-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/authors.html b/docs/authors.html
deleted file mode 100644
index e94ea29..0000000
--- a/docs/authors.html
+++ /dev/null
@@ -1,143 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Content not found. Please use links in the navbar.
-
- Page not found (404)
-`, then ``, etc.) that has more than one element. Defaults to 1 (for ``).
- getTopLevel: function($scope) {
- for (var i = 1; i <= 6; i++) {
- var $headings = this.findOrFilter($scope, 'h' + i);
- if ($headings.length > 1) {
- return i;
- }
- }
-
- return 1;
- },
-
- // returns the elements for the top level, and the next below it
- getHeadings: function($scope, topLevel) {
- var topSelector = 'h' + topLevel;
-
- var secondaryLevel = topLevel + 1;
- var secondarySelector = 'h' + secondaryLevel;
-
- return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
- },
-
- getNavLevel: function(el) {
- return parseInt(el.tagName.charAt(1), 10);
- },
-
- populateNav: function($topContext, topLevel, $headings) {
- var $context = $topContext;
- var $prevNav;
-
- var helpers = this;
- $headings.each(function(i, el) {
- var $newNav = helpers.generateNavItem(el);
- var navLevel = helpers.getNavLevel(el);
-
- // determine the proper $context
- if (navLevel === topLevel) {
- // use top level
- $context = $topContext;
- } else if ($prevNav && $context === $topContext) {
- // create a new level of the tree and switch to it
- $context = helpers.createChildNavList($prevNav);
- } // else use the current $context
-
- $context.append($newNav);
-
- $prevNav = $newNav;
- });
- },
-
- parseOps: function(arg) {
- var opts;
- if (arg.jquery) {
- opts = {
- $nav: arg
- };
- } else {
- opts = arg;
- }
- opts.$scope = opts.$scope || $(document.body);
- return opts;
- }
- },
-
- // accepts a jQuery object, or an options object
- init: function(opts) {
- opts = this.helpers.parseOps(opts);
-
- // ensure that the data attribute is in place for styling
- opts.$nav.attr('data-toggle', 'toc');
-
- var $topContext = this.helpers.createChildNavList(opts.$nav);
- var topLevel = this.helpers.getTopLevel(opts.$scope);
- var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
- this.helpers.populateNav($topContext, topLevel, $headings);
- }
- };
-
- $(function() {
- $('nav[data-toggle="toc"]').each(function(i, el) {
- var $nav = $(el);
- Toc.init($nav);
- });
- });
-})();
diff --git a/docs/docsearch.css b/docs/docsearch.css
deleted file mode 100644
index e5f1fe1..0000000
--- a/docs/docsearch.css
+++ /dev/null
@@ -1,148 +0,0 @@
-/* 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
deleted file mode 100644
index b35504c..0000000
--- a/docs/docsearch.js
+++ /dev/null
@@ -1,85 +0,0 @@
-$(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
deleted file mode 100644
index 09c2fb3..0000000
--- a/docs/index.html
+++ /dev/null
@@ -1,177 +0,0 @@
-
-
-
-
-
-
-
-Read Binary Files Saved by Igor Pro (Including Neuromatic Data) • IgorR
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Introduction
-The IgorR package for R provides routines to read binary files generated by Igor Pro.
-This includes both the standalone .ibw Igor Binary Wave format (v2 and the latest v5) and the .pxp Packed Experiment Format including both waves and variables. In addition the package provides functions to read files generated by the Neuromatic analysis suite written by Jason Rothman for Igor Pro.
-
-
-
-Installation
-
-
-
-Github Install
-To install the latest development version from github
-# install hadley's devtools if required
-if(!require('devtools')) install.packages('devtools')
-devtools::install_github('jefferis/IgorR')
-
-
-
-Development Install
-To checkout a version that can be used for development (RStudio is strongly recommended), in your terminal application.
-
-In R
-
-
-
-
-
-Details
-Details of the ibw file format were derived from the Igor Technical Note 003.
-For those interested in the source code, ReadIgorBinary.R provides code for standard pxp and ibw files, while ReadNclamp.R provides routines to read packed experiment files generated by the Nclamp data acquisition package.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/link.svg b/docs/link.svg
deleted file mode 100644
index 88ad827..0000000
--- a/docs/link.svg
+++ /dev/null
@@ -1,12 +0,0 @@
-
-
-
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
deleted file mode 100644
index c01e592..0000000
--- a/docs/pkgdown.css
+++ /dev/null
@@ -1,367 +0,0 @@
-/* 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 {
- position: relative;
-}
-
-body > .container {
- display: flex;
- height: 100%;
- flex-direction: column;
-}
-
-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%;
-}
-
-/* Fix bug in bootstrap (only seen in firefox) */
-summary {
- display: list-item;
-}
-
-/* Typographic tweaking ---------------------------------*/
-
-.contents .page-header {
- margin-top: calc(-60px + 1em);
-}
-
-dd {
- margin-left: 3em;
-}
-
-/* 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;
-}
-
-/* Navbar submenu --------------------------*/
-
-.dropdown-submenu {
- position: relative;
-}
-
-.dropdown-submenu>.dropdown-menu {
- top: 0;
- left: 100%;
- margin-top: -6px;
- margin-left: -1px;
- border-radius: 0 6px 6px 6px;
-}
-
-.dropdown-submenu:hover>.dropdown-menu {
- display: block;
-}
-
-.dropdown-submenu>a:after {
- display: block;
- content: " ";
- float: right;
- width: 0;
- height: 0;
- border-color: transparent;
- border-style: solid;
- border-width: 5px 0 5px 5px;
- border-left-color: #cccccc;
- margin-top: 5px;
- margin-right: -10px;
-}
-
-.dropdown-submenu:hover>a:after {
- border-left-color: #ffffff;
-}
-
-.dropdown-submenu.pull-left {
- float: none;
-}
-
-.dropdown-submenu.pull-left>.dropdown-menu {
- left: -100%;
- margin-left: 10px;
- border-radius: 6px 0 6px 6px;
-}
-
-/* Sidebar --------------------------*/
-
-#pkgdown-sidebar {
- margin-top: 30px;
- position: -webkit-sticky;
- position: sticky;
- top: 70px;
-}
-
-#pkgdown-sidebar h2 {
- font-size: 1.5em;
- margin-top: 1em;
-}
-
-#pkgdown-sidebar h2:first-child {
- margin-top: 0;
-}
-
-#pkgdown-sidebar .list-unstyled li {
- margin-bottom: 0.5em;
-}
-
-/* bootstrap-toc tweaks ------------------------------------------------------*/
-
-/* All levels of nav */
-
-nav[data-toggle='toc'] .nav > li > a {
- padding: 4px 20px 4px 6px;
- font-size: 1.5rem;
- font-weight: 400;
- color: inherit;
-}
-
-nav[data-toggle='toc'] .nav > li > a:hover,
-nav[data-toggle='toc'] .nav > li > a:focus {
- padding-left: 5px;
- color: inherit;
- border-left: 1px solid #878787;
-}
-
-nav[data-toggle='toc'] .nav > .active > a,
-nav[data-toggle='toc'] .nav > .active:hover > a,
-nav[data-toggle='toc'] .nav > .active:focus > a {
- padding-left: 5px;
- font-size: 1.5rem;
- font-weight: 400;
- color: inherit;
- border-left: 2px solid #878787;
-}
-
-/* Nav: second level (shown on .active) */
-
-nav[data-toggle='toc'] .nav .nav {
- display: none; /* Hide by default, but at >768px, show it */
- padding-bottom: 10px;
-}
-
-nav[data-toggle='toc'] .nav .nav > li > a {
- padding-left: 16px;
- font-size: 1.35rem;
-}
-
-nav[data-toggle='toc'] .nav .nav > li > a:hover,
-nav[data-toggle='toc'] .nav .nav > li > a:focus {
- padding-left: 15px;
-}
-
-nav[data-toggle='toc'] .nav .nav > .active > a,
-nav[data-toggle='toc'] .nav .nav > .active:hover > a,
-nav[data-toggle='toc'] .nav .nav > .active:focus > a {
- padding-left: 15px;
- font-weight: 500;
- font-size: 1.35rem;
-}
-
-/* orcid ------------------------------------------------------------------- */
-
-.orcid {
- font-size: 16px;
- color: #A6CE39;
- /* margins are required by official ORCID trademark and display guidelines */
- margin-left:4px;
- margin-right:4px;
- vertical-align: middle;
-}
-
-/* Reference index & topics ----------------------------------------------- */
-
-.ref-index th {font-weight: normal;}
-
-.ref-index td {vertical-align: top;}
-.ref-index .icon {width: 40px;}
-.ref-index .alias {width: 40%;}
-.ref-index-icons .alias {width: calc(40% - 40px);}
-.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;
-}
-
-/* headroom.js ------------------------ */
-
-.headroom {
- will-change: transform;
- transition: transform 200ms linear;
-}
-.headroom--pinned {
- transform: translateY(0%);
-}
-.headroom--unpinned {
- transform: translateY(-100%);
-}
-
-/* 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;
-}
-
-/* fontawesome ------------------------ */
-
-.fab {
- font-family: "Font Awesome 5 Brands" !important;
-}
-
-/* don't display links in code chunks when printing */
-/* source: https://stackoverflow.com/a/10781533 */
-@media print {
- code a:link:after, code a:visited:after {
- content: "";
- }
-}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
deleted file mode 100644
index 7e7048f..0000000
--- a/docs/pkgdown.js
+++ /dev/null
@@ -1,108 +0,0 @@
-/* http://gregfranko.com/blog/jquery-best-practices/ */
-(function($) {
- $(function() {
-
- $('.navbar-fixed-top').headroom();
-
- $('body').css('padding-top', $('.navbar').height() + 10);
- $(window).resize(function(){
- $('body').css('padding-top', $('.navbar').height() + 10);
- });
-
- $('[data-toggle="tooltip"]').tooltip();
-
- var cur_path = paths(location.pathname);
- var links = $("#navbar ul li a");
- var max_length = -1;
- var pos = -1;
- for (var i = 0; i < links.length; i++) {
- if (links[i].getAttribute("href") === "#")
- continue;
- // Ignore external links
- if (links[i].host !== location.host)
- continue;
-
- var nav_path = paths(links[i].pathname);
-
- var length = prefix_length(nav_path, cur_path);
- if (length > max_length) {
- max_length = length;
- pos = i;
- }
- }
-
- // Add class to parent
`).
- getTopLevel: function($scope) {
- for (var i = 1; i <= 6; i++) {
- var $headings = this.findOrFilter($scope, 'h' + i);
- if ($headings.length > 1) {
- return i;
- }
- }
-
- return 1;
- },
-
- // returns the elements for the top level, and the next below it
- getHeadings: function($scope, topLevel) {
- var topSelector = 'h' + topLevel;
-
- var secondaryLevel = topLevel + 1;
- var secondarySelector = 'h' + secondaryLevel;
-
- return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
- },
-
- getNavLevel: function(el) {
- return parseInt(el.tagName.charAt(1), 10);
- },
-
- populateNav: function($topContext, topLevel, $headings) {
- var $context = $topContext;
- var $prevNav;
-
- var helpers = this;
- $headings.each(function(i, el) {
- var $newNav = helpers.generateNavItem(el);
- var navLevel = helpers.getNavLevel(el);
-
- // determine the proper $context
- if (navLevel === topLevel) {
- // use top level
- $context = $topContext;
- } else if ($prevNav && $context === $topContext) {
- // create a new level of the tree and switch to it
- $context = helpers.createChildNavList($prevNav);
- } // else use the current $context
-
- $context.append($newNav);
-
- $prevNav = $newNav;
- });
- },
-
- parseOps: function(arg) {
- var opts;
- if (arg.jquery) {
- opts = {
- $nav: arg
- };
- } else {
- opts = arg;
- }
- opts.$scope = opts.$scope || $(document.body);
- return opts;
- }
- },
-
- // accepts a jQuery object, or an options object
- init: function(opts) {
- opts = this.helpers.parseOps(opts);
-
- // ensure that the data attribute is in place for styling
- opts.$nav.attr('data-toggle', 'toc');
-
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- var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
- this.helpers.populateNav($topContext, topLevel, $headings);
- }
- };
-
- $(function() {
- $('nav[data-toggle="toc"]').each(function(i, el) {
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- Toc.init($nav);
- });
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diff --git a/docs/docsearch.css b/docs/docsearch.css
deleted file mode 100644
index e5f1fe1..0000000
--- a/docs/docsearch.css
+++ /dev/null
@@ -1,148 +0,0 @@
-/* Docsearch -------------------------------------------------------------- */
-/*
- Source: https://github.com/algolia/docsearch/
- License: MIT
-*/
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-.algolia-autocomplete {
- display: block;
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-.algolia-autocomplete .ds-dropdown-menu {
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- box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
-}
-
-@media (min-width:768px) {
- .algolia-autocomplete .ds-dropdown-menu {
- width: 175%
- }
-}
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-.algolia-autocomplete .ds-dropdown-menu::before {
- display: none
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-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
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-.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
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-.algolia-autocomplete .algolia-docsearch-suggestion {
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-.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
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-.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
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-.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
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-.algolia-autocomplete .algolia-docsearch-suggestion--content {
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-.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
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-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
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-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
- display: block;
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-.algolia-autocomplete .algolia-docsearch-suggestion--title {
- display: block;
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-.algolia-autocomplete .algolia-docsearch-suggestion--text {
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-.algolia-autocomplete .algolia-docsearch-footer {
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-.algolia-autocomplete .algolia-docsearch-footer--logo {
- background-image: url("data:image/svg+xml;utf8,");
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-.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
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-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
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diff --git a/docs/docsearch.js b/docs/docsearch.js
deleted file mode 100644
index b35504c..0000000
--- a/docs/docsearch.js
+++ /dev/null
@@ -1,85 +0,0 @@
-$(function() {
-
- // register a handler to move the focus to the search bar
- // upon pressing shift + "/" (i.e. "?")
- $(document).on('keydown', function(e) {
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- var mark = function() {
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- var referrer = document.URL ;
- var paramKey = "q" ;
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- if (referrer.indexOf("?") !== -1) {
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- };
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- mark();
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-});
-
-/* 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);
- }
-
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- if (content) {
- words = words.concat(content.matchedWords);
- }
-
- // return unique words
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-}
-
-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
deleted file mode 100644
index 09c2fb3..0000000
--- a/docs/index.html
+++ /dev/null
@@ -1,177 +0,0 @@
-
-
-
-
-
-
-
-Read Binary Files Saved by Igor Pro (Including Neuromatic Data) • IgorR
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Introduction
-The IgorR package for R provides routines to read binary files generated by Igor Pro.
-This includes both the standalone .ibw Igor Binary Wave format (v2 and the latest v5) and the .pxp Packed Experiment Format including both waves and variables. In addition the package provides functions to read files generated by the Neuromatic analysis suite written by Jason Rothman for Igor Pro.
-
-
-
-Installation
-
-
-
-Github Install
-To install the latest development version from github
-# install hadley's devtools if required
-if(!require('devtools')) install.packages('devtools')
-devtools::install_github('jefferis/IgorR')
-
-
-
-Development Install
-To checkout a version that can be used for development (RStudio is strongly recommended), in your terminal application.
-
-In R
-
-
-
-
-
-Details
-Details of the ibw file format were derived from the Igor Technical Note 003.
-For those interested in the source code, ReadIgorBinary.R provides code for standard pxp and ibw files, while ReadNclamp.R provides routines to read packed experiment files generated by the Nclamp data acquisition package.
-
-
-
-
-
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diff --git a/docs/link.svg b/docs/link.svg
deleted file mode 100644
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--- a/docs/link.svg
+++ /dev/null
@@ -1,12 +0,0 @@
-
-
-
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
deleted file mode 100644
index c01e592..0000000
--- a/docs/pkgdown.css
+++ /dev/null
@@ -1,367 +0,0 @@
-/* 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%
- *
- */
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-html, body {
- height: 100%;
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-body {
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-img {
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-.contents .page-header {
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- background-repeat: no-repeat;
- background-size: 20px 20px;
- background-position: center center;
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-.hasAnchor:hover a.anchor {
- visibility: visible;
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- visibility: hidden;
- }
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-/* Fixes for fixed navbar --------------------------*/
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-.contents h1, .contents h2, .contents h3, .contents h4 {
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-.dropdown-submenu {
- position: relative;
-}
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-.dropdown-submenu>.dropdown-menu {
- top: 0;
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-.dropdown-submenu:hover>.dropdown-menu {
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-.dropdown-submenu:hover>a:after {
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-.dropdown-submenu.pull-left {
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-.dropdown-submenu.pull-left>.dropdown-menu {
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-/* Sidebar --------------------------*/
-
-#pkgdown-sidebar {
- margin-top: 30px;
- position: -webkit-sticky;
- position: sticky;
- top: 70px;
-}
-
-#pkgdown-sidebar h2 {
- font-size: 1.5em;
- margin-top: 1em;
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-}
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-#pkgdown-sidebar .list-unstyled li {
- margin-bottom: 0.5em;
-}
-
-/* bootstrap-toc tweaks ------------------------------------------------------*/
-
-/* All levels of nav */
-
-nav[data-toggle='toc'] .nav > li > a {
- padding: 4px 20px 4px 6px;
- font-size: 1.5rem;
- font-weight: 400;
- color: inherit;
-}
-
-nav[data-toggle='toc'] .nav > li > a:hover,
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- padding-left: 5px;
- color: inherit;
- border-left: 1px solid #878787;
-}
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-nav[data-toggle='toc'] .nav > .active > a,
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- padding-left: 5px;
- font-size: 1.5rem;
- font-weight: 400;
- color: inherit;
- border-left: 2px solid #878787;
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-.orcid {
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-.ref-index th {font-weight: normal;}
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-.ref-index-icons .alias {width: calc(40% - 40px);}
-.ref-index .title {width: 60%;}
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-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
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-code a, pre a {
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-a.sourceLine:hover {
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-
-.fl {color: #1514b5;}
-.fu {color: #000000;} /* function */
-.ch,.st {color: #036a07;} /* string */
-.kw {color: #264D66;} /* keyword */
-.co {color: #888888;} /* comment */
-
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-}
-
-/* headroom.js ------------------------ */
-
-.headroom {
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-.headroom--pinned {
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-.headroom--unpinned {
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-
-/* 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;
-}
-
-/* fontawesome ------------------------ */
-
-.fab {
- font-family: "Font Awesome 5 Brands" !important;
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-
-/* don't display links in code chunks when printing */
-/* source: https://stackoverflow.com/a/10781533 */
-@media print {
- code a:link:after, code a:visited:after {
- content: "";
- }
-}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
deleted file mode 100644
index 7e7048f..0000000
--- a/docs/pkgdown.js
+++ /dev/null
@@ -1,108 +0,0 @@
-/* http://gregfranko.com/blog/jquery-best-practices/ */
-(function($) {
- $(function() {
-
- $('.navbar-fixed-top').headroom();
-
- $('body').css('padding-top', $('.navbar').height() + 10);
- $(window).resize(function(){
- $('body').css('padding-top', $('.navbar').height() + 10);
- });
-
- $('[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") === "#")
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- if (links[i].host !== location.host)
- continue;
-
- var nav_path = paths(links[i].pathname);
-
- var length = prefix_length(nav_path, cur_path);
- if (length > max_length) {
- max_length = length;
- pos = i;
- }
- }
-
- // Add class to parent
-
-
-
-
-
-
-
-
-
-
-
-
--Introduction
-The IgorR package for R provides routines to read binary files generated by Igor Pro.
-This includes both the standalone .ibw Igor Binary Wave format (v2 and the latest v5) and the .pxp Packed Experiment Format including both waves and variables. In addition the package provides functions to read files generated by the Neuromatic analysis suite written by Jason Rothman for Igor Pro.
-
-
--Installation
- -
-
-
--Github Install
-To install the latest development version from github
-# install hadley's devtools if required -if(!require('devtools')) install.packages('devtools') -devtools::install_github('jefferis/IgorR')
-
--Development Install
-To checkout a version that can be used for development (RStudio is strongly recommended), in your terminal application.
- -In R
- -
-
-
- -Details
-Details of the ibw file format were derived from the Igor Technical Note 003.
-For those interested in the source code, ReadIgorBinary.R provides code for standard pxp and ibw files, while ReadNclamp.R provides routines to read packed experiment files generated by the Nclamp data acquisition package.
-
-
-
-
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diff --git a/docs/reference/IgorR-private.html b/docs/reference/IgorR-private.html
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- Read binary files saved by Igor Pro (including Neuromatic data)
- -IgorR-package.Rd
-
-
-
-
- This package provides function to read data from the Igor Pro data analysis
-program by Wavemetrics. The data formats supported are Igor packed experiment
-format (.pxp) and Igor binary wave (.ibw). See:
-http://www.wavemetrics.com/ for details.
Details
- -It also includes some functions to load special pxp files produced by the -Neuromatic/Nclamp packages for recording and analysing neuronal #data. See -http://www.neuromatic.thinkrandom.com/ for details.
- - -
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diff --git a/docs/reference/ReadAllNclampLogTables.html b/docs/reference/ReadAllNclampLogTables.html
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- Private functions in IgorR Package
- -IgorR-private.Rd
-
-
- Private functions in IgorR Package
-Read the a short record header from the current location in a PXP file
-Note that the recordType will be one of the constants from Igor's -enum PackedFileRecordType
-.ReadPackedHeader(con, endian)- -
Arguments
-| con | -an R connection to the file we are reading |
-
|---|---|
| endian | -either little or big |
-
Value
- -a list containing information about the current record
- -
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diff --git a/docs/reference/ReadNclampLogTable.html b/docs/reference/ReadNclampLogTable.html
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- Read all Nclamp log tables from a directory into a list
- -ReadAllNclampLogTables.Rd
-
-
- Read all Nclamp log tables from a directory into a list
-ReadAllNclampLogTables(logfiledir, pattern = "_log[0-9]+[.]pxp$", ...)- -
Arguments
-| logfiledir | -path to directory containing log files (pxp files). |
-
|---|---|
| pattern | -optional regular expression -- see |
-
| ... | -additional parameters for |
-
Value
- -A named list containing one dataframe for each parsed log file.
- -Examples
--if (FALSE) { -logfiles <- ReadAllNclampLogTables("/GD/projects/PhysiologyData/logs") -str(logfiles) -}
-
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diff --git a/docs/reference/SummariseSweepFile.html b/docs/reference/SummariseSweepFile.html
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- Read the log table produced by Nclamp acquisition software for Igor
- -ReadNclampLogTable.Rd
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- log tables are special Igor .pxp files that contain only variables. -Each entry corresponds to a single run of an Nclamp protocol, -storing information like protocol name, run time etc.
-ReadNclampLogTable(f, Verbose = FALSE)- -
Arguments
-| f | -path to the log file. |
-
|---|---|
| Verbose | -whether to print status information while reading the file. |
-
Value
- -A dataframe containing a row for each acquisition protocol run.
- -
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diff --git a/docs/reference/SweepFilesToDataFrame.html b/docs/reference/SweepFilesToDataFrame.html
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- Extract summary information from an Nclamp/Igor Sweep File
- -SummariseSweepFile.Rd
-
-
- e.g. for import into Physiology database
-SummariseSweepFile(f, Verbose = FALSE)- -
Arguments
-| f | -path to an Nclamp/Igor PXP format sweep file. |
-
|---|---|
| Verbose | -if |
-
Value
- -A list of about 25 fields summarising the sweep file.
- -Examples
--l <- SummariseSweepFile(system.file("igor", "WedJul407c2_001.pxp", package="IgorR")) -cat("There are", l$NumWaves, "waves in the file each of total duration", l$StimWaveLength, - "ms and sample duration", l$StimSampleInterval, "ms \n")#> There are 100 waves in the file each of total duration 20 ms and sample duration 0.025 ms
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diff --git a/docs/reference/UpdateSweepDataFrame.html b/docs/reference/UpdateSweepDataFrame.html
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- Summarise multiple sweep files into a single dataframe
- -SweepFilesToDataFrame.Rd
-
-
- Note that this is still a little fragile if the lists produced by
-SummariseSweepFile do not have consistent field names.
SweepFilesToDataFrame(ff)- -
Arguments
-| ff | -paths to a set of sweep files. |
-
|---|
Value
- -A dataframe with rows for each sweep file.
-See also
- -SummariseSweepFile
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diff --git a/docs/reference/WaveToTimeSeries.html b/docs/reference/WaveToTimeSeries.html
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- Update the CSV file summarising the sweeps in an Nclamp data folder
- -UpdateSweepDataFrame.Rd
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- Update the CSV file summarising the sweeps in an Nclamp data folder
-UpdateSweepDataFrame( - folder, - outfile = NULL, - action = c("update", "force"), - DryRun = FALSE -)- -
Arguments
-| folder | -path to the folder. |
-
|---|---|
| outfile | -path to outfile (default: |
-
| action | -update newer (default) or force update (not yet implemented). |
-
| DryRun | -if |
-
Value
- -TRUE if something happened, FALSE otherwise.
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diff --git a/docs/reference/index.html b/docs/reference/index.html
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- Convert an Igor wave (wave list) loaded by read.ibw into an R time series
- -WaveToTimeSeries.Rd
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-
- Where there are multiple waves, they are assumed to be of compatible lengths
-so that they can be joined together by cbind.
WaveToTimeSeries(WaveData, ReturnOriginalDataOnError = TRUE)- -
Arguments
-| WaveData, | -a wave or list of waves |
-
|---|---|
| ReturnOriginalDataOnError | -If we can't make a time series, return -return original data (default TRUE) |
-
Value
- -a time series or multi time series (ts,
- mts)
See also
- - - -
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diff --git a/docs/reference/read.ibw.html b/docs/reference/read.ibw.html
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diff --git a/docs/reference/read.pxp.html b/docs/reference/read.pxp.html
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- Read binary files in the Igor Binary Wave format (IBW)
- -read.ibw.Rd
-
-
- Read binary files in the Igor Binary Wave format (IBW)
-read.ibw( - wavefile, - Verbose = FALSE, - ReturnTimeSeries = FALSE, - MakeWave = FALSE, - HeaderOnly = FALSE -)- -
Arguments
-| wavefile | -either a character vector containing the path to a file or an -R connection. |
-
|---|---|
| Verbose | -if |
-
| ReturnTimeSeries | -if |
-
| MakeWave | -if |
-
| HeaderOnly | -if |
-
Value
- -A vector containing the wave data or, if MakeWave == TRUE,
- returns the name of a new R vector containing the data which has been made
- in the user environment
See also
- -Other igor-io:
-WaveToTimeSeries(),
-read.pxp()
Examples
--# return a list containing the wave -wavedata=read.ibw(system.file("igor","version5.ibw",package="IgorR")) -sum(wavedata)#> [1] 15-# make a list containing the wave's data in the users's environment -wavename=read.ibw(system.file("igor","version5.ibw",package="IgorR"),MakeWave=TRUE) -sum(get(wavename))#> [1] 15
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diff --git a/docs/reference/tsp.igorwave.html b/docs/reference/tsp.igorwave.html
deleted file mode 100644
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+++ /dev/null
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- Reads an Igor Pro Packed Experiment (.pxp) file
- -read.pxp.Rd
-
-
- Note that PXP files are only partially documented so some contents cannot be -parsed (e.g. image data). This function currently reads data records (Igor -waves and variables), history, procedures, recreation macros and plain text -notebooks. Formatted notebooks cannot be read.
-read.pxp( - pxpfile, - regex, - ReturnTimeSeries = FALSE, - Verbose = FALSE, - StructureOnly = FALSE, - ExtractText = FALSE, - IgorPlatform = NULL, - ... -)- -
Arguments
-| pxpfile | -character vector naming a PXP file or an R connection. |
-
|---|---|
| regex | -if |
-
| ReturnTimeSeries | -if |
-
| Verbose | -whether to print information to console during loading -(numeric values are also allowed 0=none, 1=basic, 2=all). |
-
| StructureOnly | -(TODO) if |
-
| ExtractText | -whether to extract procedures, recreation macros, history
-and plain text notebooks ( |
-
| IgorPlatform | -OS on which Igor file was saved (windows or macintosh). |
-
| ... | -optional parameters passed to read.ibw. |
-
Value
- -A list containing all the individual waves or variables in the PXP - file.
-Details
- -IgorPlatform will determine in which encoding text is read
-(WINDOWS-1252 for windows and macintosh for macintosh). Unique abbreviations
-are acceptable. Defaults to "windows" on Windows, "macintosh"
-otherwise. Note that Igor Pro 5.5 added a PlatformRecord to the PXP file
-format which is used to determine the file's platform of origin when
-available. Since this is information straight from the horse's mouth it will
-override the IgorPlatform argument.
See also
- -Other igor-io:
-WaveToTimeSeries(),
-read.ibw()
Examples
--
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diff --git a/man/IgorR-package.Rd b/man/IgorR-package.Rd
index 9b1d449..cc81b59 100644
--- a/man/IgorR-package.Rd
+++ b/man/IgorR-package.Rd
@@ -18,6 +18,15 @@ Neuromatic/Nclamp packages for recording and analysing neuronal #data. See
Key functions in the package include \code{\link{read.ibw}},
\code{\link{read.pxp}}.
+}
+\seealso{
+Useful links:
+\itemize{
+ \item \url{https://github.com/jefferis/IgorR}
+ \item \url{https://jefferis.github.io/IgorR/}
+ \item Report bugs at \url{https://github.com/jefferis/IgorR/issues}
+}
+
}
\author{
\strong{Maintainer}: Gregory Jefferis \email{jefferis@gmail.com} (\href{https://orcid.org/0000-0002-0587-9355}{ORCID})
diff --git a/tests/testthat/test-ibw.R b/tests/testthat/test-ibw.R
index ff342e4..ef5e11d 100644
--- a/tests/testthat/test-ibw.R
+++ b/tests/testthat/test-ibw.R
@@ -25,13 +25,25 @@ test_that("Read Igor v2 file", {
})
test_that("Processing of dates", {
- expect_equivalent(.convertIgorDate(3444214517),as.POSIXct("2013-02-20 14:15:17"))
+ # when in GMT timezone (Banjul, The Gambia) or BST Igor says
+ # print secs2Time(3444214517, 3)
+ # 14:15:17
+ expect_equivalent(.convertIgorDate(3444214517, tz="GMT"),as.POSIXct("2013-02-20 14:15:17", tz = 'GMT'))
+ expect_equivalent(.convertIgorDate(3444214517, tz="Africa/Banjul"),as.POSIXct("2013-02-20 14:15:17", tz = 'Africa/Banjul'))
+ expect_equivalent(.convertIgorDate(3444214517, tz="Europe/London"),as.POSIXct("2013-02-20 14:15:17", tz = 'Europe/London'))
# from nm20120811c1_016.pxp
- # current implementation says 13:37 on my laptop, lmb cluster and mac in PDT
+ # old implementation said 13:37 on my laptop, lmb cluster and mac in PDT
# but mtime of file and embedded time string is 12:37
# and this is also what I get on a sunos machine in PDT
- # DISABLED due to OS dependent results that I cannot fix
- # expect_equivalent(.convertIgorDate(3427533421),as.POSIXct("2012-08-11 13:37:01"))
+ expect_equivalent(.convertIgorDate(3427533421, tz = 'GMT'),as.POSIXct("2012-08-11 12:37:01", tz='GMT'))
+ expect_equivalent(.convertIgorDate(3427533421, tz = 'Europe/London'),as.POSIXct("2012-08-11 12:37:01", tz='Europe/London'))
+
+ # when in GMT timezone or BST Igor says
+ # print secs2Time(3805612788, 3)
+ # 10:39:48
+ expect_equivalent(.convertIgorDate(3805612788, tz='GMT'),as.POSIXct("2024-08-04 10:39:48", tz='GMT'))
+ expect_equivalent(.convertIgorDate(3805612788, tz='Europe/London'),as.POSIXct("2024-08-04 10:39:48", tz='Europe/London'))
+ expect_equivalent(.convertIgorDate(3805612788, tz='America/New_York'),as.POSIXct("2024-08-04 10:39:48", tz='America/New_York'))
})
test_that("Processing of funny null terminated strings", {
-
-
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- Return tsp attribute of Igor wave (start, end, frequency)
- -tsp.igorwave.Rd
-
-
- Note that end = (npts-1) * deltat
-tsp.igorwave(wave)- -
Arguments
-| wave | -Igor wave loaded by |
-
|---|
Value
- -numeric vector with elements start, end, frequency
-