[Stacomir-commits] r471 - in pkg/stacomir: . inst/cran-comments man/figures
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jan 27 10:12:37 CET 2018
Author: briand
Date: 2018-01-27 10:12:36 +0100 (Sat, 27 Jan 2018)
New Revision: 471
Modified:
pkg/stacomir/.Rbuildignore
pkg/stacomir/README.Rmd
pkg/stacomir/README.md
pkg/stacomir/inst/cran-comments/cran-comments-v0.5.3.1.md
pkg/stacomir/man/figures/README-rmmmult-1.png
pkg/stacomir/man/figures/README-silver-1.png
Log:
Modified: pkg/stacomir/.Rbuildignore
===================================================================
--- pkg/stacomir/.Rbuildignore 2018-01-04 13:31:37 UTC (rev 470)
+++ pkg/stacomir/.Rbuildignore 2018-01-27 09:12:36 UTC (rev 471)
@@ -4,4 +4,8 @@
^logo\.png$
^NEWS.md$
^NEWS.md.html$
-^README.md.html$
\ No newline at end of file
+^README.md.html$
+^.NEWS.md.html$
+^.README.md.html$
+^cran-comments.md$
+^cran-comments$
\ No newline at end of file
Modified: pkg/stacomir/README.Rmd
===================================================================
--- pkg/stacomir/README.Rmd 2018-01-04 13:31:37 UTC (rev 470)
+++ pkg/stacomir/README.Rmd 2018-01-27 09:12:36 UTC (rev 471)
@@ -5,6 +5,7 @@
toc: true
---
+
[](https://cran.r-project.org/package=stacomiR)
```{r echo = FALSE}
Modified: pkg/stacomir/README.md
===================================================================
--- pkg/stacomir/README.md 2018-01-04 13:31:37 UTC (rev 470)
+++ pkg/stacomir/README.md 2018-01-27 09:12:36 UTC (rev 471)
@@ -1,268 +1,218 @@
----
-title: StacomiR
-author: Marion Legrand, Cédric Briand
-output: github_document
-toc: true
----
+StacomiR
+================
+Marion Legrand, Cédric Briand
+true
+
[](https://cran.r-project.org/package=stacomiR)
-
-
# stacomiR <img src="man/figures/logo.png" align="right" />
+## Introduction
-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
+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
-Installation
--------------------------
+The package is available from CRAN, a development version is available
+from R-Forge.
-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.
+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.
+
#### 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,
-* electric guide barrier,
-* netting dam,
-* etc.
-#### Crossing device
+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, \* 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 dam. They can be of
-various type
-* fishway,
-* spillway,
-* fish elevator,
-* eel trapping ladder,
-* etc.
+migratory flow between upstream and downstream sections of a dam. They
+can be of various type \* fishway, \* spillway, \* fish elevator, \* eel
+trapping ladder, \* 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 trap,
-* an accoustic 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 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 :
-***
-* 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
-***
-Read the help files e.g. `? report_mig` to get documentation on the following
+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 **\* 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
-`database_expected=FALSE`
+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 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 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.
+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
- 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)
- ```
+`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 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).
+`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)`
+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
-
+<!-- -->
#### 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
@@ -273,9 +223,9 @@
#> 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"
@@ -295,12 +245,14 @@
#> 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 program is intended to be used by ‘non experienced’ R users.
+Launching `stacomi()` will create the interface. The interface looks
+like : [Durif et al.,
+2009](http://fishlarvae.org/common/SiteMedia/durif%20et%20al%202009b.pdf))
-License
--------
+## License
The STACOMI project is released under GPL-2.
Modified: pkg/stacomir/inst/cran-comments/cran-comments-v0.5.3.1.md
===================================================================
--- pkg/stacomir/inst/cran-comments/cran-comments-v0.5.3.1.md 2018-01-04 13:31:37 UTC (rev 470)
+++ pkg/stacomir/inst/cran-comments/cran-comments-v0.5.3.1.md 2018-01-27 09:12:36 UTC (rev 471)
@@ -5,10 +5,9 @@
Latest message from CRAN states that the package is no longer building. The packages
‘gWidgetsRGtk2’ ‘RGtk2’ are no longer available on r-release-osx-x86_64 and the packages
‘stacomirtools’ ‘RODBC’ are not available on r-oldrel-osx-x86_64. There is nothing I can do about that.
+
+There is also a fix to an error : the maintainer of Hmisc Frank E Harrell has asked me to update several of my functions namely `roundPOSIXt` and `truncPOSIXt`. This is done in this release.
-However, the maintainer of Hmisc Frank E Harrell has asked me to update several of my functions
-namely `roundPOSIXt` and `truncPOSIXt`. This is done in this release.
-
In addition this version adds :
@@ -25,3 +24,4 @@
Win Builder -- current and development.
R-forge.
+
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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