or function name should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/estimate_time_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 1 in Janzen et al. unpublished
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:8:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:12:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' J <- number_of_junctions_markers(N = 100, H_0 = 0.5, t = 200, marker_distribution = markers)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:18:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L18) *style:* **Variable or function name should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L19) *style:* **Variable or function name should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(lower_lim, upper_lim) )
                                                                      ^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
                                                        ^
```
[R/estimate_time_phased.R:108:19:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L108) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_phased.R:135:23:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:135:32:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:138:10:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L138) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:142:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:143:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L143) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:147:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:148:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L148) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:149:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L149) *style:* **Lines should not be more than 80 characters.**
```r
#' @param optim_pop_size If TRUE, population size is also optimized. Starting point of the optimizaton will then be on the given population size, and half the maximum time.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:184:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L184) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:191:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L191) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
                                                 ^
```
[R/estimate_time_unphased.R:12:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                       ^
```
[R/estimate_time_unphased.R:12:43:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                                          ^
```
[R/estimate_time_unphased.R:18:22:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- p * q * ( p * q * P[3] +
                     ^
```
[R/estimate_time_unphased.R:35:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                       ^
```
[R/estimate_time_unphased.R:88:19:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L88) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_unphased.R:115:23:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:115:32:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:118:12:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L118) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:175:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L175) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/estimate_time_unphased.R:182:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L182) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, in a backcrossing mating scheme.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:4:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:10:43:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L10) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected number of junctions between two markers separated by a given amount of recombination
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distance between two markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:12:36:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L12) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_di <- function(N = Inf,
                                   ^
```
[R/number_of_junctions_di.R:13:36:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected total number of junctions in a chromosome, given the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distribution of markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:20:41:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_markers <- function(N = Inf,
                                        ^
```
[R/number_of_junctions_markers.R:21:41:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L21) *style:* **Variable or function name should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions_markers.R:32:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L32) *warning:* **no visible global function definition for ‘number_of_junctions_di’**
```r
    expected_junctions <- number_of_junctions_di(N, H_0, t, di)
                          ^~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after t generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:13:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L13) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/optim_limits.R:5:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/optim_limits.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param calc_func function to calculate the time, should accept two arguments: upper, lower and should return a stats::optimize object with two properties: $minimum and $objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/optim_limits.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param iterations number of times the boundaries should be adjusted to obtain an estimate that is not close to the boundaries. After this number of iterations is exceeded, NA is returned
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:38:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/phased_log_likelihood.R:45:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/sim_backcrossing.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:12:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return List with five entries: average_junctions: average number of junctions over time, detected_junctions: average number of detected junctions, given the markers. markers: vector with the locations of the molecular markers, junction_distribution: distribution of junctions per time step average_heterozygosity: average heterozygosity.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with regularly distributed markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:5:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:17:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
sim_fin_chrom <- function (pop_size = 100,
                          ^
```
[R/sim_fin_chrom.R:22:28:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L22) *style:* **Variable or function name should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with an infinite number of recombination sites.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param markers The number of genetic markers superimposed on the chromosome. If markers is set to -1, no markers are superimposed (faster simulation)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is returned.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:8:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the unphased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:34:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/unphased_log_likelihood.R:41:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/util.R:22:10:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( get_states_vector(local_anc))
         ^
```
[R/util.R:22:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L22) *warning:* **no visible global function definition for ‘get_states_vector’**
```r
  return( get_states_vector(local_anc))
          ^~~~~~~~~~~~~~~~~
```
[R/util.R:56:42:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    (local_anc_matrix[, 1 ] == local_anc_matrix[, 2]))
                                         ^
```
[R/util.R:108:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:108:37:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
                                    ^
```
[R/util.R:116:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 3) cond_prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:122:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 4) cond_prob <- (p ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:146:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:146:44:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
                                           ^
```
[R/util.R:151:18:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L151) *warning:* **no visible global function definition for ‘get_expectation_O_state’**
```r
    cond_prob <- get_expectation_O_state(P, p, focal_state)
                 ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-equations.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-equations.R#L18) *style:* **Variable or function name should be snake_case.**
```r
  J <- junctions::number_of_junctions(N = 100, R = 1000,
  ^
```
[tests/testthat/test-marker_dist.R:4:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L17) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L60) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L61) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L5) *style:* **Variable or function name should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L6) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```


Tutorial 1 + Tutorial 2


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 326](https://teamcity.nice.org.uk/viewLog.html?buildId=56837&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) Build time: 00:00:25


Successfully aliased the URL <https://blog-po5siv19u.now.sh> to the following aliases:

* https://blog.cybai.dev
* https://blog.cybai.now.sh
* https://blog-git-master.cybai.now.sh


@da3dsoul oh, so you did it. haha


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 327](https://teamcity.nice.org.uk/viewLog.html?buildId=56838&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) Build time: 00:00:25


Successfully aliased the URL <https://asoiaf-gaewkhc6o.now.sh> to the following aliases:

* https://asoiaf.ahmodosama.now.sh
* https://asoiaf-git-master.ahmodosama.now.sh


Successfully aliased the URL <https://forecast-5gbjsifth.now.sh> to the following aliases:

* https://forecast.autapomorph.now.sh
* https://forecast-git-master.autapomorph.now.sh


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 328](https://teamcity.nice.org.uk/viewLog.html?buildId=56839&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) Build time: 00:00:24


Fixed what I did here but


Trim doesn't work with messages?


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 329](https://teamcity.nice.org.uk/viewLog.html?buildId=56840&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) Build time: 00:00:24


Successfully aliased the URL <https://plankawen-d1wn7gs33.now.sh> to the following aliases:

* https://rashdanrazak.com
* https://plankawen.rashdanrazak91.now.sh
* https://plankawen-git-master.rashdanrazak91.now.sh


The task here was to read your name from the console :)


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 330](https://teamcity.nice.org.uk/viewLog.html?buildId=56841&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **FAILURE**
Summary: Exit code 1 (Step: Set build number (Command Line)) Build time: 00:00:24


you can use %.2f to ensure display only to 2 digits


I think you solved a different exercise here. This is the cuboid exercise


ЕБАЛ РОТ


I opened a pull request already


Successfully aliased the URL <https://asoiaf-mebcsw5b0.now.sh> to the following aliases:

* https://asoiaf.ahmodosama.now.sh
* https://asoiaf-git-master.ahmodosama.now.sh


you should deallocate the memory here with the free function


第二次修改


Successfully aliased the URL <https://builder-ebkxcajylm.now.sh> to the following alias:

* https://builder-staging.now.sh


Бан


Successfully aliased the URL <https://hydrus-web-95jz3j0aj.now.sh> to the following aliases:

* https://hydrus.app
* https://hydrus-web.floogulinc.now.sh
* https://hydrus-web-git-master.floogulinc.now.sh


"Lisättiin sisältöä ignoreen"


The task wanted you to leave the last 5 elements as it was so you can see those are zeroes. But it's okay, I like your solution :)


Successfully aliased the URL <https://star-staff-6xfafvx87.now.sh> to the following aliases:

* https://star-staff.hanterokun.now.sh
* https://star-staff-git-master.hanterokun.now.sh


Failed to alias the deployment: Deployment not found.

[Click here](https://zeit.co/github/deployment?deploymentId=dpl_kDhvQ9eWg3xhstM53uL383XSGSrX) to access the non-aliased deployment.


Тут все-таки будет лучше сеттер, а не аксессор - мы ведь дальше делаем кастомный ридер


Это лучше сделать хэшом типа { номер: поезд } - так эффективней


I think the task here was to read your name from the console :)


trick: you could write if(scanf(%d, &guess_number)) getting rid of "int ret;"


修改


In my opinion the number of exercises you solved this day is very small. Please solve a little bit more exercises when you have free time


nice error handling!


ok


Successfully aliased the URL <https://forecast-liar13ddq.now.sh> to the following aliases:

* https://forecast.autapomorph.now.sh
* https://forecast-git-master.autapomorph.now.sh


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


Done Changes!


It is really causing problems on 32-bit perls. Values are converted to float and truncated...
```
$ perlblead32 -E 'use constant PG_MAX_BIGINT => 9223372036854775807; say PG_MAX_BIGINT;'
9.22337203685478e+18
```
On 64-bit perls it is fine:
```
$ perlblead -E 'use constant PG_MAX_BIGINT => 9223372036854775807; say PG_MAX_BIGINT;'
9223372036854775807
```


This solution only works if you start with lower guesses, than higher guesses. If I first guess with a higher number, than a lower number, then it't not going to work. Try to use a simple

```c
if(asduhad){
}
```


would be nicer with some text output instead of integer output


To be consistent with the package 'lubridate', and to be able to use its functions throughout the package , I think it's best to use it special 'Date' format rather than POSIXct


This is testing file 2


![Screenshot 2019-07-29 at 13 44 12](https://user-images.githubusercontent.com/53823738/62702762-48c53f80-ba05-11e9-93bb-9c1ec25b60ad.png)


Successfully aliased the URL <https://cnp-21ae0lxle.now.sh> to the following aliases:

* https://cnp.alexzabbey.now.sh
* https://cnp-git-master.alexzabbey.now.sh


try to define the PI variable instead of making it a variable :)


OK, You just did :D
I reviewed the commits in chronological order


For the sake of simplicity, I'd rather let the users specify in what format are the dates, rather than offering to guess them. In my opinion, it's very little additional work for the users, and it simplifies greatly the code (and improves its performances)


This is a security enhancement, rather than a patch for a specific exploit. It introduces a backwards incompatible change to the authentication endpoints, and therefore it will not be backported to stable.


you could simplify this statement by writing `return a==b`


you could simplify this statement by writing `return number % 2 == 0`


use the argument 'dateFormat' to call the functions from lubridate, that conveniently have the same names (ymd(), ydm(), ...)


This is really confusing you should write this if in a new line


could use
```C
return !flag;
```
or start flag as 1 and set it 0 in the loop


# Specs execution successful
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### Plans updated

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

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

### Deployments updated

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

|Deployment project |
----|
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Successfully aliased the URL <https://hydrus-web-4nyvo71s0.now.sh> to the following aliases:

* https://hydrus.app
* https://hydrus-web.floogulinc.now.sh
* https://hydrus-web-git-master.floogulinc.now.sh


# push전에 Pull을 사용할때는 다른 사람과 함께 이 프로젝트를 할때 사용한다.


Successfully aliased the URL <https://tech-blog-atcb8bg8g.now.sh> to the following aliases:

* https://nervous-borg.now.sh
* https://dhk.now.sh
* https://tech-blog.kimdhoe.now.sh
* https://tech-blog-git-master.kimdhoe.now.sh


I think this task could be performed by another function. It's not really a matter of date formatting, but rather a choice of how to define an hospital stay


According to your solution only the 0 and the even numbers are prime :)
Please fix this because it's way oversimplifies the task


Nice optimization! Actually it is enough to check up to sqrt(num)


I like the refactor 👍


Successfully aliased the URL <https://agrobot-5m0grxbvc.now.sh> to the following aliases:

* https://agrobot.martinsabiodun94.now.sh
* https://agrobot-git-master.martinsabiodun94.now.sh


add some explanation to the printf, eg.: "length is: %d"


Nais bruh


This is an undefined behavour because you don't have any allocated memory in `sandwich.name`, that's just a pointer. You name property should be a static array and than you could initialize it with the `strcpy` function


Isn't an error being ignore here?


what if str1 is shorter than str2? it could crash!


the sneaky space


Also now, only the wrapper function checkBase() is exported. I follow the best practices guidelines that recommend to export a minimal set of functions to avoid conflicts.


```sh
$ splint sct.c
Splint 3.1.2 --- 20 Feb 2009

sct.c: (in function get_sct_for_screen)
sct.c:63:69: Variable has unknown (implicitly int) type: root
  A variable declaration has no explicit type.  The type is implicitly int.
  (Use -imptype to inhibit warning)
sct.c:83:9: Return value (type int) ignored: XFree(crtc_gamma)
  Result returned by function call is not used. If this is intended, can cast
  result to (void) to eliminate message. (Use -retvalint to inhibit warning)
sct.c:84:6: Fresh storage crtc_gamma not released before scope exit
  A memory leak has been detected. Storage allocated locally is not released
  before the last reference to it is lost. (Use -mustfreefresh to inhibit
  warning)
   sct.c:77:9: Fresh storage crtc_gamma created
sct.c:85:5: Return value (type int) ignored: XFree(res)
sct.c:126:17: Fresh storage res not released before return
   sct.c:64:71: Fresh storage res created
sct.c: (in function sct_for_screen)
sct.c:133:69: Variable has unknown (implicitly int) type: root
sct.c:176:9: Return value (type int) ignored: XFree(crtc_gamma)
sct.c:177:6: Fresh storage crtc_gamma not released before scope exit
   sct.c:165:9: Fresh storage crtc_gamma created
sct.c:179:5: Return value (type int) ignored: XFree(res)
sct.c:180:2: Fresh storage res not released before return
   sct.c:134:71: Fresh storage res created
sct.c: (in function main)
sct.c:185:33: Null storage passed as non-null param: XOpenDisplay (NULL)
  A possibly null pointer is passed as a parameter corresponding to a formal
  parameter with no /*@null@*/ annotation.  If NULL may be used for this
  parameter, add a /*@null@*/ annotation to the function parameter declaration.
  (Use -nullpass to inhibit warning)
sct.c:196:14: Operand of ! is non-boolean (int): !strcmp(argv[1], "-h")
  The operand of a boolean operator is not a boolean. Use +ptrnegate to allow !
  to be used on pointers. (Use -boolops to inhibit warning)
sct.c:196:39: Operand of ! is non-boolean (int): !strcmp(argv[1], "--help")
sct.c:215:5: Return value (type int) ignored: XCloseDisplay(dpy)
sct.c:217:25: Fresh storage dpy not released before return
   sct.c:185:39: Fresh storage dpy created

Finished checking --- 15 code warnings
```


your file is never closed


sorry, it is :)


you should deallocate the memory with the `free` function


````C
counter--; str[counter+1]
```
is just
```C
str[counter]
```


you deallocate your array and after you are using it. It's undefined behaviour


missing null character from the end!


Successfully aliased the URL <https://namae-h3wv9l3d2.now.sh> to the following aliases:

* https://namae.dev
* https://namae.uechi.now.sh
* https://namae-git-master.uechi.now.sh


Like it says in the method name, this will apply an in-place method to `countedLink`, modifying its contents. That's probably unintended.


Why didyou delete this exercise?


Successfully aliased the URL <https://as-tickets-97h5p7kkk.now.sh> to the following aliases:

* https://as-tickets.autapomorph.now.sh
* https://as-tickets-git-master.autapomorph.now.sh


As the exercise says: you sohuld have used variables :)


In this place you should use: export APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=DontWarn, or move this line before RUN block


you should not store it in an integer


Nice solution 👍


Need to address this properly by encoding urls in REST-based classes.


✅ Device tests passed on iOS32b on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2924924)(iOS32b): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/master/200d5bf0a427ca8152681b69fff622dd4d58fc5a/2924924/device-tests/jenkins-results/tests/index.html) ✅

# Test results

# No tests selected.


[bot] 自动构建 [auto-dragalia-75c35eb3.zip](https://circleci.com/gh/NateScarlet/auto-dragalia/484/artifacts/0/home/circleci/project/artifacts/auto-dragalia-75c35eb3.zip)


you defined PI, but still you wrote 3.14 here


Looks like it is indeed. Although, even if an error is detected, we are in a complicated position (possibly with part of the object being pushed while the rest is not).
But yeah, would make sense to catch that error. At least for best practice.


yes sir


much better


You could just write `return age >= 18`


Successfully aliased the URL <https://agrobot-eo2mvj5dc.now.sh> to the following aliases:

* https://agrobot.martinsabiodun94.now.sh
* https://agrobot-git-master.martinsabiodun94.now.sh


# 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)|


Don't assign values inside the printf! It works, but makes the code confusing, and the line way too long.


2nd commit


감사합니다 ^^


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* https://gatsby-theme-carbon.now.sh
* https://gatsby-theme-carbon.carbon-design-system.now.sh
* https://gatsby-theme-carbon-git-master.carbon-design-system.now.sh


Hey @DzikuVx, Could you explain the thoughts behind changing the min and max RADIO_FREQUENCY? Because currently it doesn't match what's configured in the beacon, and I can't get my head around it.

Thanks =)


I feel this function is pointless, you just call another function in it :)


please follow the styleguide


Yeah, better to be internally consistent.


you could use the enum names here instead of integers. It would make the code much nicer


The whole sentence is about logic in `_walk_to_root()`.


what is this fish variable? It's not even declared. Does your code compile?


Build version: __`3.2.1-renovate/husky-3.x.293`__ :crossed_fingers: [`renovate/husky-3.x`](https://github.com/streamich/git-cz/tree/renovate/husky-3.x) on [*Travis*](https://travis-ci.org/streamich/git-cz/builds/122434742) :tada:


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


Successfully aliased the URL <https://ohjelmointi-19-9pbf54rv7.now.sh> to the following aliases:

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


Could write:
```C
car_t car_one = {VOLVO, 1500, 150};
```


you never deallocate memory


Ah, thanks for the clarification. Still probably OK to omit it, I think.


sorry, you do :) I just see your commits in chronological order


Pow function is waaay slower than x*x. For squaring pow should not be used imo.


Is this repository required?


Transporter les bots


css :

/* Nerdy secret: You can use "less" below! Don't tell anybody... */

.github-profile {
	margin: 1rem;
  img {
    width: 75px;
  }
  .info {
    display: inline-block;
    margin-left: 12px;
		.name {
    	font-size: 1.25rem;
      font-weight: bold;
    }
  }
}

form {
	border: thin solid #ddd;
  background-color: #fbfbfb;
  padding: 2rem;
  margin-bottom: 2rem;
  display: flex;
  justify-content: center;
}

.header {
	text-align: center;
  font-size: 1.5rem;
  margin-bottom: 1rem;
}


Successfully aliased the URL <https://mtgpricebackend-93c26gblm.now.sh> to the following aliases:

* https://mtgpricebackend.kevlavery.now.sh
* https://mtgpricebackend-git-master.kevlavery.now.sh


Nice solution. It;s much better then reallocating it every time you add another👍


If there are maven metadata naming conventions, definitely stick to those! Sorry, I wasn’t aware of those.


Successfully aliased the URL <https://topics-manager-lj56x3hhm.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


Instead of this, use
`<dependency>
    <groupId>javax.persistence</groupId>
    <artifactId>javax.persistence-api</artifactId>
    <version>2.2</version>
</dependency>
`


What's the need of this dependency?


Successfully aliased the URL <https://gatsby-theme-carbon-pz2vdj91t.now.sh> to the following aliases:

* https://gatsby-theme-carbon.now.sh
* https://gatsby-theme-carbon.carbon-design-system.now.sh
* https://gatsby-theme-carbon-git-master.carbon-design-system.now.sh


Hi Prof. @tdhock,

I am not sure about how we can move code inside the block as we already have everything inside the block.
We have everything separately defined for each censored types.

Sorry, i am not able to get it. Please explain more.


Update template for adding new Java class.


I suspect this class has been created using Netbeans from database.


Thanks for the update @wuchong


🔥 Device tests completed (Failed) on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2924139)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/alex-mono-bump-d163/17b415b3d1c294eda07f5f6a7c1a2a067ae35c82/2924139/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>10 tests failed, 103 tests passed.</summary>

## Failed tests

 * mscorlib/tvOS - device/Debug: Failed
 * monotouch-test/tvOS - device/Debug (interpreter): Failed
 * [NUnit] Mono BCL tests group 2/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * mscorlib/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * mscorlib/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * mscorlib/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * mscorlib/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * mscorlib/tvOS - device/Release: Failed (MT1032: This application executable might be too large (976 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * mscorlib/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed (MT1032: This application executable might be too large (555 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * mscorlib/tvOS - device/Debug: SGenConc: Failed
</details>


Is this license description required?


MY ART


You don't do anything with the return value :)
Pls finish this exercise but be cautios. You just allocated memory which is enough for a single line. It should look something like this:

```c
matrix = malloc(matrix_size * sizeof(int*))
for(int i = 0; i < matrix_size; ++i){
   int* line = malloc(line_size * sizeof(int));
   for(int j = 0; j < line_size; ++j){
     //add values for line
   }
}
```


Now could not deploy this pull request since it contains the following references to invalid secrets in the `env` sections of the `now.json` file:

* `infinity-service-node-env-canary` (in env: `NODE_ENV)`
* `infinity-service-port-canary` (in env: `PORT)`
* `infinity-service-database-canary` (in env: `DATABASE)`
* `infinity-service-token-secret-canary` (in env: `TOKEN_SECRET)`
* `infinity-service-host-canary` (in env: `HOST)`
* `infinity-service-mailer-apikey-canary` (in env: `MAILER_APIKEY)`
* `infinity-service-mailer-domain-canary` (in env: `MAILER_DOMAIN)`
* `infinity-service-mailer-from-canary` (in env: `MAILER_FROM)`
* `infinity-service-cors-origin-canary` (in env: `CORS_ORIGIN)`

Add those secrets or remove them from the `env` maps in the `now.json` file.


What's this needed for here? And what do relationships have to do with sparse fieldsets?
In fact, I've identified this line as causing a bug (pretty critical actually): if you have sparse fieldsets (fields in the request), relationships key remains empty and when returning multiple results, you have no way how to link included resources (`include` clause) to the proper root resource in a compound document.
Commenting it out seems to resolve this issue...


Time attendance system committed


Successfully aliased the URL <https://namae-kwrccw6vu.now.sh> to the following aliases:

* https://namae.dev
* https://namae.uechi.now.sh
* https://namae-git-master.uechi.now.sh


update


No problem, but the objective of Exercise was to create a simple Java program. The motive is to isolate other technologies from ORM/Hibernate as much as possible.


Build version: __`0.10.0-renovate/husky-3.x.1490`__ :crossed_fingers: [`renovate/husky-3.x`](https://github.com/streamich/ci-scripts/tree/renovate/husky-3.x) on [*Travis*](https://travis-ci.org/streamich/ci-scripts/builds/569336949) :tada:


You could just write `return number1 == number2`


hello，may I have the 'Src_Dst_Paths.dat' file,so I want to see how the program works.


pls follow guideline with the function and variable names


This is NOT a good practice. Sizeof will work in this case, but it is the only exception. Size should be stored before, and not calculated after.


Hi, look like you don't need to rewrite existing `NameInflector`. Just create new class which will be implement `Inflector` interface, define `inflect()` method and use `ServiceProvider` to bind your realisation.

for example:
```php
class YourInflector implements Inflector {
    public function inflect(Command $command)
    {
        return str_replace(
            '\Commands',
            '\Handlers\Commands',
            get_class($command)
        ) . 'Handler';
    }
}

class AppServiceProvider extends ServiceProvider
{
    $this->app->bind(Inflector::class, YourInflector::class);
}
```


Good thing you utilized logger!


You should make a car_type_to_string function and print a string instead of a number here


Remove the target folder and project files.


instead of saying: `car.type != 3` you could write `car.type != TESLA`
Makes your code much more readable


back


pls follow guideline with your function names


Again, please dont use sizeof on arrays!


This option has only one valid value? Then it's hardly a choice anymore.


`std::lower_bound` requires iterated elements to be sorted in ascending order to work properly (this is clearly indicated in its [doc](https://en.cppreference.com/w/cpp/algorithm/lower_bound)).

There is no guarantee the content of the `_panels` list will be sorted here so the swap might fail.

I would rather use the [swapItemsAt](https://doc.qt.io/qt-5/qlist.html#swapItemsAt) method here when Qt >= 5.13 is used.


nit: commit message subject "isntall" -> "install"


Pls solve a little bit more exercises if you have free time. It's not a lot


What's the need of all the eclipse dependencies?


Successfully aliased the URL <https://chronica-4wqimo4ls.now.sh> to the following aliases:

* https://chronica.xyz
* https://www.chronica.xyz
* https://chronica.ckipp01.now.sh
* https://chronica-git-master.ckipp01.now.sh


I used this method to configure the properties to hibernate to the program.


Pls solve dynamic memory allocation exercises. That's really important thing to practice


For easy understanding line_counter should be defined closer to where it is first used.


I'll take care next time sir.


Same as line483.


The first 3 dependencies are just enough.


These are the changes I made at the beginning to the documentation.


Update template for adding new Java class.


Successfully aliased the URL <https://doit-ii9oc7cz6.now.sh> to the following aliases:

* https://doit.umaxfun.now.sh
* https://doit-git-master.umaxfun.now.sh


[R/pir_plot.R:158:7:](https://github.com/richelbilderbeek/pirouette/blob/8f71f85016bcbed50c754aecd09e6fc52e5a7981/R/pir_plot.R#L158) *style:* **Commented code should be removed.**
```r
  #   "twin_candidate" = "#8888FF"  # Light blue
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_plot.R:170:7:](https://github.com/richelbilderbeek/pirouette/blob/8f71f85016bcbed50c754aecd09e6fc52e5a7981/R/pir_plot.R#L170) *style:* **Commented code should be removed.**
```r
  #   "twin_candidate" = "#00FF00"  # Light blue
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_plot.R:180:7:](https://github.com/richelbilderbeek/pirouette/blob/8f71f85016bcbed50c754aecd09e6fc52e5a7981/R/pir_plot.R#L180) *style:* **Commented code should be removed.**
```r
  #   "twin_candidate" = "#AAAAFF"  # Light blue
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_plot.R:192:7:](https://github.com/richelbilderbeek/pirouette/blob/8f71f85016bcbed50c754aecd09e6fc52e5a7981/R/pir_plot.R#L192) *style:* **Commented code should be removed.**
```r
  #   "twin_candidate" = "#AAFFAA"  # Light blue
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_plot.R:210:38:](https://github.com/richelbilderbeek/pirouette/blob/8f71f85016bcbed50c754aecd09e6fc52e5a7981/R/pir_plot.R#L210) *style:* **Commented code should be removed.**
```r
  bindwidth <- 0.1 / sqrt(n_error) # 0.1 * exp(-n_error)
                                     ^~~~~~~~~~~~~~~~~~~
```


It's advisable to use logging rather than sout.


Is it mandatory to implement Serializable interface?


@JuliaRegistrator register()


re-opend connection to mysqlDatabase


Successfully aliased the URL <https://lifechanger-qyrupdzzyj.now.sh> to the following alias:

* https://lifechanger.now.sh


Registration pull request created: [JuliaRegistries/General/2578](https://github.com/JuliaRegistries/General/pull/2578)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.0 -m "<description of version>" e0019e6627216a210d1d7cd4b66a15d9709a7d68
git push origin v0.1.0
```


Close the file!!


Remove target folder, IDE specific files and JAR files, if any.


Much better! ^_^


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* https://marvel-fight-club.paulomontoya5.now.sh
* https://marvel-fight-club-git-master.paulomontoya5.now.sh


I don't remember what the reasom was. You must find it with a typo: heloOthers.


If 7 is the ID, it's better left to the database engine to initialize it.


Missing.


Work Done!


What was the need to swap the author?


Free the array!


Successfully aliased the URL <https://docs-57fq0l05t.zeit.sh> to the following aliases:

* https://docs.zeit.sh
* https://docs-git-master.zeit.sh


Here you are changing the semantics of the previous operation, quoting [QModelIndex](https://doc.qt.io/archives/qt-5.5/qmodelindex.html) doc:

> The model() function returns the model that the index references as a QAbstractItemModel. The child() function is used to examine items held under the index in the model. The sibling() function allows you to traverse items in the model on the same level as the index.

Deprecation warnings tell us the following:
```
warning: 'child' is deprecated: Use QAbstractItemModel::index [-Wdeprecated-declarations]
```

So, the call to `child` must be replaced by:
```cpp
const QModelIndex &child = index.model()->index(i, 0, index);
```


Explain the need of each eclipse dependency.


Good.


This is not the place to ask this question.

Thermal printers usually have a Bluetooth interface and a specific sdk, so indeed this is out of scope (no CUPS server).


Successfully aliased the URL <https://marvel-fight-club-q8r78dddq.now.sh> to the following aliases:

* https://marvel-fight-club.paulomontoya5.now.sh
* https://marvel-fight-club-git-master.paulomontoya5.now.sh


Fhhgfcv


Is this a valid groupId: `unknown.binary`?


i was trying to create my click listener and i have to get recycler view clicked item position from another page. i just thought this should be 'public static' for reach the object. then i search on google and i found more useful and representing pretty way :

https://www.youtube.com/watch?v=69C1ljfDvl0

so, i forgot to change back this line because no need anymore the 'public static' keywords.


Nice but unnecessary.


styleguide pls


No, it's not required, i think it came because i made use of persistence class so IDE must have suggested for adding dependancy so i think it might have been added that time i removed the import package for it but forgot for depedancy.


Looks good after removing generated files.


To be removed.


Update template for adding new Java class.


lol


Always use final String variables when you need to pass constant values.


Use the below "magic_number" for this "10" too!


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @fjetter was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


[R/pir_plot.R:159:7:](https://github.com/richelbilderbeek/pirouette/blob/7f5879d53d38ba2f077070e21ab367a4e1cd36e4/R/pir_plot.R#L159) *style:* **Commented code should be removed.**
```r
  #   "twin_candidate" = "#8888FF"  # Light blue
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_plot.R:171:7:](https://github.com/richelbilderbeek/pirouette/blob/7f5879d53d38ba2f077070e21ab367a4e1cd36e4/R/pir_plot.R#L171) *style:* **Commented code should be removed.**
```r
  #   "twin_candidate" = "#00FF00"  # Light blue
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_plot.R:181:7:](https://github.com/richelbilderbeek/pirouette/blob/7f5879d53d38ba2f077070e21ab367a4e1cd36e4/R/pir_plot.R#L181) *style:* **Commented code should be removed.**
```r
  #   "twin_candidate" = "#AAAAFF"  # Light blue
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_plot.R:193:7:](https://github.com/richelbilderbeek/pirouette/blob/7f5879d53d38ba2f077070e21ab367a4e1cd36e4/R/pir_plot.R#L193) *style:* **Commented code should be removed.**
```r
  #   "twin_candidate" = "#AAFFAA"  # Light blue
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_plot.R:211:38:](https://github.com/richelbilderbeek/pirouette/blob/7f5879d53d38ba2f077070e21ab367a4e1cd36e4/R/pir_plot.R#L211) *style:* **Commented code should be removed.**
```r
  bindwidth <- 0.1 / sqrt(n_error) # 0.1 * exp(-n_error)
                                     ^~~~~~~~~~~~~~~~~~~
```


Yup


Yeah i created the database first so i used entity class build option from netbeans but later i found how to create database from POJO model by adding this property to hibernate config file
"<property name="hbm2ddl.auto">create</property>"


interesting


Could use just
```C
(rand()%50)*2
```


@gigimon глянь, пожалуйста последний #test edit, он не работает и я на нем зависла


Instead use
`<dependency>
    <groupId>javax.persistence</groupId>
    <artifactId>javax.persistence-api</artifactId>
    <version>2.2</version>
</dependency>
`


```C
(int* dst, int* src)
```
is nicer and more conventional


This is a IDE specific file. Please remove it.


No it is not i created this file using netbeans IDE so this all was auto generated


That's the radius, not PI. :D


size should be:
```C
20*sizeof(*src)
```


ID should be generated by the database engine.


you can create an array with labels of link and its href. And then use map in order to repeat a tag.
For example,
```
const footerLink = [{ label: 'About us', href: '#'}]
```

then
```
{
footerLink.map((footer) => (<a className="pr-3 text-danger" href={footer.href}>{footer.label}</a>));
```


OH yeah , I think that is very crazy.....


Missing generated value annotation.


Successfully aliased the URL <https://nextjs-vi46h0mzn.now.sh> to the following aliases:

* https://nextjs.eyale.now.sh
* https://nextjs-git-master.eyale.now.sh


Please explain the need for license description.


It was a temporary repository created by netbeans i didn't add it


Successfully aliased the URL <https://marvel-fight-club-c2d5xgtwb.now.sh> to the following aliases:

* https://marvel-fight-club.paulomontoya5.now.sh
* https://marvel-fight-club-git-master.paulomontoya5.now.sh


已经删除 rimraf 依赖，直接用 midway 内置的删除机制。


Should `PRIsize` be remove also in libpcap?


repetition could be an integer, not a pointer. It would be easier to understand, and would run just as fast.


These gs are not signed, there is no g evaluation in comp_i.
Evaluation fo clustering should be done in form_P__, per scaled g, not per G?


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


Update template for adding new Java class.


Always use final String variables when you need to pass constant values.


Ok, I see it now.


Use parentheses
```C
counter * (*repetition)
```
when multiplication and dereferencing is in the same expression. It is confusing like this.


Remove target folder, IDE specific files and JAR files, if any.


Successfully aliased the URL <https://astragalomancy-6abc9tbqs.now.sh> to the following aliases:

* https://astragalomancy.willytan-96.now.sh
* https://astragalomancy-git-master.willytan-96.now.sh


Explain the usage of this dependency.


It's advisable to use logging rather than sout.


Successfully aliased the URL <https://whatcolourhoodieiskevinwearingtodaycom-725k343eb.now.sh> to the following aliases:

* https://whatcolourhoodieiskevinwearingtoday.com
* https://whatcolourhoodieiskevinwearingtodaycom.kevincarrogan.now.sh
* https://whatcolourhoodieiskevinwearingtodaycom-git-master.kevincarrogan.now.sh


Good thing you added the length attribute.


Could you please update this to target all party members instead? This would buff the enemy otherwise


분석을위해가져간다눙


I think

> added x <- NULL; rm(x) for the check in pir_plot

would be a more appropriate commit message, it would be friendlier to the R maintainers. There is a reason you need to do this: fix it and everybody will love you!


Care to send in a PR?


atleast u will attach bootstrap  file to it


Great!


Could use
```C
#define LEVI "Levi"
```
or
```C
char levi = "Levi";
```
and use the %s of the printf.
But this is also ok.


Violation of camel case naming convention.


Successfully aliased the URL <https://marvel-fight-club-1phbzliij.now.sh> to the following aliases:

* https://marvel-fight-club.paulomontoya5.now.sh
* https://marvel-fight-club-git-master.paulomontoya5.now.sh


omg insane h4x0r


By far, the only project to have the least minimum number of dependencies. Great


Nice use of .2 formatting!


Note: as issues are disabled, I have to comment this commit instead.

Please add my account in the authors.md file as https://github.com/cmangos/mangos-wotlk/commits/master?author=jackpoz shows there are some of my commits in this project.
You might want to include also that some code changes have been merged from other projects, with a list of the projects :)


> Great work 👍

Thanks @hagronnestad. It's my first endeavor into VS 2019, so keep that in mind...

I'm focused on getting the ZiLib basics for V5/6 working. Not really taking backwards compatibility into account... We can work on that later for the GUI.

The code might not be optimal or following best practices, but I take any pointers from a pro :-D


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No manual initialization of ID values.


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No


Some text output would be nice like
```C
printf("Added: %d, added);
```


okay sir


postgres dependency -> For PostgreSQL database
hibernate-core dependency -> For Hibernate Core
javaee-web-api -> For NotNull Constraint Validation (import  javax.validation.constraints.NotNull )


fix-kiva-init (matthew-larson) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

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


Sure Sir..
I'll take care from now


Can you send this `owner` concern to its own parent contract?


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This patch just makes sure to return from try_to_free_dmap_chunks(). fuse_dax_free_mem_worker() will reschedule the job again.


fix-kiva-init (matthew-larson) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (9 of 9 tests passed, 0 test warnings)

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


I have modified the code as per your corrections. Let me know you find any corrections still.


Maybe a name other than `beneficiaries`?


@shunjou any chance of making a build with the 4.19 kernel for August?


I'll put it in .gitignore file
ok...


```C
%.0f
```
would produce the result expected by the comment above.


>  But your idea (IAsset contains pointer to its metadata) is even cleaner IMO

Let's go with that because then we won't have the stupid issues with always caching metadata thing above.


[R/pir_plot.R:183:38:](https://github.com/richelbilderbeek/pirouette/blob/21d3d9ed12e6c1b56376b23832ca4aab679608e7/R/pir_plot.R#L183) *style:* **Commented code should be removed.**
```r
  bindwidth <- 0.1 / sqrt(n_error) # 0.1 * exp(-n_error)
                                     ^~~~~~~~~~~~~~~~~~~
```


hello sir,
       Only two main dependencies "hibernate-core" and "postgresql"
included in pom.xml file, but other two dependencies are included by
default while i build the maven.


You'll also need to drop it in the travis yml file


You don't need to deploy `SafeMath` because all its functions are `internal`.
Plus, you would have to `.link` it.


I imagine they left it in for future expansion purposes. Mirrored it accordingly.