[Stacomir-commits] r479 - pkg/stacomir

[noreply at r-forge.r-project.org]

Author: legrand
Date: 2018-05-16 10:56:14 +0200 (Wed, 16 May 2018)
New Revision: 479

Added:
   pkg/stacomir/paper.bib
   pkg/stacomir/paper.md
Log:


Added: pkg/stacomir/paper.bib
===================================================================
--- pkg/stacomir/paper.bib	                        (rev 0)
+++ pkg/stacomir/paper.bib	2018-05-16 08:56:14 UTC (rev 479)
@@ -0,0 +1,39 @@
+
+ at article{mcdowall_1992,
+	
+	title = {Particular problems for the conservation of diadromous fish},
+	
+	volume = {2},
+	issn = {1099-0755},
+	
+	url = {http://onlinelibrary.wiley.com.inee.bib.cnrs.fr/doi/10.1002/aqc.3270020405/abstract},
+	
+	doi = {10.1002/aqc.3270020405},
+	
+	language = {en},
+	
+	number = {4},
+	
+	urldate = {2018-02-05},
+	
+	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
+	
+	author = {McDowall, R. M.},
+	
+	month = dec,
+	
+	year = {1992},
+	
+	pages = {351--355},
+	
+	file = {McDowall, 1992.pdf:C\:\\Users\\marion.legrand\\Zotero\\storage\\25FHWJCS\\McDowall, 1992.pdf:application/pdf;Snapshot:C\:\\Users\\marion.legrand\\Zotero\\storage\\HCSYYC4I\\pdf.html:text/html}
+	
+}
+ at Manual{R2017,
+    title = {R: A Language and Environment for Statistical Computing},
+    author = {{R Core Team}},
+    organization = {R Foundation for Statistical Computing},
+    address = {Vienna, Austria},
+    year = {2017},
+    url = {https://www.R-project.org/},
+  }
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Added: pkg/stacomir/paper.md
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--- pkg/stacomir/paper.md	                        (rev 0)
+++ pkg/stacomir/paper.md	2018-05-16 08:56:14 UTC (rev 479)
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+---
+title: 'stacomiR : a common tool for monitoring fish migration'
+authors:
+ - name: Marion Legrand
+   affiliation: "1, 2"
+ - name: Cédric Briand
+   affiliation: 3
+affiliations:
+ - name: EcoLab, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
+   index: 1
+ - name: Loire Grands Migrateurs (LOGRAMI), 5, avenue Buffon, Orléans, France
+   index: 2
+ - name: Etablissement Public Territorial du Bassin de la Vilaine (EPTB Vilaine), Boulevard de Bretagne, La Roche-Bernard, France
+   index: 3
+
+date: 15 May 2018
+bibliography: paper.bib
+---
+
+# Summary
+
+Migratory fishes population are vulnerable as they are often more prone to human impact when migrating in rivers and to the ocean [@mcdowall_1992].
+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 package[@R2017]. The program is intended to be used by a "non experienced" R user, but all the R code automatically generated by the programm is shown to the user. Thus, it is possible to copy/paste the code and modify it (for example to change the preprogrammed colors or make more complicated changes). 
+The package is available from CRAN, a development version is available
+from R-Forge.
+
+```{R}
+# Installation
+install.packages("stacomiR") # get the package from CRAN
+install.packages("stacomiR", repos="http://R-Forge.R-project.org") # get the development version
+library(stacomiR)
+
+# Launch the graphical interface
+## For user having the stacomi database
+stacomi()
+## For user without connection to the database
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE) 
+```
+
+Launching `stacomi()` will create the interface. The interface looks
+like :
+
+![](man/figures/interface_graph_taille_sat.png)
+
+```{R}
+# Plot for example, the glass eel migration in weight and number (top), the periods and type of operation for DF and DC, 
+# and the operation (trapping periods) (middle), a summary of migration per month (bottom). 
+## For user without the connection to the database
+data("r_mig")
+data("r_mig_ope")
+assign("report_ope",r_mig_ope,envir=envir_stacomi)
+data("r_mig_df")
+assign("report_df",r_mig_df,envir=envir_stacomi)
+data("r_mig_dc")
+assign("report_dc",r_mig_dc,envir=envir_stacomi)
+plot(r_mig,plot.type="standard",silent=TRUE)
+
+```
+![](man/figures/README-rmmstandard-1.png)
+
+# References
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