[Stacomir-commits] r456 - in pkg/stacomir: . man/figures
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Aug 31 16:41:16 CEST 2017
Author: briand
Date: 2017-08-31 16:41:16 +0200 (Thu, 31 Aug 2017)
New Revision: 456
Added:
pkg/stacomir/man/figures/README-rmmstandard-1.png
Modified:
pkg/stacomir/README.Rmd
pkg/stacomir/README.md
Log:
wrting examples in README.Rmd
Modified: pkg/stacomir/README.Rmd
===================================================================
--- pkg/stacomir/README.Rmd 2017-08-31 13:07:18 UTC (rev 455)
+++ pkg/stacomir/README.Rmd 2017-08-31 14:41:16 UTC (rev 456)
@@ -63,88 +63,72 @@
Data structure
-------------------
-The open source postgresql database was built on the following concepts.
-*Contact the authors to get a copy of the structure of the database*.
+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. *Contact the authors to get a copy of the database*. The
+database comprises tables related to infrastructure, operations and fish
+samples.
+*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
-fishways can have a complex structure, with the river divided into several
-branches, arriving at different dams. A fishway or river section can also be
-monitored by different counting devices.
+
#### Station
-A station of fish migration monitoring is considered to be
-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
-weirs 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.
+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.
-#### Weir
-The concept of weir used in the context of fish migration monitoring database
+#### 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 :
-* dam,
+* weir,
* electric guide barrier,
* netting dam,
* etc.
#### Crossing device
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
+migratory flow between upstream and downstream sections of a dam. They can be of
+various type
* fishway,
* spillway,
-* fish elevator,
+* fish elevator,
+* eel trapping ladder,
* etc.
-It is possible to have more than one crossing device on a same weir.
+It is possible to have more than one crossing device on a same dam.
#### Counting device
-A couting device (DC) is a set of equipment installed on a crossing devise
-to monitor fish migration.
-It can be :
+A counting device (DC) is a set of equipment installed on a crossing device used
+to monitor fish migration. It can be :
* a video counting device,
-* a trap pass,
+* a trap,
* an acoustic counting device,
-* etc.
+* ...
-#### Operating periods of the devices
-Both counting and crossing devices are monitored to have clear indications of
-operating periods. These informations are really important to better interpret
-fish migration data.
-
-#### Environmental monitoring station
-To better understand migration of fish the database allow to insert information
-about environmental condition at a fish monitoring station. Different
-environmental parameters are available like :
-* turbidity,
-* atmospheric pressure,
-* temperature (both of the river and of the air),
-* flow,
-* lunar cycle,
-* etc.
-### Migration
-Whatever infrastructure is all fishes passing through a counting device are
-monitored.
-
#### Monitoring operation
-An operation represents a monitoring varying duration of a counting device. It
-therefore includes a start and end date for a specific counting device.
+An operation corresponds to a monitoring of a counting device during a time
+span.
-#### Fishes
-Fishes passing a counting device during a monitoring operation are
-species and stage determined and counted.
+#### 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.
#### Other features
-For each fish passing the counting device features like size, weight, sex, age,
-etc. can be monitored as well as :
-* the futur of the fish (released, death, farmed, etc.),
-* tagging (2 possibilities : read of existing tag or lay of new tag),
-* pathologies,
-* genetic samples.
+The database also handles, marking-recapture operations, pathologies, samples
+collection (scale, fin sample for genetic...), fate of fishes (released, death,
+farmed, etc.), etc...
+Some tables are also used to insert information
+about environmental condition such as turbidity, atmospheric pressure,
+temperature, flow ...
Package structure
@@ -223,8 +207,8 @@
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
+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.
@@ -239,20 +223,29 @@
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
+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 for DF and DC, and the operation (trapping
+periods) (middle), a summary of migration per month (bottom).
+```{r rmmstd,eval=FALSE,echo=FALSE,fig.keep="last"}
+# chunk not evaluated as it produces 5 plot with dev.new() called in a loop
+Sys.setlocale("LC_ALL","English")
+ plot(r_mig_mult,plot.type="standard",silent=TRUE)
+```
+
+
+
+Summary of migration for different stages and counting devices
+
```{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
Modified: pkg/stacomir/README.md
===================================================================
--- pkg/stacomir/README.md 2017-08-31 13:07:18 UTC (rev 455)
+++ pkg/stacomir/README.md 2017-08-31 14:41:16 UTC (rev 456)
@@ -57,59 +57,72 @@
Data structure
-------------------
+<<<<<<< .mine
+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. *Contact the authors to get a copy of the database*. The
+database comprises tables related to infrastructure, operations and fish
+samples.
+||||||| .r454
The open source postgresql database was built on the following concepts.
+*Contact the authors to get a copy of the database*.
+=======
+The open source postgresql database was built on the following concepts.
*Contact the authors to get a copy of the structure of the database*.
+>>>>>>> .r455
### Infrastructure
-A migration report is always built on a section of a river. However, dam and
-fishways can have a complex structure, with the river divided into several
-branches, arriving at different dams. A fishway or river section can also be
-monitored by different counting devices.
+
#### Station
-A station of fish migration monitoring is considered to be
-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
-weirs 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.
+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.
-#### Weir
-The concept of weir used in the context of fish migration monitoring database
+#### 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 :
-* dam,
+* weir,
* electric guide barrier,
* netting dam,
* etc.
#### Crossing device
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
+migratory flow between upstream and downstream sections of a dam. They can be of
+various type
* fishway,
* spillway,
-* fish elevator,
+* fish elevator,
+* eel trapping ladder,
* etc.
-It is possible to have more than one crossing device on a same weir.
+It is possible to have more than one crossing device on a same dam.
#### Counting device
-A couting device (DC) is a set of equipment installed on a crossing devise
-to monitor fish migration.
-It can be :
+A counting device (DC) is a set of equipment installed on a crossing device used
+to monitor fish migration. It can be :
* a video counting device,
-* a trap pass,
+* a trap,
* an acoustic counting device,
-* etc.
+* ...
+<<<<<<< .mine
+||||||| .r454
+#### Environmental monitoring station
+=======
#### Operating periods of the devices
Both counting and crossing devices are monitored to have clear indications of
operating periods. These informations are really important to better interpret
fish migration data.
#### Environmental monitoring station
+>>>>>>> .r455
To better understand migration of fish the database allow to insert information
about environmental condition at a fish monitoring station. Different
environmental parameters are available like :
@@ -120,25 +133,46 @@
* lunar cycle,
* etc.
+<<<<<<< .mine
+||||||| .r454
+
### Migration
Whatever infrastructure is all fishes passing through a counting device are
monitored.
+=======
+### Migration
+Whatever infrastructure is all fishes passing through a counting device are
+monitored.
+
+>>>>>>> .r455
#### Monitoring operation
-An operation represents a monitoring varying duration of a counting device. It
-therefore includes a start and end date for a specific counting device.
+An operation corresponds to a monitoring of a counting device during a time
+span.
-#### Fishes
-Fishes passing a counting device during a monitoring operation are
-species and stage determined and counted.
+#### 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.
#### Other features
+<<<<<<< .mine
+The database also handles, marking-recapture operations, pathologies, samples
+collection (scale, fin sample for genetic...), fate of fishes (released, death,
+farmed, etc.), etc...
+Some tables are also used to insert information
+about environmental condition such as turbidity, atmospheric pressure,
+temperature, flow ...
+||||||| .r454
+=======
For each fish passing the counting device features like size, weight, sex, age,
etc. can be monitored as well as :
* the futur of the fish (released, death, farmed, etc.),
* tagging (2 possibilities : read of existing tag or lay of new tag),
* pathologies,
* genetic samples.
+>>>>>>> .r455
Package structure
@@ -219,8 +253,8 @@
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
+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.
@@ -234,25 +268,25 @@
data("r_mig_mult_dc")
assign("report_dc",r_mig_mult_dc,envir=envir_stacomi)
r_mig_mult<-calcule(r_mig_mult,silent=TRUE)
- #> Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'calcule' for signature '"report_mig_mult"'
```
-Individual plot for all DC, taxa and stage where data present
-Silent=TRUE to turn off messages
+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 for DF and DC, and the operation (trapping
+periods) (middle), a summary of migration per month (bottom).
-```
-#> Error in as.double(y): cannot coerce type 'S4' to vector of type 'double'
-```
-Ci dessous ne marche pas générer à la main puis expliquer et lien
-```
-#> Error in as.double(y): cannot coerce type 'S4' to vector of type 'double'
-```
-
+
+Summary of migration for different stages and counting devices
+
+
+
+
+
### R-GTK2 graphical interface
Added: pkg/stacomir/man/figures/README-rmmstandard-1.png
===================================================================
(Binary files differ)
Property changes on: pkg/stacomir/man/figures/README-rmmstandard-1.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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