[Stacomir-commits] r474 - in pkg/stacomir: . man/figures
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 15 14:37:39 CET 2018
Author: briand
Date: 2018-02-15 14:37:38 +0100 (Thu, 15 Feb 2018)
New Revision: 474
Modified:
pkg/stacomir/README.Rmd
pkg/stacomir/README.md
pkg/stacomir/man/figures/README-rmmmult-1.png
pkg/stacomir/man/figures/README-silver-1.png
Log:
Modified: pkg/stacomir/README.Rmd
===================================================================
--- pkg/stacomir/README.Rmd 2018-02-06 14:32:40 UTC (rev 473)
+++ pkg/stacomir/README.Rmd 2018-02-15 13:37:38 UTC (rev 474)
@@ -1,6 +1,6 @@
---
title: StacomiR
-author: Marion Legrand, Cédric Briand
+author: Marion Legrand, C�dric Briand
output: github_document
---
@@ -208,7 +208,8 @@
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)
```
@@ -255,17 +256,8 @@
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)
-```
+
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
Modified: pkg/stacomir/README.md
===================================================================
--- pkg/stacomir/README.md 2018-02-06 14:32:40 UTC (rev 473)
+++ pkg/stacomir/README.md 2018-02-15 13:37:38 UTC (rev 474)
@@ -1,226 +1,246 @@
-StacomiR
-================
-Marion Legrand, Cédric Briand
+---
+title: StacomiR
+author: Marion Legrand, C�dric Briand
+output: github_document
+---
+
+
[](https://cran.r-project.org/package=stacomiR)
+
+
# 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
+```
+#> 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 ([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.
+Migratory fishes population are vulnerable as they are often more prone 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
-The package is available from CRAN, a development version is available
-from R-Forge.
+Installation
+-------------------------
-``` r
+The package is available from CRAN, a development version is available from
+R-Forge.
+
+
+```r
install.packages("stacomiR") # get the package from CRAN
install.packages("stacomiR", repos="http://R-Forge.R-project.org") # get the development version
```
-## Usage
+Usage
+-------------------------
Launch the graphical interface
-``` r
+
+```r
stacomi()
```
-The program can be launched to use from the command
-line
+The program can be launched to use from the command line
-``` r
+
+```r
stacomi(gr_interface = FALSE, login_window = TRUE, database_expected = TRUE)
```
-## Data structure
-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. The database comprises tables
-related to infrastructure, operations and fish samples. *Contact the
-authors to get a copy of the database*.
+Data structure
+-------------------
+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. The
+database comprises tables related to infrastructure, operations and fish
+samples.
+*Contact the authors to get a copy of the database*.
### Infrastructure
+
#### 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 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. 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).
+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. 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
+The concept of dam used in the context of fish migration monitoring database
+refers to a system blocking or guiding the migratory flow like :
-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,
- - weir,
+* electric guide barrier,
- - electric guide barrier,
+* netting dam,
- - netting dam,
+* etc.
- - etc.
-#### Crossing device
-
+#### Crossing device
A crossing device (DF) is a passageway that allows and concentrates the
-migratory flow between upstream and downstream sections of a dam. They
-can be of various type :
+migratory flow between upstream and downstream sections of a dam. They can be of
+various type :
- - fishway,
+* fishway,
- - spillway,
+* spillway,
- - fish elevator,
+* fish elevator,
- - eel trapping ladder,
+* eel trapping ladder,
- - etc.
+* etc.
It is possible to have more than one crossing device on a same dam.
#### Counting device
+A counting device (DC) is a set of equipment installed on a crossing device used
+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 video counting device,
+* a trap,
- - a trap,
+* an accoustic counting device,
- - an accoustic counting device,
+* ...
- - …
#### Monitoring operation
+An operation corresponds to a monitoring of a counting device during a time
+span.
-An operation corresponds to a monitoring of a counting device during a
-time span.
-
#### 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.
-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
+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 ...
-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
-
-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
+ 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 : \*\*\*
+method*, or plot results.
+For instance, the migration report class comprises slots for :
+***
- - DC The counting device (camera, trap, acoustic device…)
+* DC The counting device (camera, trap, acoustic device...)
- - taxa The species list from the database and the taxa selected
+* taxa The species list from the database and the taxa selected
- - stage The stages list from the database and the stage selected
+* stage The stages list from the database and the stage selected
- - starting date The date of beginning
+* starting date The date of beginning
- - ending date The last date of the report
+* ending date The last date of the report
------
-
-Read the help files e.g. `? report_mig` to get documentation on the
-following
+***
+Read the help files e.g. `? report_mig` to get documentation on the following
classes.
-| Class | Command | description |
-| ------------------------ | :------------------------------ | :---------------------------------- |
-| report\_mig | `new("report_mig")` | Migration report (single) |
-| report\_mig\_mult | `new("report_mig_mult")` | Migr. (several DC,taxa…) |
-| report\_annual | `new("report_annual")` | Multi year migration counts |
-| report\_dc | `new("report_dc")` | Counting device operation |
-| report\_df | `new("report_df")` | Fishway operation |
-| report\_mig\_env | `new("report_env")` | Migration crossed with env. factors |
-| report\_mig\_char | `new("report_df")` | Migration with fish characteristics |
-| report\_mig\_interannual | `new("report_mig_interannual")` | Comp. between years |
-| report\_sample\_char | `new("report_sample_char")` | Sample characteristics |
-| report\_ge\_weight | `new("report_ge_weight")` | Trend in glass eel weight |
-| report\_silver\_eel | `new("report_siver_eel")` | Silver eel migration & stage |
-| report\_sea\_age | `new("report_sea_age")` | Set sea age for Salmon |
-| report\_species | `new("report_species")` | Species composition |
+| Class | Command | description|
+| ------------- |:----------|:--------------------------------------- |
+|report_mig | `new("report_mig")` | Migration report (single) |
+| report_mig_mult| `new("report_mig_mult")`| Migr. (several DC,taxa...) |
+| report_annual| `new("report_annual")`| Multi year migration counts |
+| report_dc | `new("report_dc")`| Counting device operation |
+| report_df | `new("report_df")`| Fishway operation |
+| report_mig_env | `new("report_env")`| Migration crossed with env. factors |
+| report_mig_char | `new("report_df")`| Migration with fish characteristics |
+|report_mig_interannual | `new("report_mig_interannual")`| Comp. between years|
+|report_sample_char | `new("report_sample_char")`| Sample characteristics |
+|report_ge_weight | `new("report_ge_weight")`| Trend in glass eel weight |
+|report_silver_eel | `new("report_siver_eel")`| Silver eel migration & stage|
+|report_sea_age | `new("report_sea_age")`| Set sea age for Salmon |
+|report_species | `new("report_species")`| Species composition |
-## Working examples
-### Command line
+Working examples
+-------------------------
+### Command line
+
#### Migration report
-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
+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
+
+ ```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 AGG).
-Glass eel and yellow eel migrate to the watershed while silver eels 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.
+Glass
+eel and yellow eel migrate to the watershed while silver eels
+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
+```r
stacomi(gr_interface=FALSE,
- login_window=FALSE,
- database_expected=TRUE)
+ 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"),
+ 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)
@@ -230,51 +250,45 @@
# 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.
-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)
-#> 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
-for DF and DC, and the operation (trapping periods) (middle), a summary
-of migration per month (bottom).
+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).
+
+
+
Summary of migration for different stages and counting devices
-<!-- -->
+```
+#> Error in object at calcdata[[i]]: subscript out of bounds
+```
+
#### Silver eels
-This section provides a short example for the function calculating
-Durif’s stages. Those maturity stages for silver eels are calculated
-from body characteristics. The dataset `coef_durif` corresponds to
-classification scores are calculated by multiplying the metrics BL =
-body length, W = weight, MD = mean eye diameter (Dv+Dh)/2, and FL length
-of the pectoral fin, with each parameter p as
-S=Constant+BL*p(bl)+W*p(W)… The function `fun_stage_durif` choose the
-stage achieving the highest score ([Durif et al.,
+This section provides a short example for the function
+calculating Durif's stages. Those maturity stages for silver eels are
+calculated from body characteristics. The dataset `coef_durif`
+corresponds to classification scores are calculated by multiplying the metrics
+BL = body length, W = weight, MD = mean eye diameter (Dv+Dh)/2, and FL length of
+the pectoral fin, with each parameter p as S=Constant+BL*p(bl)+W*p(W)... The
+function `fun_stage_durif` choose the stage achieving the highest
+score ([Durif et al.,
2009](http://fishlarvae.org/common/SiteMedia/durif%20et%20al%202009b.pdf))
-``` r
+
+```r
require(stacomiR)
data("coef_durif")
# load a dataset of class report_silver_eel with data slot already prepared
@@ -285,9 +299,9 @@
#> Warning in predict.lm(rlmmodb, newdata = newdata, se.fit = TRUE, type = "response", : Assuming constant prediction variance even though model fit is weighted
```
-<!-- -->
+
-``` r
+```r
#######################################
# To use the function fun_stage_durif manually
# create a matrix with columns BL","W","Dv","Dh","FL"
@@ -307,15 +321,14 @@
#> 25710 25711 25712 25713 25714 25715 25716 25717 25718 25719
#> "FIII" "FIII" "FIII" "FIV" "FIII" "FIII" "FV" "FV" "FIII" "FIII"
```
-
### R-GTK2 graphical interface
-The program is intended to be used by ‘non experienced’ R users.
-Launching `stacomi()` will create the interface. The interface looks
-like :
+The program is intended to be used by 'non experienced' R users. Launching
+`stacomi()` will create the interface. The interface looks like :
-## License
+License
+-------
The STACOMI project is released under GPL-2.
Modified: pkg/stacomir/man/figures/README-rmmmult-1.png
===================================================================
(Binary files differ)
Modified: pkg/stacomir/man/figures/README-silver-1.png
===================================================================
(Binary files differ)
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