[Stacomir-commits] r451 - / pkg/stacomir
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 30 16:50:07 CEST 2017
Author: briand
Date: 2017-08-30 16:50:06 +0200 (Wed, 30 Aug 2017)
New Revision: 451
Added:
LICENSE
Modified:
pkg/stacomir/README.Rmd
pkg/stacomir/README.md
Log:
further writing of the README file
Added: LICENSE
===================================================================
--- LICENSE (rev 0)
+++ LICENSE 2017-08-30 14:50:06 UTC (rev 451)
@@ -0,0 +1,280 @@
+ GNU GENERAL PUBLIC LICENSE
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\ No newline at end of file
Modified: pkg/stacomir/README.Rmd
===================================================================
--- pkg/stacomir/README.Rmd 2017-08-30 14:21:32 UTC (rev 450)
+++ pkg/stacomir/README.Rmd 2017-08-30 14:50:06 UTC (rev 451)
@@ -21,8 +21,20 @@
library(stacomiR)
```
+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.
+
Installation
-------------------------
@@ -47,42 +59,41 @@
```{r example2, eval=FALSE}
stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = FALSE)
```
-Introduction
----------------------------
-Link with open source database,
-objective evaluation and sharing stock indicators for migratory fishes.
-No R package
-JAVA + postgres + R
-
Data structure
-------------------
-The structure of the data contained in the open source postgresql database
-"bd_contmig_nat" is based on the following concepts.
+The open source postgresql database was built on the following concepts.
-### Station
-Station is a fish migration monitoring and in general, it is considered to be a
-section of a watercourse allowing the evaluation of fish upstream or downstream
-migration.
-Station may extend to the whole section of the migration axis to evaluate a
-migratory flow on a section subdivided into several natural or artificial
-channels. A station consists physically of as many weirs as hydrographic
-sections monitored (river, channels, etc.).
+### 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 (DC).
-### Weir
+#### 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.
+
+#### Weir
The concept of weir used in the context of fish migration monitoring database
refers to a system blocking or guiding the migratory flow like : (i) dam, (ii)
electric guide barrier, (iii) netting dam, etc.
-### Crossing device
+#### 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
:(i) fishway, (ii) spillway, (iii) fish elevator, etc.
It is possible to have more than one crossing device on a same weir.
-### Counting device
+#### 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.
@@ -93,7 +104,26 @@
Package structure
--------------------
+The package relies on S4 classes. *Referential classes* are used to access data
+from the database (taxa, stages, counting devices...).
+*Report classes* are built from referential classes and have different methods
+to access the database *connect methods*, generate calculations *calcule
+method*, or plot results.
+For instance, the migration report class comprises slots for :
+***
+* DC The counting device (camera, trap, acoustic device...)
+* taxa The species list from the database and the taxa selected
+* stage The stages list from the database and the stage selected
+* 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 |
+| report_mig_mult| Annual migration| Annual migration (several DC, taxa...) |
+
+
Working examples
-------------------------
@@ -103,4 +133,5 @@
License
-------
-Released under GPL-2.
\ No newline at end of file
+
+The STACOMI project is released under GPL-2.
\ No newline at end of file
Modified: pkg/stacomir/README.md
===================================================================
--- pkg/stacomir/README.md 2017-08-30 14:21:32 UTC (rev 450)
+++ pkg/stacomir/README.md 2017-08-30 14:50:06 UTC (rev 451)
@@ -12,8 +12,20 @@
# stacomiR <img src="man/figures/logo.png" align="right" />
+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.
+
Installation
-------------------------
@@ -41,21 +53,19 @@
```r
stacomi(gr_interface = TRUE, login_window = TRUE, database_expected = FALSE)
```
-Introduction
----------------------------
-Link with open source database,
-objective evaluation and sharing stock indicators for migratory fishes.
-No R package
-JAVA + postgres + R
-
Data structure
-------------------
-The structure of the data contained in the open source postgresql database
-"bd_contmig_nat" is based on the following concepts.
+The open source postgresql database was built on the following concepts.
-### Station
+### 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 (DC).
+
+#### Station
Station is a fish migration monitoring and in general, it is considered to be a
section of a watercourse allowing the evaluation of fish upstream or downstream
migration.
@@ -64,19 +74,19 @@
channels. A station consists physically of as many weirs as hydrographic
sections monitored (river, channels, etc.).
-### Weir
+#### Weir
The concept of weir used in the context of fish migration monitoring database
refers to a system blocking or guiding the migratory flow like : (i) dam, (ii)
electric guide barrier, (iii) netting dam, etc.
-### Crossing device
+#### 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
:(i) fishway, (ii) spillway, (iii) fish elevator, etc.
It is possible to have more than one crossing device on a same weir.
-### Counting device
+#### 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.
@@ -87,7 +97,26 @@
Package structure
--------------------
+The package relies on S4 classes. *Referential classes* are used to access data
+from the database (taxa, stages, counting devices...).
+*Report classes* are built from referential classes and have different methods
+to access the database *connect methods*, generate calculations *calcule
+method*, or plot results.
+For instance, the migration report class comprises slots for :
+***
+* DC The counting device (camera, trap, acoustic device...)
+* taxa The species list from the database and the taxa selected
+* stage The stages list from the database and the stage selected
+* 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 |
+| report_mig_mult| Annual migration| Annual migration (several DC, taxa...) |
+
+
Working examples
-------------------------
@@ -97,4 +126,5 @@
License
-------
-Released under GPL-2.
+
+The STACOMI project is released under GPL-2.
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