[Stacomir-commits] r478 - in pkg/stacomir: man/figures vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Feb 18 20:37:14 CET 2018 

Author: briand
Date: 2018-02-18 20:37:14 +0100 (Sun, 18 Feb 2018)
New Revision: 478

Added:
   pkg/stacomir/vignettes/stacomir.html
   pkg/stacomir/vignettes/stacomir.pdf
Modified:
   pkg/stacomir/man/figures/README-silver-1.png
   pkg/stacomir/vignettes/stacomir.Rmd
Log:


Modified: pkg/stacomir/man/figures/README-silver-1.png
===================================================================
(Binary files differ)

Modified: pkg/stacomir/vignettes/stacomir.Rmd
===================================================================
--- pkg/stacomir/vignettes/stacomir.Rmd	2018-02-16 09:01:14 UTC (rev 477)
+++ pkg/stacomir/vignettes/stacomir.Rmd	2018-02-18 19:37:14 UTC (rev 478)
@@ -1,6 +1,6 @@
 ---
 title: "StacomiR"
-author: "Marion Legrand, Cédric Briand"
+author: "Marion Legrand, Cédric Briand"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
@@ -21,7 +21,7 @@
 
 # stacomiR <img src="../man/figures/logo.png" align="right" />
 
-```{r echo=FALSE}
+```{r echo=FALSE, include=FALSE}
 library(stacomiR)
 
 ```
@@ -139,14 +139,16 @@
 
 
 #### Monitoring operation
-An operation corresponds to a monitoring of a counting device during a time
+An operation corresponds to the monitoring of a counting device during a time
 span. 
 
 #### Sample
 A sample corresponds to a batch of fishes passing during a monitoring operation.
 Sample characteristics (length, weight, sex, body measurements) are attached to
 the sample. For each sample the species and the stage (which corresponds to a
-maturation stage and is related to migratory behaviour) is recorded. 
+maturation stage and is related to migratory behaviour) is recorded. Samples
+correspond to multiple fish of the same species and stage or to individual
+records.
 
 #### Other features
 The database also handles, marking-recapture operations, pathologies, samples
@@ -255,9 +257,10 @@
 ```
 
 The previous line generates data not only about the report_mig_mult class,
-but also run dependent classes which describe how the fishway (DF) and counting devices (DC) have been operated.
-Sometimes there is no data but only because the camera was not working. There are also information
-about the operations (e.g. periods at wich a trap content has been evaluated). Here we load what
+but also runs dependent classes which describe how the fishway (DF) and counting
+devices (DC) have been operated. Sometimes there are no data but only because
+the camera was not working. There are also information about the operations
+(e.g. periods at wich a trap content has been evaluated). Here we load what
 would have been generated if we had run the previous lines.
 
 

Added: pkg/stacomir/vignettes/stacomir.html
===================================================================
--- pkg/stacomir/vignettes/stacomir.html	                        (rev 0)
+++ pkg/stacomir/vignettes/stacomir.html	2018-02-18 19:37:14 UTC (rev 478)
@@ -0,0 +1,531 @@
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+
+<meta name="author" content="Marion Legrand, Cédric Briand" />
+
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+<h1 class="title toc-ignore">StacomiR</h1>
+<h4 class="author"><em>Marion Legrand, Cédric Briand</em></h4>
+<h4 class="date"><em>2018-02-18</em></h4>
+
+
+
+<div id="stacomir" class="section level1">
+<h1>stacomiR <img 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" align="right" /></h1>
+<div id="introduction" class="section level2">
+<h2>Introduction</h2>
+<p>Migratory fishes population are vulnerable as they are often more prone to human impact when migrating in rivers and to the ocean (<a href="http://onlinelibrary.wiley.com.inee.bib.cnrs.fr/doi/10.1002/aqc.3270020405/pdf">McDowall, 1992</a>). They are often counted at stations when they perform the migrations at some of their lifestages, and these counts provide valuable indices to the population size and trend. The objective of the stacomi project is to provide a common database for people monitoring fish migration, so that data from watershed are shared, and stocks exchanging between different basins are better managed. The stacomi database, is an open-source database, it managed with a JAVA interface, and results from that database are treated directly with the stacomiR project.</p>
+</div>
+<div id="installation" class="section level2">
+<h2>Installation</h2>
+<p>The package is available from CRAN, a development version is available from R-Forge.</p>
+<pre class="sourceCode r"><code class="sourceCode r"><div class="sourceLine" id="1" href="#1" data-line-number="1"><span class="kw">install.packages</span>(<span class="st">"stacomiR"</span>) <span class="co"># get the package from CRAN</span></div>
+<div class="sourceLine" id="2" href="#2" data-line-number="2"><span class="kw">install.packages</span>(<span class="st">"stacomiR"</span>, <span class="dt">repos=</span><span class="st">"http://R-Forge.R-project.org"</span>) <span class="co"># get the development version</span></div></code></pre>
+</div>
+<div id="usage" class="section level2">
+<h2>Usage</h2>
+<p>Launch the graphical interface</p>
+<pre class="sourceCode r"><code class="sourceCode r"><div class="sourceLine" id="1" href="#1" data-line-number="1"><span class="kw">stacomi</span>()</div></code></pre>
+<p>The program can be launched to use from the command line</p>
+<pre class="sourceCode r"><code class="sourceCode r"><div class="sourceLine" id="1" href="#1" data-line-number="1"><span class="kw">stacomi</span>(<span class="dt">gr_interface =</span> <span class="ot">FALSE</span>, <span class="dt">login_window =</span> <span class="ot">TRUE</span>, <span class="dt">database_expected =</span> <span class="ot">TRUE</span>)</div></code></pre>
+</div>
+<div id="data-structure" class="section level2">
+<h2>Data structure</h2>
+<p>The open source postgresql database comprises a common schema with dictionaries, and different schema for different users. Each user can save its own schema and send it to others. The database comprises tables related to infrastructure, operations and fish samples. <em>Contact the authors to get a copy of the database</em>.</p>
+<div id="infrastructure" class="section level3">
+<h3>Infrastructure</h3>
+<div id="station" class="section level4">
+<h4>Station</h4>
+<p>A migration report is always built on a section of a river, this is called the station. A station of fish migration monitoring is a section of a watercourse where fish upstream or downstream migration is monitored. The station covers the whole section of a single river, but can extend to several natural or artificial channels. A station consists physically of as many dams as hydrographic sections monitored (river, channels, etc.). According to the local settings, it corresponds to one river location with a counting device, or to one or several dams. For example, in the figure below we can see a station with three crossing device (DF 1 to 3) and two counting device (DC 1 to 2), the first one beeing a trap counting device (DC1) and the other a video-counting device (DC2).</p>
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/stacomir -r 478

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