[Stacomir-commits] r475 - in pkg/stacomir: . man/figures vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Feb 15 17:14:22 CET 2018 

Author: briand
Date: 2018-02-15 17:14:22 +0100 (Thu, 15 Feb 2018)
New Revision: 475

Added:
   pkg/stacomir/man/figures/README-rmmmult-1.pdf
   pkg/stacomir/man/figures/README-silver-1.pdf
   pkg/stacomir/vignettes/
   pkg/stacomir/vignettes/stacomir.Rmd
Modified:
   pkg/stacomir/DESCRIPTION
   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/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION	2018-02-15 13:37:38 UTC (rev 474)
+++ pkg/stacomir/DESCRIPTION	2018-02-15 16:14:22 UTC (rev 475)
@@ -104,10 +104,13 @@
     mgcv
 Suggests:
     testthat,
-    viridis
+    viridis,
+    knitr,
+    rmarkdown
 Author: Cedric Briand [aut, cre],
     Marion Legrand [aut],
     Timothee Besse [aut]
 Maintainer: Cedric Briand <cedric.briand00 at gmail.com>
 RoxygenNote: 5.0.1
 NeedsCompilation: no
+VignetteBuilder: knitr

Modified: pkg/stacomir/README.Rmd
===================================================================
--- pkg/stacomir/README.Rmd	2018-02-15 13:37:38 UTC (rev 474)
+++ pkg/stacomir/README.Rmd	2018-02-15 16:14:22 UTC (rev 475)
@@ -1,13 +1,17 @@
 ---
 title: StacomiR
-author: Marion Legrand, C�dric Briand
+author: Marion Legrand, Cédric Briand
 output: github_document
-
 ---  
 
 
 [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/stacomiR)](https://cran.r-project.org/package=stacomiR)
 
+```{r knitropt, include=FALSE}
+ require(knitr)
+opts_knit$set(message=FALSE, warnings=FALSE,error=FALSE,include=FALSE) 
+```
+
 ```{r echo = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -162,7 +166,6 @@
 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...)
 
@@ -174,7 +177,6 @@
 
 * ending date The last date of the report
 
-***
 Read the help files e.g. `? report_mig` to get documentation on the following
 classes.
 
@@ -209,7 +211,7 @@
 `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) 
 ```
@@ -232,7 +234,8 @@
 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=TRUE,echo=TRUE}
    stacomi(gr_interface=FALSE,
 	  login_window=FALSE,
 	  database_expected=TRUE)	

Modified: pkg/stacomir/README.md
===================================================================
--- pkg/stacomir/README.md	2018-02-15 13:37:38 UTC (rev 474)
+++ pkg/stacomir/README.md	2018-02-15 16:14:22 UTC (rev 475)
@@ -1,294 +1,267 @@
----
-title: StacomiR
-author: Marion Legrand, C�dric Briand
-output: github_document
+StacomiR
+================
+Marion Legrand, Cédric Briand
 
----  
-
-
 [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/stacomiR)](https://cran.r-project.org/package=stacomiR)
 
-
-
 # stacomiR <img src="man/figures/logo.png" align="right" />
 
+## 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
--------------------------
-
-The package is available from CRAN, a development version is available from
-R-Forge.
-
-
-```r
+``` 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
 
-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*.
+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).
 
 ![plot](man/figures/StationComptage.png)
 
-
-
 #### 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, 
+The concept of dam used in the context of fish migration monitoring
+database refers to a system blocking or guiding the migratory flow like
+:
 
-* electric guide barrier, 
+  - weir,
 
-* netting dam, 
+  - electric guide barrier,
 
-* etc.
+  - netting dam,
 
+  - 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 video 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 trap, 
+  - a video counting device,
 
-* an accoustic counting device, 
+  - a trap,
 
-* ...
+  - 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
 
-Working examples
--------------------------
+### Command line
 
-###        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) 
+```
 
- 
- ```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
+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")
+#> [1] Choice made, and object report_mig_mult assigned in envir_stacomi
   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)
+#> data collected from the database nrow=400
+#> [1] Loading data for operations
+#> [1] Time steps loaded fot this counting device\n
+#> [1] Time steps of the fishway loaded\n
   # 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.
 
+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).
-
-
-
-
 ![plot of chunk rmmmult](man/figures/README-rmmstandard-1.png)
 
 Summary of migration for different stages and counting devices
 
+![](man/figures/README-rmmmult-1.png)<!-- -->
 
-```
-#> 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
@@ -299,9 +272,9 @@
 #> Warning in predict.lm(rlmmodb, newdata = newdata, se.fit = TRUE, type = "response", : Assuming constant prediction variance even though model fit is weighted
 ```
 
-![plot of chunk silver](man/figures/README-silver-1.png)
+![](man/figures/README-silver-1.png)<!-- -->
 
-```r
+``` r
 #######################################
 # To use the function fun_stage_durif manually
 # create a matrix with columns BL","W","Dv","Dh","FL"
@@ -321,14 +294,15 @@
 #>  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 :
 
 ![plot](man/figures/interface_graph_taille_sat.png)
 
-License
--------
+## License
 
 The STACOMI project is released under GPL-2.

Added: pkg/stacomir/man/figures/README-rmmmult-1.pdf
===================================================================
--- pkg/stacomir/man/figures/README-rmmmult-1.pdf	                        (rev 0)
+++ pkg/stacomir/man/figures/README-rmmmult-1.pdf	2018-02-15 16:14:22 UTC (rev 475)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/stacomir -r 475

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