[Stacomir-commits] r472 - / pkg/stacomir pkg/stacomir/man/figures
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 5 16:54:34 CET 2018
Author: legrand
Date: 2018-02-05 16:54:34 +0100 (Mon, 05 Feb 2018)
New Revision: 472
Added:
pkg/stacomir/man/figures/StationComptage.png
pkg/stacomir/man/figures/interface_graph_taille_sat.png
Modified:
README
pkg/stacomir/README.Rmd
pkg/stacomir/README.md
pkg/stacomir/man/figures/README-silver-1.png
Log:
Add diagram of station + add reference about migratory fish + add picture of graphical interface
Modified: README
===================================================================
--- README 2018-01-27 09:12:36 UTC (rev 471)
+++ README 2018-02-05 15:54:34 UTC (rev 472)
@@ -5,7 +5,7 @@
Theußl and Zeileis (2010) [1] and the R-Forge Administration and
Development Team (2009) [2].
-1. Introduction
+1. Introduction
-----------------------------------------------------------------------
R is free software distributed under a GNU-style copyleft. R-Forge is
a central platform for the development of R packages, R-related
Modified: pkg/stacomir/README.Rmd
===================================================================
--- pkg/stacomir/README.Rmd 2018-01-27 09:12:36 UTC (rev 471)
+++ pkg/stacomir/README.Rmd 2018-02-05 15:54:34 UTC (rev 472)
@@ -26,7 +26,8 @@
--------------------------
Migratory fishes population are vulnerable as they are often more prone to human
-impact when migrating in rivers and to the ocean. They are often counted at
+impact when migrating in rivers and to the ocean ([McDowall,
+1992](http://onlinelibrary.wiley.com.inee.bib.cnrs.fr/doi/10.1002/aqc.3270020405/pdf)). 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
@@ -76,6 +77,7 @@
#### Station
+
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
@@ -83,9 +85,14 @@
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.
+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).
-#### dams
+
+
+
+
+#### Dams
The concept of dam used in the context of fish migration monitoring database
refers to a system blocking or guiding the migratory flow like :
* weir,
@@ -181,7 +188,7 @@
without access, use the arguments `login_windows=FALSE` and
`database_expected=FALSE`
- ```{r , eval=TRUE, echo=TRUE}
+```{r , eval=TRUE, echo=TRUE}
## launches the application in the command line without connection to the database
stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
```
@@ -204,7 +211,7 @@
daily
migration from monitoring operations which do not necessarily span a day, and convert the glass eel
weight in numbers.
- ```{r ,eval=FALSE,echo=TRUE}
+```{r ,eval=FALSE,echo=TRUE}
stacomi(gr_interface=FALSE,
login_window=FALSE,
database_expected=TRUE)
@@ -228,7 +235,7 @@
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.
- ```{r ,eval=TRUE,echo=TRUE}
+```{r ,eval=TRUE,echo=TRUE}
data("r_mig_mult")
data("r_mig_mult_ope")
assign("report_ope",r_mig_mult_ope,envir=envir_stacomi)
@@ -293,9 +300,9 @@
The program is intended to be used by 'non experienced' R users. Launching
`stacomi()` will create the interface. The interface looks like :
-[Durif et al.,
-2009](http://fishlarvae.org/common/SiteMedia/durif%20et%20al%202009b.pdf))
+
+
License
-------
Modified: pkg/stacomir/README.md
===================================================================
--- pkg/stacomir/README.md 2018-01-27 09:12:36 UTC (rev 471)
+++ pkg/stacomir/README.md 2018-02-05 15:54:34 UTC (rev 472)
@@ -1,6 +1,6 @@
StacomiR
================
-Marion Legrand, Cédric Briand
+Marion Legrand, Cédric Briand
true
@@ -8,18 +8,23 @@
# stacomiR <img src="man/figures/logo.png" align="right" />
+ #> Warning: package 'stacomiR' was built under R version 3.4.3
+ #> Loading required package: stacomirtools
+ #> Loading required package: RODBC
+
## Introduction
Migratory fishes population are vulnerable as they are often more prone
-to human impact when migrating in rivers and to the ocean. 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.
+to human impact when migrating in rivers and to the ocean ([McDowall,
+1992](http://onlinelibrary.wiley.com.inee.bib.cnrs.fr/doi/10.1002/aqc.3270020405/pdf)).
+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.
## Installation
@@ -65,10 +70,16 @@
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.
+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).
-#### dams
+
+#### Dams
+
The concept of dam used in the context of fish migration monitoring
database refers to a system blocking or guiding the migratory flow like
: \* weir, \* electric guide barrier, \* netting dam, \* etc.
@@ -149,11 +160,14 @@
Examples are provided with each of the class, you can access them simply
by typing `? report_mig_mult` The program is intented to be used in
conjuntion with the database, to test it without access, use the
-arguments `login_windows=FALSE` and `database_expected=FALSE`
+arguments `login_windows=FALSE` and
+`database_expected=FALSE`
-`r ## launches the application in the command line without connection to
-the database
-stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)`
+``` r
+## launches the application in the command line without connection to the database
+stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
+```
+
The following code is only run when there is a connection to the
database. The program will create an object of the class
report\_mig\_mult, and run it for several DC, here 5 is a vertical slot
@@ -166,28 +180,44 @@
migration from monitoring operations which do not necessarily span a
day, and convert the glass eel weight in numbers.
-`r stacomi(gr_interface=FALSE, login_window=FALSE,
-database_expected=TRUE) r_mig_mult=new("report_mig_mult")
-r_mig_mult=choice_c(r_mig_mult, dc=c(5,6,12), taxa=c("Anguilla
-anguilla"), stage=c("AGG","AGJ","CIV"), datedebut="2011-01-01",
-datefin="2011-12-31") r_mig_mult<-charge(r_mig_mult) # launching charge
-will also load classes associated with the report # e.g. report_ope,
-report_df, report_dc r_mig_mult<-connect(r_mig_mult) # calculations
-r_mig_mult<-calcule(r_mig_mult,silent=TRUE)` 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 would have been generated if we had run the previous lines.
+``` r
+ stacomi(gr_interface=FALSE,
+ login_window=FALSE,
+ database_expected=TRUE)
+ r_mig_mult=new("report_mig_mult")
+ r_mig_mult=choice_c(r_mig_mult,
+ dc=c(5,6,12),
+ taxa=c("Anguilla anguilla"),
+ stage=c("AGG","AGJ","CIV"),
+ datedebut="2011-01-01",
+ datefin="2011-12-31")
+ r_mig_mult<-charge(r_mig_mult)
+ # launching charge will also load classes associated with the report
+ # e.g. report_ope, report_df, report_dc
+ r_mig_mult<-connect(r_mig_mult)
+ # calculations
+ r_mig_mult<-calcule(r_mig_mult,silent=TRUE)
+```
-`r data("r_mig_mult") data("r_mig_mult_ope")
+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 would have been generated if we
+had run the previous lines.
+
+``` r
+data("r_mig_mult")
+data("r_mig_mult_ope")
assign("report_ope",r_mig_mult_ope,envir=envir_stacomi)
data("r_mig_mult_df")
assign("report_df",r_mig_mult_df,envir=envir_stacomi)
data("r_mig_mult_dc")
assign("report_dc",r_mig_mult_dc,envir=envir_stacomi)
-r_mig_mult<-calcule(r_mig_mult,silent=TRUE)`
+r_mig_mult<-calcule(r_mig_mult,silent=TRUE)
+#> Loading required package: DBI
+```
One graph per DC, taxa and stage. Below as an example, the glass eel
migration in weight and number (top), the periods and type of operation
@@ -250,9 +280,10 @@
The program is intended to be used by ‘non experienced’ R users.
Launching `stacomi()` will create the interface. The interface looks
-like : [Durif et al.,
-2009](http://fishlarvae.org/common/SiteMedia/durif%20et%20al%202009b.pdf))
+like :
+
+
## License
The STACOMI project is released under GPL-2.
Modified: pkg/stacomir/man/figures/README-silver-1.png
===================================================================
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Added: pkg/stacomir/man/figures/StationComptage.png
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Property changes on: pkg/stacomir/man/figures/interface_graph_taille_sat.png
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