R/write_test_data.R

In cstawitz/RMAS: Read and Write Input and Output for MAS Model

#' This function writes dummy data that is used in the "Introduction" vignette
#' @name write_test_data
#' @param nyears scalar, number of years in the model
#' @param ewaa_vector vector of empirical weight-at-age, length nyears * nages
#' @param catch_index_v list with two entries, one named "values" and one named "errors" corresponding to catch, each list entry has length nyears
#' @param survey_index_v list with two entries, one named "values" and one named "errors" corresponding to index, each list entry has length nyears
#' @param catch_comp_csv a string with the name of the .csv file containing the catch age composition data, if NULL (the default) dummy data are used
#' @param survey_comp_csv a string with the name of the .csv file containing the survey age composition data, if NULL (the default) dummy data are used
write_test_data <- function(nyears, ewaa_vector = NULL, catch_index_v = NULL, survey_index_v = NULL, catch_comp_csv = NULL, survey_comp_csv = NULL){

  if(!is.null(ewaa_vector)){
    empirical_weight <- ewaa_vector
  } else{
empirical_weight<- c(0.5306555, 1.1963283, 2.0582654, 3.0349873, 4.0552124, 5.0646975, 6.0262262, 6.9169206, 7.7248909, 8.4461128, 9.0818532, 9.636695, 
    rep(c(0.5306555, 1.1963283, 2.0582654, 3.0349873, 4.0552124, 5.0646975, 6.0262262, 6.9169206, 7.7248909, 8.4461128, 9.0818532, 9.636695),29)) 
  }
  
  if(!is.null(catch_index_v)){
    if(!names(catch_index_v)==c("values","error")){
      stop("Error: catch index must have names of values and error.")
    } else{
      if((length(catch_index_v$values)!=nyears)|(length(catch_index_v$error))){
        stop("Error: catch_index$values and catch_index$error must have one entry corresponding to each year.")
      }
    }
    catch_index <- catch_index_v
  } else{
    
    catch_index <- list("values"=c(160.9729922, 469.039834, 767.2392242, 995.4491466, 760.1287713, 1330.812956, 
                                   1293.228597, 2476.815314, 1325.554509, 1523.691282, 1621.524464, 1611.573564, 
                                   1113.866103, 1538.117519, 1508.500687, 1266.046142, 2238.86148, 1607.917363, 
                                   1453.868581, 1295.528013, 1613.812022, 1072.966713, 1636.167979, 1210.822294, 
                                   1129.045115, 964.3269465, 923.3521247, 1218.20288, 881.6275361, 1270.847518), "error"=rep(0.01,30))
  }
  
  if(!is.null(survey_index_v)){
    if(!names(survey_index_v)==c("values","error")){
      stop("Error: survey index must have names of values and error.")
    } else{
      if((length(survey_index_v$values)!=nyears)|(length(survey_index_v$error))){
        stop("Error: survey_index$values and survey_index$error must have one entry corresponding to each year.")
      }
    }
    survey_index <- survey_index_v
  } else{
    
    survey_index<- list("values" = c(1.769444064, 1.507772568, 1.533016092, 1.616248667, 1.383168775, 1.616386391, 1.412438781, 1.312749108, 
                                     1.196086699, 1.100803192, 1.237393383, 1.059375707, 0.960531835, 0.975227232, 1.029677793, 0.859372577, 
                                     0.920958391, 0.702236849, 0.910970335, 0.671124274, 0.771789588, 0.636336668,  0.602957579, 0.66842653, 
                                     0.501908084, 0.462440308, 0.537562886, 0.564409646, 0.566285357, 0.495778669),
                        "error"=rep(0.2, 30))
    
  }

if(!is.null(catch_comp_csv)){
catch_comp<- read.csv(catch_comp_csv)
} else{
  
  catch_comp <- list("values"=c(0.075, 0.085, 0.105, 0.11, 0.1, 0.08, 0.1, 0.065, 0.065, 0.005, 0.055, 0.155,
                                                  0.07, 0.15, 0.125, 0.13, 0.095, 0.04, 0.07, 0.075, 0.025, 0.055, 0.05, 0.115,
                                                  0.075, 0.155, 0.11, 0.11, 0.135, 0.045, 0.075, 0.065, 0.04, 0.035, 0.025, 0.13,
                                                  0.075, 0.09, 0.12, 0.165, 0.095, 0.07, 0.09, 0.06, 0.06, 0.03, 0.02, 0.125,
                                                  0.115, 0.05, 0.11, 0.175, 0.1, 0.04, 0.085, 0.05, 0.045, 0.03, 0.035, 0.165,
                                                  0.075, 0.14, 0.12, 0.085, 0.085, 0.105, 0.085, 0.06, 0.055, 0.04, 0.025, 0.125,
                                                  0.09, 0.125, 0.195, 0.06, 0.105, 0.075, 0.055, 0.095, 0.055, 0.035, 0.015, 0.095,
                                                  0.065, 0.11, 0.135, 0.195, 0.075, 0.07, 0.095, 0.035, 0.055, 0.03, 0.015, 0.12,
                                                  0.105, 0.165, 0.155, 0.155, 0.12, 0.065, 0.05, 0.05, 0.02, 0.015, 0.015, 0.085,
                                                  0.07, 0.115, 0.145, 0.125, 0.17, 0.105, 0.035, 0.04, 0.045, 0.03, 0.02, 0.1,
                                                  0.085, 0.18, 0.115, 0.14, 0.095, 0.07, 0.075, 0.055, 0.02, 0.025, 0.045, 0.095,
                                                  0.105, 0.13, 0.16, 0.095, 0.13, 0.06, 0.085, 0.085, 0.03, 0.015, 0.025, 0.08,
                                                  0.1, 0.135, 0.16, 0.135, 0.09, 0.1, 0.065, 0.07, 0.055, 0.01, 0.01, 0.07,
                                                  0.085, 0.12, 0.18, 0.17, 0.11, 0.06, 0.075, 0.035, 0.055, 0.03, 0.01, 0.07,
                                                  0.075, 0.145, 0.215, 0.09, 0.135, 0.085, 0.06, 0.025, 0.055, 0.015, 0.02, 0.08,
                                                  0.125, 0.105, 0.205, 0.125, 0.095, 0.09, 0.05, 0.035, 0.045, 0.035, 0.02, 0.07,
                                                  0.12, 0.14, 0.155, 0.145, 0.125, 0.075, 0.075, 0.03, 0.045, 0.025, 0.01, 0.055,
                                                  0.085, 0.215, 0.16, 0.12, 0.12, 0.04, 0.075, 0.075, 0.04, 0.015, 0.03, 0.025,
                                                  0.105, 0.135, 0.22, 0.18, 0.095, 0.085, 0.065, 0.05, 0.02, 0.015, 0.005, 0.025,
                                                  0.12, 0.14, 0.16, 0.215, 0.135, 0.035, 0.065, 0.04, 0.015, 0.015, 0.01, 0.05,
                                                  0.16, 0.14, 0.145, 0.14, 0.125, 0.085, 0.06, 0.045, 0.02, 0.025, 0.01, 0.045,
                                                  0.165, 0.265, 0.135, 0.135, 0.06, 0.07, 0.055, 0.02, 0.01, 0.03, 0.015, 0.04,
                                                  0.11, 0.245, 0.23, 0.085, 0.11, 0.09, 0.055, 0.025, 0, 0.01, 0, 0.04,
                                                  0.165, 0.235, 0.23, 0.17, 0.055, 0.06, 0.03, 0.02, 0.005, 0.005, 0.01, 0.015,
                                                  0.165, 0.155, 0.205, 0.18, 0.13, 0.06, 0.035, 0.02, 0.02, 0.005, 0.005, 0.02,
                                                  0.12, 0.185, 0.19, 0.14, 0.185, 0.085, 0.02, 0.015, 0.03, 0.015, 0.005, 0.01,
                                                  0.165, 0.185, 0.19, 0.13, 0.11, 0.085, 0.05, 0.03, 0.01, 0.025, 0, 0.02,
                                                  0.19, 0.2, 0.135, 0.175, 0.09, 0.07, 0.07, 0.045, 0.01, 0, 0, 0.015,
                                                  0.18, 0.22, 0.155, 0.135, 0.125, 0.065, 0.07, 0.025, 0.015, 0.005, 0.005, 0,
                                                  0.145, 0.255, 0.215, 0.135, 0.07, 0.08, 0.02, 0.035, 0.02, 0.005, 0.005, 0.015),
                                           "sample_size"=rep(200,30))
  
  #write.csv(catch_comp, file="inst/extdata/catch_comp_1.csv")
                           
}

if(!is.null(survey_comp_csv)){
survey_comp <- read.csv(survey_comp_csv)
} else{
survey_comp<- list("values"=c(0.04, 0.12, 0.155, 0.15, 0.15, 0.06, 0.085, 0.03, 0.035, 0.03, 0.01, 0.135,
                      0.07, 0.135, 0.135, 0.095, 0.11, 0.07, 0.105, 0.045, 0.045, 0.025, 0.04, 0.125,
                      0.085, 0.165, 0.12, 0.13, 0.115, 0.065, 0.045, 0.045, 0.04, 0.045, 0.01, 0.135,
                      0.05, 0.12, 0.195, 0.15, 0.125, 0.085, 0.06, 0.03, 0.035, 0.035, 0.025, 0.09,
                      0.04, 0.17, 0.12, 0.17, 0.105, 0.07, 0.045, 0.065, 0.035, 0.045, 0.01, 0.125,
                      0.085, 0.155, 0.13, 0.155, 0.105, 0.055, 0.06, 0.055, 0.045, 0.045, 0.01, 0.1,
                      0.085, 0.17, 0.235, 0.08, 0.13, 0.065, 0.055, 0.045, 0.025, 0.01, 0.04, 0.06,
                      0.07, 0.125, 0.2, 0.18, 0.07, 0.075, 0.065, 0.03, 0.045, 0.02, 0.02, 0.1,
                      0.07, 0.165, 0.145, 0.135, 0.15, 0.07, 0.06, 0.05, 0.035, 0.015, 0.025, 0.08,
                      0.065, 0.16, 0.16, 0.12, 0.14, 0.085, 0.055, 0.03, 0.035, 0.05, 0.01, 0.09,
                      0.105, 0.205, 0.14, 0.12, 0.08, 0.105, 0.055, 0.04, 0.02, 0.025, 0.02, 0.085,
                      0.09, 0.21, 0.155, 0.095, 0.12, 0.07, 0.07, 0.05, 0.04, 0.02, 0.02, 0.06,
                      0.115, 0.1, 0.19, 0.175, 0.09, 0.075, 0.055, 0.045, 0.025, 0.005, 0.02, 0.105,
                      0.065, 0.16, 0.18, 0.155, 0.095, 0.055, 0.075, 0.025, 0.025, 0.04, 0.025, 0.1,
                      0.09, 0.205, 0.15, 0.095, 0.15, 0.1, 0.07, 0.045, 0.01, 0.03, 0.02, 0.035,
                      0.09, 0.16, 0.18, 0.165, 0.095, 0.11, 0.035, 0.045, 0.025, 0.02, 0.025, 0.05,
                      0.14, 0.19, 0.17, 0.145, 0.065, 0.06, 0.07, 0.045, 0.03, 0.015, 0.005, 0.065,
                      0.055, 0.225, 0.28, 0.115, 0.105, 0.07, 0.045, 0.035, 0.015, 0.01, 0.015, 0.03,
                      0.08, 0.155, 0.255, 0.2, 0.085, 0.055, 0.025, 0.02, 0.035, 0.015, 0.025, 0.05,
                      0.07, 0.23, 0.175, 0.145, 0.135, 0.045, 0.06, 0.04, 0.035, 0.02, 0.015, 0.03,
                      0.16, 0.205, 0.21, 0.105, 0.1, 0.045, 0.05, 0.035, 0.015, 0.02, 0.005, 0.05,
                      0.12, 0.255, 0.16, 0.09, 0.095, 0.105, 0.065, 0.025, 0.025, 0.015, 0.005, 0.04,
                      0.115, 0.225, 0.29, 0.125, 0.065, 0.055, 0.03, 0.03, 0.015, 0.01, 0.015, 0.025,
                      0.095, 0.23, 0.24, 0.2, 0.085, 0.025, 0.04, 0.02, 0.01, 0.025, 0.005, 0.025,
                      0.11, 0.23, 0.185, 0.19, 0.125, 0.055, 0.025, 0.025, 0.02, 0.01, 0, 0.025,
                      0.08, 0.265, 0.165, 0.13, 0.185, 0.075, 0.055, 0.015, 0.01, 0.015, 0, 0.005,
                      0.125, 0.225, 0.275, 0.135, 0.1, 0.06, 0.045, 0.02, 0.005, 0, 0.005, 0.005,
                      0.13, 0.285, 0.185, 0.195, 0.1, 0.025, 0.045, 0.02, 0, 0, 0.005, 0.01,
                      0.135, 0.3, 0.245, 0.1, 0.1, 0.035, 0.02, 0.025, 0.025, 0.01, 0.005, 0,
                      0.11, 0.285, 0.225, 0.17, 0.05, 0.065, 0.02, 0.01, 0.035, 0.01, 0.005, 0.015), "sample_size"=rep(200,30))
#write.csv(survey_comp,"inst/extdata/survey_comp_1.csv")
}

return(list("ewaa"=empirical_weight,
            "catch_index"=catch_index,
            "survey_index"=survey_index,
            "catch_comp"=catch_comp,
            "survey_comp"=survey_comp))
}