WritingSSfiles
Christine Stawitz
May 14, 2019
Introduction
This page discusses reading in an existing stock assessment file and replacing the data values with those from the atlantisom package. To read in the Stock Synthesis files, first ensure you have the latest version of r4ss. You will need to ensure the relevant Stock Synthesis files are stored in the inst/extdata/ folder, with each species example in its own folder.
devtools::install_github("r4ss/r4ss", dependencies = FALSE)Sardine example
Dummy files are in the package directory; use r4ss to load the dummy data file. Use the relevant species config file to load the configuration variables for each run. Note: this script will extract conditional age-at-length data, length composition data, and a CPUE in biomass for one survey during the specified time interval, and age composition data, length composition data, and catch in numbers from a single fishery. The timing and duration of the survey and fishery should be set in the config file. Unless otherwise stated, numbers going into Stock Synthesis are in thousands of fish. Weight of a single fish is in grams or kilograms, and weight of biomass is in metric tons. We assume a single sex model with a sex ratio fixed at 0.5 - different assumptions require modifying the Stock Synthesis control file. This script only runs with Stock Synthesis 3.30.
## Loading required package: r4ss## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 45## N_agebins: 10## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999Below, we can see the structure of the catch and CPUE data
names(stocksynthesis.data$catch) <- names(stocksynthesis.data$CPUE)
stocksynthesis.data$CPUE## year seas index obs se_log
## 1 30 7 2 474849 0.1
## 2 31 7 2 435870 0.1
## 3 32 7 2 464053 0.1
## 4 33 7 2 548864 0.1
## 5 34 7 2 424040 0.1
## 6 35 7 2 481492 0.1
## 7 36 7 2 461319 0.1
## 8 37 7 2 450456 0.1
## 9 38 7 2 515847 0.1
## 10 39 7 2 482477 0.1
## 11 40 7 2 401372 0.1
## 12 41 7 2 446629 0.1
## 13 42 7 2 408634 0.1
## 14 43 7 2 433813 0.1
## 15 44 7 2 443037 0.1
## 16 45 7 2 444108 0.1
## 17 46 7 2 457172 0.1
## 18 47 7 2 469495 0.1
## 19 48 7 2 379074 0.1
## 20 49 7 2 389817 0.1
## 21 50 7 2 517128 0.1
## 22 51 7 2 431072 0.1
## 23 52 7 2 490912 0.1
## 24 53 7 2 404384 0.1
## 25 54 7 2 431618 0.1
## 26 55 7 2 488595 0.1
## 27 56 7 2 447789 0.1
## 28 57 7 2 373234 0.1
## 29 58 7 2 414667 0.1
## 30 59 7 2 483665 0.1
## 31 60 7 2 403390 0.1
## 32 61 7 2 430583 0.1
## 33 62 7 2 426524 0.1
## 34 63 7 2 488542 0.1
## 35 64 7 2 470796 0.1
## 36 65 7 2 430163 0.1
## 37 66 7 2 408388 0.1
## 38 67 7 2 467931 0.1
## 39 68 7 2 478608 0.1
## 40 69 7 2 375026 0.1
## 41 70 7 2 393498 0.1
## 42 71 7 2 367955 0.1
## 43 72 7 2 345888 0.1
## 44 73 7 2 416815 0.1
## 45 74 7 2 460000 0.1
## 46 75 7 2 432399 0.1
## 47 76 7 2 479237 0.1
## 48 77 7 2 488663 0.1
## 49 78 7 2 400375 0.1
## 50 79 7 2 404726 0.1We can next look at age composition data
stocksynthesis.data$agecomp## Yr Seas FltSvy Gender Part Ageerr Lbin_lo Lbin_hi Nsamp a1
## 1 30 7 2 0 0 1 10 11 0.002 0.002
## 2 30 7 2 0 0 1 11 12 0.0131 0.0131
## 3 30 7 2 0 0 1 12 13 0.0394 0.0394
## 4 30 7 2 0 0 1 13 14 0.0627 0.0627
## 5 30 7 2 0 0 1 14 15 0.0616 0.0586
## 6 30 7 2 0 0 1 15 16 0.0445 0.0344
## 7 30 7 2 0 0 1 16 17 0.0375 0.0142
## 8 30 7 2 0 0 1 17 18 0.0414 0.004
## 9 30 7 2 0 0 1 18 19 0.0455 0.001
## 10 30 7 2 0 0 1 19 20 0.0394 0
## 11 30 7 2 0 0 1 20 21 0.0314 0
## 12 30 7 2 0 0 1 21 22 0.0273 0
## 13 30 7 2 0 0 1 22 23 0.0273 0
## 14 30 7 2 0 0 1 23 24 0.0293 0
## 15 30 7 2 0 0 1 24 25 0.0333 0
## 16 30 7 2 0 0 1 25 26 0.0324 0
## 17 30 7 2 0 0 1 26 27 0.0313 0
## 18 30 7 2 0 0 1 27 28 0.0283 0
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## 20 30 7 2 0 0 1 29 30 0.0264 0
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## 47 31 7 2 0 0 1 13 14 0.0677 0.0677
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## 1629 0 0.002 0.0162 0.0081 0.002 0 0 0 0
## 1630 0 0.001 0.0131 0.0101 0.003 0.001 0 0 0
## 1631 0 0 0.0101 0.0111 0.004 0.001 0 0 0
## 1632 0 0 0.0071 0.0111 0.0061 0.002 0 0 0
## 1633 0 0 0.004 0.0101 0.0071 0.003 0.001 0 0
## 1634 0 0 0.002 0.0081 0.0071 0.004 0.001 0 0
## 1635 0 0 0.001 0.0061 0.0081 0.0051 0.001 0 0
## 1636 0 0 0.001 0.004 0.0071 0.0061 0.002 0.001 0
## 1637 0 0 0 0.003 0.0061 0.0061 0.002 0.001 0
## 1638 0 0 0 0.002 0.0051 0.0061 0.003 0.001 0
## 1639 0 0 0 0.001 0.004 0.0061 0.003 0.002 0.001
## 1640 0 0 0 0.001 0.003 0.0051 0.003 0.002 0.001
## 1641 0 0 0 0 0.002 0.004 0.003 0.002 0.001
## 1642 0 0 0 0 0.001 0.003 0.002 0.002 0.001
## 1643 0 0 0 0 0.001 0.002 0.002 0.002 0.001
## 1644 0 0 0 0 0.001 0.002 0.002 0.002 0.001
## 1645 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1646 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1647 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1648 0 0 0 0 0 0 0 0.001 0.001
## 1649 0 0 0 0 0 0 0 0.001 0
## 1650 0 0 0 0 0 0 0 0 0
## 1651 0 0 0 0 0 0 0 0 0
## 1652 0 0 0 0 0 0 0 0 0
## 1653 0 0 0 0 0 0 0 0 0
## 1654 0.003 0 0 0 0 0 0 0 0
## 1655 0.0111 0 0 0 0 0 0 0 0
## 1656 0.0242 0 0 0 0 0 0 0 0
## 1657 0.0373 0 0 0 0 0 0 0 0
## 1658 0.0404 0.001 0 0 0 0 0 0 0
## 1659 0.0333 0.003 0 0 0 0 0 0 0
## 1660 0.0212 0.0071 0 0 0 0 0 0 0
## 1661 0.0111 0.0131 0 0 0 0 0 0 0
## 1662 0.005 0.0202 0.001 0 0 0 0 0 0
## 1663 0.002 0.0252 0.002 0 0 0 0 0 0
## 1664 0.001 0.0262 0.005 0 0 0 0 0 0
## 1665 0 0.0232 0.0091 0.001 0 0 0 0 0
## 1666 0 0.0182 0.0131 0.001 0 0 0 0 0
## 1667 0 0.0121 0.0161 0.003 0 0 0 0 0
## 1668 0 0.0071 0.0182 0.005 0 0 0 0 0
## 1669 0 0.004 0.0182 0.0071 0.001 0 0 0 0
## 1670 0 0.002 0.0161 0.0091 0.002 0 0 0 0
## 1671 0 0.001 0.0121 0.0111 0.003 0.001 0 0 0
## 1672 0 0 0.0091 0.0121 0.004 0.001 0 0 0
## 1673 0 0 0.0061 0.0121 0.0061 0.002 0 0 0
## 1674 0 0 0.004 0.0101 0.0071 0.002 0.001 0 0
## 1675 0 0 0.002 0.0081 0.0071 0.003 0.001 0 0
## 1676 0 0 0.001 0.0061 0.0071 0.004 0.002 0.001 0
## 1677 0 0 0.001 0.005 0.0071 0.004 0.002 0.001 0
## 1678 0 0 0 0.003 0.0061 0.005 0.003 0.001 0.001
## 1679 0 0 0 0.002 0.005 0.005 0.003 0.002 0.001
## 1680 0 0 0 0.001 0.004 0.004 0.004 0.002 0.001
## 1681 0 0 0 0.001 0.003 0.004 0.004 0.002 0.001
## 1682 0 0 0 0 0.002 0.003 0.003 0.002 0.002
## 1683 0 0 0 0 0.001 0.002 0.003 0.002 0.002
## 1684 0 0 0 0 0.001 0.002 0.003 0.002 0.002
## 1685 0 0 0 0 0 0.001 0.002 0.002 0.002
## 1686 0 0 0 0 0 0.001 0.002 0.002 0.002
## 1687 0 0 0 0 0 0.001 0.001 0.001 0.002
## 1688 0 0 0 0 0 0 0.001 0.001 0.001
## 1689 0 0 0 0 0 0 0.001 0.001 0.001
## 1690 0 0 0 0 0 0 0 0.001 0.001
## 1691 0 0 0 0 0 0 0 0 0.001
## 1692 0 0 0 0 0 0 0 0 0
## 1693 0 0 0 0 0 0 0 0 0
## 1694 0 0 0 0 0 0 0 0 0
## 1695 0.001 0 0 0 0 0 0 0 0
## 1696 0.0041 0 0 0 0 0 0 0 0
## 1697 0.0132 0 0 0 0 0 0 0 0
## 1698 0.0294 0 0 0 0 0 0 0 0
## 1699 0.0437 0 0 0 0 0 0 0 0
## 1700 0.0467 0.001 0 0 0 0 0 0 0
## 1701 0.0376 0.003 0 0 0 0 0 0 0
## 1702 0.0234 0.0071 0 0 0 0 0 0 0
## 1703 0.0122 0.0142 0 0 0 0 0 0 0
## 1704 0.0051 0.0213 0.001 0 0 0 0 0 0
## 1705 0.002 0.0264 0.002 0 0 0 0 0 0
## 1706 0.001 0.0264 0.0051 0 0 0 0 0 0
## 1707 0 0.0234 0.0091 0.001 0 0 0 0 0
## 1708 0 0.0173 0.0132 0.001 0 0 0 0 0
## 1709 0 0.0112 0.0162 0.002 0 0 0 0 0
## 1710 0 0.0071 0.0183 0.0041 0 0 0 0 0
## 1711 0 0.003 0.0173 0.0061 0.001 0 0 0 0
## 1712 0 0.002 0.0152 0.0081 0.002 0 0 0 0
## 1713 0 0.001 0.0122 0.0091 0.003 0 0 0 0
## 1714 0 0 0.0081 0.0102 0.0041 0.001 0 0 0
## 1715 0 0 0.0051 0.0091 0.0051 0.001 0 0 0
## 1716 0 0 0.003 0.0081 0.0061 0.002 0.001 0 0
## 1717 0 0 0.002 0.0071 0.0061 0.002 0.001 0.001 0
## 1718 0 0 0.001 0.0051 0.0061 0.003 0.002 0.001 0
## 1719 0 0 0.001 0.0041 0.0061 0.003 0.002 0.001 0
## 1720 0 0 0 0.002 0.0051 0.003 0.003 0.002 0
## 1721 0 0 0 0.001 0.0041 0.003 0.003 0.002 0
## 1722 0 0 0 0.001 0.003 0.003 0.003 0.003 0.001
## 1723 0 0 0 0 0.002 0.003 0.003 0.003 0.001
## 1724 0 0 0 0 0.001 0.002 0.003 0.003 0.001
## 1725 0 0 0 0 0.001 0.002 0.003 0.003 0.001
## 1726 0 0 0 0 0.001 0.001 0.002 0.003 0.001
## 1727 0 0 0 0 0 0.001 0.002 0.003 0.001
## 1728 0 0 0 0 0 0.001 0.001 0.002 0.001
## 1729 0 0 0 0 0 0 0.001 0.002 0.001
## 1730 0 0 0 0 0 0 0.001 0.001 0.001
## 1731 0 0 0 0 0 0 0.001 0.001 0.001
## 1732 0 0 0 0 0 0 0 0.001 0
## 1733 0 0 0 0 0 0 0 0.001 0
## 1734 0 0 0 0 0 0 0 0 0
## 1735 0 0 0 0 0 0 0 0 0
## 1736 0 0 0 0 0 0 0 0 0
## 1737 0.001 0 0 0 0 0 0 0 0
## 1738 0.003 0 0 0 0 0 0 0 0
## 1739 0.012 0 0 0 0 0 0 0 0
## 1740 0.0271 0 0 0 0 0 0 0 0
## 1741 0.0411 0 0 0 0 0 0 0 0
## 1742 0.0441 0.001 0 0 0 0 0 0 0
## 1743 0.0361 0.003 0 0 0 0 0 0 0
## 1744 0.0231 0.007 0 0 0 0 0 0 0
## 1745 0.012 0.012 0 0 0 0 0 0 0
## 1746 0.005 0.0191 0.001 0 0 0 0 0 0
## 1747 0.002 0.0231 0.002 0 0 0 0 0 0
## 1748 0.001 0.0231 0.005 0 0 0 0 0 0
## 1749 0 0.0201 0.008 0.001 0 0 0 0 0
## 1750 0 0.015 0.012 0.001 0 0 0 0 0
## 1751 0 0.01 0.015 0.003 0 0 0 0 0
## 1752 0 0.006 0.016 0.005 0.001 0 0 0 0
## 1753 0 0.003 0.016 0.007 0.001 0 0 0 0
## 1754 0 0.001 0.013 0.009 0.002 0 0 0 0
## 1755 0 0.001 0.01 0.011 0.004 0.001 0 0 0
## 1756 0 0 0.007 0.011 0.005 0.002 0 0 0
## 1757 0 0 0.005 0.01 0.006 0.002 0 0 0
## 1758 0 0 0.003 0.009 0.008 0.004 0.001 0 0
## 1759 0 0 0.002 0.007 0.008 0.005 0.001 0 0
## 1760 0 0 0.001 0.005 0.008 0.006 0.002 0.001 0
## 1761 0 0 0 0.004 0.007 0.006 0.002 0.001 0
## 1762 0 0 0 0.003 0.006 0.006 0.003 0.001 0.001
## 1763 0 0 0 0.002 0.005 0.006 0.003 0.002 0.001
## 1764 0 0 0 0.001 0.004 0.006 0.003 0.002 0.001
## 1765 0 0 0 0.001 0.003 0.005 0.003 0.002 0.001
## 1766 0 0 0 0 0.002 0.004 0.003 0.002 0.002
## 1767 0 0 0 0 0.001 0.003 0.002 0.002 0.002
## 1768 0 0 0 0 0.001 0.002 0.002 0.002 0.002
## 1769 0 0 0 0 0 0.002 0.002 0.002 0.002
## 1770 0 0 0 0 0 0.001 0.001 0.002 0.002
## 1771 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1772 0 0 0 0 0 0 0.001 0.001 0.001
## 1773 0 0 0 0 0 0 0 0.001 0.001
## 1774 0 0 0 0 0 0 0 0.001 0.001
## 1775 0 0 0 0 0 0 0 0 0.001
## 1776 0 0 0 0 0 0 0 0 0
## 1777 0 0 0 0 0 0 0 0 0
## 1778 0 0 0 0 0 0 0 0 0
## 1779 0 0 0 0 0 0 0 0 0
## 1780 0.003 0 0 0 0 0 0 0 0
## 1781 0.011 0 0 0 0 0 0 0 0
## 1782 0.0261 0 0 0 0 0 0 0 0
## 1783 0.0391 0 0 0 0 0 0 0 0
## 1784 0.0431 0.001 0 0 0 0 0 0 0
## 1785 0.0351 0.003 0 0 0 0 0 0 0
## 1786 0.0231 0.007 0 0 0 0 0 0 0
## 1787 0.012 0.013 0 0 0 0 0 0 0
## 1788 0.005 0.0201 0.001 0 0 0 0 0 0
## 1789 0.002 0.0251 0.002 0 0 0 0 0 0
## 1790 0.001 0.0261 0.005 0 0 0 0 0 0
## 1791 0 0.0231 0.008 0.001 0 0 0 0 0
## 1792 0 0.0171 0.012 0.001 0 0 0 0 0
## 1793 0 0.011 0.015 0.003 0 0 0 0 0
## 1794 0 0.007 0.0171 0.005 0.001 0 0 0 0
## 1795 0 0.004 0.016 0.007 0.001 0 0 0 0
## 1796 0 0.002 0.014 0.009 0.002 0 0 0 0
## 1797 0 0.001 0.011 0.011 0.003 0.001 0 0 0
## 1798 0 0 0.008 0.011 0.005 0.001 0 0 0
## 1799 0 0 0.005 0.011 0.006 0.002 0.001 0 0
## 1800 0 0 0.003 0.009 0.007 0.003 0.001 0 0
## 1801 0 0 0.002 0.008 0.007 0.003 0.002 0 0
## 1802 0 0 0.001 0.006 0.007 0.004 0.002 0.001 0
## 1803 0 0 0 0.004 0.007 0.004 0.003 0.001 0
## 1804 0 0 0 0.003 0.006 0.005 0.003 0.001 0
## 1805 0 0 0 0.002 0.005 0.004 0.004 0.002 0.001
## 1806 0 0 0 0.001 0.003 0.004 0.004 0.002 0.001
## 1807 0 0 0 0.001 0.002 0.004 0.004 0.002 0.001
## 1808 0 0 0 0 0.002 0.003 0.004 0.002 0.001
## 1809 0 0 0 0 0.001 0.002 0.003 0.002 0.001
## 1810 0 0 0 0 0.001 0.002 0.003 0.002 0.001
## 1811 0 0 0 0 0 0.001 0.002 0.002 0.001
## 1812 0 0 0 0 0 0.001 0.002 0.002 0.001
## 1813 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1814 0 0 0 0 0 0 0.001 0.001 0.001
## 1815 0 0 0 0 0 0 0.001 0.001 0.001
## 1816 0 0 0 0 0 0 0 0.001 0
## 1817 0 0 0 0 0 0 0 0 0
## 1818 0 0 0 0 0 0 0 0 0
## 1819 0 0 0 0 0 0 0 0 0
## 1820 0 0 0 0 0 0 0 0 0
## 1821 0.003 0 0 0 0 0 0 0 0
## 1822 0.0111 0 0 0 0 0 0 0 0
## 1823 0.0253 0 0 0 0 0 0 0 0
## 1824 0.0395 0 0 0 0 0 0 0 0
## 1825 0.0436 0.001 0 0 0 0 0 0 0
## 1826 0.0365 0.002 0 0 0 0 0 0 0
## 1827 0.0233 0.0061 0 0 0 0 0 0 0
## 1828 0.0122 0.0122 0 0 0 0 0 0 0
## 1829 0.0051 0.0182 0.001 0 0 0 0 0 0
## 1830 0.002 0.0233 0.002 0 0 0 0 0 0
## 1831 0.001 0.0243 0.0041 0 0 0 0 0 0
## 1832 0 0.0213 0.0081 0.001 0 0 0 0 0
## 1833 0 0.0162 0.0111 0.001 0 0 0 0 0
## 1834 0 0.0111 0.0142 0.003 0 0 0 0 0
## 1835 0 0.0061 0.0162 0.0051 0 0 0 0 0
## 1836 0 0.003 0.0152 0.0071 0.001 0 0 0 0
## 1837 0 0.002 0.0132 0.0091 0.002 0 0 0 0
## 1838 0 0.001 0.0101 0.0111 0.003 0.001 0 0 0
## 1839 0 0 0.0081 0.0122 0.0041 0.001 0 0 0
## 1840 0 0 0.0051 0.0111 0.0051 0.002 0.001 0 0
## 1841 0 0 0.003 0.0101 0.0061 0.002 0.001 0 0
## 1842 0 0 0.002 0.0081 0.0061 0.003 0.001 0 0
## 1843 0 0 0.001 0.0061 0.0061 0.0041 0.002 0 0
## 1844 0 0 0 0.0041 0.0061 0.0041 0.003 0.001 0
## 1845 0 0 0 0.003 0.0051 0.0051 0.003 0.001 0.001
## 1846 0 0 0 0.002 0.0041 0.0041 0.003 0.001 0.001
## 1847 0 0 0 0.001 0.003 0.0041 0.0041 0.001 0.001
## 1848 0 0 0 0.001 0.002 0.003 0.0041 0.001 0.002
## 1849 0 0 0 0 0.001 0.003 0.003 0.001 0.002
## 1850 0 0 0 0 0.001 0.002 0.003 0.001 0.002
## 1851 0 0 0 0 0.001 0.002 0.002 0.001 0.002
## 1852 0 0 0 0 0 0.001 0.002 0.001 0.002
## 1853 0 0 0 0 0 0.001 0.002 0.001 0.002
## 1854 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1855 0 0 0 0 0 0 0.001 0.001 0.001
## 1856 0 0 0 0 0 0 0.001 0 0.001
## 1857 0 0 0 0 0 0 0 0 0.001
## 1858 0 0 0 0 0 0 0 0 0.001
## 1859 0 0 0 0 0 0 0 0 0
## 1860 0 0 0 0 0 0 0 0 0
## 1861 0 0 0 0 0 0 0 0 0
## 1862 0 0 0 0 0 0 0 0 0
## 1863 0.003 0 0 0 0 0 0 0 0
## 1864 0.0101 0 0 0 0 0 0 0 0
## 1865 0.0232 0 0 0 0 0 0 0 0
## 1866 0.0363 0 0 0 0 0 0 0 0
## 1867 0.0413 0.001 0 0 0 0 0 0 0
## 1868 0.0342 0.003 0 0 0 0 0 0 0
## 1869 0.0232 0.0081 0 0 0 0 0 0 0
## 1870 0.0121 0.0151 0 0 0 0 0 0 0
## 1871 0.005 0.0242 0.001 0 0 0 0 0 0
## 1872 0.002 0.0302 0.002 0 0 0 0 0 0
## 1873 0.001 0.0312 0.004 0 0 0 0 0 0
## 1874 0 0.0282 0.007 0.001 0 0 0 0 0
## 1875 0 0.0222 0.0111 0.001 0 0 0 0 0
## 1876 0 0.0151 0.0141 0.003 0 0 0 0 0
## 1877 0 0.0091 0.0161 0.005 0 0 0 0 0
## 1878 0 0.005 0.0161 0.007 0.001 0 0 0 0
## 1879 0 0.002 0.0141 0.0091 0.002 0 0 0 0
## 1880 0 0.001 0.0111 0.0111 0.003 0 0 0 0
## 1881 0 0 0.0081 0.0111 0.004 0.001 0 0 0
## 1882 0 0 0.005 0.0111 0.005 0.001 0 0 0
## 1883 0 0 0.003 0.0101 0.006 0.002 0.001 0 0
## 1884 0 0 0.002 0.0081 0.007 0.003 0.001 0.001 0
## 1885 0 0 0.001 0.006 0.007 0.003 0.002 0.001 0
## 1886 0 0 0.001 0.004 0.006 0.004 0.002 0.001 0
## 1887 0 0 0 0.003 0.005 0.004 0.002 0.002 0.001
## 1888 0 0 0 0.002 0.004 0.004 0.003 0.002 0.001
## 1889 0 0 0 0.001 0.003 0.004 0.003 0.002 0.001
## 1890 0 0 0 0.001 0.002 0.003 0.003 0.003 0.001
## 1891 0 0 0 0 0.002 0.003 0.003 0.003 0.002
## 1892 0 0 0 0 0.001 0.002 0.002 0.003 0.002
## 1893 0 0 0 0 0.001 0.001 0.002 0.003 0.002
## 1894 0 0 0 0 0 0.001 0.002 0.002 0.002
## 1895 0 0 0 0 0 0.001 0.001 0.002 0.002
## 1896 0 0 0 0 0 0 0.001 0.002 0.001
## 1897 0 0 0 0 0 0 0.001 0.001 0.001
## 1898 0 0 0 0 0 0 0 0.001 0.001
## 1899 0 0 0 0 0 0 0 0.001 0.001
## 1900 0 0 0 0 0 0 0 0.001 0.001
## 1901 0 0 0 0 0 0 0 0 0
## 1902 0 0 0 0 0 0 0 0 0
## 1903 0 0 0 0 0 0 0 0 0
## 1904 0 0 0 0 0 0 0 0 0
## 1905 0.003 0 0 0 0 0 0 0 0
## 1906 0.0111 0 0 0 0 0 0 0 0
## 1907 0.0251 0 0 0 0 0 0 0 0
## 1908 0.0402 0 0 0 0 0 0 0 0
## 1909 0.0452 0.001 0 0 0 0 0 0 0
## 1910 0.0382 0.002 0 0 0 0 0 0 0
## 1911 0.0251 0.006 0 0 0 0 0 0 0
## 1912 0.0141 0.0121 0 0 0 0 0 0 0
## 1913 0.006 0.0191 0.001 0 0 0 0 0 0
## 1914 0.002 0.0251 0.002 0 0 0 0 0 0
## 1915 0.001 0.0261 0.005 0 0 0 0 0 0
## 1916 0 0.0241 0.009 0 0 0 0 0 0
## 1917 0 0.0181 0.0131 0.001 0 0 0 0 0
## 1918 0 0.0131 0.0171 0.002 0 0 0 0 0
## 1919 0 0.008 0.0191 0.004 0 0 0 0 0
## 1920 0 0.004 0.0181 0.006 0.001 0 0 0 0
## 1921 0 0.002 0.0161 0.008 0.002 0 0 0 0
## 1922 0 0.001 0.0131 0.009 0.003 0 0 0 0
## 1923 0 0 0.0101 0.0101 0.004 0.001 0 0 0
## 1924 0 0 0.006 0.0101 0.005 0.001 0 0 0
## 1925 0 0 0.004 0.009 0.006 0.002 0 0 0
## 1926 0 0 0.002 0.007 0.006 0.003 0.001 0 0
## 1927 0 0 0.001 0.005 0.006 0.003 0.001 0.001 0
## 1928 0 0 0.001 0.004 0.006 0.004 0.001 0.001 0
## 1929 0 0 0 0.003 0.005 0.004 0.002 0.001 0.001
## 1930 0 0 0 0.002 0.004 0.004 0.002 0.001 0.001
## 1931 0 0 0 0.001 0.003 0.004 0.002 0.002 0.001
## 1932 0 0 0 0.001 0.002 0.003 0.002 0.002 0.001
## 1933 0 0 0 0 0.002 0.003 0.002 0.002 0.001
## 1934 0 0 0 0 0.001 0.002 0.002 0.002 0.002
## 1935 0 0 0 0 0.001 0.002 0.002 0.002 0.002
## 1936 0 0 0 0 0 0.001 0.001 0.002 0.002
## 1937 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1938 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1939 0 0 0 0 0 0 0.001 0.001 0.001
## 1940 0 0 0 0 0 0 0 0.001 0.001
## 1941 0 0 0 0 0 0 0 0.001 0.001
## 1942 0 0 0 0 0 0 0 0 0.001
## 1943 0 0 0 0 0 0 0 0 0
## 1944 0 0 0 0 0 0 0 0 0
## 1945 0 0 0 0 0 0 0 0 0
## 1946 0 0 0 0 0 0 0 0 0
## 1947 0.003 0 0 0 0 0 0 0 0
## 1948 0.0111 0 0 0 0 0 0 0 0
## 1949 0.0262 0 0 0 0 0 0 0 0
## 1950 0.0423 0 0 0 0 0 0 0 0
## 1951 0.0483 0.001 0 0 0 0 0 0 0
## 1952 0.0412 0.002 0 0 0 0 0 0 0
## 1953 0.0272 0.006 0 0 0 0 0 0 0
## 1954 0.0151 0.0121 0 0 0 0 0 0 0
## 1955 0.007 0.0181 0.001 0 0 0 0 0 0
## 1956 0.003 0.0241 0.002 0 0 0 0 0 0
## 1957 0.001 0.0262 0.004 0 0 0 0 0 0
## 1958 0 0.0231 0.007 0 0 0 0 0 0
## 1959 0 0.0181 0.0111 0.001 0 0 0 0 0
## 1960 0 0.0131 0.0141 0.002 0 0 0 0 0
## 1961 0 0.008 0.0161 0.004 0 0 0 0 0
## 1962 0 0.004 0.0161 0.006 0.001 0 0 0 0
## 1963 0 0.002 0.0141 0.008 0.002 0 0 0 0
## 1964 0 0.001 0.0121 0.0091 0.003 0.001 0 0 0
## 1965 0 0 0.0091 0.0101 0.004 0.001 0 0 0
## 1966 0 0 0.006 0.0101 0.005 0.002 0 0 0
## 1967 0 0 0.004 0.0091 0.006 0.002 0.001 0 0
## 1968 0 0 0.002 0.007 0.006 0.003 0.001 0 0
## 1969 0 0 0.001 0.006 0.006 0.004 0.001 0.001 0
## 1970 0 0 0.001 0.004 0.006 0.005 0.002 0.001 0
## 1971 0 0 0 0.003 0.005 0.005 0.002 0.001 0
## 1972 0 0 0 0.002 0.004 0.005 0.002 0.002 0.001
## 1973 0 0 0 0.001 0.003 0.004 0.002 0.002 0.001
## 1974 0 0 0 0.001 0.002 0.004 0.002 0.002 0.001
## 1975 0 0 0 0 0.002 0.003 0.002 0.002 0.001
## 1976 0 0 0 0 0.001 0.003 0.002 0.002 0.001
## 1977 0 0 0 0 0.001 0.002 0.002 0.002 0.001
## 1978 0 0 0 0 0 0.001 0.001 0.002 0.001
## 1979 0 0 0 0 0 0.001 0.001 0.002 0.001
## 1980 0 0 0 0 0 0.001 0.001 0.001 0.001
## 1981 0 0 0 0 0 0 0.001 0.001 0.001
## 1982 0 0 0 0 0 0 0 0.001 0.001
## 1983 0 0 0 0 0 0 0 0.001 0
## 1984 0 0 0 0 0 0 0 0 0
## 1985 0 0 0 0 0 0 0 0 0
## 1986 0 0 0 0 0 0 0 0 0
## 1987 0 0 0 0 0 0 0 0 0
## 1988 0.003 0 0 0 0 0 0 0 0
## 1989 0.01 0 0 0 0 0 0 0 0
## 1990 0.0241 0 0 0 0 0 0 0 0
## 1991 0.0392 0 0 0 0 0 0 0 0
## 1992 0.0452 0.001 0 0 0 0 0 0 0
## 1993 0.0392 0.002 0 0 0 0 0 0 0
## 1994 0.0261 0.006 0 0 0 0 0 0 0
## 1995 0.0141 0.0131 0 0 0 0 0 0 0
## 1996 0.007 0.0201 0.001 0 0 0 0 0 0
## 1997 0.003 0.0271 0.002 0 0 0 0 0 0
## 1998 0.001 0.0291 0.004 0 0 0 0 0 0
## 1999 0 0.0261 0.007 0 0 0 0 0 0
## 2000 0 0.0211 0.01 0.001 0 0 0 0 0
## 2001 0 0.0141 0.0131 0.002 0 0 0 0 0
## 2002 0 0.009 0.0151 0.003 0 0 0 0 0
## 2003 0 0.005 0.0151 0.005 0.001 0 0 0 0
## 2004 0 0.003 0.0141 0.007 0.002 0 0 0 0
## 2005 0 0.001 0.011 0.008 0.003 0.001 0 0 0
## 2006 0 0.001 0.008 0.009 0.004 0.001 0 0 0
## 2007 0 0 0.006 0.009 0.005 0.002 0 0 0
## 2008 0 0 0.004 0.008 0.006 0.003 0.001 0 0
## 2009 0 0 0.002 0.006 0.007 0.004 0.001 0 0
## 2010 0 0 0.001 0.005 0.007 0.004 0.002 0 0
## 2011 0 0 0.001 0.004 0.007 0.005 0.002 0.001 0
## 2012 0 0 0 0.002 0.006 0.005 0.002 0.001 0.001
## 2013 0 0 0 0.002 0.005 0.005 0.003 0.001 0.001
## 2014 0 0 0 0.001 0.004 0.005 0.003 0.001 0.001
## 2015 0 0 0 0.001 0.003 0.004 0.003 0.002 0.001
## 2016 0 0 0 0 0.002 0.004 0.003 0.002 0.002
## 2017 0 0 0 0 0.001 0.003 0.003 0.002 0.002
## 2018 0 0 0 0 0.001 0.002 0.002 0.002 0.002
## 2019 0 0 0 0 0.001 0.002 0.002 0.001 0.002
## 2020 0 0 0 0 0 0.001 0.001 0.001 0.002
## 2021 0 0 0 0 0 0.001 0.001 0.001 0.002
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## 46 17 17 16 14 13 11 10 9 9 6 4 4 3 2 2 1 0
## 47 19 19 16 16 13 12 10 9 8 5 5 4 3 2 1 0 0
## 48 19 20 17 17 15 14 13 11 9 8 5 5 3 3 1 1 0
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## 50 20 19 16 16 15 13 11 9 8 7 6 4 3 3 2 1 0
## 51 31 29 28 25 23 22 20 19 18 15 15 13 11 10 10 7 6
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## 68 35 35 32 29 30 26 24 21 16 15 15 11 8 6 5 4 3
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## 88 33 31 30 27 27 24 21 19 17 15 13 10 8 6 4 3 3
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## 98 36 35 32 29 29 27 22 21 18 16 12 9 8 6 4 3 3
## 99 28 27 26 23 20 19 17 14 13 11 10 7 6 4 3 3 1
## 100 29 28 26 24 26 23 22 19 17 16 13 12 11 6 6 4 3
## l53 l54
## 1 0 0
## 2 0 0
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## 69 2 1
## 70 3 2
## 71 3 3
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## 73 1 1
## 74 2 1
## 75 3 2
## 76 4 3
## 77 7 5
## 78 2 2
## 79 2 1
## 80 2 2
## 81 4 3
## 82 5 4
## 83 3 1
## 84 2 1
## 85 3 2
## 86 3 3
## 87 7 4
## 88 2 1
## 89 2 1
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## 94 2 0
## 95 2 1
## 96 4 3
## 97 5 4
## 98 1 0
## 99 1 0
## 100 3 2We may also need to access or modify the setup variables before the data matrices.
#CPUE units, SD and error structure
stocksynthesis.data$CPUEinfo## Fleet Units Errtype SD_Report
## Fishery 1 2 0 0
## Survey 2 1 0 0#Number of length bins
stocksynthesis.data$N_lbins## [1] 45#Length bin method
stocksynthesis.data$Lbin_method## [1] 3#Vector of age bins
stocksynthesis.data$agebin_vector## [1] 1 2 3 4 5 6 7 8 9 10Writing index data
To edit index data, use the atlantisom sampling functions to extract survey biomass and numbers. These can then be written using the SS_write_CPUE function.
results <- get(load(atlantis_output_name))
devtools::load_all()## Loading atlantisomspecies=c(species)
#Sample all boxes
boxes <- unique(results$nums$polygon)
#Efficiency of the survey
effic <- data.frame(species=species, efficiency=eff_case)
# Assume uniform selectivity
sel<- data.frame(species=rep(species,length(age_classes)),
agecl=age_classes,
selex=sel_by_age)
#Sample survey - 3rd timestep simulates a summer survey
survey_out <- create_survey(dat=results$nums, time=survey_sample_full, species=species, boxes=boxes, effic=effic, selex=sel)
#Set effective sample size for age compositions
effN <- surveyEffN
highEffN <- data.frame(species=species, effN=rep(effN, length(species)))
#Sample fish for age composition
age_comp_data <- sample_fish(survey_out, highEffN)
# aggregate true resn per survey design
survey_aggresnstd <- aggregateDensityData(dat = results$resn,
time = unique(results$nums$time),
species = species,
boxes = boxes)
# aggregate true structn per survey design
survey_aggstructnstd <- aggregateDensityData(dat = results$structn,
time = unique(results$nums$time),
species = species,
boxes = boxes)
ss_structnstd <- sample_fish(survey_aggstructnstd,
effN,
sample=FALSE)
ss_resnstd <- sample_fish(survey_aggresnstd,
effN,
sample=FALSE)
#Extract length composition data
ss_length_stdsurv <- calc_age2length(structn = ss_structnstd,
resn = ss_resnstd,
nums = age_comp_data,
biolprm = results$biolprm, fgs = results$fgs,
CVlenage = CVs$lenage, remove.zeroes=TRUE)
#Need to replace with interp function
wtAtAge <- ss_length_stdsurv$muweight %>%
select(species, agecl, time, wtAtAge = atoutput) %>%
mutate(wtAtAge = wtAtAge/1000)## Warning: package 'bindrcpp' was built under R version 3.5.1##
## Attaching package: 'bindrcpp'## The following object is masked from 'package:atlantisom':
##
## create_env# CV function
cv <- data.frame(species="Pacific_sardine", cv=CVs$survey)
#Sample survey biomass
survObsBiom <- sample_survey_biomass(dat=survey_out,cv=cv,wtAtAge)Catch data
catch_numbers <- create_fishery_subset(dat = results$catch,
time = fish_years,
species = species,
boxes = boxes)
#Sample catch in numbers
catch_total <- catch_numbers %>%
group_by(time) %>%
summarise(catch=sum(atoutput))
#Test writing CPUE in biomass
stocksynthesis.data <- SS_write_ts(ss_data_list = stocksynthesis.data,
ts_data = list(survObsBiom$atoutput[fish_years],
catch_total$catch[catch_total$time==fish_years]),
CVs = c(CVs$survey,
CVs$fishery),
data_years = list((survObsBiom$time[fish_years]-survey_sample_time)/timestep+1, fish_years),
sampling_month = list(rep(survey_month,nyears),
rep(fishing_month,nyears)),
units = c("biomass","numbers"),
data_type=c("CPUE","catch"),
fleets = c(2,1))Writing age composition data
age_comp_data## species agecl polygon layer time atoutput
## 1 Pacific_sardine 1 NA NA 3 79
## 2 Pacific_sardine 2 NA NA 3 423
## 3 Pacific_sardine 3 NA NA 3 243
## 4 Pacific_sardine 4 NA NA 3 107
## 5 Pacific_sardine 5 NA NA 3 65
## 6 Pacific_sardine 6 NA NA 3 42
## 7 Pacific_sardine 7 NA NA 3 13
## 8 Pacific_sardine 8 NA NA 3 19
## 9 Pacific_sardine 9 NA NA 3 7
## 10 Pacific_sardine 10 NA NA 3 2
## 11 Pacific_sardine 1 NA NA 8 484
## 12 Pacific_sardine 2 NA NA 8 43
## 13 Pacific_sardine 3 NA NA 8 242
## 14 Pacific_sardine 4 NA NA 8 117
## 15 Pacific_sardine 5 NA NA 8 58
## 16 Pacific_sardine 6 NA NA 8 31
## 17 Pacific_sardine 7 NA NA 8 16
## 18 Pacific_sardine 8 NA NA 8 5
## 19 Pacific_sardine 9 NA NA 8 4
## 20 Pacific_sardine 10 NA NA 8 0
## 21 Pacific_sardine 1 NA NA 13 407
## 22 Pacific_sardine 2 NA NA 13 278
## 23 Pacific_sardine 3 NA NA 13 27
## 24 Pacific_sardine 4 NA NA 13 149
## 25 Pacific_sardine 5 NA NA 13 65
## 26 Pacific_sardine 6 NA NA 13 42
## 27 Pacific_sardine 7 NA NA 13 11
## 28 Pacific_sardine 8 NA NA 13 11
## 29 Pacific_sardine 9 NA NA 13 5
## 30 Pacific_sardine 10 NA NA 13 5
## 31 Pacific_sardine 1 NA NA 18 321
## 32 Pacific_sardine 2 NA NA 18 298
## 33 Pacific_sardine 3 NA NA 18 211
## 34 Pacific_sardine 4 NA NA 18 18
## 35 Pacific_sardine 5 NA NA 18 77
## 36 Pacific_sardine 6 NA NA 18 37
## 37 Pacific_sardine 7 NA NA 18 21
## 38 Pacific_sardine 8 NA NA 18 12
## 39 Pacific_sardine 9 NA NA 18 5
## 40 Pacific_sardine 10 NA NA 18 0
## 41 Pacific_sardine 1 NA NA 23 280
## 42 Pacific_sardine 2 NA NA 23 249
## 43 Pacific_sardine 3 NA NA 23 206
## 44 Pacific_sardine 4 NA NA 23 140
## 45 Pacific_sardine 5 NA NA 23 14
## 46 Pacific_sardine 6 NA NA 23 58
## 47 Pacific_sardine 7 NA NA 23 27
## 48 Pacific_sardine 8 NA NA 23 15
## 49 Pacific_sardine 9 NA NA 23 10
## 50 Pacific_sardine 10 NA NA 23 1
## 51 Pacific_sardine 1 NA NA 28 271
## 52 Pacific_sardine 2 NA NA 28 213
## 53 Pacific_sardine 3 NA NA 28 202
## 54 Pacific_sardine 4 NA NA 28 151
## 55 Pacific_sardine 5 NA NA 28 90
## 56 Pacific_sardine 6 NA NA 28 4
## 57 Pacific_sardine 7 NA NA 28 32
## 58 Pacific_sardine 8 NA NA 28 19
## 59 Pacific_sardine 9 NA NA 28 10
## 60 Pacific_sardine 10 NA NA 28 8
## 61 Pacific_sardine 1 NA NA 33 272
## 62 Pacific_sardine 2 NA NA 33 219
## 63 Pacific_sardine 3 NA NA 33 174
## 64 Pacific_sardine 4 NA NA 33 134
## 65 Pacific_sardine 5 NA NA 33 99
## 66 Pacific_sardine 6 NA NA 33 57
## 67 Pacific_sardine 7 NA NA 33 5
## 68 Pacific_sardine 8 NA NA 33 22
## 69 Pacific_sardine 9 NA NA 33 12
## 70 Pacific_sardine 10 NA NA 33 6
## 71 Pacific_sardine 1 NA NA 38 259
## 72 Pacific_sardine 2 NA NA 38 195
## 73 Pacific_sardine 3 NA NA 38 180
## 74 Pacific_sardine 4 NA NA 38 126
## 75 Pacific_sardine 5 NA NA 38 85
## 76 Pacific_sardine 6 NA NA 38 64
## 77 Pacific_sardine 7 NA NA 38 56
## 78 Pacific_sardine 8 NA NA 38 4
## 79 Pacific_sardine 9 NA NA 38 18
## 80 Pacific_sardine 10 NA NA 38 13
## 81 Pacific_sardine 1 NA NA 43 272
## 82 Pacific_sardine 2 NA NA 43 208
## 83 Pacific_sardine 3 NA NA 43 181
## 84 Pacific_sardine 4 NA NA 43 103
## 85 Pacific_sardine 5 NA NA 43 94
## 86 Pacific_sardine 6 NA NA 43 49
## 87 Pacific_sardine 7 NA NA 43 41
## 88 Pacific_sardine 8 NA NA 43 41
## 89 Pacific_sardine 9 NA NA 43 2
## 90 Pacific_sardine 10 NA NA 43 9
## 91 Pacific_sardine 1 NA NA 48 293
## 92 Pacific_sardine 2 NA NA 48 195
## 93 Pacific_sardine 3 NA NA 48 146
## 94 Pacific_sardine 4 NA NA 48 125
## 95 Pacific_sardine 5 NA NA 48 81
## 96 Pacific_sardine 6 NA NA 48 57
## 97 Pacific_sardine 7 NA NA 48 37
## 98 Pacific_sardine 8 NA NA 48 37
## 99 Pacific_sardine 9 NA NA 48 27
## 100 Pacific_sardine 10 NA NA 48 2
## 101 Pacific_sardine 1 NA NA 53 269
## 102 Pacific_sardine 2 NA NA 53 219
## 103 Pacific_sardine 3 NA NA 53 157
## 104 Pacific_sardine 4 NA NA 53 104
## 105 Pacific_sardine 5 NA NA 53 88
## 106 Pacific_sardine 6 NA NA 53 54
## 107 Pacific_sardine 7 NA NA 53 42
## 108 Pacific_sardine 8 NA NA 53 32
## 109 Pacific_sardine 9 NA NA 53 21
## 110 Pacific_sardine 10 NA NA 53 14
## 111 Pacific_sardine 1 NA NA 58 249
## 112 Pacific_sardine 2 NA NA 58 208
## 113 Pacific_sardine 3 NA NA 58 165
## 114 Pacific_sardine 4 NA NA 58 124
## 115 Pacific_sardine 5 NA NA 58 85
## 116 Pacific_sardine 6 NA NA 58 58
## 117 Pacific_sardine 7 NA NA 58 50
## 118 Pacific_sardine 8 NA NA 58 28
## 119 Pacific_sardine 9 NA NA 58 20
## 120 Pacific_sardine 10 NA NA 58 13
## 121 Pacific_sardine 1 NA NA 63 246
## 122 Pacific_sardine 2 NA NA 63 210
## 123 Pacific_sardine 3 NA NA 63 164
## 124 Pacific_sardine 4 NA NA 63 127
## 125 Pacific_sardine 5 NA NA 63 78
## 126 Pacific_sardine 6 NA NA 63 68
## 127 Pacific_sardine 7 NA NA 63 40
## 128 Pacific_sardine 8 NA NA 63 33
## 129 Pacific_sardine 9 NA NA 63 18
## 130 Pacific_sardine 10 NA NA 63 16
## 131 Pacific_sardine 1 NA NA 68 223
## 132 Pacific_sardine 2 NA NA 68 204
## 133 Pacific_sardine 3 NA NA 68 190
## 134 Pacific_sardine 4 NA NA 68 111
## 135 Pacific_sardine 5 NA NA 68 74
## 136 Pacific_sardine 6 NA NA 68 77
## 137 Pacific_sardine 7 NA NA 68 55
## 138 Pacific_sardine 8 NA NA 68 40
## 139 Pacific_sardine 9 NA NA 68 18
## 140 Pacific_sardine 10 NA NA 68 8
## 141 Pacific_sardine 1 NA NA 73 226
## 142 Pacific_sardine 2 NA NA 73 217
## 143 Pacific_sardine 3 NA NA 73 169
## 144 Pacific_sardine 4 NA NA 73 118
## 145 Pacific_sardine 5 NA NA 73 93
## 146 Pacific_sardine 6 NA NA 73 49
## 147 Pacific_sardine 7 NA NA 73 47
## 148 Pacific_sardine 8 NA NA 73 38
## 149 Pacific_sardine 9 NA NA 73 21
## 150 Pacific_sardine 10 NA NA 73 22
## 151 Pacific_sardine 1 NA NA 78 259
## 152 Pacific_sardine 2 NA NA 78 206
## 153 Pacific_sardine 3 NA NA 78 142
## 154 Pacific_sardine 4 NA NA 78 128
## 155 Pacific_sardine 5 NA NA 78 81
## 156 Pacific_sardine 6 NA NA 78 81
## 157 Pacific_sardine 7 NA NA 78 36
## 158 Pacific_sardine 8 NA NA 78 34
## 159 Pacific_sardine 9 NA NA 78 18
## 160 Pacific_sardine 10 NA NA 78 15
## 161 Pacific_sardine 1 NA NA 83 240
## 162 Pacific_sardine 2 NA NA 83 215
## 163 Pacific_sardine 3 NA NA 83 183
## 164 Pacific_sardine 4 NA NA 83 92
## 165 Pacific_sardine 5 NA NA 83 84
## 166 Pacific_sardine 6 NA NA 83 64
## 167 Pacific_sardine 7 NA NA 83 63
## 168 Pacific_sardine 8 NA NA 83 26
## 169 Pacific_sardine 9 NA NA 83 20
## 170 Pacific_sardine 10 NA NA 83 13
## 171 Pacific_sardine 1 NA NA 88 250
## 172 Pacific_sardine 2 NA NA 88 206
## 173 Pacific_sardine 3 NA NA 88 144
## 174 Pacific_sardine 4 NA NA 88 116
## 175 Pacific_sardine 5 NA NA 88 87
## 176 Pacific_sardine 6 NA NA 88 70
## 177 Pacific_sardine 7 NA NA 88 48
## 178 Pacific_sardine 8 NA NA 88 45
## 179 Pacific_sardine 9 NA NA 88 16
## 180 Pacific_sardine 10 NA NA 88 18
## 181 Pacific_sardine 1 NA NA 93 223
## 182 Pacific_sardine 2 NA NA 93 218
## 183 Pacific_sardine 3 NA NA 93 141
## 184 Pacific_sardine 4 NA NA 93 122
## 185 Pacific_sardine 5 NA NA 93 89
## 186 Pacific_sardine 6 NA NA 93 69
## 187 Pacific_sardine 7 NA NA 93 59
## 188 Pacific_sardine 8 NA NA 93 31
## 189 Pacific_sardine 9 NA NA 93 25
## 190 Pacific_sardine 10 NA NA 93 23
## 191 Pacific_sardine 1 NA NA 98 244
## 192 Pacific_sardine 2 NA NA 98 209
## 193 Pacific_sardine 3 NA NA 98 169
## 194 Pacific_sardine 4 NA NA 98 123
## 195 Pacific_sardine 5 NA NA 98 80
## 196 Pacific_sardine 6 NA NA 98 60
## 197 Pacific_sardine 7 NA NA 98 43
## 198 Pacific_sardine 8 NA NA 98 31
## 199 Pacific_sardine 9 NA NA 98 23
## 200 Pacific_sardine 10 NA NA 98 18
## 201 Pacific_sardine 1 NA NA 103 228
## 202 Pacific_sardine 2 NA NA 103 208
## 203 Pacific_sardine 3 NA NA 103 169
## 204 Pacific_sardine 4 NA NA 103 123
## 205 Pacific_sardine 5 NA NA 103 82
## 206 Pacific_sardine 6 NA NA 103 69
## 207 Pacific_sardine 7 NA NA 103 52
## 208 Pacific_sardine 8 NA NA 103 32
## 209 Pacific_sardine 9 NA NA 103 14
## 210 Pacific_sardine 10 NA NA 103 23
## 211 Pacific_sardine 1 NA NA 108 273
## 212 Pacific_sardine 2 NA NA 108 198
## 213 Pacific_sardine 3 NA NA 108 165
## 214 Pacific_sardine 4 NA NA 108 114
## 215 Pacific_sardine 5 NA NA 108 81
## 216 Pacific_sardine 6 NA NA 108 71
## 217 Pacific_sardine 7 NA NA 108 38
## 218 Pacific_sardine 8 NA NA 108 29
## 219 Pacific_sardine 9 NA NA 108 19
## 220 Pacific_sardine 10 NA NA 108 12
## 221 Pacific_sardine 1 NA NA 113 219
## 222 Pacific_sardine 2 NA NA 113 191
## 223 Pacific_sardine 3 NA NA 113 185
## 224 Pacific_sardine 4 NA NA 113 124
## 225 Pacific_sardine 5 NA NA 113 92
## 226 Pacific_sardine 6 NA NA 113 64
## 227 Pacific_sardine 7 NA NA 113 57
## 228 Pacific_sardine 8 NA NA 113 31
## 229 Pacific_sardine 9 NA NA 113 17
## 230 Pacific_sardine 10 NA NA 113 20
## 231 Pacific_sardine 1 NA NA 118 242
## 232 Pacific_sardine 2 NA NA 118 207
## 233 Pacific_sardine 3 NA NA 118 161
## 234 Pacific_sardine 4 NA NA 118 126
## 235 Pacific_sardine 5 NA NA 118 83
## 236 Pacific_sardine 6 NA NA 118 55
## 237 Pacific_sardine 7 NA NA 118 53
## 238 Pacific_sardine 8 NA NA 118 35
## 239 Pacific_sardine 9 NA NA 118 23
## 240 Pacific_sardine 10 NA NA 118 15
## 241 Pacific_sardine 1 NA NA 123 198
## 242 Pacific_sardine 2 NA NA 123 215
## 243 Pacific_sardine 3 NA NA 123 165
## 244 Pacific_sardine 4 NA NA 123 129
## 245 Pacific_sardine 5 NA NA 123 82
## 246 Pacific_sardine 6 NA NA 123 85
## 247 Pacific_sardine 7 NA NA 123 50
## 248 Pacific_sardine 8 NA NA 123 33
## 249 Pacific_sardine 9 NA NA 123 32
## 250 Pacific_sardine 10 NA NA 123 11
## 251 Pacific_sardine 1 NA NA 128 246
## 252 Pacific_sardine 2 NA NA 128 191
## 253 Pacific_sardine 3 NA NA 128 166
## 254 Pacific_sardine 4 NA NA 128 121
## 255 Pacific_sardine 5 NA NA 128 84
## 256 Pacific_sardine 6 NA NA 128 70
## 257 Pacific_sardine 7 NA NA 128 50
## 258 Pacific_sardine 8 NA NA 128 33
## 259 Pacific_sardine 9 NA NA 128 20
## 260 Pacific_sardine 10 NA NA 128 19
## 261 Pacific_sardine 1 NA NA 133 249
## 262 Pacific_sardine 2 NA NA 133 212
## 263 Pacific_sardine 3 NA NA 133 159
## 264 Pacific_sardine 4 NA NA 133 113
## 265 Pacific_sardine 5 NA NA 133 77
## 266 Pacific_sardine 6 NA NA 133 66
## 267 Pacific_sardine 7 NA NA 133 38
## 268 Pacific_sardine 8 NA NA 133 41
## 269 Pacific_sardine 9 NA NA 133 26
## 270 Pacific_sardine 10 NA NA 133 19
## 271 Pacific_sardine 1 NA NA 138 232
## 272 Pacific_sardine 2 NA NA 138 183
## 273 Pacific_sardine 3 NA NA 138 188
## 274 Pacific_sardine 4 NA NA 138 130
## 275 Pacific_sardine 5 NA NA 138 92
## 276 Pacific_sardine 6 NA NA 138 69
## 277 Pacific_sardine 7 NA NA 138 43
## 278 Pacific_sardine 8 NA NA 138 30
## 279 Pacific_sardine 9 NA NA 138 19
## 280 Pacific_sardine 10 NA NA 138 14
## 281 Pacific_sardine 1 NA NA 143 258
## 282 Pacific_sardine 2 NA NA 143 196
## 283 Pacific_sardine 3 NA NA 143 156
## 284 Pacific_sardine 4 NA NA 143 128
## 285 Pacific_sardine 5 NA NA 143 79
## 286 Pacific_sardine 6 NA NA 143 60
## 287 Pacific_sardine 7 NA NA 143 57
## 288 Pacific_sardine 8 NA NA 143 24
## 289 Pacific_sardine 9 NA NA 143 25
## 290 Pacific_sardine 10 NA NA 143 17
## 291 Pacific_sardine 1 NA NA 148 227
## 292 Pacific_sardine 2 NA NA 148 181
## 293 Pacific_sardine 3 NA NA 148 179
## 294 Pacific_sardine 4 NA NA 148 133
## 295 Pacific_sardine 5 NA NA 148 80
## 296 Pacific_sardine 6 NA NA 148 83
## 297 Pacific_sardine 7 NA NA 148 51
## 298 Pacific_sardine 8 NA NA 148 34
## 299 Pacific_sardine 9 NA NA 148 19
## 300 Pacific_sardine 10 NA NA 148 13
## 301 Pacific_sardine 1 NA NA 153 222
## 302 Pacific_sardine 2 NA NA 153 211
## 303 Pacific_sardine 3 NA NA 153 168
## 304 Pacific_sardine 4 NA NA 153 115
## 305 Pacific_sardine 5 NA NA 153 90
## 306 Pacific_sardine 6 NA NA 153 73
## 307 Pacific_sardine 7 NA NA 153 46
## 308 Pacific_sardine 8 NA NA 153 37
## 309 Pacific_sardine 9 NA NA 153 21
## 310 Pacific_sardine 10 NA NA 153 17
## 311 Pacific_sardine 1 NA NA 158 253
## 312 Pacific_sardine 2 NA NA 158 201
## 313 Pacific_sardine 3 NA NA 158 166
## 314 Pacific_sardine 4 NA NA 158 122
## 315 Pacific_sardine 5 NA NA 158 98
## 316 Pacific_sardine 6 NA NA 158 51
## 317 Pacific_sardine 7 NA NA 158 44
## 318 Pacific_sardine 8 NA NA 158 32
## 319 Pacific_sardine 9 NA NA 158 15
## 320 Pacific_sardine 10 NA NA 158 18
## 321 Pacific_sardine 1 NA NA 163 226
## 322 Pacific_sardine 2 NA NA 163 221
## 323 Pacific_sardine 3 NA NA 163 177
## 324 Pacific_sardine 4 NA NA 163 114
## 325 Pacific_sardine 5 NA NA 163 90
## 326 Pacific_sardine 6 NA NA 163 61
## 327 Pacific_sardine 7 NA NA 163 36
## 328 Pacific_sardine 8 NA NA 163 37
## 329 Pacific_sardine 9 NA NA 163 25
## 330 Pacific_sardine 10 NA NA 163 13
## 331 Pacific_sardine 1 NA NA 168 240
## 332 Pacific_sardine 2 NA NA 168 189
## 333 Pacific_sardine 3 NA NA 168 163
## 334 Pacific_sardine 4 NA NA 168 127
## 335 Pacific_sardine 5 NA NA 168 89
## 336 Pacific_sardine 6 NA NA 168 66
## 337 Pacific_sardine 7 NA NA 168 51
## 338 Pacific_sardine 8 NA NA 168 37
## 339 Pacific_sardine 9 NA NA 168 19
## 340 Pacific_sardine 10 NA NA 168 19
## 341 Pacific_sardine 1 NA NA 173 229
## 342 Pacific_sardine 2 NA NA 173 213
## 343 Pacific_sardine 3 NA NA 173 164
## 344 Pacific_sardine 4 NA NA 173 124
## 345 Pacific_sardine 5 NA NA 173 86
## 346 Pacific_sardine 6 NA NA 173 57
## 347 Pacific_sardine 7 NA NA 173 49
## 348 Pacific_sardine 8 NA NA 173 35
## 349 Pacific_sardine 9 NA NA 173 22
## 350 Pacific_sardine 10 NA NA 173 21
## 351 Pacific_sardine 1 NA NA 178 223
## 352 Pacific_sardine 2 NA NA 178 192
## 353 Pacific_sardine 3 NA NA 178 176
## 354 Pacific_sardine 4 NA NA 178 133
## 355 Pacific_sardine 5 NA NA 178 87
## 356 Pacific_sardine 6 NA NA 178 62
## 357 Pacific_sardine 7 NA NA 178 51
## 358 Pacific_sardine 8 NA NA 178 34
## 359 Pacific_sardine 9 NA NA 178 26
## 360 Pacific_sardine 10 NA NA 178 16
## 361 Pacific_sardine 1 NA NA 183 236
## 362 Pacific_sardine 2 NA NA 183 198
## 363 Pacific_sardine 3 NA NA 183 169
## 364 Pacific_sardine 4 NA NA 183 108
## 365 Pacific_sardine 5 NA NA 183 107
## 366 Pacific_sardine 6 NA NA 183 68
## 367 Pacific_sardine 7 NA NA 183 48
## 368 Pacific_sardine 8 NA NA 183 27
## 369 Pacific_sardine 9 NA NA 183 20
## 370 Pacific_sardine 10 NA NA 183 19
## 371 Pacific_sardine 1 NA NA 188 239
## 372 Pacific_sardine 2 NA NA 188 206
## 373 Pacific_sardine 3 NA NA 188 139
## 374 Pacific_sardine 4 NA NA 188 103
## 375 Pacific_sardine 5 NA NA 188 103
## 376 Pacific_sardine 6 NA NA 188 81
## 377 Pacific_sardine 7 NA NA 188 51
## 378 Pacific_sardine 8 NA NA 188 38
## 379 Pacific_sardine 9 NA NA 188 22
## 380 Pacific_sardine 10 NA NA 188 18
## 381 Pacific_sardine 1 NA NA 193 218
## 382 Pacific_sardine 2 NA NA 193 182
## 383 Pacific_sardine 3 NA NA 193 166
## 384 Pacific_sardine 4 NA NA 193 125
## 385 Pacific_sardine 5 NA NA 193 102
## 386 Pacific_sardine 6 NA NA 193 77
## 387 Pacific_sardine 7 NA NA 193 59
## 388 Pacific_sardine 8 NA NA 193 39
## 389 Pacific_sardine 9 NA NA 193 17
## 390 Pacific_sardine 10 NA NA 193 15
## 391 Pacific_sardine 1 NA NA 198 246
## 392 Pacific_sardine 2 NA NA 198 199
## 393 Pacific_sardine 3 NA NA 198 156
## 394 Pacific_sardine 4 NA NA 198 122
## 395 Pacific_sardine 5 NA NA 198 86
## 396 Pacific_sardine 6 NA NA 198 71
## 397 Pacific_sardine 7 NA NA 198 44
## 398 Pacific_sardine 8 NA NA 198 40
## 399 Pacific_sardine 9 NA NA 198 26
## 400 Pacific_sardine 10 NA NA 198 10
## 401 Pacific_sardine 1 NA NA 203 235
## 402 Pacific_sardine 2 NA NA 203 225
## 403 Pacific_sardine 3 NA NA 203 174
## 404 Pacific_sardine 4 NA NA 203 114
## 405 Pacific_sardine 5 NA NA 203 82
## 406 Pacific_sardine 6 NA NA 203 50
## 407 Pacific_sardine 7 NA NA 203 46
## 408 Pacific_sardine 8 NA NA 203 35
## 409 Pacific_sardine 9 NA NA 203 21
## 410 Pacific_sardine 10 NA NA 203 18
## 411 Pacific_sardine 1 NA NA 208 235
## 412 Pacific_sardine 2 NA NA 208 202
## 413 Pacific_sardine 3 NA NA 208 161
## 414 Pacific_sardine 4 NA NA 208 113
## 415 Pacific_sardine 5 NA NA 208 109
## 416 Pacific_sardine 6 NA NA 208 52
## 417 Pacific_sardine 7 NA NA 208 46
## 418 Pacific_sardine 8 NA NA 208 33
## 419 Pacific_sardine 9 NA NA 208 26
## 420 Pacific_sardine 10 NA NA 208 23
## 421 Pacific_sardine 1 NA NA 213 242
## 422 Pacific_sardine 2 NA NA 213 184
## 423 Pacific_sardine 3 NA NA 213 160
## 424 Pacific_sardine 4 NA NA 213 121
## 425 Pacific_sardine 5 NA NA 213 83
## 426 Pacific_sardine 6 NA NA 213 72
## 427 Pacific_sardine 7 NA NA 213 48
## 428 Pacific_sardine 8 NA NA 213 34
## 429 Pacific_sardine 9 NA NA 213 26
## 430 Pacific_sardine 10 NA NA 213 30
## 431 Pacific_sardine 1 NA NA 218 251
## 432 Pacific_sardine 2 NA NA 218 215
## 433 Pacific_sardine 3 NA NA 218 166
## 434 Pacific_sardine 4 NA NA 218 119
## 435 Pacific_sardine 5 NA NA 218 67
## 436 Pacific_sardine 6 NA NA 218 69
## 437 Pacific_sardine 7 NA NA 218 47
## 438 Pacific_sardine 8 NA NA 218 28
## 439 Pacific_sardine 9 NA NA 218 25
## 440 Pacific_sardine 10 NA NA 218 13
## 441 Pacific_sardine 1 NA NA 223 228
## 442 Pacific_sardine 2 NA NA 223 211
## 443 Pacific_sardine 3 NA NA 223 183
## 444 Pacific_sardine 4 NA NA 223 120
## 445 Pacific_sardine 5 NA NA 223 84
## 446 Pacific_sardine 6 NA NA 223 66
## 447 Pacific_sardine 7 NA NA 223 47
## 448 Pacific_sardine 8 NA NA 223 29
## 449 Pacific_sardine 9 NA NA 223 18
## 450 Pacific_sardine 10 NA NA 223 14
## 451 Pacific_sardine 1 NA NA 228 250
## 452 Pacific_sardine 2 NA NA 228 218
## 453 Pacific_sardine 3 NA NA 228 134
## 454 Pacific_sardine 4 NA NA 228 122
## 455 Pacific_sardine 5 NA NA 228 78
## 456 Pacific_sardine 6 NA NA 228 47
## 457 Pacific_sardine 7 NA NA 228 63
## 458 Pacific_sardine 8 NA NA 228 36
## 459 Pacific_sardine 9 NA NA 228 28
## 460 Pacific_sardine 10 NA NA 228 24
## 461 Pacific_sardine 1 NA NA 233 231
## 462 Pacific_sardine 2 NA NA 233 195
## 463 Pacific_sardine 3 NA NA 233 176
## 464 Pacific_sardine 4 NA NA 233 113
## 465 Pacific_sardine 5 NA NA 233 79
## 466 Pacific_sardine 6 NA NA 233 69
## 467 Pacific_sardine 7 NA NA 233 52
## 468 Pacific_sardine 8 NA NA 233 33
## 469 Pacific_sardine 9 NA NA 233 32
## 470 Pacific_sardine 10 NA NA 233 20
## 471 Pacific_sardine 1 NA NA 238 229
## 472 Pacific_sardine 2 NA NA 238 205
## 473 Pacific_sardine 3 NA NA 238 166
## 474 Pacific_sardine 4 NA NA 238 109
## 475 Pacific_sardine 5 NA NA 238 89
## 476 Pacific_sardine 6 NA NA 238 65
## 477 Pacific_sardine 7 NA NA 238 53
## 478 Pacific_sardine 8 NA NA 238 35
## 479 Pacific_sardine 9 NA NA 238 33
## 480 Pacific_sardine 10 NA NA 238 16
## 481 Pacific_sardine 1 NA NA 243 221
## 482 Pacific_sardine 2 NA NA 243 206
## 483 Pacific_sardine 3 NA NA 243 182
## 484 Pacific_sardine 4 NA NA 243 113
## 485 Pacific_sardine 5 NA NA 243 89
## 486 Pacific_sardine 6 NA NA 243 69
## 487 Pacific_sardine 7 NA NA 243 44
## 488 Pacific_sardine 8 NA NA 243 32
## 489 Pacific_sardine 9 NA NA 243 26
## 490 Pacific_sardine 10 NA NA 243 18
## 491 Pacific_sardine 1 NA NA 248 229
## 492 Pacific_sardine 2 NA NA 248 220
## 493 Pacific_sardine 3 NA NA 248 153
## 494 Pacific_sardine 4 NA NA 248 121
## 495 Pacific_sardine 5 NA NA 248 96
## 496 Pacific_sardine 6 NA NA 248 69
## 497 Pacific_sardine 7 NA NA 248 48
## 498 Pacific_sardine 8 NA NA 248 20
## 499 Pacific_sardine 9 NA NA 248 27
## 500 Pacific_sardine 10 NA NA 248 17
## 501 Pacific_sardine 1 NA NA 253 238
## 502 Pacific_sardine 2 NA NA 253 221
## 503 Pacific_sardine 3 NA NA 253 151
## 504 Pacific_sardine 4 NA NA 253 122
## 505 Pacific_sardine 5 NA NA 253 78
## 506 Pacific_sardine 6 NA NA 253 58
## 507 Pacific_sardine 7 NA NA 253 51
## 508 Pacific_sardine 8 NA NA 253 29
## 509 Pacific_sardine 9 NA NA 253 32
## 510 Pacific_sardine 10 NA NA 253 20
## 511 Pacific_sardine 1 NA NA 258 252
## 512 Pacific_sardine 2 NA NA 258 193
## 513 Pacific_sardine 3 NA NA 258 170
## 514 Pacific_sardine 4 NA NA 258 122
## 515 Pacific_sardine 5 NA NA 258 83
## 516 Pacific_sardine 6 NA NA 258 57
## 517 Pacific_sardine 7 NA NA 258 51
## 518 Pacific_sardine 8 NA NA 258 37
## 519 Pacific_sardine 9 NA NA 258 18
## 520 Pacific_sardine 10 NA NA 258 17
## 521 Pacific_sardine 1 NA NA 263 227
## 522 Pacific_sardine 2 NA NA 263 228
## 523 Pacific_sardine 3 NA NA 263 159
## 524 Pacific_sardine 4 NA NA 263 97
## 525 Pacific_sardine 5 NA NA 263 90
## 526 Pacific_sardine 6 NA NA 263 70
## 527 Pacific_sardine 7 NA NA 263 44
## 528 Pacific_sardine 8 NA NA 263 31
## 529 Pacific_sardine 9 NA NA 263 31
## 530 Pacific_sardine 10 NA NA 263 23
## 531 Pacific_sardine 1 NA NA 268 252
## 532 Pacific_sardine 2 NA NA 268 205
## 533 Pacific_sardine 3 NA NA 268 161
## 534 Pacific_sardine 4 NA NA 268 118
## 535 Pacific_sardine 5 NA NA 268 78
## 536 Pacific_sardine 6 NA NA 268 60
## 537 Pacific_sardine 7 NA NA 268 44
## 538 Pacific_sardine 8 NA NA 268 33
## 539 Pacific_sardine 9 NA NA 268 24
## 540 Pacific_sardine 10 NA NA 268 25
## 541 Pacific_sardine 1 NA NA 273 245
## 542 Pacific_sardine 2 NA NA 273 195
## 543 Pacific_sardine 3 NA NA 273 155
## 544 Pacific_sardine 4 NA NA 273 130
## 545 Pacific_sardine 5 NA NA 273 81
## 546 Pacific_sardine 6 NA NA 273 67
## 547 Pacific_sardine 7 NA NA 273 46
## 548 Pacific_sardine 8 NA NA 273 31
## 549 Pacific_sardine 9 NA NA 273 29
## 550 Pacific_sardine 10 NA NA 273 21
## 551 Pacific_sardine 1 NA NA 278 231
## 552 Pacific_sardine 2 NA NA 278 212
## 553 Pacific_sardine 3 NA NA 278 180
## 554 Pacific_sardine 4 NA NA 278 104
## 555 Pacific_sardine 5 NA NA 278 101
## 556 Pacific_sardine 6 NA NA 278 58
## 557 Pacific_sardine 7 NA NA 278 36
## 558 Pacific_sardine 8 NA NA 278 29
## 559 Pacific_sardine 9 NA NA 278 28
## 560 Pacific_sardine 10 NA NA 278 21
## 561 Pacific_sardine 1 NA NA 283 225
## 562 Pacific_sardine 2 NA NA 283 218
## 563 Pacific_sardine 3 NA NA 283 143
## 564 Pacific_sardine 4 NA NA 283 128
## 565 Pacific_sardine 5 NA NA 283 107
## 566 Pacific_sardine 6 NA NA 283 55
## 567 Pacific_sardine 7 NA NA 283 46
## 568 Pacific_sardine 8 NA NA 283 44
## 569 Pacific_sardine 9 NA NA 283 17
## 570 Pacific_sardine 10 NA NA 283 17
## 571 Pacific_sardine 1 NA NA 288 222
## 572 Pacific_sardine 2 NA NA 288 222
## 573 Pacific_sardine 3 NA NA 288 168
## 574 Pacific_sardine 4 NA NA 288 124
## 575 Pacific_sardine 5 NA NA 288 92
## 576 Pacific_sardine 6 NA NA 288 69
## 577 Pacific_sardine 7 NA NA 288 31
## 578 Pacific_sardine 8 NA NA 288 28
## 579 Pacific_sardine 9 NA NA 288 22
## 580 Pacific_sardine 10 NA NA 288 22
## 581 Pacific_sardine 1 NA NA 293 257
## 582 Pacific_sardine 2 NA NA 293 225
## 583 Pacific_sardine 3 NA NA 293 145
## 584 Pacific_sardine 4 NA NA 293 111
## 585 Pacific_sardine 5 NA NA 293 101
## 586 Pacific_sardine 6 NA NA 293 48
## 587 Pacific_sardine 7 NA NA 293 42
## 588 Pacific_sardine 8 NA NA 293 34
## 589 Pacific_sardine 9 NA NA 293 18
## 590 Pacific_sardine 10 NA NA 293 19
## 591 Pacific_sardine 1 NA NA 298 266
## 592 Pacific_sardine 2 NA NA 298 188
## 593 Pacific_sardine 3 NA NA 298 157
## 594 Pacific_sardine 4 NA NA 298 107
## 595 Pacific_sardine 5 NA NA 298 101
## 596 Pacific_sardine 6 NA NA 298 60
## 597 Pacific_sardine 7 NA NA 298 44
## 598 Pacific_sardine 8 NA NA 298 38
## 599 Pacific_sardine 9 NA NA 298 23
## 600 Pacific_sardine 10 NA NA 298 16
## 601 Pacific_sardine 1 NA NA 303 235
## 602 Pacific_sardine 2 NA NA 303 193
## 603 Pacific_sardine 3 NA NA 303 168
## 604 Pacific_sardine 4 NA NA 303 116
## 605 Pacific_sardine 5 NA NA 303 106
## 606 Pacific_sardine 6 NA NA 303 62
## 607 Pacific_sardine 7 NA NA 303 52
## 608 Pacific_sardine 8 NA NA 303 25
## 609 Pacific_sardine 9 NA NA 303 28
## 610 Pacific_sardine 10 NA NA 303 15
## 611 Pacific_sardine 1 NA NA 308 249
## 612 Pacific_sardine 2 NA NA 308 205
## 613 Pacific_sardine 3 NA NA 308 157
## 614 Pacific_sardine 4 NA NA 308 124
## 615 Pacific_sardine 5 NA NA 308 68
## 616 Pacific_sardine 6 NA NA 308 64
## 617 Pacific_sardine 7 NA NA 308 57
## 618 Pacific_sardine 8 NA NA 308 34
## 619 Pacific_sardine 9 NA NA 308 26
## 620 Pacific_sardine 10 NA NA 308 16
## 621 Pacific_sardine 1 NA NA 313 235
## 622 Pacific_sardine 2 NA NA 313 193
## 623 Pacific_sardine 3 NA NA 313 156
## 624 Pacific_sardine 4 NA NA 313 132
## 625 Pacific_sardine 5 NA NA 313 102
## 626 Pacific_sardine 6 NA NA 313 64
## 627 Pacific_sardine 7 NA NA 313 43
## 628 Pacific_sardine 8 NA NA 313 31
## 629 Pacific_sardine 9 NA NA 313 22
## 630 Pacific_sardine 10 NA NA 313 22
## 631 Pacific_sardine 1 NA NA 318 228
## 632 Pacific_sardine 2 NA NA 318 206
## 633 Pacific_sardine 3 NA NA 318 171
## 634 Pacific_sardine 4 NA NA 318 111
## 635 Pacific_sardine 5 NA NA 318 96
## 636 Pacific_sardine 6 NA NA 318 66
## 637 Pacific_sardine 7 NA NA 318 41
## 638 Pacific_sardine 8 NA NA 318 39
## 639 Pacific_sardine 9 NA NA 318 26
## 640 Pacific_sardine 10 NA NA 318 16
## 641 Pacific_sardine 1 NA NA 323 238
## 642 Pacific_sardine 2 NA NA 323 192
## 643 Pacific_sardine 3 NA NA 323 169
## 644 Pacific_sardine 4 NA NA 323 117
## 645 Pacific_sardine 5 NA NA 323 91
## 646 Pacific_sardine 6 NA NA 323 63
## 647 Pacific_sardine 7 NA NA 323 52
## 648 Pacific_sardine 8 NA NA 323 35
## 649 Pacific_sardine 9 NA NA 323 22
## 650 Pacific_sardine 10 NA NA 323 21
## 651 Pacific_sardine 1 NA NA 328 238
## 652 Pacific_sardine 2 NA NA 328 204
## 653 Pacific_sardine 3 NA NA 328 162
## 654 Pacific_sardine 4 NA NA 328 127
## 655 Pacific_sardine 5 NA NA 328 87
## 656 Pacific_sardine 6 NA NA 328 71
## 657 Pacific_sardine 7 NA NA 328 40
## 658 Pacific_sardine 8 NA NA 328 32
## 659 Pacific_sardine 9 NA NA 328 20
## 660 Pacific_sardine 10 NA NA 328 19
## 661 Pacific_sardine 1 NA NA 333 249
## 662 Pacific_sardine 2 NA NA 333 196
## 663 Pacific_sardine 3 NA NA 333 171
## 664 Pacific_sardine 4 NA NA 333 109
## 665 Pacific_sardine 5 NA NA 333 103
## 666 Pacific_sardine 6 NA NA 333 47
## 667 Pacific_sardine 7 NA NA 333 46
## 668 Pacific_sardine 8 NA NA 333 34
## 669 Pacific_sardine 9 NA NA 333 29
## 670 Pacific_sardine 10 NA NA 333 16
## 671 Pacific_sardine 1 NA NA 338 234
## 672 Pacific_sardine 2 NA NA 338 212
## 673 Pacific_sardine 3 NA NA 338 162
## 674 Pacific_sardine 4 NA NA 338 125
## 675 Pacific_sardine 5 NA NA 338 94
## 676 Pacific_sardine 6 NA NA 338 57
## 677 Pacific_sardine 7 NA NA 338 36
## 678 Pacific_sardine 8 NA NA 338 41
## 679 Pacific_sardine 9 NA NA 338 16
## 680 Pacific_sardine 10 NA NA 338 23
## 681 Pacific_sardine 1 NA NA 343 232
## 682 Pacific_sardine 2 NA NA 343 209
## 683 Pacific_sardine 3 NA NA 343 176
## 684 Pacific_sardine 4 NA NA 343 117
## 685 Pacific_sardine 5 NA NA 343 92
## 686 Pacific_sardine 6 NA NA 343 55
## 687 Pacific_sardine 7 NA NA 343 52
## 688 Pacific_sardine 8 NA NA 343 33
## 689 Pacific_sardine 9 NA NA 343 24
## 690 Pacific_sardine 10 NA NA 343 10
## 691 Pacific_sardine 1 NA NA 348 217
## 692 Pacific_sardine 2 NA NA 348 195
## 693 Pacific_sardine 3 NA NA 348 171
## 694 Pacific_sardine 4 NA NA 348 117
## 695 Pacific_sardine 5 NA NA 348 85
## 696 Pacific_sardine 6 NA NA 348 82
## 697 Pacific_sardine 7 NA NA 348 47
## 698 Pacific_sardine 8 NA NA 348 37
## 699 Pacific_sardine 9 NA NA 348 27
## 700 Pacific_sardine 10 NA NA 348 22
## 701 Pacific_sardine 1 NA NA 353 241
## 702 Pacific_sardine 2 NA NA 353 219
## 703 Pacific_sardine 3 NA NA 353 156
## 704 Pacific_sardine 4 NA NA 353 121
## 705 Pacific_sardine 5 NA NA 353 84
## 706 Pacific_sardine 6 NA NA 353 64
## 707 Pacific_sardine 7 NA NA 353 39
## 708 Pacific_sardine 8 NA NA 353 38
## 709 Pacific_sardine 9 NA NA 353 26
## 710 Pacific_sardine 10 NA NA 353 12
## 711 Pacific_sardine 1 NA NA 358 229
## 712 Pacific_sardine 2 NA NA 358 216
## 713 Pacific_sardine 3 NA NA 358 168
## 714 Pacific_sardine 4 NA NA 358 114
## 715 Pacific_sardine 5 NA NA 358 95
## 716 Pacific_sardine 6 NA NA 358 57
## 717 Pacific_sardine 7 NA NA 358 43
## 718 Pacific_sardine 8 NA NA 358 38
## 719 Pacific_sardine 9 NA NA 358 19
## 720 Pacific_sardine 10 NA NA 358 21
## 721 Pacific_sardine 1 NA NA 363 233
## 722 Pacific_sardine 2 NA NA 363 175
## 723 Pacific_sardine 3 NA NA 363 162
## 724 Pacific_sardine 4 NA NA 363 134
## 725 Pacific_sardine 5 NA NA 363 102
## 726 Pacific_sardine 6 NA NA 363 71
## 727 Pacific_sardine 7 NA NA 363 53
## 728 Pacific_sardine 8 NA NA 363 24
## 729 Pacific_sardine 9 NA NA 363 29
## 730 Pacific_sardine 10 NA NA 363 17
## 731 Pacific_sardine 1 NA NA 368 227
## 732 Pacific_sardine 2 NA NA 368 215
## 733 Pacific_sardine 3 NA NA 368 154
## 734 Pacific_sardine 4 NA NA 368 125
## 735 Pacific_sardine 5 NA NA 368 88
## 736 Pacific_sardine 6 NA NA 368 72
## 737 Pacific_sardine 7 NA NA 368 46
## 738 Pacific_sardine 8 NA NA 368 31
## 739 Pacific_sardine 9 NA NA 368 25
## 740 Pacific_sardine 10 NA NA 368 17
## 741 Pacific_sardine 1 NA NA 373 257
## 742 Pacific_sardine 2 NA NA 373 186
## 743 Pacific_sardine 3 NA NA 373 162
## 744 Pacific_sardine 4 NA NA 373 109
## 745 Pacific_sardine 5 NA NA 373 89
## 746 Pacific_sardine 6 NA NA 373 71
## 747 Pacific_sardine 7 NA NA 373 43
## 748 Pacific_sardine 8 NA NA 373 36
## 749 Pacific_sardine 9 NA NA 373 27
## 750 Pacific_sardine 10 NA NA 373 20
## 751 Pacific_sardine 1 NA NA 378 241
## 752 Pacific_sardine 2 NA NA 378 189
## 753 Pacific_sardine 3 NA NA 378 166
## 754 Pacific_sardine 4 NA NA 378 119
## 755 Pacific_sardine 5 NA NA 378 84
## 756 Pacific_sardine 6 NA NA 378 80
## 757 Pacific_sardine 7 NA NA 378 44
## 758 Pacific_sardine 8 NA NA 378 28
## 759 Pacific_sardine 9 NA NA 378 25
## 760 Pacific_sardine 10 NA NA 378 24
## 761 Pacific_sardine 1 NA NA 383 237
## 762 Pacific_sardine 2 NA NA 383 207
## 763 Pacific_sardine 3 NA NA 383 185
## 764 Pacific_sardine 4 NA NA 383 98
## 765 Pacific_sardine 5 NA NA 383 85
## 766 Pacific_sardine 6 NA NA 383 61
## 767 Pacific_sardine 7 NA NA 383 51
## 768 Pacific_sardine 8 NA NA 383 30
## 769 Pacific_sardine 9 NA NA 383 27
## 770 Pacific_sardine 10 NA NA 383 19
## 771 Pacific_sardine 1 NA NA 388 213
## 772 Pacific_sardine 2 NA NA 388 212
## 773 Pacific_sardine 3 NA NA 388 171
## 774 Pacific_sardine 4 NA NA 388 125
## 775 Pacific_sardine 5 NA NA 388 95
## 776 Pacific_sardine 6 NA NA 388 54
## 777 Pacific_sardine 7 NA NA 388 47
## 778 Pacific_sardine 8 NA NA 388 40
## 779 Pacific_sardine 9 NA NA 388 21
## 780 Pacific_sardine 10 NA NA 388 22
## 781 Pacific_sardine 1 NA NA 393 215
## 782 Pacific_sardine 2 NA NA 393 208
## 783 Pacific_sardine 3 NA NA 393 179
## 784 Pacific_sardine 4 NA NA 393 122
## 785 Pacific_sardine 5 NA NA 393 82
## 786 Pacific_sardine 6 NA NA 393 77
## 787 Pacific_sardine 7 NA NA 393 39
## 788 Pacific_sardine 8 NA NA 393 39
## 789 Pacific_sardine 9 NA NA 393 30
## 790 Pacific_sardine 10 NA NA 393 9
## 791 Pacific_sardine 1 NA NA 398 250
## 792 Pacific_sardine 2 NA NA 398 194
## 793 Pacific_sardine 3 NA NA 398 155
## 794 Pacific_sardine 4 NA NA 398 131
## 795 Pacific_sardine 5 NA NA 398 93
## 796 Pacific_sardine 6 NA NA 398 55
## 797 Pacific_sardine 7 NA NA 398 41
## 798 Pacific_sardine 8 NA NA 398 33
## 799 Pacific_sardine 9 NA NA 398 33
## 800 Pacific_sardine 10 NA NA 398 15
## 801 Pacific_sardine 1 NA NA 403 244
## 802 Pacific_sardine 2 NA NA 403 203
## 803 Pacific_sardine 3 NA NA 403 164
## 804 Pacific_sardine 4 NA NA 403 135
## 805 Pacific_sardine 5 NA NA 403 76
## 806 Pacific_sardine 6 NA NA 403 51
## 807 Pacific_sardine 7 NA NA 403 48
## 808 Pacific_sardine 8 NA NA 403 40
## 809 Pacific_sardine 9 NA NA 403 29
## 810 Pacific_sardine 10 NA NA 403 10
## 811 Pacific_sardine 1 NA NA 408 221
## 812 Pacific_sardine 2 NA NA 408 219
## 813 Pacific_sardine 3 NA NA 408 186
## 814 Pacific_sardine 4 NA NA 408 130
## 815 Pacific_sardine 5 NA NA 408 70
## 816 Pacific_sardine 6 NA NA 408 57
## 817 Pacific_sardine 7 NA NA 408 40
## 818 Pacific_sardine 8 NA NA 408 40
## 819 Pacific_sardine 9 NA NA 408 24
## 820 Pacific_sardine 10 NA NA 408 13
## 821 Pacific_sardine 1 NA NA 413 213
## 822 Pacific_sardine 2 NA NA 413 215
## 823 Pacific_sardine 3 NA NA 413 185
## 824 Pacific_sardine 4 NA NA 413 120
## 825 Pacific_sardine 5 NA NA 413 88
## 826 Pacific_sardine 6 NA NA 413 68
## 827 Pacific_sardine 7 NA NA 413 40
## 828 Pacific_sardine 8 NA NA 413 32
## 829 Pacific_sardine 9 NA NA 413 23
## 830 Pacific_sardine 10 NA NA 413 16
## 831 Pacific_sardine 1 NA NA 418 275
## 832 Pacific_sardine 2 NA NA 418 199
## 833 Pacific_sardine 3 NA NA 418 161
## 834 Pacific_sardine 4 NA NA 418 112
## 835 Pacific_sardine 5 NA NA 418 88
## 836 Pacific_sardine 6 NA NA 418 62
## 837 Pacific_sardine 7 NA NA 418 46
## 838 Pacific_sardine 8 NA NA 418 27
## 839 Pacific_sardine 9 NA NA 418 18
## 840 Pacific_sardine 10 NA NA 418 12
## 841 Pacific_sardine 1 NA NA 423 243
## 842 Pacific_sardine 2 NA NA 423 207
## 843 Pacific_sardine 3 NA NA 423 162
## 844 Pacific_sardine 4 NA NA 423 99
## 845 Pacific_sardine 5 NA NA 423 96
## 846 Pacific_sardine 6 NA NA 423 72
## 847 Pacific_sardine 7 NA NA 423 47
## 848 Pacific_sardine 8 NA NA 423 29
## 849 Pacific_sardine 9 NA NA 423 24
## 850 Pacific_sardine 10 NA NA 423 21
## 851 Pacific_sardine 1 NA NA 428 225
## 852 Pacific_sardine 2 NA NA 428 221
## 853 Pacific_sardine 3 NA NA 428 170
## 854 Pacific_sardine 4 NA NA 428 117
## 855 Pacific_sardine 5 NA NA 428 79
## 856 Pacific_sardine 6 NA NA 428 62
## 857 Pacific_sardine 7 NA NA 428 46
## 858 Pacific_sardine 8 NA NA 428 38
## 859 Pacific_sardine 9 NA NA 428 18
## 860 Pacific_sardine 10 NA NA 428 24
## 861 Pacific_sardine 1 NA NA 433 243
## 862 Pacific_sardine 2 NA NA 433 202
## 863 Pacific_sardine 3 NA NA 433 149
## 864 Pacific_sardine 4 NA NA 433 128
## 865 Pacific_sardine 5 NA NA 433 90
## 866 Pacific_sardine 6 NA NA 433 69
## 867 Pacific_sardine 7 NA NA 433 50
## 868 Pacific_sardine 8 NA NA 433 37
## 869 Pacific_sardine 9 NA NA 433 16
## 870 Pacific_sardine 10 NA NA 433 16
## 871 Pacific_sardine 1 NA NA 438 207
## 872 Pacific_sardine 2 NA NA 438 234
## 873 Pacific_sardine 3 NA NA 438 170
## 874 Pacific_sardine 4 NA NA 438 122
## 875 Pacific_sardine 5 NA NA 438 91
## 876 Pacific_sardine 6 NA NA 438 67
## 877 Pacific_sardine 7 NA NA 438 39
## 878 Pacific_sardine 8 NA NA 438 32
## 879 Pacific_sardine 9 NA NA 438 25
## 880 Pacific_sardine 10 NA NA 438 13
## 881 Pacific_sardine 1 NA NA 443 226
## 882 Pacific_sardine 2 NA NA 443 215
## 883 Pacific_sardine 3 NA NA 443 160
## 884 Pacific_sardine 4 NA NA 443 133
## 885 Pacific_sardine 5 NA NA 443 91
## 886 Pacific_sardine 6 NA NA 443 50
## 887 Pacific_sardine 7 NA NA 443 48
## 888 Pacific_sardine 8 NA NA 443 41
## 889 Pacific_sardine 9 NA NA 443 21
## 890 Pacific_sardine 10 NA NA 443 15
## 891 Pacific_sardine 1 NA NA 448 244
## 892 Pacific_sardine 2 NA NA 448 193
## 893 Pacific_sardine 3 NA NA 448 162
## 894 Pacific_sardine 4 NA NA 448 129
## 895 Pacific_sardine 5 NA NA 448 86
## 896 Pacific_sardine 6 NA NA 448 57
## 897 Pacific_sardine 7 NA NA 448 54
## 898 Pacific_sardine 8 NA NA 448 37
## 899 Pacific_sardine 9 NA NA 448 25
## 900 Pacific_sardine 10 NA NA 448 13
## 901 Pacific_sardine 1 NA NA 453 239
## 902 Pacific_sardine 2 NA NA 453 199
## 903 Pacific_sardine 3 NA NA 453 159
## 904 Pacific_sardine 4 NA NA 453 126
## 905 Pacific_sardine 5 NA NA 453 98
## 906 Pacific_sardine 6 NA NA 453 55
## 907 Pacific_sardine 7 NA NA 453 43
## 908 Pacific_sardine 8 NA NA 453 36
## 909 Pacific_sardine 9 NA NA 453 25
## 910 Pacific_sardine 10 NA NA 453 20
## 911 Pacific_sardine 1 NA NA 458 245
## 912 Pacific_sardine 2 NA NA 458 203
## 913 Pacific_sardine 3 NA NA 458 155
## 914 Pacific_sardine 4 NA NA 458 134
## 915 Pacific_sardine 5 NA NA 458 96
## 916 Pacific_sardine 6 NA NA 458 57
## 917 Pacific_sardine 7 NA NA 458 49
## 918 Pacific_sardine 8 NA NA 458 31
## 919 Pacific_sardine 9 NA NA 458 16
## 920 Pacific_sardine 10 NA NA 458 14
## 921 Pacific_sardine 1 NA NA 463 237
## 922 Pacific_sardine 2 NA NA 463 205
## 923 Pacific_sardine 3 NA NA 463 195
## 924 Pacific_sardine 4 NA NA 463 112
## 925 Pacific_sardine 5 NA NA 463 99
## 926 Pacific_sardine 6 NA NA 463 51
## 927 Pacific_sardine 7 NA NA 463 49
## 928 Pacific_sardine 8 NA NA 463 30
## 929 Pacific_sardine 9 NA NA 463 15
## 930 Pacific_sardine 10 NA NA 463 7
## 931 Pacific_sardine 1 NA NA 468 232
## 932 Pacific_sardine 2 NA NA 468 198
## 933 Pacific_sardine 3 NA NA 468 158
## 934 Pacific_sardine 4 NA NA 468 110
## 935 Pacific_sardine 5 NA NA 468 103
## 936 Pacific_sardine 6 NA NA 468 84
## 937 Pacific_sardine 7 NA NA 468 40
## 938 Pacific_sardine 8 NA NA 468 26
## 939 Pacific_sardine 9 NA NA 468 34
## 940 Pacific_sardine 10 NA NA 468 15
## 941 Pacific_sardine 1 NA NA 473 224
## 942 Pacific_sardine 2 NA NA 473 216
## 943 Pacific_sardine 3 NA NA 473 165
## 944 Pacific_sardine 4 NA NA 473 112
## 945 Pacific_sardine 5 NA NA 473 94
## 946 Pacific_sardine 6 NA NA 473 65
## 947 Pacific_sardine 7 NA NA 473 49
## 948 Pacific_sardine 8 NA NA 473 34
## 949 Pacific_sardine 9 NA NA 473 24
## 950 Pacific_sardine 10 NA NA 473 17
## 951 Pacific_sardine 1 NA NA 478 228
## 952 Pacific_sardine 2 NA NA 478 221
## 953 Pacific_sardine 3 NA NA 478 166
## 954 Pacific_sardine 4 NA NA 478 120
## 955 Pacific_sardine 5 NA NA 478 87
## 956 Pacific_sardine 6 NA NA 478 63
## 957 Pacific_sardine 7 NA NA 478 48
## 958 Pacific_sardine 8 NA NA 478 35
## 959 Pacific_sardine 9 NA NA 478 23
## 960 Pacific_sardine 10 NA NA 478 9
## 961 Pacific_sardine 1 NA NA 483 234
## 962 Pacific_sardine 2 NA NA 483 201
## 963 Pacific_sardine 3 NA NA 483 168
## 964 Pacific_sardine 4 NA NA 483 130
## 965 Pacific_sardine 5 NA NA 483 83
## 966 Pacific_sardine 6 NA NA 483 53
## 967 Pacific_sardine 7 NA NA 483 50
## 968 Pacific_sardine 8 NA NA 483 38
## 969 Pacific_sardine 9 NA NA 483 24
## 970 Pacific_sardine 10 NA NA 483 19
## 971 Pacific_sardine 1 NA NA 488 250
## 972 Pacific_sardine 2 NA NA 488 212
## 973 Pacific_sardine 3 NA NA 488 165
## 974 Pacific_sardine 4 NA NA 488 133
## 975 Pacific_sardine 5 NA NA 488 82
## 976 Pacific_sardine 6 NA NA 488 64
## 977 Pacific_sardine 7 NA NA 488 44
## 978 Pacific_sardine 8 NA NA 488 24
## 979 Pacific_sardine 9 NA NA 488 18
## 980 Pacific_sardine 10 NA NA 488 8
## 981 Pacific_sardine 1 NA NA 493 245
## 982 Pacific_sardine 2 NA NA 493 217
## 983 Pacific_sardine 3 NA NA 493 156
## 984 Pacific_sardine 4 NA NA 493 120
## 985 Pacific_sardine 5 NA NA 493 90
## 986 Pacific_sardine 6 NA NA 493 49
## 987 Pacific_sardine 7 NA NA 493 51
## 988 Pacific_sardine 8 NA NA 493 32
## 989 Pacific_sardine 9 NA NA 493 20
## 990 Pacific_sardine 10 NA NA 493 20#Get the age bins
age_bin_names <- names(stocksynthesis.data$agecomp)[10:length(names(stocksynthesis.data$agecomp))]
age_bins <- sub("a","",age_bin_names)
age_comp_flat <- reformat_compositions(age_comp_data,
round.places = 4,
comp_type = "agecomp")
## Write age composition data for survey
stocksynthesis.data <- SS_write_comps(ss_data_list = stocksynthesis.data,
comp_matrix = list(age_comp_flat[burnin:(burnin+nyears-1),]),
data_rows = list(stocksynthesis.data$styr:(stocksynthesis.data$styr+nyears-1)),
sampling_month = list(rep(survey_month,nyears)),
data_type = c("agecomp"),
fleet_number = c(1),
bins = list(age_bins),
caal_bool = c(FALSE))
stocksynthesis.data$agecomp## Yr Seas FltSvy Gender Part Ageerr Lbin_lo Lbin_hi Nsamp a1 a2
## 1 1 7 1 0 0 1 -1 -1 1 0.227 0.181
## 2 2 7 1 0 0 1 -1 -1 1 0.222 0.211
## 3 3 7 1 0 0 1 -1 -1 1 0.253 0.201
## 4 4 7 1 0 0 1 -1 -1 1 0.226 0.221
## 5 5 7 1 0 0 1 -1 -1 1 0.24 0.189
## 6 6 7 1 0 0 1 -1 -1 1 0.229 0.213
## 7 7 7 1 0 0 1 -1 -1 1 0.223 0.192
## 8 8 7 1 0 0 1 -1 -1 1 0.236 0.198
## 9 9 7 1 0 0 1 -1 -1 1 0.239 0.206
## 10 10 7 1 0 0 1 -1 -1 1 0.218 0.182
## 11 11 7 1 0 0 1 -1 -1 1 0.246 0.199
## 12 12 7 1 0 0 1 -1 -1 1 0.235 0.225
## 13 13 7 1 0 0 1 -1 -1 1 0.235 0.202
## 14 14 7 1 0 0 1 -1 -1 1 0.242 0.184
## 15 15 7 1 0 0 1 -1 -1 1 0.251 0.215
## 16 16 7 1 0 0 1 -1 -1 1 0.228 0.211
## 17 17 7 1 0 0 1 -1 -1 1 0.25 0.218
## 18 18 7 1 0 0 1 -1 -1 1 0.231 0.195
## 19 19 7 1 0 0 1 -1 -1 1 0.229 0.205
## 20 20 7 1 0 0 1 -1 -1 1 0.221 0.206
## 21 21 7 1 0 0 1 -1 -1 1 0.229 0.22
## 22 22 7 1 0 0 1 -1 -1 1 0.238 0.221
## 23 23 7 1 0 0 1 -1 -1 1 0.252 0.193
## 24 24 7 1 0 0 1 -1 -1 1 0.227 0.228
## 25 25 7 1 0 0 1 -1 -1 1 0.252 0.205
## 26 26 7 1 0 0 1 -1 -1 1 0.245 0.195
## 27 27 7 1 0 0 1 -1 -1 1 0.231 0.212
## 28 28 7 1 0 0 1 -1 -1 1 0.225 0.218
## 29 29 7 1 0 0 1 -1 -1 1 0.222 0.222
## 30 30 7 1 0 0 1 -1 -1 1 0.257 0.225
## 31 31 7 1 0 0 1 -1 -1 1 0.266 0.188
## 32 32 7 1 0 0 1 -1 -1 1 0.235 0.193
## 33 33 7 1 0 0 1 -1 -1 1 0.249 0.205
## 34 34 7 1 0 0 1 -1 -1 1 0.235 0.193
## 35 35 7 1 0 0 1 -1 -1 1 0.228 0.206
## 36 36 7 1 0 0 1 -1 -1 1 0.238 0.192
## 37 37 7 1 0 0 1 -1 -1 1 0.238 0.204
## 38 38 7 1 0 0 1 -1 -1 1 0.249 0.196
## 39 39 7 1 0 0 1 -1 -1 1 0.234 0.212
## 40 40 7 1 0 0 1 -1 -1 1 0.232 0.209
## 41 41 7 1 0 0 1 -1 -1 1 0.217 0.195
## 42 42 7 1 0 0 1 -1 -1 1 0.241 0.219
## 43 43 7 1 0 0 1 -1 -1 1 0.229 0.216
## 44 44 7 1 0 0 1 -1 -1 1 0.233 0.175
## 45 45 7 1 0 0 1 -1 -1 1 0.227 0.215
## 46 46 7 1 0 0 1 -1 -1 1 0.257 0.186
## 47 47 7 1 0 0 1 -1 -1 1 0.241 0.189
## 48 48 7 1 0 0 1 -1 -1 1 0.237 0.207
## 49 49 7 1 0 0 1 -1 -1 1 0.213 0.212
## 50 50 7 1 0 0 1 -1 -1 1 0.215 0.208
## a3 a4 a5 a6 a7 a8 a9 a10
## 1 0.179 0.133 0.08 0.083 0.051 0.034 0.019 0.013
## 2 0.168 0.115 0.09 0.073 0.046 0.037 0.021 0.017
## 3 0.166 0.122 0.098 0.051 0.044 0.032 0.015 0.018
## 4 0.177 0.114 0.09 0.061 0.036 0.037 0.025 0.013
## 5 0.163 0.127 0.089 0.066 0.051 0.037 0.019 0.019
## 6 0.164 0.124 0.086 0.057 0.049 0.035 0.022 0.021
## 7 0.176 0.133 0.087 0.062 0.051 0.034 0.026 0.016
## 8 0.169 0.108 0.107 0.068 0.048 0.027 0.02 0.019
## 9 0.139 0.103 0.103 0.081 0.051 0.038 0.022 0.018
## 10 0.166 0.125 0.102 0.077 0.059 0.039 0.017 0.015
## 11 0.156 0.122 0.086 0.071 0.044 0.04 0.026 0.01
## 12 0.174 0.114 0.082 0.05 0.046 0.035 0.021 0.018
## 13 0.161 0.113 0.109 0.052 0.046 0.033 0.026 0.023
## 14 0.16 0.121 0.083 0.072 0.048 0.034 0.026 0.03
## 15 0.166 0.119 0.067 0.069 0.047 0.028 0.025 0.013
## 16 0.183 0.12 0.084 0.066 0.047 0.029 0.018 0.014
## 17 0.134 0.122 0.078 0.047 0.063 0.036 0.028 0.024
## 18 0.176 0.113 0.079 0.069 0.052 0.033 0.032 0.02
## 19 0.166 0.109 0.089 0.065 0.053 0.035 0.033 0.016
## 20 0.182 0.113 0.089 0.069 0.044 0.032 0.026 0.018
## 21 0.153 0.121 0.096 0.069 0.048 0.02 0.027 0.017
## 22 0.151 0.122 0.078 0.058 0.051 0.029 0.032 0.02
## 23 0.17 0.122 0.083 0.057 0.051 0.037 0.018 0.017
## 24 0.159 0.097 0.09 0.07 0.044 0.031 0.031 0.023
## 25 0.161 0.118 0.078 0.06 0.044 0.033 0.024 0.025
## 26 0.155 0.13 0.081 0.067 0.046 0.031 0.029 0.021
## 27 0.18 0.104 0.101 0.058 0.036 0.029 0.028 0.021
## 28 0.143 0.128 0.107 0.055 0.046 0.044 0.017 0.017
## 29 0.168 0.124 0.092 0.069 0.031 0.028 0.022 0.022
## 30 0.145 0.111 0.101 0.048 0.042 0.034 0.018 0.019
## 31 0.157 0.107 0.101 0.06 0.044 0.038 0.023 0.016
## 32 0.168 0.116 0.106 0.062 0.052 0.025 0.028 0.015
## 33 0.157 0.124 0.068 0.064 0.057 0.034 0.026 0.016
## 34 0.156 0.132 0.102 0.064 0.043 0.031 0.022 0.022
## 35 0.171 0.111 0.096 0.066 0.041 0.039 0.026 0.016
## 36 0.169 0.117 0.091 0.063 0.052 0.035 0.022 0.021
## 37 0.162 0.127 0.087 0.071 0.04 0.032 0.02 0.019
## 38 0.171 0.109 0.103 0.047 0.046 0.034 0.029 0.016
## 39 0.162 0.125 0.094 0.057 0.036 0.041 0.016 0.023
## 40 0.176 0.117 0.092 0.055 0.052 0.033 0.024 0.01
## 41 0.171 0.117 0.085 0.082 0.047 0.037 0.027 0.022
## 42 0.156 0.121 0.084 0.064 0.039 0.038 0.026 0.012
## 43 0.168 0.114 0.095 0.057 0.043 0.038 0.019 0.021
## 44 0.162 0.134 0.102 0.071 0.053 0.024 0.029 0.017
## 45 0.154 0.125 0.088 0.072 0.046 0.031 0.025 0.017
## 46 0.162 0.109 0.089 0.071 0.043 0.036 0.027 0.02
## 47 0.166 0.119 0.084 0.08 0.044 0.028 0.025 0.024
## 48 0.185 0.098 0.085 0.061 0.051 0.03 0.027 0.019
## 49 0.171 0.125 0.095 0.054 0.047 0.04 0.021 0.022
## 50 0.179 0.122 0.082 0.077 0.039 0.039 0.03 0.009#We end up using CAAL for the survey below, so let's generate fishery age comps instead
effN <- data.frame(species=species, effN=effN)
catch_numssshigh <- sample_fish(catch_numbers, effN)
#Get weights
# aggregate true resn per survey or fishery subset design
catch_aggresnss <- aggregateDensityData(dat = results$resn,
time = c(0:111),
species = species,
boxes = boxes)
# aggregate true structn per survey or fishery subsetdesign
catch_aggstructnss <- aggregateDensityData(dat = results$structn,
time = c(0:111),
species = species,
boxes = boxes)
#dont sample these, just aggregate them using median
catch_structnss <- sample_fish(catch_aggstructnss, effN, sample = FALSE)
catch_resnss <- sample_fish(catch_aggresnss, effN, sample = FALSE)
str(catch_numssshigh)## 'data.frame': 500 obs. of 6 variables:
## $ species : Factor w/ 1 level "Pacific_sardine": 1 1 1 1 1 1 1 1 1 1 ...
## $ agecl : num 1 2 3 4 5 6 7 8 9 10 ...
## $ polygon : logi NA NA NA NA NA NA ...
## $ layer : logi NA NA NA NA NA NA ...
## $ time : int 30 30 30 30 30 30 30 30 30 30 ...
## $ atoutput: int 134 110 231 167 113 75 64 43 35 28 ...catch_length <- calc_age2length(structn = catch_structnss,
resn = catch_resnss,
nums = catch_numssshigh,
biolprm = results$biolprm, fgs = results$fgs,
maxbin = maxbin,
CVlenage = CVs$lenage, remove.zeroes=TRUE)Setting up EM
For the EM, we want conditional age-at-length (CAAL) and length composition data only. So we use the same function with our matrices of length and CAAL comp data to write to the data file.
#Check length compositions match age compositions
ss_length_stdsurv$natlength %>%
group_by(time,agecl) %>%
summarise(sum(atoutput))## # A tibble: 976 x 3
## # Groups: time [?]
## time agecl `sum(atoutput)`
## <int> <dbl> <dbl>
## 1 3 1 78
## 2 3 2 421
## 3 3 3 242
## 4 3 4 107
## 5 3 5 64
## 6 3 6 42
## 7 3 7 10
## 8 3 8 19
## 9 3 9 7
## 10 8 1 483
## # ... with 966 more rowslen_comp_data <- ss_length_stdsurv$natlength
fish_len_comp_data <- catch_length$natlengthOnce we have the natlength matrix, we can munge the data into the proper CAAL and length bin format for SS
caal_comp_flat <- reformat_compositions(len_comp_data, round.places=4,
comp_type="caalcomp")
#remove burnin
caal_comp_final <- filter(caal_comp_flat,
time %in% survey_years)
#Add over age classes to get sample size
len_comp_flat <- reformat_compositions(len_comp_data,
round.places = 0,
comp_type="lencomp")
#remove burnin
len_comp_final <- filter(len_comp_flat,
time %in% survey_years)
length_bins <- as.integer(names(len_comp_final))## Warning: NAs introduced by coercionlength_bins <- length_bins[!is.na(length_bins)]
fish_len_comp_flat <- reformat_compositions(catch_length$natlength,
round.places = 0,
comp_type="lencomp")
#remove burnin
fish_len_comp_final <- filter(fish_len_comp_flat,
time %in% fish_years)
fish_age_comp_flat <- reformat_compositions(catch_numssshigh,
comp_type="agecomp")
#remove burnin
fish_age_comp_final <- filter(fish_age_comp_flat,
time %in% fish_years)
comp_list <- list(caal_comp_final,len_comp_final, fish_age_comp_final, fish_len_comp_final)
apply_month <- list(rep(survey_month, nrow(comp_list[[1]])), rep(survey_month, nrow(comp_list[[2]])), rep(fishing_month,nrow(comp_list[[3]])),rep(fishing_month,nrow(comp_list[[4]])))
# Write CAAL and length composition data
stocksynthesis.data <- SS_write_comps(ss_data_list = stocksynthesis.data, comp_matrix = comp_list, data_rows = list((comp_list[[1]]$time-survey_sample_time)/timestep + 1 ,(survey_years-survey_sample_time)/timestep + 1,fish_years,fish_years),
sampling_month = apply_month, data_type = rep(c("agecomp", "lencomp"),2), fleet_number = c(2,2,1,1), bins = list(age_bins, length_bins, age_bins, length_bins), caal_bool = c(TRUE, rep(FALSE,3)))
head(stocksynthesis.data$lencomp)## Yr Seas FltSvy Gender Part Nsamp l10 l11 l12 l13 l14 l15 l16 l17 l18 l19
## 1 30 7 2 0 0 991 2 13 39 62 59 43 35 37 41 35
## 2 31 7 2 0 0 989 2 12 38 61 58 43 37 42 46 42
## 3 32 7 2 0 0 989 2 14 43 69 66 47 36 39 43 40
## 4 33 7 2 0 0 988 2 12 38 61 60 43 36 40 47 44
## 5 34 7 2 0 0 991 2 13 40 65 62 43 33 35 40 38
## 6 35 7 2 0 0 992 2 12 39 62 60 43 35 39 45 42
## l20 l21 l22 l23 l24 l25 l26 l27 l28 l29 l30 l31 l32 l33 l34 l35 l36 l37
## 1 28 25 28 31 34 34 33 32 30 29 28 26 26 24 24 23 21 22
## 2 33 27 25 28 31 31 31 29 27 26 25 25 25 24 24 24 20 21
## 3 32 25 24 27 30 31 31 30 28 27 27 28 26 24 22 21 19 18
## 4 36 28 25 28 30 32 33 30 29 26 26 25 24 24 21 21 19 19
## 5 31 25 22 25 28 30 31 30 28 28 28 27 27 24 23 22 21 20
## 6 34 26 24 26 28 30 30 30 28 27 27 25 25 23 22 21 20 19
## l38 l39 l40 l41 l42 l43 l44 l45 l46 l47 l48 l49 l50 l51 l52 l53 l54
## 1 19 18 16 15 13 11 9 8 5 4 4 3 2 0 0 0 0
## 2 20 18 16 16 13 11 9 8 6 4 4 3 3 1 0 0 0
## 3 17 16 15 13 11 9 9 8 6 4 4 3 3 1 1 0 0
## 4 17 16 16 14 13 10 9 9 7 6 4 3 3 2 0 0 0
## 5 21 19 17 15 14 12 11 10 9 6 4 4 3 3 1 1 0
## 6 18 18 16 15 14 13 11 10 9 7 5 4 3 3 1 1 0head(stocksynthesis.data$agecomp)## Yr Seas FltSvy Gender Part Ageerr Lbin_lo Lbin_hi Nsamp a1 a2
## 1 30 7 2 0 0 1 10 11 0.002 0.002 0
## 2 30 7 2 0 0 1 11 12 0.0131 0.0131 0
## 3 30 7 2 0 0 1 12 13 0.0394 0.0394 0
## 4 30 7 2 0 0 1 13 14 0.0626 0.0626 0
## 5 30 7 2 0 0 1 14 15 0.0595 0.0575 0.002
## 6 30 7 2 0 0 1 15 16 0.0434 0.0343 0.0091
## a3 a4 a5 a6 a7 a8 a9 a10
## 1 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0#Change length bin structure to match atlantis data
stocksynthesis.data$lbin_vector <- length_bins
#Set lbin_method to 1 - this makes the population length bins match the data bins
#When lbin_method==1, we just comment out the binwidth, minimum, and maximum size arguments since they aren't used
stocksynthesis.data$lbin_method <- 1
stocksynthesis.data$binwidth <- "#"
stocksynthesis.data$minimum_size <- "#"
stocksynthesis.data$maximum_size <- "#"
#Change minimum sample size to 0.001 for CAAL data (SS won't let it go lower than this)
stocksynthesis.data$age_info$minsamplesize <- rep(0.001,2)
SS_writedat(stocksynthesis.data, outfile = paste0("./inst/extdata/",model_dir,
datfile_name),
overwrite=TRUE)## running SS_writedat## running SS_writedat_3.30## opening connection to ./inst/extdata/Sardine_SS_files/sardEM_3_3.dat## file written to ./inst/extdata/Sardine_SS_files/sardEM_3_3.datComing up with dynamic life history parameters
Below we get the weight-length relationship parameters from atlantis, calculate h and R0 from Atlantis \(\alpha\) and \(\beta\) parameters, use the function to back out natural mortality (M) from Atlantis, and use the survey length-at-age from Atlantis to estimate a growth curve.
#Get biological parameters
biolprm <- results$biolprm
fgs <- results$fgs
li_a_use <- biolprm$wl[match(fgs$Code[match(species,fgs$Name)],biolprm$wl[, 1]), 2]/1000
li_b_use <- biolprm$wl[match(fgs$Code[match(species,fgs$Name)],biolprm$wl[, 1]), 3]
len_nonburn <- ss_length_stdsurv$mulen %>%
filter(time > burnin*timestep)
plot(len_nonburn$atoutput~len_nonburn$agecl, col=len_nonburn$time)
length.data <- data.frame("Year"=(len_nonburn$time-survey_sample_time)/timestep+1, length=len_nonburn$atoutput, Weight=NA, Sex="Female", age=as.integer(len_nonburn$agecl))
#require(bbmle)
#vb_estimates <-sample_fit_vbgf(length.data, 25, 45, 0.4,
# 0.1, 0.1, 20, 40, 0.05, 0.01, 0.01,
# 30, 50, 0.6, 0.3, 0.3, 0.5, 10)Running stock synthesis
After the data and control file modifications, ensure you copy the local SS 3.3 executable into the folder containing the model files. Then run the following chunk.
#Run stock synthesis model
run_stocksynthesis(species = species, model_dir = model_dir, show_output = TRUE)## Running ss EM for species: Pacific_sardine