#################################
# generates calcmig data
# In data :
#For sets of data, set up a package to use lazy-loading of data. 
#
#For objects which are system data, for example lookup tables used in bilcalculations
#within the function, use a file ‘R/sysdata.rda’ in the package sources or create the 
#objects by R code at package installation time. 
#
#
#A sometimes important distinction is that the second approach places 
#objects in the namespace but the first does not. So if it is important
#that the function sees mytable as an object from the package, 
#it is system data and the second approach should be used.

##################################
filecsv<-"C:/Program Files/stacomi/calcmig.csv"
calcmig<-utils::read.csv(filecsv,header=TRUE,sep=";")
setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(calcmig,internal=FALSE,overwrite=TRUE)

#################################
# generates a dataset with Durif coefficients
# source Laurent Beaulaton
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
coef_durif = matrix(NA, nrow=5, ncol=6)
colnames(coef_durif) = c("I", "FII", "FIII", "FIV", "FV", "MII")
rownames(coef_durif) = c("Constant", "BL", "W", "MD", "FL")
coef_durif[,1] = c(-61.276, 0.242, -0.108, 5.546, 0.614)
coef_durif[,2] = c(-87.995, 0.286, -0.125, 6.627, 0.838)
coef_durif[,3] = c(-109.014, 0.280, -0.127, 9.108, 1.182)
coef_durif[,4] = c(-113.556, 0.218, -0.103, 12.187, 1.230)
coef_durif[,5] = c(-128.204, 0.242, -0.136, 12.504, 1.821)
coef_durif[,6] = c(-84.672, 0.176, -0.116, 12.218, 1.295)
devtools::use_data(coef_durif,internal=FALSE,overwrite=TRUE)
#################################
# generates dataset for report_mig_mult
# from iav three dc with eels
##################################
require(stacomiR)
stacomi(FALSE,FALSE,FALSE)
r_mig_mult=new("report_mig_mult")
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("iav",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi) # "iav."
assign("sch","iav.",envir_stacomi)
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)
r_mig_mult<-connect(r_mig_mult,silent=FALSE)
# to avoid warnings at package checks
r_mig_mult@dc@data[,"dis_commentaires"]<-iconv(r_mig_mult@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_mult@dc@data[,"type_df"]<-iconv(r_mig_mult@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_mult@dc@data[,"type_dc"]<-iconv(r_mig_mult@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_mult@dc@data[,"dif_localisation"]<-iconv(r_mig_mult@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_mig_mult@taxa@data[,"tax_nom_commun"]<-iconv(r_mig_mult@taxa@data[,"tax_nom_commun"],from="latin1",to="UTF8")
r_mig_mult@stage@data[,"std_libelle"]<-iconv(r_mig_mult@stage@data[,"std_libelle"],from="latin1",to="UTF8")
r_mig_mult<-calcule(r_mig_mult,silent=FALSE)
setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(r_mig_mult,internal=FALSE,overwrite=TRUE)
r_mig_mult_ope<-get("report_ope",envir=envir_stacomi)
r_mig_mult_ope@data$ope_commentaires<-iconv(r_mig_mult_ope@data$ope_commentaires,from="latin1",to="UTF8")
r_mig_mult_ope@data$ope_operateur<-iconv(r_mig_mult_ope@data$ope_operateur,from="latin1",to="UTF8")
r_mig_mult_ope@dc@data[,"dis_commentaires"]<-iconv(r_mig_mult_ope@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_mult_ope@dc@data[,"type_df"]<-iconv(r_mig_mult_ope@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_mult_ope@dc@data[,"type_dc"]<-iconv(r_mig_mult_ope@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_mult_ope@dc@data[,"dif_localisation"]<-iconv(r_mig_mult_ope@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
devtools::use_data(r_mig_mult_ope,internal=FALSE,overwrite=TRUE)


r_mig_mult_df<-get("report_df",envir=envir_stacomi)
r_mig_mult_df@df@data[,"dis_commentaires"]<-iconv(r_mig_mult_df@df@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_mult_df@df@data[,"type_df"]<-iconv(r_mig_mult_df@df@data[,"type_df"],from="latin1",to="UTF8")
#r_mig_mult_df@df@data[,"type_dc"]<-iconv(r_mig_mult_df@df@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_mult_df@df@data[,"dif_localisation"]<-iconv(r_mig_mult_df@df@data[,"dif_localisation"],from="latin1",to="UTF8")
r_mig_mult_df@data$per_commentaires<-iconv(r_mig_mult_df@data$per_commentaires,from="latin1",to="UTF8")
devtools::use_data(r_mig_mult_df,internal=FALSE,overwrite=TRUE)


r_mig_mult_dc<-get("report_dc",envir=envir_stacomi)
r_mig_mult_dc@dc@data[,"dis_commentaires"]<-iconv(r_mig_mult_dc@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_mult_dc@dc@data[,"ouv_libelle"]<-iconv(r_mig_mult_dc@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_mig_mult_dc@dc@data[,"type_dc"]<-iconv(r_mig_mult_dc@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_mult_dc@dc@data[,"type_df"]<-iconv(r_mig_mult_dc@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_mult_dc@dc@data[,"dif_localisation"]<-iconv(r_mig_mult_dc@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_mig_mult_dc@data$per_commentaires<-iconv(r_mig_mult_dc@data$per_commentaires,from="latin1",to="UTF8")

devtools::use_data(r_mig_mult_dc,internal=FALSE,overwrite=TRUE)
#################################
# generates dataset for report_mig
# from the vertical slot fishway located at the estuary of the Vilaine (Brittany)
# Taxa Liza Ramada (Thinlip grey mullet) in 2015
##################################

stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=TRUE)	
r_mig=new("report_mig")
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("iav",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi) # "iav."
assign("sch","iav.",envir_stacomi)
r_mig=choice_c(r_mig,
	dc=5,
	taxa=c("Liza ramada"),
	stage=c("IND"),
	datedebut="2015-01-01",
	datefin="2015-12-31")
r_mig<-charge(r_mig)
r_mig<-connect(r_mig)

r_mig@dc@data[,"dis_commentaires"]<-iconv(r_mig@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig@dc@data[,"type_df"]<-iconv(r_mig@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig@dc@data[,"type_dc"]<-iconv(r_mig@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig@dc@data[,"dif_localisation"]<-iconv(r_mig@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_mig@taxa@data[,"tax_nom_commun"]<-iconv(r_mig@taxa@data[,"tax_nom_commun"],from="latin1",to="UTF8")
r_mig@stage@data[,"std_libelle"]<-iconv(r_mig@stage@data[,"std_libelle"],from="latin1",to="UTF8")
r_mig<-calcule(r_mig,silent=TRUE)
setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(r_mig,internal=FALSE,overwrite=TRUE)



r_mig_ope<-get("report_ope",envir=envir_stacomi)
r_mig_ope@data$ope_commentaires<-iconv(r_mig_ope@data$ope_commentaires,from="latin1",to="UTF8")
r_mig_ope@data$ope_operateur<-iconv(r_mig_ope@data$ope_operateur,from="latin1",to="UTF8")
r_mig_ope@dc@data[,"dis_commentaires"]<-iconv(r_mig_ope@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_ope@dc@data[,"type_df"]<-iconv(r_mig_ope@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_ope@dc@data[,"type_dc"]<-iconv(r_mig_ope@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_ope@dc@data[,"dif_localisation"]<-iconv(r_mig_ope@dc@data[,"dif_localisation"],from="latin1",to="UTF8")

devtools::use_data(r_mig_ope,internal=FALSE,overwrite=TRUE)


r_mig_df<-get("report_df",envir=envir_stacomi)
r_mig_df@df@data[,"dis_commentaires"]<-iconv(r_mig_df@df@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_df@df@data[,"type_df"]<-iconv(r_mig_df@df@data[,"type_df"],from="latin1",to="UTF8")
#r_mig_df@df@data[,"type_dc"]<-iconv(r_mig_df@df@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_df@df@data[,"dif_localisation"]<-iconv(r_mig_df@df@data[,"dif_localisation"],from="latin1",to="UTF8")
r_mig_df@data$per_commentaires<-iconv(r_mig_df@data$per_commentaires,from="latin1",to="UTF8")
devtools::use_data(r_mig_df,internal=FALSE,overwrite=TRUE)

r_mig_dc<-get("report_dc",envir=envir_stacomi)
r_mig_dc@dc@data[,"ouv_libelle"]<-iconv(r_mig_dc@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_mig_dc@dc@data[,"dis_commentaires"]<-iconv(r_mig_dc@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_dc@dc@data[,"type_dc"]<-iconv(r_mig_dc@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_dc@dc@data[,"type_df"]<-iconv(r_mig_dc@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_dc@dc@data[,"dif_localisation"]<-iconv(r_mig_dc@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_mig_dc@data$per_commentaires<-iconv(r_mig_dc@data$per_commentaires,from="latin1",to="UTF8")
devtools::use_data(r_mig_dc,internal=FALSE,overwrite=TRUE)

#################################
# generates dataset for report_df
##################################
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_df=new("report_df")
r_df<-choice_c(r_df,
	1,
	horodatedebut="2015-01-01",
	horodatefin="2015-12-31",
	silent=TRUE)
tz<-Sys.timezone()
Sys.setenv(TZ='GMT') # there are data when hour shift, without this the graph will fail
r_df<-charge(r_df)
r_df<-connect(r_df)

r_df@df@data[,"dis_commentaires"]<-iconv(r_df@df@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_df@df@data[,"type_df"]<-iconv(r_df@df@data[,"type_df"],from="latin1",to="UTF8")
#r_df@df@data[,"type_dc"]<-iconv(r_df@df@data[,"type_dc"],from="latin1",to="UTF8")
r_df@df@data[,"dif_localisation"]<-iconv(r_df@df@data[,"dif_localisation"],from="latin1",to="UTF8")
r_df@data$per_commentaires<-iconv(r_df@data$per_commentaires,from="latin1",to="UTF8")
#plot(r_df,plot.type="1")
#plot(r_df,plot.type="2",title="A nice title")
setwd("C:/workspace/stacomir/pkg/stacomir")
Sys.setenv(TZ=tz)
devtools::use_data(r_df,internal=FALSE,overwrite=TRUE)


#################################
# generates dataset for report_dc
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_dc=new("report_dc")
r_dc<-choice_c(r_dc,
	5,
	horodatedebut="2000-01-01",
	horodatefin="2015-12-31",
	silent=TRUE)
tz<-Sys.timezone()
Sys.setenv(TZ='GMT') # there are data when hour shift, without this the graph will fail
r_dc<-charge(r_dc)
r_dc<-connect(r_dc)
r_dc@dc@data[,"ouv_libelle"]<-iconv(r_dc@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_dc@dc@data[,"dis_commentaires"]<-iconv(r_dc@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_dc@dc@data[,"type_df"]<-iconv(r_dc@dc@data[,"type_df"],from="latin1",to="UTF8")
r_dc@dc@data[,"type_dc"]<-iconv(r_dc@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_dc@dc@data[,"dif_localisation"]<-iconv(r_dc@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_dc@data$per_commentaires<-iconv(r_dc@data$per_commentaires,from="latin1",to="UTF8")
setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(r_dc,internal=FALSE,overwrite=TRUE)
Sys.setenv(TZ=tz)
#################################
# generates dataset for report_sample_char
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_sample_char<-new("report_sample_char")
# the following will load data for size, 
# parameters  1786 (total size) and C001 (size at video control)
# are all size measures
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
r_sample_char<-choice_c(r_sample_char,
	dc=c(5,6),
	taxa=c("Anguilla anguilla"),
	stage=c("AGJ","CIV"),
	par=c(1786,"C001"),
	horodatedebut="2013-01-01",
	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)

r_sample_char@dc@data[,"ouv_libelle"]<-iconv(r_sample_char@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_sample_char@dc@data[,"dis_commentaires"]<-iconv(r_sample_char@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_sample_char@dc@data[,"type_df"]<-iconv(r_sample_char@dc@data[,"type_df"],from="latin1",to="UTF8")
r_sample_char@dc@data[,"type_dc"]<-iconv(r_sample_char@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_sample_char@dc@data[,"dif_localisation"]<-iconv(r_sample_char@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_sample_char@par@data[,"par_nom"]<-iconv(r_sample_char@par@data[,"par_nom"],from="latin1",to="UTF8")
r_sample_char@data$dev_libelle<-iconv(r_sample_char@data$dev_libelle,from="latin1",to="UTF8")
r_sample_char@data$std_libelle<-iconv(r_sample_char@data$std_libelle,from="latin1",to="UTF8")
r_sample_char@data$val_libelle<-iconv(r_sample_char@data$val_libelle,from="latin1",to="UTF8")
r_sample_char@data$par_nom<-iconv(r_sample_char@data$par_nom,from="latin1",to="UTF8")
r_sample_char<-calcule(r_sample_char)
setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(r_sample_char,internal=FALSE,overwrite=TRUE)

#################################
# generates dataset for report_mig_interannual
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
require(stacomiR)
stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)

baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("pmp",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi)
assign("sch","pmp.",envir_stacomi)
r_mig_interannual<-new("report_mig_interannual")

r_mig_interannual<-choice_c(r_mig_interannual,
	dc=16,
	taxa=c("Anguilla anguilla"),
	stage=c("AGJ"),
	anneedebut=1984,
	anneefin=2015,
	silent=TRUE)
# this will just test that the object is valid... not really a necessary step for this class
#r_mig_interannual<-charge(r_mig_interannual,silent=TRUE)
r_mig_interannual<-connect(r_mig_interannual,silent=TRUE)	


r_mig_interannual@dc@data[,"ouv_libelle"]<-iconv(r_mig_interannual@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_mig_interannual@dc@data[,"dis_commentaires"]<-iconv(r_mig_interannual@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_interannual@dc@data[,"type_df"]<-iconv(r_mig_interannual@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_interannual@dc@data[,"type_dc"]<-iconv(r_mig_interannual@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_interannual@dc@data[,"dif_localisation"]<-iconv(r_mig_interannual@dc@data[,"dif_localisation"],from="latin1",to="UTF8")

setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(r_mig_interannual,internal=FALSE,overwrite=TRUE)
#################################
# generates dataset for report_annual
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("iav",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi)
assign("sch","iav.",envir_stacomi)
r_ann<-new("report_annual")
r_ann<-choice_c(r_ann,
	dc=c(5,6,12),
	taxa=c("Anguilla anguilla"),
	stage=c("AGJ","AGG"),
	anneedebut="1996",
	anneefin="2015",
	silent=FALSE)
r_ann <- connect(r_ann)
r_ann@dc@data[,"ouv_libelle"] <- iconv(r_ann@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_ann@dc@data[,"dis_commentaires"] <- iconv(r_ann@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_ann@dc@data[,"type_df"] <- iconv(r_ann@dc@data[,"type_df"],from="latin1",to="UTF8")
r_ann@dc@data[,"type_dc"] <- iconv(r_ann@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_ann@dc@data[,"dif_localisation"] <- iconv(r_ann@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_ann@taxa@data[,"tax_nom_commun"] <- iconv(r_ann@taxa@data[,"tax_nom_commun"],from="latin1",to="UTF8")
r_ann@stage@data[,"std_libelle"] <- iconv(r_ann@stage@data[,"std_libelle"],from="latin1",to="UTF8")
setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(r_ann,internal=FALSE,overwrite=TRUE)

#################################
# generates dataset for report_annual : migradour
##################################


baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("migradour",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi)
assign("sch","migradour.",envir_stacomi)
r_ann_adour<-new("report_annual")
r_ann_adour<-choice_c(r_ann_adour,
	dc=c(33:40),
	taxa=c("Salmo salar"),
	stage=c(11),
	anneedebut="1996",
	anneefin="2015",
	silent=FALSE)
r_ann_adour<-connect(r_ann_adour)
r_ann_adour@dc@data[,"ouv_libelle"]<-iconv(r_ann_adour@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_ann_adour@dc@data[,"dis_commentaires"]<-iconv(r_ann_adour@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_ann_adour@dc@data[,"type_df"]<-iconv(r_ann_adour@dc@data[,"type_df"],from="latin1",to="UTF8")
r_ann_adour@dc@data[,"type_dc"]<-iconv(r_ann_adour@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_ann_adour@dc@data[,"dc_code"]<-iconv(r_ann_adour@dc@data[,"dc_code"],from="latin1",to="UTF8")
r_ann_adour@dc@data[,"dif_localisation"]<-iconv(r_ann_adour@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_ann_adour@taxa@data[,"tax_nom_commun"]<-iconv(r_ann_adour@taxa@data[,"tax_nom_commun"],from="latin1",to="UTF8")
r_ann_adour@stage@data[,"std_libelle"]<-iconv(r_ann_adour@stage@data[,"std_libelle"],from="latin1",to="UTF8")
setwd("C:/workspace/stacomir/pkg/stacomir")
devtools::use_data(r_ann_adour,internal=FALSE,overwrite=TRUE)



#################################
# generates dataset for reportArgenture : fd80 the somme
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_silver<-new("report_silver_eel")
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("fd80",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi)
assign("sch","fd80.",envir_stacomi)
r_silver<-choice_c(r_silver,
	dc=c(2,6),			
	horodatedebut="2010-09-01",
	horodatefin="2016-10-04",
	silent=FALSE)
# two warning produced, ignored if silent=TRUE
r_silver<-connect(r_silver)
r_silver@dc@data[,"ouv_libelle"]<-iconv(r_silver@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_silver@dc@data[,"dis_commentaires"]<-iconv(r_silver@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_silver@dc@data[,"type_df"]<-iconv(r_silver@dc@data[,"type_df"],from="latin1",to="UTF8")
r_silver@dc@data[,"type_dc"]<-iconv(r_silver@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_silver@dc@data[,"dif_localisation"]<-iconv(r_silver@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_silver@taxa@data[,"tax_nom_commun"]<-iconv(r_silver@taxa@data[,"tax_nom_commun"],from="latin1",to="UTF8")
r_silver@stage@data[,"std_libelle"]<-iconv(r_silver@stage@data[,"std_libelle"],from="latin1",to="UTF8")
r_silver@par@data[,"par_nom"]<-iconv(r_silver@par@data[,"par_nom"],from="latin1",to="UTF8")
r_silver@data$dev_libelle<-iconv(r_silver@data$dev_libelle,from="latin1",to="UTF8")
r_silver@data$std_libelle<-iconv(r_silver@data$std_libelle,from="latin1",to="UTF8")
r_silver@data$val_libelle<-iconv(r_silver@data$val_libelle,from="latin1",to="UTF8")
r_silver@data$par_nom<-iconv(r_silver@data$par_nom,from="latin1",to="UTF8")

devtools::use_data(r_silver,internal=FALSE,overwrite=TRUE)

#################################
# generates dataset for report_ge_weight : iav
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
Sys.setenv(LANG = "EN")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_gew<-new("report_ge_weight")
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("iav",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi)
assign("sch","iav.",envir_stacomi)
r_gew@liste<-charge(object=r_gew@liste,listechoice=c("=1",">1","tous"),label="")
r_gew<-choice_c(r_gew,
	dc=c(6),			
	anneedebut="2009",
	anneefin="2016",
	selectedvalue=">1",
	silent=FALSE)
r_gew<-connect(r_gew)	
r_gew@dc@data[,"ouv_libelle"]<-iconv(r_gew@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_gew@dc@data[,"dis_commentaires"]<-iconv(r_gew@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_gew@dc@data[,"type_df"]<-iconv(r_gew@dc@data[,"type_df"],from="latin1",to="UTF8")
r_gew@dc@data[,"type_dc"]<-iconv(r_gew@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_gew@dc@data[,"dif_localisation"]<-iconv(r_gew@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_gew<-calcule(r_gew)
devtools::use_data(r_gew,internal=FALSE,overwrite=TRUE)


#################################
# generates dataset for report_sea_age r_seaa
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_seaa<-new("report_sea_age")
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("logrami",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi)
assign("sch","logrami.",envir_stacomi)

r_seaa<-choice_c(r_seaa,
	dc=c(107,108,101),			
	horodatedebut="2012-01-01",
	horodatefin="2012-12-31",
	limit1hm=675,
	limit2hm=875,
	silent=FALSE)
r_seaa<-connect(r_seaa)
r_seaa@dc@data[,"ouv_libelle"]<-iconv(r_seaa@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_seaa@dc@data[,"dis_commentaires"]<-iconv(r_seaa@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_seaa@dc@data[,"type_df"]<-iconv(r_seaa@dc@data[,"type_df"],from="latin1",to="UTF8")
r_seaa@dc@data[,"type_dc"]<-iconv(r_seaa@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_seaa@dc@data[,"dif_localisation"]<-iconv(r_seaa@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_seaa@data[,"car_valeur_quantitatif"]<-r_seaa@data[,"car_valeur_quantitatif"]*10
r_seaa@data[,"par_nom"]<-iconv(r_seaa@data[,"par_nom"],from="latin1",to="UTF8")
r_seaa@data[,"dev_libelle"]<-iconv(r_seaa@data[,"dev_libelle"],from="latin1",to="UTF8")
r_seaa@data[,"std_libelle"]<-iconv(r_seaa@data[,"std_libelle"],from="latin1",to="UTF8")
r_seaa@taxa@data[,"tax_nom_commun"]<-iconv(r_seaa@taxa@data[,"tax_nom_commun"],from="latin1",to="UTF8")
r_seaa@par@data[,"par_nom"]<-iconv(r_seaa@par@data[,"par_nom"],from="latin1",to="UTF8")
r_seaa@stage@data[,"std_libelle"]<-iconv(r_seaa@stage@data[,"std_libelle"],from="latin1",to="UTF8")
r_seaa@data$car_valeur_quantitatif[r_seaa@data$car_par_code=="C001"]<-
	r_seaa@data$car_valeur_quantitatif[r_seaa@data$car_par_code=="C001"]/10
r_seaa<-calcule(r_seaa)
devtools::use_data(r_seaa,internal=FALSE,overwrite=TRUE)


#################################
# generates dataset for report_mig_interannual with two dc
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_mig_interannual_vichy<-new("report_mig_interannual")
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("logrami",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi)
assign("sch","logrami.",envir_stacomi)

r_mig_interannual_vichy<-choice_c(r_mig_interannual_vichy,
	dc=c(107,108),			
	taxa=c("Salmo salar"),
	stage=c("5"),
	anneedebut="1997",
	anneefin="2012",
	silent=FALSE)
#r_mig_interannual_vichy<-charge(r_mig_interannual_vichy)
r_mig_interannual_vichy<-connect(r_mig_interannual_vichy)
r_mig_interannual_vichy@dc@data[,"ouv_libelle"]<-iconv(r_mig_interannual_vichy@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_mig_interannual_vichy@dc@data[,"dis_commentaires"]<-iconv(r_mig_interannual_vichy@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_interannual_vichy@dc@data[,"type_df"]<-iconv(r_mig_interannual_vichy@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_interannual_vichy@dc@data[,"type_dc"]<-iconv(r_mig_interannual_vichy@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_interannual_vichy@dc@data[,"dif_localisation"]<-iconv(r_mig_interannual_vichy@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
devtools::use_data(r_mig_interannual_vichy,internal=FALSE,overwrite=TRUE)

#################################
# generates dataset for report_env
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_env<-new("report_env")
r_env<-choice_c(r_env,
	stationMesure=c("temp_gabion","coef_maree"),
	datedebut="2008-01-01",
	datefin="2008-12-31",
	silent=FALSE)	
r_env<-connect(r_env)
r_env@stationMesure@data$stm_description<-iconv(r_env@stationMesure@data$stm_description,from="latin1",to="UTF8")
devtools::use_data(r_env,internal=FALSE,overwrite=TRUE)

#################################
# generates dataset for report_mig_char
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)
r_mig_char<-new("report_mig_char")
baseODBC<-get("baseODBC",envir=envir_stacomi)
baseODBC[c(2,3)]<-rep("logrami",2)
assign("baseODBC",baseODBC,envir_stacomi)
sch<-get("sch",envir=envir_stacomi)
assign("sch","logrami.",envir_stacomi)
# here parqual is not in the list
# so this is equivalent to parqual=NULL
r_mig_char<-choice_c(r_mig_char,
	dc=c(107,108,101),
	taxa=c("Salmo salar"),
	stage=c('5','11','BEC','BER','IND'),
	parquan=c('A124','C001','1786','1785'),
	horodatedebut="2012-01-01",
	horodatefin="2012-12-31",
	silent=FALSE)
# r_mig_char<-charge(r_mig_char) not necessary there
r_mig_char<-connect(r_mig_char)
r_mig_char@dc@data[,"ouv_libelle"]<-iconv(r_mig_char@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_mig_char@dc@data[,"dis_commentaires"]<-iconv(r_mig_char@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_char@dc@data[,"type_df"]<-iconv(r_mig_char@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_char@dc@data[,"type_dc"]<-iconv(r_mig_char@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_char@dc@data[,"dif_localisation"]<-iconv(r_mig_char@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
devtools::use_data(r_mig_char,internal=FALSE,overwrite=TRUE)


#################################
# generates dataset for report_mig_env
##################################
setwd("C:/workspace/stacomir/pkg/stacomir")
require(stacomiR)
stacomi(gr_interface=FALSE,
	login_window=FALSE,
	database_expected=FALSE)

r_mig_env<-new("report_mig_env")
r_mig_env<-choice_c(r_mig_env,
	dc=c(5,6,12),
	taxa=c("Anguilla anguilla"),
	stage=c("AGJ","AGG","CIV"),
	stationMesure=c("temp_gabion","coef_maree","phases_lune"),
	datedebut="2008-01-01",
	datefin="2008-12-31",
	silent=FALSE)	
r_mig_env<-charge(r_mig_env)
r_mig_env<-connect(r_mig_env)
r_mig_env<-calcule(r_mig_env,silent=TRUE)

r_mig_env@report_mig_mult@dc@data[,"ouv_libelle"]<-iconv(r_mig_env@report_mig_mult@dc@data[,"ouv_libelle"],from="latin1",to="UTF8")
r_mig_env@report_mig_mult@dc@data[,"dis_commentaires"]<-iconv(r_mig_env@report_mig_mult@dc@data[,"dis_commentaires"],from="latin1",to="UTF8")
r_mig_env@report_mig_mult@dc@data[,"type_df"]<-iconv(r_mig_env@report_mig_mult@dc@data[,"type_df"],from="latin1",to="UTF8")
r_mig_env@report_mig_mult@dc@data[,"type_dc"]<-iconv(r_mig_env@report_mig_mult@dc@data[,"type_dc"],from="latin1",to="UTF8")
r_mig_env@report_mig_mult@dc@data[,"dif_localisation"]<-iconv(r_mig_env@report_mig_mult@dc@data[,"dif_localisation"],from="latin1",to="UTF8")
r_mig_env@report_env@stationMesure@data$stm_description<-iconv(r_mig_env@report_env@stationMesure@data$stm_description,from="latin1",to="UTF8")
r_mig_env@report_mig_mult@stage@data[,"std_libelle"]<-iconv(r_mig_env@report_mig_mult@stage@data[,"std_libelle"],from="latin1",to="UTF8")

devtools::use_data(r_mig_env,internal=FALSE,overwrite=TRUE)
