[Stacomir-commits] r587 - pkg/stacomir/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 9 11:59:39 CET 2021
Author: briand
Date: 2021-11-09 11:59:39 +0100 (Tue, 09 Nov 2021)
New Revision: 587
Modified:
pkg/stacomir/man/report_annual-class.Rd
pkg/stacomir/man/report_dc-class.Rd
pkg/stacomir/man/report_df-class.Rd
pkg/stacomir/man/report_env-class.Rd
pkg/stacomir/man/report_ge_weight-class.Rd
pkg/stacomir/man/report_mig-class.Rd
pkg/stacomir/man/report_mig_char-class.Rd
pkg/stacomir/man/report_mig_env-class.Rd
pkg/stacomir/man/report_mig_interannual-class.Rd
pkg/stacomir/man/report_mig_mult-class.Rd
pkg/stacomir/man/report_sample_char-class.Rd
pkg/stacomir/man/report_sea_age-class.Rd
pkg/stacomir/man/report_silver_eel-class.Rd
pkg/stacomir/man/report_species-class.Rd
pkg/stacomir/man/write_database-report_mig-method.Rd
Log:
manual
Modified: pkg/stacomir/man/report_annual-class.Rd
===================================================================
--- pkg/stacomir/man/report_annual-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_annual-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -26,13 +26,26 @@
}}
\examples{
-require(stacomiR)
-# launching stacomi without selecting the scheme or interface
-stacomi(
- database_expected=FALSE, sch='iav')
-# the following script will load the Arzal dataset if connected to iav schema
-
+# launching stacomi without database for demo
+stacomi(database_expected=FALSE)
+# the following piece of script will load the Arzal dataset and connected to iav postgres schema
+# it requires a working database
+# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
+ stacomi(database_expected=TRUE, sch='iav')
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
r_ann<-new("report_annual")
r_ann<-choice_c(r_ann,
dc=c(5,6,12),
Modified: pkg/stacomir/man/report_dc-class.Rd
===================================================================
--- pkg/stacomir/man/report_dc-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_dc-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -29,14 +29,27 @@
}
\examples{
-require(stacomiR)
-stacomi(
- database_expected=FALSE)
-###########################################################
-## An example that will work only if the database is present
-## and the program installed and comprises the schema iav
-###########################################################"
+
+# this option allows to launch the program without the interface to display some of the program features.
+stacomi(database_expected=FALSE)
+# An example that will work only if the database is present
+# and the program installed and comprises the schema iav
+# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
+
r_dc=new("report_dc")
r_dc<-choice_c(r_dc,
5,
Modified: pkg/stacomir/man/report_df-class.Rd
===================================================================
--- pkg/stacomir/man/report_df-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_df-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -37,11 +37,26 @@
}
\examples{
-require(stacomiR)
stacomi(
database_expected=FALSE)
-## An example that will work with the database installed only
+# An example that will work with the database installed only and schema iav in the database
+# prompt for user and password but you can set appropriate options for host, port and dbname
+stacomi(
+ database_expected=TRUE, sch='iav')
\dontrun{
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
r_df=new("report_df")
r_df<-choice_c(r_df,
1,
Modified: pkg/stacomir/man/report_env-class.Rd
===================================================================
--- pkg/stacomir/man/report_env-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_env-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -23,10 +23,22 @@
}}
\examples{
-require(stacomiR)
stacomi(
database_expected=FALSE)
\dontrun{
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
r_env<-new("report_env")
r_env<-choice_c(r_env,
stationMesure=c("temp_gabion","coef_maree"),
Modified: pkg/stacomir/man/report_ge_weight-class.Rd
===================================================================
--- pkg/stacomir/man/report_ge_weight-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_ge_weight-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -51,7 +51,24 @@
# launching stacomi without selecting the scheme or interface
stacomi(
database_expected=FALSE, sch='iav')
+# this requires a working database with the schema iav
+# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
+ stacomi(
+ database_expected=TRUE, sch='iav')
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
#create an instance of the class
r_gew<-new("report_ge_weight")
r_gew at liste<-charge(object=r_gew at liste,listechoice=c("=1",">1","tous"),label="")
Modified: pkg/stacomir/man/report_mig-class.Rd
===================================================================
--- pkg/stacomir/man/report_mig-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_mig-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -37,14 +37,24 @@
In practise, the report_mig class uses methods (calcule, connect...) from the more elaborate \link{report_mig_mult-class}
}
\examples{
-library(stacomiR)
-
stacomi(database_expected=FALSE)
-## launches the application in the command line
-## here an example of loading
-## not run as the program is possibly not installed
-## this example generates the r_mig dataset
-\dontrun{
+# If you have a working database
+# the following line of code will create the r_mig dataset from the iav (default) schema in the database
+\dontrun{
+ stacomi(database_expected=TRUE)
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
stacomi(
database_expected=TRUE)
r_mig=new("report_mig")
Modified: pkg/stacomir/man/report_mig_char-class.Rd
===================================================================
--- pkg/stacomir/man/report_mig_char-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_mig_char-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -55,8 +55,24 @@
stacomi(
database_expected=FALSE, sch='logrami')
-
+# this requires a database with the schema logrami
+# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
+ stacomi(
+ database_expected=TRUE, sch='logrami')
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
r_mig_char<-new("report_mig_char")
# here parqual is not in the list
# so this is equivalent to parqual=NULL
Modified: pkg/stacomir/man/report_mig_env-class.Rd
===================================================================
--- pkg/stacomir/man/report_mig_env-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_mig_env-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -31,7 +31,23 @@
database_expected=FALSE)
# the following will load the data provided the user has access to the database
# with data in the iav example scheme.
+# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
+ stacomi(
+ database_expected=TRUE)
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
r_mig_env<-new("report_mig_env")
r_mig_env<-choice_c(r_mig_env,
dc=c(5,6,12),
Modified: pkg/stacomir/man/report_mig_interannual-class.Rd
===================================================================
--- pkg/stacomir/man/report_mig_interannual-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_mig_interannual-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -41,9 +41,24 @@
# launching stacomi without selecting the scheme or interface
stacomi(
database_expected=FALSE, sch='pmp')
-###### If you have connection to the database with the pmp scheme ############
+# If you have connection to the database with the pmp scheme
+# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
-
+ stacomi(
+ database_expected=TRUE)
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
# overriding user schema to point to Parc Marais Poitevin
# (longest historical dataset available
# in France for eel ...) this suppose you have access to the pmp schema...
Modified: pkg/stacomir/man/report_mig_mult-class.Rd
===================================================================
--- pkg/stacomir/man/report_mig_mult-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_mig_mult-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -53,9 +53,23 @@
## the following lines will only run if you have the program installed
## and the iav scheme available in the database
## this example generates the r_mig_mult dataset
+# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
stacomi(
database_expected=TRUE)
+if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+}
+options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+)
r_mig_mult=new("report_mig_mult")
r_mig_mult=choice_c(r_mig_mult,
dc=c(5,6,12),
Modified: pkg/stacomir/man/report_sample_char-class.Rd
===================================================================
--- pkg/stacomir/man/report_sample_char-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_sample_char-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -38,20 +38,33 @@
}
\examples{
-require(stacomiR)
-# launching stacomi without selecting the scheme or interface
-stacomi(
- database_expected=FALSE)
-# the following script will load the Arzal dataset
-#if connected to iav schema
+# launching stacomi without connection to the database
+stacomi( database_expected=FALSE)
+# If you have a working database
+# the following line of code will create the r_sample_char dataset from the iav (default) schema in the database
\dontrun{
+ stacomi(database_expected=TRUE) # uses default option sch = 'iav'
+ # prompt for user and password, you can set these in the options, including dbname and host
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
#create an instance of the class
- r_sample_char<-new("report_sample_char")
+ r_sample_char <- new("report_sample_char")
# the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
- r_sample_char<-choice_c(r_sample_char,
+ r_sample_char <- choice_c(r_sample_char,
dc=c(5,6),
taxa=c("Anguilla anguilla"),
stage=c("AGJ","CIV"),
@@ -60,8 +73,8 @@
horodatefin="2013-12-31",
silent=FALSE)
# two warning produced, ignored if silent=TRUE
- r_sample_char<-connect(r_sample_char)
- r_sample_char<-calcule(r_sample_char,silent=TRUE)
+ r_sample_char <- connect(r_sample_char)
+ r_sample_char <- calcule(r_sample_char,silent=TRUE)
}
# load the dataset generated by previous lines
Modified: pkg/stacomir/man/report_sea_age-class.Rd
===================================================================
--- pkg/stacomir/man/report_sea_age-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_sea_age-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -49,8 +49,25 @@
\examples{
require(stacomiR)
stacomi(
- database_expected=FALSE, sch= 'logrami')
+ database_expected=FALSE)
+# If you have a working database
+# the following line of code will create the r_seaa dataset from the logrami schema in the database
\dontrun{
+ stacomi(database_expected=TRUE, sch='logrami') # overrides the default option sch = 'iav'
+ # prompt for user and password, you can set these in the options, including dbname and host
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
#create an instance of the class
r_seaa<-new("report_sea_age")
r_seaa<-choice_c(r_seaa,
Modified: pkg/stacomir/man/report_silver_eel-class.Rd
===================================================================
--- pkg/stacomir/man/report_silver_eel-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_silver_eel-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -47,17 +47,31 @@
}
\examples{
-require(stacomiR)
# launching stacomi without selecting the scheme or interface
-stacomi(
- database_expected=FALSE, sch ='fd80')
+stacomi( database_expected=FALSE)
# the following script will load data from the two Anguillere monitored in the Somme
+# If you have a working database
+# the following line of code will create the r_silver dataset from the "fd80." schema in the database
\dontrun{
+ stacomi(database_expected=TRUE, sch="fd80.") # overrides the default option sch = 'iav'
+ # prompt for user and password, you can set these in the options, including dbname and host
+ if (interactive()){
+ if (!exists("user")){
+ user <- readline(prompt="Enter user: ")
+ password <- readline(prompt="Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host ="localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
+
#create an instance of the class
r_silver<-new("report_silver_eel")
- sch<-rlang::env_get(envir_stacomi, "sch")
- assign("sch","fd80.",envir_stacomi)
r_silver<-choice_c(r_silver,
dc=c(2,6),
horodatedebut="2010-09-01",
Modified: pkg/stacomir/man/report_species-class.Rd
===================================================================
--- pkg/stacomir/man/report_species-class.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/report_species-class.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -33,9 +33,13 @@
}}
\examples{
-require(stacomiR)
-stacomi(
- database_expected=FALSE)
+# launching stacomi without selecting the scheme or interface
+stacomi( database_expected=FALSE)
+# the following script will load data from the two Anguillere monitored in the Somme
+
+# If you have a working database
+# the following line of code will create the bilesp dataset from the "iav." schema in the database
+
\dontrun{
bilesp<-new("report_species")
# split is one of "none", "year", "week", "month
@@ -45,27 +49,34 @@
anneedebut="2008",
anneefin="2012",
silent=FALSE)
- #bilesp<-charge(bilesp) this is used by the graphical interface
- bilesp<-connect(bilesp)
- bilesp<-calcule(bilesp)
- plot(bilesp,plot.type="pie",silent=FALSE)
- plot(bilesp,plot.type="barplot",silent=FALSE)
- bilesp<-choice_c(bilesp,
+ bilesp <- connect(bilesp)
+ bilesp <- calcule(bilesp)
+ plot(bilesp, plot.type="pie", silent=FALSE)
+ plot(bilesp, plot.type="barplot", silent=FALSE)
+ bilesp <- choice_c(bilesp,
dc=c(5,6,12),
split="month",
anneedebut="2015",
anneefin="2016",
silent=FALSE)
- bilesp<-charge(bilesp)
- bilesp<-connect(bilesp)
- plot(bilesp,plot.type="pie",silent=FALSE)
- plot(bilesp,plot.type="barplot",silent=FALSE)
+ bilesp <- charge(bilesp)
+ bilesp <- connect(bilesp)
+ plot(bilesp, plot.type="pie", silent=FALSE)
+ plot(bilesp, plot.type="barplot", silent=FALSE)
#length(unique(bilesp at calcdata$taxa_stage)) # 15
# here creating a vector of length 15 with nice blending colours
+ if (requireNamespace("grDevices", quietly = TRUE) {
+ mycolorrampblue <-
+ grDevices::colorRampPalette(c("#395B74", "#010F19"))
+ mycolorrampyellow <-
+ grDevices::colorRampPalette(c("#B59C53", "#271D00"))
+ mycolorrampred <-
+ grDevices::colorRampPalette(c("#B56F53", "#270B00"))
color<-c(mycolorrampblue(5),
mycolorrampyellow(5),
mycolorrampred(5))
plot(bilesp,plot.type="barplot",color=color,silent=TRUE)
+ }
summary(bilesp)
}
Modified: pkg/stacomir/man/write_database-report_mig-method.Rd
===================================================================
--- pkg/stacomir/man/write_database-report_mig-method.Rd 2021-11-09 10:52:03 UTC (rev 586)
+++ pkg/stacomir/man/write_database-report_mig-method.Rd 2021-11-09 10:59:39 UTC (rev 587)
@@ -3,8 +3,7 @@
\name{write_database,report_mig-method}
\alias{write_database,report_mig-method}
\alias{write_database.report_mig}
-\title{handler h_report_migwrite
-Allows the saving of daily and monthly counts in the database}
+\title{Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table}
\usage{
\S4method{write_database}{report_mig}(object, silent = TRUE, check_for_bjo = TRUE)
}
@@ -15,19 +14,12 @@
\item{check_for_bjo}{: do you want to check if data are already present in the bjo table, and delete them,
this param was added otherwise connect method when called from report_mig_interannual runs in loops}
-
-\item{h}{a handler}
-
-\item{...}{Additional parameters}
}
\description{
-handler h_report_migwrite
-Allows the saving of daily and monthly counts in the database
+Daily values are needed to compare migrations from year to year, by the class \link{report_mig_interannual-class}. They are added by
+by this function.
}
\note{
-these entries are necessary to run the Interannual Migration class.
-then no entry will be written to the database
-
the user is asked whether or not he wants to overwrite data only when silent is FALSE, if no
data are present in the database, the import is done anyway.
}
@@ -41,35 +33,4 @@
}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-
-Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
}
-\keyword{Command}
-\keyword{Daily}
-\keyword{They}
-\keyword{\link{report_mig_interannual-class}.}
-\keyword{added}
-\keyword{and}
-\keyword{are}
-\keyword{by}
-\keyword{class}
-\keyword{compare}
-\keyword{counts}
-\keyword{daily}
-\keyword{from}
-\keyword{function.}
-\keyword{internal}
-\keyword{line}
-\keyword{method}
-\keyword{migrations}
-\keyword{monthly}
-\keyword{needed}
-\keyword{t_bilanmigrationjournalier_bjo}
-\keyword{table}
-\keyword{the}
-\keyword{this}
-\keyword{to}
-\keyword{values}
-\keyword{write}
-\keyword{year}
-\keyword{year,}
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