[Stacomir-commits] r453 - pkg/stacomir
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 30 18:25:56 CEST 2017
Author: briand
Date: 2017-08-30 18:25:55 +0200 (Wed, 30 Aug 2017)
New Revision: 453
Modified:
pkg/stacomir/README.Rmd
pkg/stacomir/README.md
Log:
wrting examples in README.Rmd
Modified: pkg/stacomir/README.Rmd
===================================================================
--- pkg/stacomir/README.Rmd 2017-08-30 15:37:14 UTC (rev 452)
+++ pkg/stacomir/README.Rmd 2017-08-30 16:25:55 UTC (rev 453)
@@ -31,7 +31,7 @@
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
+open-source database, it managed with a JAVA interface, and results from that
database are treated directly with the stacomiR project.
@@ -41,7 +41,7 @@
The package is available from CRAN, a development version is available from
R-Forge.
-```{r install, eval=FALSE}
+```{r , eval=FALSE}
install.packages("stacomiR", repos="http://R-Forge.R-project.org")
```
@@ -50,20 +50,21 @@
Launch the graphical interface
-```{r example1, eval=FALSE}
-stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = TRUE)
+```{r , eval=FALSE}
+stacomi()
```
The program can be launched to use from the command line
-```{r example2, eval=FALSE}
-stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = FALSE)
+```{r , eval=FALSE}
+stacomi(gr_interface = FALSE, login_window = TRUE, database_expected = TRUE)
```
Data structure
-------------------
The open source postgresql database was built on the following concepts.
+*Contact the authors to get a copy of the database*.
### Infrastructure
A migration report is always built on a section of a river. However, dam and
@@ -90,9 +91,9 @@
* etc.
#### Crossing device
-A crossing device is a passageway that allows and concentrates the migratory
-flow between upstream and downstream of a weir. We can have several types like
-:
+A crossing device (DF) is a passageway that allows and concentrates the
+migratory flow between upstream and downstream sections of a weir. They can be
+of various type
* fishway,
* spillway,
* fish elevator,
@@ -101,8 +102,8 @@
It is possible to have more than one crossing device on a same weir.
#### Counting device
-A couting device is a set of equipment installed on a crossing devise used to
-monitor the migratory flow that passes through it.
+A couting device (DC) is a set of equipment installed on a crossing devise
+to monitor fish migration.
It can be :
* a video counting device,
* a trap pass,
@@ -141,6 +142,7 @@
* starting date The date of beginning
* ending date The last date of the report
***
+
| Class | Report type | description|
| ------------- |:----------| ---------------------------------: |
|report_mig | Annual migration | Annual migration report |
@@ -151,10 +153,89 @@
Working examples
-------------------------
-### Interface
-
### Command line
+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`
+
+ ```{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)
+```
+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 fishway, and 6 and 12 are two glass eel trapping ladder located
+at the Arzal dam in the
+Vilaine river (France).
+We are evaluating the migration
+of all stages of eel (glass eel CIV, yellow eel AGJ and silver eel AGJ).
+Glass
+eel and yellow eel migrate to the watershed while silver eel
+are migrating back
+to the ocean.
+Data are loaded from the database with the `charge` method and the `calcule`
+method
+will
+interpolate
+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}
+ 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 describing how the fishway (DF) and counting devices (DC) have been operated.
+Sometimes there is no migration but only because the camera was jammed. 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 ,eval=TRUE,echo=TRUE}
+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)
+```
+
+Individual plot for all DC, taxa and stage where data present
+Silent=TRUE to turn off messages
+
+
+```{r rmmmult,eval=TRUE,echo=FALSE,fig.keep="all"}
+ plot(r_mig_mult,plot.type="multiple",silent=TRUE)
+```
+Ci dessous ne marche pas générer à la main puis expliquer et lien
+```{r rmmstd,eval=TRUE,echo=FALSE,fig.keep="last"}
+ plot(r_mig_mult,plot.type="standard",silent=TRUE)
+```
+
+
+
+### R-GTK2 graphical interface
+
+
License
-------
Modified: pkg/stacomir/README.md
===================================================================
--- pkg/stacomir/README.md 2017-08-30 15:37:14 UTC (rev 452)
+++ pkg/stacomir/README.md 2017-08-30 16:25:55 UTC (rev 453)
@@ -22,7 +22,7 @@
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
+open-source database, it managed with a JAVA interface, and results from that
database are treated directly with the stacomiR project.
@@ -44,20 +44,21 @@
```r
-stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = TRUE)
+stacomi()
```
The program can be launched to use from the command line
```r
-stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = FALSE)
+stacomi(gr_interface = FALSE, login_window = TRUE, database_expected = TRUE)
```
Data structure
-------------------
The open source postgresql database was built on the following concepts.
+*Contact the authors to get a copy of the database*.
### Infrastructure
A migration report is always built on a section of a river. However, dam and
@@ -84,9 +85,9 @@
* etc.
#### Crossing device
-A crossing device is a passageway that allows and concentrates the migratory
-flow between upstream and downstream of a weir. We can have several types like
-:
+A crossing device (DF) is a passageway that allows and concentrates the
+migratory flow between upstream and downstream sections of a weir. They can be
+of various type
* fishway,
* spillway,
* fish elevator,
@@ -95,8 +96,8 @@
It is possible to have more than one crossing device on a same weir.
#### Counting device
-A couting device is a set of equipment installed on a crossing devise used to
-monitor the migratory flow that passes through it.
+A couting device (DC) is a set of equipment installed on a crossing devise
+to monitor fish migration.
It can be :
* a video counting device,
* a trap pass,
@@ -135,6 +136,7 @@
* starting date The date of beginning
* ending date The last date of the report
***
+
| Class | Report type | description|
| ------------- |:----------| ---------------------------------: |
|report_mig | Annual migration | Annual migration report |
@@ -145,10 +147,88 @@
Working examples
-------------------------
-### Interface
-
### Command line
+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`
+
+
+ ```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 fishway, and 6 and 12 are two glass eel trapping ladder located
+at the Arzal dam in the
+Vilaine river (France).
+We are evaluating the migration
+of all stages of eel (glass eel CIV, yellow eel AGJ and silver eel AGJ).
+Glass
+eel and yellow eel migrate to the watershed while silver eel
+are migrating back
+to the ocean.
+Data are loaded from the database with the `charge` method and the `calcule`
+method
+will
+interpolate
+daily
+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 describing how the fishway (DF) and counting devices (DC) have been operated.
+Sometimes there is no migration but only because the camera was jammed. 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)
+ ```
+
+Individual plot for all DC, taxa and stage where data present
+Silent=TRUE to turn off messages
+
+
+
+Ci dessous ne marche pas générer à la main puis expliquer et lien
+
+
+
+
+### R-GTK2 graphical interface
+
+
License
-------
More information about the Stacomir-commits
mailing list