From de4238e355fee6a1c09a5db0866989a5377983fc Mon Sep 17 00:00:00 2001 From: Iago Mosqueira Date: Fri, 10 Aug 2018 15:28:03 +0200 Subject: [PATCH] v2.5.1.9001 --- DESCRIPTION | 4 +- R/swon.R | 8 - README.md | 4 +- docs/articles/index.html | 132 +++++++++++++ docs/authors.html | 132 +++++++++++++ docs/docsearch.css | 148 ++++++++++++++ docs/docsearch.js | 85 ++++++++ docs/index.html | 187 ++++++++++++++++++ docs/link.svg | 12 ++ docs/pkgdown.css | 232 ++++++++++++++++++++++ docs/pkgdown.js | 110 +++++++++++ docs/pkgdown.yml | 5 + docs/reference/ages.html | 177 +++++++++++++++++ docs/reference/cas.html | 158 +++++++++++++++ docs/reference/cc.html | 184 ++++++++++++++++++ docs/reference/dnormal.html | 181 +++++++++++++++++ docs/reference/elas.html | 180 +++++++++++++++++ docs/reference/gascuel.html | 188 ++++++++++++++++++ docs/reference/gislason.html | 194 +++++++++++++++++++ docs/reference/gompertz.html | 183 ++++++++++++++++++ docs/reference/grwdd.html | 224 +++++++++++++++++++++ docs/reference/index.html | 364 +++++++++++++++++++++++++++++++++++ docs/reference/knife.html | 193 +++++++++++++++++++ docs/reference/lambda.html | 183 ++++++++++++++++++ docs/reference/len2wt.html | 181 +++++++++++++++++ docs/reference/leslie.html | 185 ++++++++++++++++++ docs/reference/lhEql.html | 228 ++++++++++++++++++++++ docs/reference/lhPar.html | 215 +++++++++++++++++++++ docs/reference/lhRef.html | 201 +++++++++++++++++++ docs/reference/logistic.html | 176 +++++++++++++++++ docs/reference/lopt.html | 208 ++++++++++++++++++++ docs/reference/loptAge.html | 196 +++++++++++++++++++ docs/reference/lorenzen.html | 180 +++++++++++++++++ docs/reference/m.html | 211 ++++++++++++++++++++ docs/reference/matdd.html | 223 +++++++++++++++++++++ docs/reference/mdd.html | 226 ++++++++++++++++++++++ docs/reference/moment.html | 180 +++++++++++++++++ docs/reference/powh.html | 261 +++++++++++++++++++++++++ docs/reference/refs.html | 200 +++++++++++++++++++ docs/reference/richards.html | 181 +++++++++++++++++ docs/reference/rnoise.html | 232 ++++++++++++++++++++++ docs/reference/rod.html | 182 ++++++++++++++++++ docs/reference/sigmoid.html | 190 ++++++++++++++++++ docs/reference/sv.html | 180 +++++++++++++++++ docs/reference/teleost.html | 164 ++++++++++++++++ docs/reference/unbin.html | 176 +++++++++++++++++ docs/reference/vonB.html | 185 ++++++++++++++++++ docs/reference/wklife.html | 168 ++++++++++++++++ docs/reference/wt2len.html | 181 +++++++++++++++++ 49 files changed, 8366 insertions(+), 12 deletions(-) delete mode 100644 R/swon.R create mode 100644 docs/articles/index.html create mode 100644 docs/authors.html create mode 100644 docs/docsearch.css create mode 100644 docs/docsearch.js create mode 100644 docs/index.html create mode 100644 docs/link.svg create mode 100644 docs/pkgdown.css create mode 100644 docs/pkgdown.js create mode 100644 docs/pkgdown.yml create mode 100644 docs/reference/ages.html create mode 100644 docs/reference/cas.html create mode 100644 docs/reference/cc.html create mode 100644 docs/reference/dnormal.html create mode 100644 docs/reference/elas.html create mode 100644 docs/reference/gascuel.html create mode 100644 docs/reference/gislason.html create mode 100644 docs/reference/gompertz.html create mode 100644 docs/reference/grwdd.html create mode 100644 docs/reference/index.html create mode 100644 docs/reference/knife.html create mode 100644 docs/reference/lambda.html create mode 100644 docs/reference/len2wt.html create mode 100644 docs/reference/leslie.html create mode 100644 docs/reference/lhEql.html create mode 100644 docs/reference/lhPar.html create mode 100644 docs/reference/lhRef.html create mode 100644 docs/reference/logistic.html create mode 100644 docs/reference/lopt.html create mode 100644 docs/reference/loptAge.html create mode 100644 docs/reference/lorenzen.html create mode 100644 docs/reference/m.html create mode 100644 docs/reference/matdd.html create mode 100644 docs/reference/mdd.html create mode 100644 docs/reference/moment.html create mode 100644 docs/reference/powh.html create mode 100644 docs/reference/refs.html create mode 100644 docs/reference/richards.html create mode 100644 docs/reference/rnoise.html create mode 100644 docs/reference/rod.html create mode 100644 docs/reference/sigmoid.html create mode 100644 docs/reference/sv.html create mode 100644 docs/reference/teleost.html create mode 100644 docs/reference/unbin.html create mode 100644 docs/reference/vonB.html create mode 100644 docs/reference/wklife.html create mode 100644 docs/reference/wt2len.html diff --git a/DESCRIPTION b/DESCRIPTION index 15cbb6b..d59ab35 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: FLife Type: Package Title: Methods for Modelling Life History Traits -Version: 3.2.0 -Date: 2018-04-18 +Version: 3.2.1.9001 +Date: 2018-07-25 Authors@R: person(given = "Laurence", family = "Kell", role = c("aut", "cre"), email = "laurie@seaplusplus.co.uk") Maintainer: Laurence Kell diff --git a/R/swon.R b/R/swon.R deleted file mode 100644 index d52842e..0000000 --- a/R/swon.R +++ /dev/null @@ -1,8 +0,0 @@ -Six operational objectives are: - -1. stock has a greater than ___% probability of occurring in the green quadrant of the Kobe matrix for (period). -2. stock has a less than ___% probability of entering the red quadrant of the Kobe matrix for (period). -3. less than ___% probability of the NSWO stock falling below BLIM (to be defined) for (period). -4. Maximize catch levels, achieving BMSY. -5. Limit change in TAC to ___% between management periods. -6. Ensure that fishing mortality of juveniles is below ___ for (period). \ No newline at end of file diff --git a/README.md b/README.md index c120dfa..c1ddc7e 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # FLife -- Version: 3.0.0 -- Date: 2018-04-17 +- Version: 3.2.1 +- Date: 2018-07-19 - Author: %USER% - Maintainer: %USER2% - Repository: diff --git a/docs/articles/index.html b/docs/articles/index.html new file mode 100644 index 0000000..3fada84 --- /dev/null +++ b/docs/articles/index.html @@ -0,0 +1,132 @@ + + + + + + + + +Articles • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Articles

+
+ +
+

All vignettes

+

+ + +
+
+
+ +
+
+

Developed by Laurence Kell.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + + + diff --git a/docs/authors.html b/docs/authors.html new file mode 100644 index 0000000..8942e69 --- /dev/null +++ b/docs/authors.html @@ -0,0 +1,132 @@ + + + + + + + + +Authors • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Authors

+
+ +
    +
  • +

    Laurence Kell. Author, maintainer. +

    +
    • +
+ +
+ +
+ + +
+
+

Developed by Laurence Kell.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + + + diff --git a/docs/docsearch.css b/docs/docsearch.css new file mode 100644 index 0000000..e5f1fe1 --- /dev/null +++ b/docs/docsearch.css @@ -0,0 +1,148 @@ +/* Docsearch -------------------------------------------------------------- */ +/* + Source: https://github.com/algolia/docsearch/ + License: MIT +*/ + +.algolia-autocomplete { + display: block; + -webkit-box-flex: 1; + -ms-flex: 1; + flex: 1 +} + +.algolia-autocomplete .ds-dropdown-menu { + width: 100%; + min-width: none; + max-width: none; + padding: .75rem 0; + background-color: #fff; + background-clip: padding-box; + border: 1px solid rgba(0, 0, 0, .1); + box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175); +} + +@media (min-width:768px) { + .algolia-autocomplete .ds-dropdown-menu { + width: 175% + } +} + +.algolia-autocomplete .ds-dropdown-menu::before { + display: none +} + +.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] { + padding: 0; + background-color: rgb(255,255,255); + border: 0; + max-height: 80vh; +} + +.algolia-autocomplete .ds-dropdown-menu .ds-suggestions { + margin-top: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion { + padding: 0; + overflow: visible +} + +.algolia-autocomplete .algolia-docsearch-suggestion--category-header { + padding: .125rem 1rem; + margin-top: 0; + font-size: 1.3em; + font-weight: 500; + color: #00008B; + border-bottom: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--wrapper { + float: none; + padding-top: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column { + float: none; + width: auto; + padding: 0; + text-align: left +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content { + float: none; + width: auto; + padding: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content::before { + display: none +} + +.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header { + padding-top: .75rem; + margin-top: .75rem; + border-top: 1px solid rgba(0, 0, 0, .1) +} + +.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column { + display: block; + padding: .1rem 1rem; + margin-bottom: 0.1; + font-size: 1.0em; + font-weight: 400 + /* display: none */ +} + +.algolia-autocomplete .algolia-docsearch-suggestion--title { + display: block; + padding: .25rem 1rem; + margin-bottom: 0; + font-size: 0.9em; + font-weight: 400 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--text { + padding: 0 1rem .5rem; + margin-top: -.25rem; + font-size: 0.8em; + font-weight: 400; + line-height: 1.25 +} + +.algolia-autocomplete .algolia-docsearch-footer { + width: 110px; + height: 20px; + z-index: 3; + margin-top: 10.66667px; + float: right; + font-size: 0; + line-height: 0; +} + +.algolia-autocomplete .algolia-docsearch-footer--logo { + background-image: url("data:image/svg+xml;utf8,"); + background-repeat: no-repeat; + background-position: 50%; + background-size: 100%; + overflow: hidden; + text-indent: -9000px; + width: 100%; + height: 100%; + display: block; + transform: translate(-8px); +} + +.algolia-autocomplete .algolia-docsearch-suggestion--highlight { + color: #FF8C00; + background: rgba(232, 189, 54, 0.1) +} + + +.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight { + box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5) +} + +.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content { + background-color: rgba(192, 192, 192, .15) +} diff --git a/docs/docsearch.js b/docs/docsearch.js new file mode 100644 index 0000000..b35504c --- /dev/null +++ b/docs/docsearch.js @@ -0,0 +1,85 @@ +$(function() { + + // register a handler to move the focus to the search bar + // upon pressing shift + "/" (i.e. "?") + $(document).on('keydown', function(e) { + if (e.shiftKey && e.keyCode == 191) { + e.preventDefault(); + $("#search-input").focus(); + } + }); + + $(document).ready(function() { + // do keyword highlighting + /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */ + var mark = function() { + + var referrer = document.URL ; + var paramKey = "q" ; + + if (referrer.indexOf("?") !== -1) { + var qs = referrer.substr(referrer.indexOf('?') + 1); + var qs_noanchor = qs.split('#')[0]; + var qsa = qs_noanchor.split('&'); + var keyword = ""; + + for (var i = 0; i < qsa.length; i++) { + var currentParam = qsa[i].split('='); + + if (currentParam.length !== 2) { + continue; + } + + if (currentParam[0] == paramKey) { + keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20")); + } + } + + if (keyword !== "") { + $(".contents").unmark({ + done: function() { + $(".contents").mark(keyword); + } + }); + } + } + }; + + mark(); + }); +}); + +/* Search term highlighting ------------------------------*/ + +function matchedWords(hit) { + var words = []; + + var hierarchy = hit._highlightResult.hierarchy; + // loop to fetch from lvl0, lvl1, etc. + for (var idx in hierarchy) { + words = words.concat(hierarchy[idx].matchedWords); + } + + var content = hit._highlightResult.content; + if (content) { + words = words.concat(content.matchedWords); + } + + // return unique words + var words_uniq = [...new Set(words)]; + return words_uniq; +} + +function updateHitURL(hit) { + + var words = matchedWords(hit); + var url = ""; + + if (hit.anchor) { + url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; + } else { + url = hit.url + '?q=' + escape(words.join(" ")); + } + + return url; +} diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..925b1dc --- /dev/null +++ b/docs/index.html @@ -0,0 +1,187 @@ + + + + + + + +Methods for Modelling Life History Traits • FLife + + + + + + + + + +
+
+ + + +
+
+
+

+FLife

+
    +
  • Version: 3.2.1
    • +
  • Date: 2018-07-19
    • +
  • Author: %USER%
    • +
  • Maintainer: %USER2% +
    • +
  • Repository: https://github.com/flr/FLife/ +
    • +
  • Bug reports: https://github.com/flr/FLife/issues +
    • +
+
+

+Overview

+

ONE LINE OVERVIEW, SAME AS IN DESCRIPTION

+

To install this package, start R and enter:

+
install.packages("FLife", repos="http:///flr-project.org/R")
+

or download from the FLife releases page

+
+
+

+Documentation

+ +
+
+

+Build Status

+

Travis Build Status AppVeyor Build Status

+
+
+

+Releases

+ +
+
+

+License

+

Copyright (c) %YEAR% Somebody. Released under the %LICENCE%.

+
+
+

+Contact

+

You are welcome to:

+
    +
  • Submit suggestions and bug-reports at: https://github.com/flr/FLife/issues +
    • +
  • Send a pull request on: https://github.com/flr/FLife/ +
    • +
  • Compose a friendly e-mail to: +
    • +
+
+
+
+ + +
+ + +
+

Developed by Laurence Kell.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + + + diff --git a/docs/link.svg b/docs/link.svg new file mode 100644 index 0000000..88ad827 --- /dev/null +++ b/docs/link.svg @@ -0,0 +1,12 @@ + + + + + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css new file mode 100644 index 0000000..6ca2f37 --- /dev/null +++ b/docs/pkgdown.css @@ -0,0 +1,232 @@ +/* Sticky footer */ + +/** + * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ + * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css + * + * .Site -> body > .container + * .Site-content -> body > .container .row + * .footer -> footer + * + * Key idea seems to be to ensure that .container and __all its parents__ + * have height set to 100% + * + */ + +html, body { + height: 100%; +} + +body > .container { + display: flex; + height: 100%; + flex-direction: column; + + padding-top: 60px; +} + +body > .container .row { + flex: 1 0 auto; +} + +footer { + margin-top: 45px; + padding: 35px 0 36px; + border-top: 1px solid #e5e5e5; + color: #666; + display: flex; + flex-shrink: 0; +} +footer p { + margin-bottom: 0; +} +footer div { + flex: 1; +} +footer .pkgdown { + text-align: right; +} +footer p { + margin-bottom: 0; +} + +img.icon { + float: right; +} + +img { + max-width: 100%; +} + +/* Typographic tweaking ---------------------------------*/ + +.contents h1.page-header { + margin-top: calc(-60px + 1em); +} + +/* Section anchors ---------------------------------*/ + +a.anchor { + margin-left: -30px; + display:inline-block; + width: 30px; + height: 30px; + visibility: hidden; + + background-image: url(./link.svg); + background-repeat: no-repeat; + background-size: 20px 20px; + background-position: center center; +} + +.hasAnchor:hover a.anchor { + visibility: visible; +} + +@media (max-width: 767px) { + .hasAnchor:hover a.anchor { + visibility: hidden; + } +} + + +/* Fixes for fixed navbar --------------------------*/ + +.contents h1, .contents h2, .contents h3, .contents h4 { + padding-top: 60px; + margin-top: -40px; +} + +/* Static header placement on mobile devices */ +@media (max-width: 767px) { + .navbar-fixed-top { + position: absolute; + } + .navbar { + padding: 0; + } +} + + +/* Sidebar --------------------------*/ + +#sidebar { + margin-top: 30px; +} +#sidebar h2 { + font-size: 1.5em; + margin-top: 1em; +} + +#sidebar h2:first-child { + margin-top: 0; +} + +#sidebar .list-unstyled li { + margin-bottom: 0.5em; +} + +.orcid { + height: 16px; + vertical-align: middle; +} + +/* Reference index & topics ----------------------------------------------- */ + +.ref-index th {font-weight: normal;} + +.ref-index td {vertical-align: top;} +.ref-index .alias {width: 40%;} +.ref-index .title {width: 60%;} + +.ref-index .alias {width: 40%;} +.ref-index .title {width: 60%;} + +.ref-arguments th {text-align: right; padding-right: 10px;} +.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments .name {width: 20%;} +.ref-arguments .desc {width: 80%;} + +/* Nice scrolling for wide elements --------------------------------------- */ + +table { + display: block; + overflow: auto; +} + +/* Syntax highlighting ---------------------------------------------------- */ + +pre { + word-wrap: normal; + word-break: normal; + border: 1px solid #eee; +} + +pre, code { + background-color: #f8f8f8; + color: #333; +} + +pre code { + overflow: auto; + word-wrap: normal; + white-space: pre; +} + +pre .img { + margin: 5px 0; +} + +pre .img img { + background-color: #fff; + display: block; + height: auto; +} + +code a, pre a { + color: #375f84; +} + +a.sourceLine:hover { + text-decoration: none; +} + +.fl {color: #1514b5;} +.fu {color: #000000;} /* function */ +.ch,.st {color: #036a07;} /* string */ +.kw {color: #264D66;} /* keyword */ +.co {color: #888888;} /* comment */ + +.message { color: black; font-weight: bolder;} +.error { color: orange; font-weight: bolder;} +.warning { color: #6A0366; font-weight: bolder;} + +/* Clipboard --------------------------*/ + +.hasCopyButton { + position: relative; +} + +.btn-copy-ex { + position: absolute; + right: 0; + top: 0; + visibility: hidden; +} + +.hasCopyButton:hover button.btn-copy-ex { + visibility: visible; +} + +/* mark.js ----------------------------*/ + +mark { + background-color: rgba(255, 255, 51, 0.5); + border-bottom: 2px solid rgba(255, 153, 51, 0.3); + padding: 1px; +} + +/* vertical spacing after htmlwidgets */ +.html-widget { + margin-bottom: 10px; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js new file mode 100644 index 0000000..de9bd72 --- /dev/null +++ b/docs/pkgdown.js @@ -0,0 +1,110 @@ +/* http://gregfranko.com/blog/jquery-best-practices/ */ +(function($) { + $(function() { + + $("#sidebar") + .stick_in_parent({offset_top: 40}) + .on('sticky_kit:bottom', function(e) { + $(this).parent().css('position', 'static'); + }) + .on('sticky_kit:unbottom', function(e) { + $(this).parent().css('position', 'relative'); + }); + + $('body').scrollspy({ + target: '#sidebar', + offset: 60 + }); + + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + var links = $("#navbar ul li a"); + var max_length = -1; + var pos = -1; + for (var i = 0; i < links.length; i++) { + if (links[i].getAttribute("href") === "#") + continue; + var path = paths(links[i].pathname); + + var length = prefix_length(cur_path, path); + if (length > max_length) { + max_length = length; + pos = i; + } + } + + // Add class to parent
  • , and enclosing
  • if in dropdown + if (pos >= 0) { + var menu_anchor = $(links[pos]); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); + + function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); + } + + function prefix_length(needle, haystack) { + if (needle.length > haystack.length) + return(0); + + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0 ? 1 : 0); + } + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(i); + } + + return(haystack.length); + } + + /* Clipboard --------------------------*/ + + function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); + } + + if(Clipboard.isSupported()) { + $(document).ready(function() { + var copyButton = ""; + + $(".examples, div.sourceCode").addClass("hasCopyButton"); + + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); + + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); + + // Initialize clipboard: + var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); + + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); + + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); + }); + } +})(window.jQuery || window.$) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml new file mode 100644 index 0000000..a1134d3 --- /dev/null +++ b/docs/pkgdown.yml @@ -0,0 +1,5 @@ +pandoc: 1.16.0.2 +pkgdown: 1.1.0 +pkgdown_sha: ~ +articles: [] + diff --git a/docs/reference/ages.html b/docs/reference/ages.html new file mode 100644 index 0000000..6c4d17b --- /dev/null +++ b/docs/reference/ages.html @@ -0,0 +1,177 @@ + + + + + + + + +Fills an <code>FLQuant</code> with ages — ages,FLQuant-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Fills an FLQuant with ages

    + + +
    + +
    + +

    Creates FLQuant and FLCohort with ages as entries

    + +
    + + 
    # S4 method for FLQuant
+ages(object)
    + +

    Arguments

    + + + + + + + + + + +
    object

    FLQuant or FLCohort

    ...

    any other arguments

    + +

    Value

    + +

    FLQuant or FLCohort depending on what the first argument was

    + +

    See also

    + +

    knife gascuel sigmoid gompertz vonB dnormal logistic

    + + +

    Examples

    + 
    # NOT RUN {
+data(ple4)
+ages(m(ple4))
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/cas.html b/docs/reference/cas.html new file mode 100644 index 0000000..74d8a13 --- /dev/null +++ b/docs/reference/cas.html @@ -0,0 +1,158 @@ + + + + + + + + +cas — cas • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    cas

    + + +
    + +
    + +

    A dataset containing lengths by year

    + +
    + + +

    Format

    + +

    An data.frame object

    +
    year

    of capture

    +
    len

    at capture

    +
    n

    frequency

    +
    + +

    See also

    + +

    teleost

    + + +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/cc.html b/docs/reference/cc.html new file mode 100644 index 0000000..9eef54a --- /dev/null +++ b/docs/reference/cc.html @@ -0,0 +1,184 @@ + + + + + + + + +Catch curve analysis — cc,numeric,numeric-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Catch curve analysis

    + + +
    + +
    + +

    Catch curve analysis

    + +
    + + 
    # S4 method for numeric,numeric
+cc(age, n, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    age

    n

    frequency

    ...

    any other arguments

    + +

    Value

    + +

    Returns an object of same class age

    + +

    See also

    + +

    powh

    +

    powh

    + + +

    Examples

    + 
    # NOT RUN {
+data(ple4)
+ctc=as.data.frame(catch.n(ple4))
+dat=cc(age=ctc$age,n=ctc$data)
+head(dat)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/dnormal.html b/docs/reference/dnormal.html new file mode 100644 index 0000000..2643b13 --- /dev/null +++ b/docs/reference/dnormal.html @@ -0,0 +1,181 @@ + + + + + + + + +Double normal ogive — dnormal,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Double normal ogive

    + + +
    + +
    + +

    Double normal ogive

    + +
    + + 
    # S4 method for FLQuant,FLPar
+dnormal(age, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    FLQuant or FLCohort

    params

    FLPar with parameters a1 age at maximum, sl SD for lefthand limb and sr SD for righthand limb.

    ...

    any other arguments

    + +

    Value

    + +

    Returns an object of same class as age e.g. FLQuant

    + +

    See also

    + +

    sigmoid, dnormal, logistic

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(a1=4,sl=2,sr=5000)
+dnormal(FLQuant(1:10,dimnames=list(age=1:10)),params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/elas.html b/docs/reference/elas.html new file mode 100644 index 0000000..60c1454 --- /dev/null +++ b/docs/reference/elas.html @@ -0,0 +1,180 @@ + + + + + + + + +elas analysis for reference points — elas • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    elas analysis for reference points

    + + +
    + +
    + +

    Estimates elas

    + +
    + + 
    elas(params, sel, fn)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    params

    parameters

    sel

    selection pattern

    fn

    user supplied function

    + +

    Value

    + +

    FLPar with elas of reference points by input parameters

    + +

    See also

    + +

    lhPar, lhEql, lhRef

    + + +

    Examples

    + 
    # NOT RUN {
+#bug
+# }
+
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/gascuel.html b/docs/reference/gascuel.html new file mode 100644 index 0000000..419c474 --- /dev/null +++ b/docs/reference/gascuel.html @@ -0,0 +1,188 @@ + + + + + + + + +Gascuel growth curve — gascuel,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Gascuel growth curve

    + + +
    + +
    + +

    Gascuel growth equation

    + +
    + + 
    # S4 method for FLQuant,FLPar
+gascuel(age, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    FLQuant, FLPar or numeric with ages

    params

    FLPar

    ...

    any other arguments

    + +

    Value

    + +

    Returns a class of same type as age e.g. FLQuant

    + +

    Details

    + +

    Gascuel D., Fonteneau, A., and Capisano, C. (1992). +Modelisation d'une croissance en deux stances chez #l'albacore (Thunnus albacares) de l'Atlantique Est. +Aquat. Living Resour. 5: 155-172.

    + +

    See also

    + +

    gompertz, vonB , richards

    + + +

    Examples

    + 
    # NOT RUN {
+gascuel(10)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/gislason.html b/docs/reference/gislason.html new file mode 100644 index 0000000..8cd6a3b --- /dev/null +++ b/docs/reference/gislason.html @@ -0,0 +1,194 @@ + + + + + + + + +gislason — gislason,FLQuant,numeric-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    gislason

    + + +
    + +
    + +

    gislason natural mortality relatoinship estimate M as a function of length. +M=a*length^b;

    + +
    + + 
    # S4 method for FLQuant,numeric
+gislason(length, params, a = 0.55, b = 1.44,
+  c = -1.61, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + +
    length

    mass at which M is to be predicted

    params

    FLPar with two values; i.e. a equal to M at unit mass +and b a power term; defaults are a=0.3 and b=-0.288

    a

    0.55

    b

    1.44

    c

    -1.61

    ...

    any other arguments

    + +

    See also

    + +

    lorenzen

    + + +

    Examples

    + 
    # NOT RUN {
+params=lhPar(FLPar(linf=111))
+len=FLQuant(c( 1.90, 4.23, 7.47,11.48,16.04,20.96,26.07,31.22,
+               36.28,41.17,45.83,50.20,54.27,58.03,61.48,64.62),
+             dimnames=list(age=1:16))
+gislason(length,params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/gompertz.html b/docs/reference/gompertz.html new file mode 100644 index 0000000..9bf048c --- /dev/null +++ b/docs/reference/gompertz.html @@ -0,0 +1,183 @@ + + + + + + + + +Gompertz growth equation — gompertz,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Gompertz growth equation

    + + +
    + +
    + +

    gompertz growth equation

    + +
    + + 
    # S4 method for FLQuant,FLPar
+gompertz(age, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    FLQuant, FLPar or numeric with ages

    params

    FLPar with parameters for linf, a, k

    ...

    any other arguments

    + +

    Value

    + +

    Returns an object of same class as age e.g. FLQuant

    + +

    See also

    + +

    gascuel, vonB, richards

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(linf=100,a=2,b=.4)
+age=FLQuant(1:10,dimnames=list(age=1:10))
+gompertz(age,params)
+# }
    
+
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/grwdd.html b/docs/reference/grwdd.html new file mode 100644 index 0000000..e46ac3e --- /dev/null +++ b/docs/reference/grwdd.html @@ -0,0 +1,224 @@ + + + + + + + + +grwdd — grwdd,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    grwdd

    + + +
    + +
    + +

    Lorenzen natural mortality relationship where M is a function of weight, modified to +explicitly included M as a function of numbers in a cohort, i.e. density dependence

    + +
    + + 
    # S4 method for FLQuant,FLPar
+grwdd(age, params, scale, k = 1, fn = vonB)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + +
    age

    mass at which length is to be predicted

    params

    an FLPar with two values; i.e. a equal to M at unit mass and b a power term; defaults are a=0.3 and b=-0.288

    scale

    reference

    k

    rate of change in density dependence

    fn

    function with growth model, with args age params

    ...

    other arguments, such as scale, e.g. stock numbers now relative to a reference level, e.g. at virgin biomass and k steepness of relationship

    + +

    Details

    + +

    @details

    +

    The Lorenzen natural mortality relationship is a function of mass-at-age i.e. + M=a*wt^b

    +

    The relationship can be explained by population density, since as fish grow they +also die and so there is potentially less competition for resources between larger and +older fish. Density dependence can be modelled by a logistic function, a sigmoid +curve (or S shaped) curve, with equation

    +

    f(x)=L/(1+exp(-k(x-x0)))

    +

    where +e is the natural logarithm base (also known as Euler's number), +x0 is the x-value of the sigmoid's midpoint, +L is the curve's maximum value, and +k the steepness of the curve.

    +

    Combining the two functions gives

    +

    M=aL/(1+exp(-k(n-ref)))*wt^b;

    + +

    See also

    + +

    vonB

    + + +

    Examples

    + 
    # NOT RUN {
+library(FLBRP)
+library(FLife)
+
+data(teleost)
+par=teleost[,"Hucho hucho"]
+par=lhPar(par)
+hutchen=lhEql(par)
+
+scale=stock.n(hutchen)[,25]%*%stock.wt(hutchen)
+scale=(stock.n(hutchen)%*%stock.wt(hutchen)%-%scale)%/%scale
+
+grw=grwdd(wt2len(stock.wt(hutchen),par),params=par,scale,k=.2)
+
+ggplot(as.data.frame(grw))+
+   geom_line(aes(age,data,col=factor(year)))+
+   theme(legend.position="none")+
+   scale_x_continuous(limits=c(0,15))
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html new file mode 100644 index 0000000..238f45d --- /dev/null +++ b/docs/reference/index.html @@ -0,0 +1,364 @@ + + + + + + + + +Function reference • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Reference

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +

    All functions

    +

    +
    +

    ages(<FLQuant>)

    +

    Fills an FLQuant with ages

    +

    cas

    +

    cas

    +

    cc(<numeric>,<numeric>)

    +

    Catch curve analysis

    +

    dnormal(<FLQuant>,<FLPar>)

    +

    Double normal ogive

    +

    elas()

    +

    elas analysis for reference points

    +

    gascuel(<FLQuant>,<FLPar>)

    +

    Gascuel growth curve

    +

    gislason(<FLQuant>,<numeric>)

    +

    gislason

    +

    gompertz(<FLQuant>,<FLPar>)

    +

    Gompertz growth equation

    +

    grwdd(<FLQuant>,<FLPar>)

    +

    grwdd

    +

    knife(<FLQuant>,<FLPar>)

    +

    knife edge ogive

    +

    r(<FLPar>,<missing>)

    +

    Population growth rate

    +

    len2wt(<FLQuant>,<FLPar>)

    +

    Length to weight conversion

    +

    leslie(<FLBRP>)

    +

    Leslie matrix

    +

    lhEql(<FLPar>)

    +

    Derives an FLBRP from life history parameters

    +

    lhPar()

    +

    Generates life history parameters

    +

    lhRef()

    +

    Reference points based on life histories

    +

    logistic(<FLQuant>,<FLPar>)

    +

    logistic

    +

    lopt(<FLPar>)

    +

    Lopt

    +

    loptAge(<FLPar>)

    +

    Age at maximum biomass

    +

    lorenzen(<FLQuant>,<FLPar>)

    +

    lorenzen

    +

    roff()

    +

    Natural mortality

    +

    matdd(<FLQuant>,<FLPar>)

    +

    matdd

    +

    mdd(<FLQuant>,<FLPar>)

    +

    mdd

    +

    moment(<numeric>)

    +

    Calculates moments of a distribution

    +

    powh(<numeric>,<numeric>)

    +

    Powell Weatherall method for estimating Z and Linfinity

    +

    refs()

    +

    refs

    +

    richards(<FLQuant>,<FLPar>)

    +

    Richards growth curve

    +

    rnoise(<numeric>,<FLQuant>)

    +

    Random noise with different frequencies

    +

    rod(<FLQuant>)

    +

    rod

    +

    sigmoid(<FLQuant>,<FLPar>)

    +

    Sigmoid ogive

    +

    sv(<FLPar>,<character>)

    +

    Calculates steepness and virgin biomass

    +

    teleost

    +

    teleost

    +

    unbin()

    +

    unbin frequency distributions

    +

    vonB(<FLQuant>,<FLPar>)

    +

    von Bertalanffy growth curve

    +

    wklife

    +

    wklife

    +

    wt2len(<FLQuant>,<FLPar>)

    +

    Mass to length conversion

    +
    + + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/knife.html b/docs/reference/knife.html new file mode 100644 index 0000000..c246e32 --- /dev/null +++ b/docs/reference/knife.html @@ -0,0 +1,193 @@ + + + + + + + + +knife edge ogive — knife,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    knife edge ogive

    + + +
    + +
    + +

    A method to simulate a knife edge ogive where at a given age the proportion chnages from 0 to 1

    + +
    + + 
    # S4 method for FLQuant,FLPar
+knife(age, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    FLQuant, FLPar or numeric with ages

    params

    FLPar

    ...

    any other arguments

    + +

    Value

    + +

    returns an object of same type as age e.g. FLQuant

    + +

    Details

    + +

    The knife ogive is an S-shaped or knife curve or knifeal functions, +Verhulst hypothesizes that small populations increase geometrically, because the supply of +resources exceeds demand. Then, as supply and demand balance, population growth is constant. +Finally, as demand exceeds supply, population growth decreases at the same rate that it had +increased. Verhulst describes this process with an equation that enables him to predict when +a population will reach any given size (see Verhulst's Figure):

    + +

    See also

    + +

    sigmoid, dnormal, logistic

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(a1=4)
+age=FLQuant(1:10,dimnames=list(age=1:10))
+knife(age,params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/lambda.html b/docs/reference/lambda.html new file mode 100644 index 0000000..3527a67 --- /dev/null +++ b/docs/reference/lambda.html @@ -0,0 +1,183 @@ + + + + + + + + +Population growth rate — r,FLPar,missing-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Population growth rate

    + + +
    + +
    + +

    Estimates population growth rate for a Leslie matrix

    + +
    + + 
    # S4 method for FLPar,missing
+r(m, fec, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    m

    FLPar

    fec

    missing

    ...

    any other arguments

    + +

    Value

    + +

    FLPar with growth rate a small population size

    + +

    See also

    + +

    leslie, lhRef

    + + +

    Examples

    + 
    # NOT RUN {
+library(popbio)
+eql=lhEql(lhPar(FLPar(linf=100)))
+L=leslie(eql)
+lambda(L[drop=TRUE])
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/len2wt.html b/docs/reference/len2wt.html new file mode 100644 index 0000000..e926c51 --- /dev/null +++ b/docs/reference/len2wt.html @@ -0,0 +1,181 @@ + + + + + + + + +Length to weight conversion — len2wt,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Length to weight conversion

    + + +
    + +
    + +

    Converts length to weight based on $W=aL^b$

    + +
    + + 
    # S4 method for FLQuant,FLPar
+len2wt(length, params)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    length

    age FLQuant, FLPar or numeric

    params

    FLPar

    ...

    any other arguments

    + +

    Value

    + +

    Returns a class of same type as length e.g. FLQuant

    + +

    See also

    + +

    wt2len

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(a=1,b=3)
+len2wt(FLQuant(10),params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/leslie.html b/docs/reference/leslie.html new file mode 100644 index 0000000..5262781 --- /dev/null +++ b/docs/reference/leslie.html @@ -0,0 +1,185 @@ + + + + + + + + +Leslie matrix — leslie,FLBRP-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Leslie matrix

    + + +
    + +
    + +

    Creates a Leslie Matrix from a FLBRP object that represents a population at equilibrium

    + +
    + + 
    # S4 method for FLBRP
+leslie(object, fbar = FLQuant(0), numbers = TRUE, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    object

    FLBRP

    fbar

    numeric F at whicj survival calculated

    numbers

    boolean numbers or biomass, numbers bt default

    ...

    any other arguments

    + +

    Value

    + +

    matrix

    + +

    See also

    + +

    lhRef, lhPar, lhEql

    + + +

    Examples

    + 
    # NOT RUN {
+eql=lhEql(lhPar(FLPar(linf=100)))
+leslie(eql)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/lhEql.html b/docs/reference/lhEql.html new file mode 100644 index 0000000..2662d3b --- /dev/null +++ b/docs/reference/lhEql.html @@ -0,0 +1,228 @@ + + + + + + + + +Derives an <code>FLBRP</code> from life history parameters — lhEql,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Derives an FLBRP from life history parameters

    + + +
    + +
    + +

    Takes an FLPar object with life history and selectivity parameters +and generates an corresponding FLBRP object. Can uses a range of functional forms

    + +
    + + 
    # S4 method for FLPar
+lhEql(params, growth = FLife::vonB, m = function(length,
+  params) exp(0.55) * (length^-1.61) %*% (params["linf"]^1.44) %*%
+  params["k"], mat = FLife::logistic, sel = FLife::dnormal,
+  sr = "bevholt", range = c(min = 0, max = 40, minfbar = 1, maxfbar = 40,
+  plusgroup = 40), spwn = c(params["a50"] - floor(params["a50"])),
+  fish = 0.5, units = if ("units" %in% names(attributes(params)))
+  attributes(params)$units else NULL, midyear = 0.5, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    params

    an FLPar object with life history parameters

    growth

    A function that takes an FLPar oject with parameters, by default vonB

    m

    A function that takes an FLPar oject with parameters, by default gislason

    mat

    A function that takes an FLPar oject with parameters, by default logistic

    sel

    A function that takes an FLPar oject with parameters, by default dnormal

    sr

    A character value, "bevholt" by default

    range

    A numeric with age range by default from 0 to 40

    spwn

    A numeric give propotion of year when spawning occurs, by default is params["a50"]-floor(params["a50"])

    fish

    A numeric give propotion of year when fishing occurs, by default 0.5

    units

    Acharacter for vectors in FLBRP returned by method

    midyear

    when growth measured, default 0.5

    ...

    any other arguments

    + +

    Value

    + +

    FLBRP object

    + +

    See also

    + +

    lhPar, lhRef

    +

    vonB lorenzen sigmoid

    + + +

    Examples

    + 
    # NOT RUN {
+data(teleost)
+alb=teleost[,"Thunnus alalunga"]
+eql=lhEql(lhPar(alb))
+# }
    
+
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/lhPar.html b/docs/reference/lhPar.html new file mode 100644 index 0000000..6522bb9 --- /dev/null +++ b/docs/reference/lhPar.html @@ -0,0 +1,215 @@ + + + + + + + + +Generates life history parameters — lhPar • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Generates life history parameters

    + + +
    + +
    + +

    Uses life history theory to derive parameters for biological relationships, i.e. or growth, +maturity, natural mortality. Selectivity by default is set so age at peak selectivity is the +same as age at 50/ +length of the von Bertalannfy growth equation.

    + +
    + + 
    lhPar(params, t0 = function(params) -exp(-0.3922 - 0.2752 *
+  log(params["linf"]) %-% (1.038 * log(params["k"]))), a = 3e-04, b = 3,
+  ato95 = 1, sl = 1, sr = 5000, s = 0.9, v = 1000)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    params

    FLPar object with parameters for life history equations and selection pattern. +Need Linfinity to estimate other parameters, if any other parameters supplied in code then +these are not provided by the algorithm

    t0

    of von Bertalanffy. This is a default that isnt normally derived +from life history theory, as are the following args.

    a

    coefficient of length weight relationship

    b

    exponent of length weight relationship

    ato95

    age at which 95% of fish are mature, offset to age at which 50% are mature

    sl

    selectivity-at-age parameter, standard deviation of lefthand limb of double normal

    sr

    stock recruitment relationship

    s

    steepness of stock recruitment relationship

    v

    virgin biomass

    + +

    Value

    + +

    object of class FLPar with missing parameters calculated from life history theory

    + +

    See also

    + +

    loptAge, lhRef, lhPar, lhEql

    + + +

    Examples

    + 
    # NOT RUN {
+lhPar(FLPar(linf=200))
+# }
    
+
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/lhRef.html b/docs/reference/lhRef.html new file mode 100644 index 0000000..29b7174 --- /dev/null +++ b/docs/reference/lhRef.html @@ -0,0 +1,201 @@ + + + + + + + + +Reference points based on life histories — lhRef • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Reference points based on life histories

    + + +
    + +
    + +

    lhRef calculates a variety of reference points i.e. population growth rate at small +population sizs (r), and at B~MSY (rc), ratio of virgin biomass to B~MSY (sk), life +time reproductive output (srp0) and reproductive output at B~MSY (sprmsy)

    + +
    + + 
    lhRef(params, m = function(length, params) exp(0.55) * (length^-1.61) %*%
+  (params["linf"]^1.44) %*% params["k"], sr = "bevholt", range = c(min =
+  0, max = 40, minfbar = 1, maxfbar = 40, plusgroup = 40), what = c("r", "rc",
+  "msy", "lopt", "sk", "spr0", "sprmsy"), msy = "msy")
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + +
    params

    FLPar

    m

    function for natural mortality

    sr

    character with stock recruitment relationship, e.g. "bevholt","ricker",...

    range

    ages used i.e. c(min=0,max=40,minfbar=1,maxfbar=40,plusgroup=40)

    what

    quantities to calculate "r","lopt","rc","sk","spr0","sprmsy"

    msy,

    character with "msy", "f0.1", ...

    + +

    Value

    + +

    object of class FLPar with reference points, i.e r, rc, sk, lopt,

    + +

    See also

    + +

    lhPar, lhEql

    + + +

    Examples

    + 
    # NOT RUN {
+library(FLBRP)
+params=FLPar(linf=100,t0=0,k=.4)
+params=lhPar(params)
+lhRef(params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/logistic.html b/docs/reference/logistic.html new file mode 100644 index 0000000..146b66e --- /dev/null +++ b/docs/reference/logistic.html @@ -0,0 +1,176 @@ + + + + + + + + +logistic — logistic,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    logistic

    + + +
    + +
    + +

    logistic function

    + +
    + + 
    # S4 method for FLQuant,FLPar
+logistic(age, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    FLQuant with ages

    params

    FLPar with parameters a50,ato95 and asym

    ...

    other arguments

    + +

    See also

    + +

    gompertz

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(a50=4,ato95=1,asym=1.0)
+age=FLQuant(1:10,dimnames=list(age=1:10))
+logistic(age,params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/lopt.html b/docs/reference/lopt.html new file mode 100644 index 0000000..909f3c3 --- /dev/null +++ b/docs/reference/lopt.html @@ -0,0 +1,208 @@ + + + + + + + + +Lopt — lopt,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Lopt

    + + +
    + +
    + +

    Lopt, the length at which a cohort achives its maximum biomass, can be used as a +reference point to identify growth over- or underfishing. Since taking fish below or above +this size results in potential loss of yield. The total biomass of a cohort changes through +time as a result of gains due to an increase in mean size-at-age and losses due to natural +mortality. Lopt can therefore be estimated from the natural mortality and weight-at-age vectors.

    + +
    + + 
    # S4 method for FLPar
+lopt(params, m = function(length, params) exp(0.55) *
+  (length^-1.61) %*% (params["linf"]^1.44) %*% params["k"],
+  growth = FLife:::vonB, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    params

    an FLPar object with parameter values for the natural mortality and growth +functions, and the exponent b of the length/weight relationship.

    m

    natural mortality function, by default Gislason

    growth

    length or weight-at-age function, by default von Bertalanffy

    ...

    any other arguments

    + +

    Value

    + +

    FLPar with $L_opt$ the length at which a cohort achives its maximum biomass

    + +

    Details

    + +

    Lopt is a function of growth and natural mortality-at-age and there are several +approximations such as \(2/3 L_{\infty}\) and \(L_{\infty}\frac{3}{3+k/m}\). If the life +history parameters and relationships are known then $L_opt$ can be found by finding the +time (t) and hence length at which the maximum biomass is achieved i.e. + \(L(T)^a e^{\int_0^T m(t)}\) +where \(m(t)\) can be found from the relationship of mortality at length using the relationship +of Gislason, assuming the von Bertalanffy growth curve.

    + +

    See also

    + +

    gislason, vonB, lhRef, lhPar, lhEql,

    + + +

    Examples

    + 
    # NOT RUN {
+params=lhPar(FLPar(linf=100,k=0.1,t0=-0.1,b=3))
+lopt(params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/loptAge.html b/docs/reference/loptAge.html new file mode 100644 index 0000000..b0b10a0 --- /dev/null +++ b/docs/reference/loptAge.html @@ -0,0 +1,196 @@ + + + + + + + + +Age at maximum biomass — loptAge,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Age at maximum biomass

    + + +
    + +
    + +

    Finds length at maximum biomass

    + +
    + + 
    # S4 method for FLPar
+loptAge(params, m = function(length, params) params["m1"]
+  %*% (exp(log(length) %*% params["m2"])), growth = vonB, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    params

    FLPar

    m

    A function, i.e. gislason

    growth

    A function, i.e. vonB

    ...

    any other arguments

    + +

    Value

    + +

    FLPar with length at maximum biomass of a cohort

    + +

    Details

    + +

    There are several ways to calculate \(L_{opt}\), i.e. +i) \({2/3}^{rds} L_{\infty}\) +ii) \(L_{\infty}\frac{3}{3+k/m}\) +iii) by maximising the biomass of +iv) from an FLBRP object by fishing at F=0 and finding age where biomass is a maximum

    + +

    See also

    + +

    loptAge, lhRef, lhPar, lhEql,

    + + +

    Examples

    + 
    # NOT RUN {
+params=lhPar(FLPar(linf=100))
+loptAge(params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/lorenzen.html b/docs/reference/lorenzen.html new file mode 100644 index 0000000..f28a763 --- /dev/null +++ b/docs/reference/lorenzen.html @@ -0,0 +1,180 @@ + + + + + + + + +lorenzen — lorenzen,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    lorenzen

    + + +
    + +
    + +

    Lorenzen natural mortality relationship estimate M as a function of weight. +M=a*wt^b;

    + +
    + + 
    # S4 method for FLQuant,FLPar
+lorenzen(wt, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    wt

    mass at which M is to be predicted

    params

    an FLPar with two values; i.e. a equal to M at unit mass +and b a power term; defaults are a=0.3 and b=-0.288

    ...

    any other arguments

    + +

    See also

    + +

    gislason

    + + +

    Examples

    + 
    # NOT RUN {
+mass=FLQuant(c( 1.90, 4.23, 7.47,11.48,16.04,20.96,26.07,31.22,
+               36.28,41.17,45.83,50.20,54.27,58.03,61.48,64.62),
+             dimnames=list(age=1:16))
+lorenzen(mass)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/m.html b/docs/reference/m.html new file mode 100644 index 0000000..4669435 --- /dev/null +++ b/docs/reference/m.html @@ -0,0 +1,211 @@ + + + + + + + + +Natural mortality — roff • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Natural mortality

    + + +
    + +
    + +

    Methods to provide estimates of natural mortality based on growth and reproduction parameters

    + +
    + + 
    roff(params, ...)
    + +

    Arguments

    + + + + + + + + + + +
    params

    FLPar

    ...

    any other arguments

    + +

    Value

    + +

    returns an object of FLQuant

    + +

    Details

    + +

    Natural Mortality +For larger species securing sufficient food to maintain a fast growth rate may entail +exposure to a higher natural mortality @gislason2008does. While many small demersal species +seem to be partly protected against predation by hiding, cryptic behaviour, being flat +or by possessing spines have the lowest rates of natural mortality @griffiths2007natural. +Hence, at a given length individuals belonging to species with a high $$L_{\infty}$$ may +generally be exposed to a higher M than individuals belonging to species with a low $$L_{\infty}$$.

    +

    $$ log(M) = 0.55-1.61log(L) + 1.44log(L_{\infty}) + log(k)$$

    +

    Functional forms

    +

    Many estimators have been propose for M, based on growth and reproduction,

    +

    Age at maturity + $$M=\frac{1.521}{a_{50}^{0.72}}-0.155$$ + $$M=\frac{1.65}{a_{50}}$$

    +

    Growth +$$M=1.5k$$ +$$M=1.406W_{\infty}^{-0.096}k^{0.78}$$

    +

    $$M=1.0661L_{\infty}^{-0.1172}k^{0.5092}$$ +Growth and length at maturity

    +

    $$M=3kL_{\infty}\frac{(1-\frac{L_{50}}{L_{\infty}})}{L_{50}}$$ +$$M=\frac{\beta k}{e^{k(a_{50}-t_0)}-1}$$

    +

    Varing by length, weight or age

    + +

    See also

    + +

    gislason, lorenzen

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(FLPar(linf=120,k=.15,t0=-0.1,l50=60,a=0.0001,b=3))
+age=FLQuant(1:10,dimnames=list(age=1:10))
+
+
+roff(params)
+rikhter(params)
+rikhter2(params)
+griffiths(params)
+djababli(params)
+jensen(params)
+jensen2(params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/matdd.html b/docs/reference/matdd.html new file mode 100644 index 0000000..c511a6c --- /dev/null +++ b/docs/reference/matdd.html @@ -0,0 +1,223 @@ + + + + + + + + +matdd — matdd,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    matdd

    + + +
    + +
    + +

    Logistic ogive for proportion mature-at-age, modified to explicitly included maturity +as a function of numbers in a cohort, i.e. density dependence

    + +
    + + 
    # S4 method for FLQuant,FLPar
+matdd(age, params, scale, k = 1, flagAge = TRUE)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + +
    age

    ages

    params

    an FLPar with two values; i.e. a equal to M at unit mass and b a power term; defaults are a=0.3 and b=-0.288

    scale

    reference

    k

    rate of change in density dependence

    flagAge

    default is FALSE, i.e. density dependence is based on length ratherv than age

    ...

    other arguments, such as scale, e.g. stock numbers now relative to a reference level, e.g. at virgin biomass and k steepness of relationship

    + +

    Details

    + +

    The relationship can be explained by population density, since as fish grow they +also die and so there is potentially less competition for resources between larger and +older fish. Density dependence can be modelled by a logistic function, a sigmoid +curve (or S shaped) curve, with equation

    +

    f(x)=L/(1+exp(-k(x-x0)))

    +

    where +e is the natural logarithm base (also known as Euler's number), +x0 is the x-value of the sigmoid's midpoint, +L is the curve's maximum value, and +k the steepness of the curve.

    +

    Combining the two functions gives

    +

    O=aL/(1+exp(-k(n-ref)))*wt^b;

    + +

    See also

    + +

    logistic,mdd

    + + +

    Examples

    + 
    # NOT RUN {
+library(FLBRP)
+library(FLife)
+
+data(teleost)
+par=teleost[,"Hucho hucho"]
+par=lhPar(par)
+hutchen=lhEql(par)
+
+scale=stock.n(hutchen)[,25]%*%stock.wt(hutchen)
+scale=(stock.n(hutchen)%*%stock.wt(hutchen)%-%scale)%/%scale
+
+mat=matdd(ages(scale),par,scale,k=.5)
+
+ggplot(as.data.frame(mat))+
+   geom_line(aes(age,data,col=factor(year)))+
+   theme(legend.position="none")+
+   scale_x_continuous(limits=c(0,15))
+
+
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/mdd.html b/docs/reference/mdd.html new file mode 100644 index 0000000..a5ccb85 --- /dev/null +++ b/docs/reference/mdd.html @@ -0,0 +1,226 @@ + + + + + + + + +mdd — mdd,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    mdd

    + + +
    + +
    + +

    Lorenzen natural mortality relationship where M is a function of weight, modified to +explicitly included M as a function of numbers in a cohort, i.e. density dependence

    + +
    + + 
    # S4 method for FLQuant,FLPar
+mdd(object, params, scale, k = 1, m = gislason)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + +
    object

    mass at which M is to be predicted

    params

    an FLPar with two values; i.e. a equal to M at unit mass and b a power term; defaults are a=0.3 and b=-0.288

    scale

    reference

    k

    rate of change in density dependence

    m

    function with mortality model, by default gisalson

    ...

    other arguments, such as scale, e.g. stock numbers now relative to a reference level, e.g. at virgin biomass and k steepness of relationship

    + +

    Details

    + +

    @details

    +

    The Lorenzen natural mortality relationship is a function of mass-at-age i.e. + M=a*wt^b

    +

    The relationship can be explained by population density, since as fish grow they +also die and so there is potentially less competition for resources between larger and +older fish. Density dependence can be modelled by a logistic function, a sigmoid +curve (or S shaped) curve, with equation

    +

    f(x)=L/(1+exp(-k(x-x0)))

    +

    where +e is the natural logarithm base (also known as Euler's number), +x0 is the x-value of the sigmoid's midpoint, +L is the curve's maximum value, and +k the steepness of the curve.

    +

    Combining the two functions gives

    +

    M=aL/(1+exp(-k(n-ref)))*wt^b;

    + +

    See also

    + +

    lorenzen

    + + +

    Examples

    + 
    # NOT RUN {
+library(FLBRP)
+library(FLife)
+
+data(teleost)
+par=teleost[,"Hucho hucho"]
+par=lhPar(par)
+hutchen=lhEql(par)
+
+scale=stock.n(hutchen)[,25]%*%stock.wt(hutchen)
+scale=(stock.n(hutchen)%*%stock.wt(hutchen)%-%scale)%/%scale
+
+m=mdd(wt2len(stock.wt(hutchen),par),params=par,scale,k=.9)
+
+ggplot(as.data.frame(m))+
+   geom_line(aes(age,data,col=factor(year)))+
+   theme(legend.position="none")+
+   scale_x_continuous(limits=c(0,15))
+
+m=mdd(stock.wt(hutchen),params=FLPar(m1=3,m2=-0.288),scale,k=1.2,m=lorenzen)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/moment.html b/docs/reference/moment.html new file mode 100644 index 0000000..fbe7b23 --- /dev/null +++ b/docs/reference/moment.html @@ -0,0 +1,180 @@ + + + + + + + + +Calculates moments of a distribution — moment,numeric-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Calculates moments of a distribution

    + + +
    + +
    + +

    The calculates moments of a distribution, i.e. mean, standard deviation, skew and kurtosis

    + +
    + + 
    # S4 method for numeric
+moment(object, n = rep(1, length(object)), na.rm = T)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    object

    a vector holding a time series

    n

    number of observations equal to length og object by default

    na.rm

    boolean whether to remove NAs, TRUE by default

    ...

    any other arguments, i.e. x,n=rep(1,length(x)),na.rm=T

    + +

    Value

    + +

    a vector with the inter-annual variation each time step

    + + +

    Examples

    + 
    # NOT RUN {
+x=rlnorm(100)
+moment(x)
+# }
    
+
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/powh.html b/docs/reference/powh.html new file mode 100644 index 0000000..a10c5fa --- /dev/null +++ b/docs/reference/powh.html @@ -0,0 +1,261 @@ + + + + + + + + +Powell Weatherall method for estimating Z and Linfinity — powh,numeric,numeric-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Powell Weatherall method for estimating Z and Linfinity

    + + +
    + +
    + +

    Estimates growth and mortality parameters from length frequency data.

    + +
    + + 
    # S4 method for numeric,numeric
+powh(len, n, weights = FALSE, fromMode = FALSE,
+  linf = 0)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + +
    len

    vector with length distribution

    n

    vector with numbers in each length bin

    weights

    weights for observations

    fromMode

    booelean set to FALSE by default

    linf

    allows linf to be fixed if >0

    ...

    any other argument, i.e. weights =TRUE, fromMode =FALSE

    + +

    Value

    + +

    a data.frame with mn (mean), diff (difference), +len (length) and n (frequency)

    + +

    Details

    + +

    Beverton and Holt (1956) developed a method to estimate population parameters + such as total mortality (Z) from length data i.e.

    +

    $$Z=K\frac{L_{infinity}-\overline{L}}{\overline{L}-L'}$$

    +

    Powell (1979) then developed a method, extended by Wetherall et al. (1987), +to estimate growth and mortality parameters. This assumes that the right hand tail +of a length frequency distribution is determined by the asymptotic length L +and the ratio between Z and the growth rate K.

    +

    The Beverton and Holt methods assumes good estimates for K and $L_infinity$, +while the Powell-Wetherall method only requires an estimate +of K, since $L_infinity$ is estimated by the method as well as Z/K. These method +therefore provide estimates for Z/K, if K is unknown and +Z if K is known.

    +

    As well as assuming that growth follows the von Bertalanffy growth function, +it is also assumed that the population is in a steady state +with constant exponential mortality, no changes in selection pattern of the +fishery and constant recruitment.

    +

    In the Powell-Wetherall method L' can take any value between the +smallest and largest sizes. Equation 1 then provides a series of estimates of +Z and since

    +

    $$ +\overline{L}-L'=a+bL' +$$

    +

    a and b can be estimated by a regression analysis where

    +

    $$b={-K}/{Z+K}$$ +$$a=-bL_{infinity}$$

    +

    Therefore plotting $$\overline{L}-L$$ against $L'$ provides an estimate +of $L_infinity$ and Z/K from

    +

    $$L_{infinity}=-a/b$$ +$$Z/K={-1-b}/{b}$$

    +

    If K is known Z can also be esimated

    + +

    References

    + +

    R. Beverton and S. Holt. Review of method for estimating mortality rates in + exploited fish populations, with special reference to sources of bias in + catch sampling. Rapports et Proces-Verbaux., 140(1): 67--83, 1956.

    +

    D. G. Powell. + Estimation of mortality and growth parameters from the length + frequency of a catch [model]. + Rapports et Proces-Verbaux des Reunions, 175, 1979.

    +

    J. Wetherall, J. Polovina, and S. Ralston. + Estimating growth and mortality in steady-state fish stocks from + length-frequency data. + ICLARM Conf. Proc, pages 53--74, 1987.

    + +

    See also

    + +

    cc

    + + +

    Examples

    + 
    # NOT RUN {
+data(cas)
+pw=ddply(subset(cas), .(year),
+  function(cas) powh(cas$len,cas$n)$data)
+
+  pw=transform(pw, lustrum=(year%/%5)*5,
+        yr    =year-(year%/%5)*5,
+        weight=ifelse(len>=100&len<=200,1,0))
+
+ggplot(pw)+
+  geom_line(aes(len,diff,colour=factor(yr),group=year))+
+  scale_x_continuous(limits=c(0,300)) +
+  xlab("Length (cm)")+
+  ylab("Difference between Length and Mean Size")+
+  geom_smooth(aes(len,diff,weight=weight),
+  method="lm",col="red",size=1.25,alpha=.1)+
+  theme_bw()+theme(legend.position="none")
+
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/refs.html b/docs/reference/refs.html new file mode 100644 index 0000000..5df2cf7 --- /dev/null +++ b/docs/reference/refs.html @@ -0,0 +1,200 @@ + + + + + + + + +refs — refs • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    refs

    + + +
    + +
    + +

    Returns a variety of reference points based on spawner per recruit (S/R) and stock recruitment +relationships.

    +

    $F_MSY$ corresponds to the level of exploitation that provides the maximum, derived from a +spawner and yield curves combined with a stock recruitment relationship, while $F_Crash$ is +the level of F that will drive the stock to extinction.

    +

    Reference points can also be derived from the spawner and yield curves alone. For example +$F_0.1$ is a proxy for $F_MSY$ and is the fishing mortality that corresponds to a point +on the yield per recruit curve where the slope is 10% of that at the origin; $F_Max$ is +the maximum of the yield per recruit and $SPR_O$ is the spawner per recruit at virgin biomass, +and $SPR_30$ corressponds to the point on the curve where SPR is 30% of $SPR_0$. In these +cases the biomass, ssb and yield values are derived by multiplying the per recruit values by +the average recruitment.

    + +
    + + 
    refs(object, ...)
    + +

    Arguments

    + + + + + + + + + + +
    object

    FLStock

    ...

    other arguments

    + +

    Value

    + +

    data.frame

    + + +

    Examples

    + 
    # NOT RUN {
+ library(FLCore)
+ library(FLBRP)
+ library(ggplotFL)
+ library(FLife)
+ library(popbio)
+ library(plyr)
+
+ data(ple4)
+
+ refs(ple4)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/richards.html b/docs/reference/richards.html new file mode 100644 index 0000000..835594f --- /dev/null +++ b/docs/reference/richards.html @@ -0,0 +1,181 @@ + + + + + + + + +Richards growth curve — richards,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Richards growth curve

    + + +
    + +
    + +

    Richards growth equation

    + +
    + + 
    # S4 method for FLQuant,FLPar
+richards(age, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    FLQuant, FLPar or numeric object with values corresponding to ages

    params

    FLPar object with parameters linf, k and t0

    ...

    other arguments

    + +

    Value

    + +

    Returns an object of same class as age e.g. FLQuant

    + +

    See also

    + +

    vonB, gompertz, gascuel

    + + +

    Examples

    + 
    # NOT RUN {
+age=FLQuant(1:10,dimnames=list(age=1:10))
+len=richards(age,FLPar(linf=100,k=.4,b=.1,m=2))
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/rnoise.html b/docs/reference/rnoise.html new file mode 100644 index 0000000..9403b32 --- /dev/null +++ b/docs/reference/rnoise.html @@ -0,0 +1,232 @@ + + + + + + + + +Random noise with different frequencies — rnoise,numeric,FLQuant-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Random noise with different frequencies

    + + +
    + +
    + +

    A noise generator

    + +
    + + 
    # S4 method for numeric,FLQuant
+rnoise(n = n, len = len, sd = 0.3, b = 0,
+  burn = 0, trunc = 0, what = c("year", "cohort", "age"))
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    n

    number of iterations

    len

    an FLQuant

    sd

    standard error for simulated series

    b

    autocorrelation parameter a real number in [0,1]

    burn

    gets rid of 1st values i series

    trunc

    get rid of values > abs(trunc)

    what

    returns time series for year, cohort or age"

    ...

    anyl

    + +

    Value

    + +

    A FLQuant with autocorrelation equal to B.

    + +

    References

    + +

    Ranta and Kaitala 2001 Proc. R. Soc. +vt = b * vt-1 + s * sqrt(1 - b^2) +s is normally distributed random variable with mean = 0 +b is the autocorrelation parameter

    + + +

    Examples

    + 
    # NOT RUN {
+flq=FLQuant(1:100)
+white <- rnoise(1000,flq,sd=.3,b=0)
+plot(white)
+acf(white)
+
+red <- rnoise(1000,flq,sd=.3,b=0.7)
+plot(red)
+acf(red)
+
+data(ple4)
+res=rnoise(1000,flq,sd=.3,b=0)
+
+ggplot()+
+geom_point(aes(year,age,size= data),
+            data=subset(as.data.frame(res),data>0))+
+geom_point(aes(year,age,size=-data),
+            data=subset(as.data.frame(res),data<=0),colour="red")+
+scale_size_area(max_size=4, guide="none")+
+facet_wrap(~iter)
+
+res=rnoise(4,m(ple4),burn=10,b=0.9,cohort=TRUE)
+ggplot()+
+geom_point(aes(year,age,size= data),
+          data=subset(as.data.frame(res),data>0))+
+geom_point(aes(year,age,size=-data),
+          data=subset(as.data.frame(res),data<=0),colour="red")+
+scale_size_area(max_size=4, guide="none")+
+facet_wrap(~iter)
+
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/rod.html b/docs/reference/rod.html new file mode 100644 index 0000000..a784729 --- /dev/null +++ b/docs/reference/rod.html @@ -0,0 +1,182 @@ + + + + + + + + +rod — rod,FLQuant-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    rod

    + + +
    + +
    + +

    Regime shifts +Evidence for regime shifts are explored using a a sequential t-test algorithm +(STARS; rodionov2004sequential) as modified by Szuwalski et al., (submitted)

    + +
    + + 
    # S4 method for FLQuant
+rod(object, ...)
    + +

    Arguments

    + + + + + + + + + + +
    object

    an object of class FLQuant

    ...

    any other arguments

    + +

    Details

    + +

    Returns a data.frame

    + + +

    Examples

    + 
    # NOT RUN {
+ object=rlnorm(1,FLQuant(0,dimnames=list(year=1:30)),.3)
+ pg=rod(object)
+ ggplot(object) +
+     geom_polygon(aes(year,data,group=regime),
+         fill="lavender",col="blue",
+         lwd=.25,data=pg,alpha=.75)+
+     geom_point(aes(year,data))+
+     geom_line(aes(year,data))
+# }
    
+
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/sigmoid.html b/docs/reference/sigmoid.html new file mode 100644 index 0000000..3baf014 --- /dev/null +++ b/docs/reference/sigmoid.html @@ -0,0 +1,190 @@ + + + + + + + + +Sigmoid ogive — sigmoid,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Sigmoid ogive

    + + +
    + +
    + +

    sigmoid ogive

    + +
    + + 
    # S4 method for FLQuant,FLPar
+sigmoid(age, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    FLQuant, FLPar or numeric with ages

    params

    FLPar with age at whick probability is 0.5 (a50) and offset to 0.95 (ato95)

    ...

    any other arguments

    + +

    Value

    + +

    returns an object of same type as age e.g. FLQuant

    + +

    Details

    + +

    The sigmoid ogive is an S-shaped or sigmoid curve or sigmoidal functions, +Verhulst hypothesizes that small populations increase geometrically, because the supply of resources exceeds demand. Then, as supply and demand balance, population growth is constant. Finally, as demand exceeds supply, population growth decreases at the same rate that it had increased. Verhulst describes this process with an equation that enables him to predict when a population will reach any given size (see Verhulst's Figure):

    + +

    See also

    + +

    knife, dnormal, logistic

    +

    dnormal,knife

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(a50=4,ato95=1)
+age=FLQuant(1:10,dimnames=list(age=1:10))
+sigmoid(age,params)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/sv.html b/docs/reference/sv.html new file mode 100644 index 0000000..cf1bbe8 --- /dev/null +++ b/docs/reference/sv.html @@ -0,0 +1,180 @@ + + + + + + + + +Calculates steepness and virgin biomass — sv,FLPar,character-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Calculates steepness and virgin biomass

    + + +
    + +
    + +

    Calculates steepness and virgin biomass given a and b for a Beverton and Holt SRR

    + +
    + + 
    # S4 method for FLPar,character
+sv(x, model, spr0 = NA)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    x

    FLPar with a and b

    model

    character with name of stock recruitment relationship, by default "bevholt"

    spr0

    spawner per recruit at F=0

    ...

    any other arguments

    + +

    Value

    + +

    FLPar with values for steepness (s) and virgin biomass (v)

    + + +

    Examples

    + 
    # NOT RUN {
+#bug
+params=FLPar(a=37.8,b=8.93)
+sv(params,"bevholt",.4)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/teleost.html b/docs/reference/teleost.html new file mode 100644 index 0000000..2136b9d --- /dev/null +++ b/docs/reference/teleost.html @@ -0,0 +1,164 @@ + + + + + + + + +teleost — teleost • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    teleost

    + + +
    + +
    + +

    A dataset containing life history parameters for a range of teleost species

    + +
    + + +

    Format

    + +

    A data frame with 139 rows (i.e. species) and 13 variables:

    +
    species,genus,family,order,class

    +
    linf

    asymptotic length of the Von Bertalanffy growth equation

    +
    k

    rate at which length reaches linf

    +
    t0

    adjusts the growth equation for the initial size at birth

    +
    l50

    length at which 50% are mature

    +
    a

    scaling factor of the length weight relationship

    +
    b

    exponent of the length weight relationship

    +
    temp

    temperature

    +
    habit

    e.g. pelagic or demeresal

    +
    + +

    See also

    + +

    cas

    + + +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/unbin.html b/docs/reference/unbin.html new file mode 100644 index 0000000..b736fca --- /dev/null +++ b/docs/reference/unbin.html @@ -0,0 +1,176 @@ + + + + + + + + +unbin frequency distributions — unbin • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    unbin frequency distributions

    + + +
    + +
    + +

    For a vector with labels corresponding to intervals i.e. "(0,10]" + returns a data.frame with left and right boundaries and mid point.

    + +
    + + 
    unbin(x)
    + +

    Arguments

    + + + + + + +
    x

    a vector of with intervals as names

    + +

    Value

    + +

    a data.frame with left and right boundaries and mid points.

    + + +

    Examples

    + 
    x=summary(cut(runif(100),seq(0,1,.1)))
+unbin(x)
    #>           left right  mid  n
+#> (0,0.1]    0.0   0.1 0.05 12
+#> (0.1,0.2]  0.1   0.2 0.15  8
+#> (0.2,0.3]  0.2   0.3 0.25 11
+#> (0.3,0.4]  0.3   0.4 0.35 11
+#> (0.4,0.5]  0.4   0.5 0.45 14
+#> (0.5,0.6]  0.5   0.6 0.55 10
+#> (0.6,0.7]  0.6   0.7 0.65 10
+#> (0.7,0.8]  0.7   0.8 0.75 10
+#> (0.8,0.9]  0.8   0.9 0.85  6
+#> (0.9,1]    0.9   1.0 0.95  8
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/vonB.html b/docs/reference/vonB.html new file mode 100644 index 0000000..d5c2fba --- /dev/null +++ b/docs/reference/vonB.html @@ -0,0 +1,185 @@ + + + + + + + + +von Bertalanffy growth curve — vonB,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    von Bertalanffy growth curve

    + + +
    + +
    + +

    Von Bertalanffy growth equation

    + +
    + + 
    # S4 method for FLQuant,FLPar
+vonB(age, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    age

    FLQuant, FLPar or numeric object with values corresponding to ages

    params

    FLPar object with parameters linf, k and t0

    ...

    other arguments

    + +

    Value

    + +

    Returns an object of same class as age e.g. FLQuant

    + +

    See also

    + +

    gompertz, gascuel, richards

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(linf=100,t0=0,k=.4)
+age=FLQuant(1:10,dimnames=list(age=1:10))
+len=vonB(age,params)
+
+#inverse growth curve
+vonB(params=params,length=len)
+# }
    +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/wklife.html b/docs/reference/wklife.html new file mode 100644 index 0000000..2c384bf --- /dev/null +++ b/docs/reference/wklife.html @@ -0,0 +1,168 @@ + + + + + + + + +wklife — wklife • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    wklife

    + + +
    + +
    + +

    A dataset containing life history parameters for a range of teleost species

    + +
    + + +

    Format

    + +

    A data frame with 15 rows (i.e. species) and 13 variables:

    +
    species

    +
    name

    +
    area

    +
    stock

    +
    sex

    +
    a

    scaling factor of the length weight relationship

    +
    b

    exponent of the length weight relationship

    +
    linf

    asymptotic length of the Von Bertalanffy growth equation

    +
    k

    rate at which length reaches linf

    +
    t0

    adjusts the growth equation for the initial size at birth

    +
    lmax

    asymptotic length of the Von Bertalanffy growth equation

    +
    l50

    length at which 50% are mature

    +
    a50

    age at which 50% are mature

    +
    + +

    See also

    + +

    teleost

    + + +
    + +
    + +
    +
    +

    Developed by Laurence Kell.

    +
    + +
    +

    Site built with pkgdown.

    +
    + +
    +
    + + + + + + diff --git a/docs/reference/wt2len.html b/docs/reference/wt2len.html new file mode 100644 index 0000000..631efcd --- /dev/null +++ b/docs/reference/wt2len.html @@ -0,0 +1,181 @@ + + + + + + + + +Mass to length conversion — wt2len,FLQuant,FLPar-method • FLife + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + +
    + +
    +
    +
    +

    Mass to length conversion

    + + +
    + +
    + +

    converts weight to length

    + +
    + + 
    # S4 method for FLQuant,FLPar
+wt2len(wt, params, ...)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    wt

    FLQuant, FLPar or numeric with length

    params

    FLPar with a and b, i.e. condition and scaling factors

    ...

    any other arguments

    + +

    Value

    + +

    Returns an object of same class as wt e.g. FLQuant

    + +

    See also

    + +

    len2wt

    + + +

    Examples

    + 
    # NOT RUN {
+params=FLPar(a=0.1,b=3)
+wt2len(FLQuant(10),params)
+# }
    +
    + +
    + + +
    + + + + + +