[Stacomir-commits] r586 - in pkg/stacomir: inst/examples man/figures
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 9 11:52:03 CET 2021
Author: briand
Date: 2021-11-09 11:52:03 +0100 (Tue, 09 Nov 2021)
New Revision: 586
Added:
pkg/stacomir/man/figures/StationComptage.png
pkg/stacomir/man/figures/interface_graph_taille_sat.png
pkg/stacomir/man/figures/logo.png
Modified:
pkg/stacomir/inst/examples/report_annual-example.R
pkg/stacomir/inst/examples/report_dc-example.R
pkg/stacomir/inst/examples/report_df-example.R
pkg/stacomir/inst/examples/report_env-example.R
pkg/stacomir/inst/examples/report_ge_weight-example.R
pkg/stacomir/inst/examples/report_mig-example.R
pkg/stacomir/inst/examples/report_mig_char-example.R
pkg/stacomir/inst/examples/report_mig_env-example.R
pkg/stacomir/inst/examples/report_mig_interannual-example.R
pkg/stacomir/inst/examples/report_mig_mult-example.R
pkg/stacomir/inst/examples/report_sample_char-example.R
pkg/stacomir/inst/examples/report_sea_age-example.R
pkg/stacomir/inst/examples/report_silver_eel-example.R
pkg/stacomir/inst/examples/report_species-example.R
Log:
edited all examples
Modified: pkg/stacomir/inst/examples/report_annual-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_annual-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_annual-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,10 +1,23 @@
-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/inst/examples/report_dc-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_dc-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_dc-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,11 +1,24 @@
-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/inst/examples/report_df-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_df-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_df-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,8 +1,23 @@
-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/inst/examples/report_env-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_env-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_env-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,7 +1,19 @@
-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/inst/examples/report_ge_weight-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_ge_weight-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_ge_weight-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -2,7 +2,24 @@
# 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/inst/examples/report_mig-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_mig-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_mig-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,11 +1,21 @@
-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/inst/examples/report_mig_char-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_mig_char-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_mig_char-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -2,8 +2,24 @@
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/inst/examples/report_mig_env-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_mig_env-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_mig_env-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -3,7 +3,23 @@
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/inst/examples/report_mig_interannual-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_mig_interannual-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_mig_interannual-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -2,9 +2,24 @@
# 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/inst/examples/report_mig_mult-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_mig_mult-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_mig_mult-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -6,9 +6,23 @@
## 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/inst/examples/report_sample_char-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_sample_char-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_sample_char-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,17 +1,30 @@
-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"),
@@ -20,8 +33,8 @@
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/inst/examples/report_sea_age-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_sea_age-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_sea_age-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,7 +1,24 @@
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/inst/examples/report_silver_eel-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_silver_eel-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_silver_eel-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,14 +1,28 @@
-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/inst/examples/report_species-example.R
===================================================================
--- pkg/stacomir/inst/examples/report_species-example.R 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/inst/examples/report_species-example.R 2021-11-09 10:52:03 UTC (rev 586)
@@ -1,6 +1,10 @@
-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
@@ -10,27 +14,34 @@
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)
}
Added: pkg/stacomir/man/figures/StationComptage.png
===================================================================
(Binary files differ)
Index: pkg/stacomir/man/figures/StationComptage.png
===================================================================
--- pkg/stacomir/man/figures/StationComptage.png 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/man/figures/StationComptage.png 2021-11-09 10:52:03 UTC (rev 586)
Property changes on: pkg/stacomir/man/figures/StationComptage.png
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Added: svn:mime-type
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Added: pkg/stacomir/man/figures/interface_graph_taille_sat.png
===================================================================
(Binary files differ)
Index: pkg/stacomir/man/figures/interface_graph_taille_sat.png
===================================================================
--- pkg/stacomir/man/figures/interface_graph_taille_sat.png 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/man/figures/interface_graph_taille_sat.png 2021-11-09 10:52:03 UTC (rev 586)
Property changes on: pkg/stacomir/man/figures/interface_graph_taille_sat.png
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Added: pkg/stacomir/man/figures/logo.png
===================================================================
(Binary files differ)
Index: pkg/stacomir/man/figures/logo.png
===================================================================
--- pkg/stacomir/man/figures/logo.png 2021-11-09 10:05:16 UTC (rev 585)
+++ pkg/stacomir/man/figures/logo.png 2021-11-09 10:52:03 UTC (rev 586)
Property changes on: pkg/stacomir/man/figures/logo.png
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Added: svn:mime-type
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+application/octet-stream
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