Last updated: 2018-07-17

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  • ✖ R Markdown file: uncommitted changes The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

  • ✔ Environment: empty

    Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

  • ✔ Seed: set.seed(20180716)

    The command set.seed(20180716) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

  • ✔ Session information: recorded

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  • ✔ Repository version: 54a8a35

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    code/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    docs/.DS_Store
    Ignored:    figures/

Untracked files:
    Untracked:  .drake/
    Untracked:  analysis/model_functions.Rmd
    Untracked:  analysis/plot_model.Rmd
    Untracked:  analysis/run_model.Rmd
    Untracked:  data/mating_type_tables/
    Untracked:  data/sim_results/
    Untracked:  manuscript/
    Untracked:  output/my_manuscript.pdf
    Untracked:  output/supplementary_material.pdf
    Untracked:  run.R
    Untracked:  sex_shredder.Rproj
    Untracked:  sim_results/

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   analysis/index.Rmd
    Deleted:    myproject.Rproj
    Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes. 

Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Attaching package: 'reshape2'
The following object is masked from 'package:tidyr':

    smiths

Define the parameter space

parameters <- expand.grid(
  generations = 1000,
  W_shredding_rate = c(0, 0.95),
  Z_conversion_rate = c(0, 0.95),
  Zr_creation_rate = c(0, 0.01, 0.1),
  Zr_mutation_rate = c(0.0, 0.0001),
  Wr_mutation_rate = c(0.0, 0.0001),
  cost_Zdrive_female = c(0.01, 0.01, 0.5),
  cost_Zdrive_male = 0.01,
  cost_Wr = 0.01,
  cost_Zr = 0.01,
  cost_A = 0.01,
  cost_B = 0.01,
  n_patches = 20,
  male_migration_prob = c(0.01, 0.5),
  female_migration_prob = c(0.01, 0.5),
  max_fecundity = 20,
  softness = c(0, 0.5, 1),
  male_weighting = 1,
  density_dependence_shape = 0.5,
  carrying_capacity = 10000,
  initial_pop_size = 5000,
  initial_Zdrive = 0.05,
  initial_Zr = 0.01,
  initial_Wr = 0.00,
  initial_A = 0.00,
  initial_B = 0.00,
  realisations = 1:100
)

Run the model on each parameter space

do_all_parameters(parameters, over_write = FALSE, cores = 6)
Warning in mclapply(i, fun, cores): all scheduled cores encountered errors
in user code
[1] "Done all parameters"
combine_results_files() %>% saveRDS(file = "data/all_results.rds")

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] bindrcpp_0.2.2 reshape2_1.4.3 stringr_1.3.1  tidyr_0.8.1   
[5] purrr_0.2.5    dplyr_0.7.6   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      rstudioapi_0.7    knitr_1.20       
 [4] bindr_0.1.1       whisker_0.3-2     magrittr_1.5     
 [7] workflowr_1.1.1   tidyselect_0.2.4  R6_2.2.2         
[10] rlang_0.2.1       plyr_1.8.4        tools_3.5.1      
[13] R.oo_1.22.0       git2r_0.22.1      htmltools_0.3.6  
[16] yaml_2.1.19       rprojroot_1.3-2   digest_0.6.15    
[19] assertthat_0.2.0  tibble_1.4.2      crayon_1.3.4     
[22] R.utils_2.6.0     glue_1.2.0        evaluate_0.10.1  
[25] rmarkdown_1.10    stringi_1.2.3     pillar_1.3.0     
[28] compiler_3.5.1    backports_1.1.2   R.methodsS3_1.7.1
[31] pkgconfig_2.0.1

This reproducible R Markdown analysis was created with workflowr 1.1.1