doc/Introduction.R
In ldbk/CLEFRDB: What the Package Does (One Line, Title Case)
## ---- include = FALSE----------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----compilnopack,eval=F,include=F---------------------------------------
# NA
## ----setup---------------------------------------------------------------
library(CLEFRDB)
## ----time1---------------------------------------------------------------
new("Time")
## ----time2---------------------------------------------------------------
print(Timetype)
## ----time3,eval=T--------------------------------------------------------
hauldate<-as.POSIXct(strptime("2011-03-27 01:30:03",
"%Y-%m-%d %H:%M:%S"))
new("Time",TimeType="date",TimeDate=hauldate)
## ----time4---------------------------------------------------------------
haultime<-c("2011-03-27 01:30:03",
"2011-03-27 12:00:00",
"2011-03-15 12:00:00",
"2011-02-14 00:00:00")
haultime<-as.POSIXct(strptime(haultime,
"%Y-%m-%d %H:%M:%S"))
haultime<-new("Time",TimeType=c("date","day","month","quarter"),
TimeDate=haultime)
print(haultime)
## ----time5---------------------------------------------------------------
substr(haultime@TimeDate,1,4)
## ----time6,eval=F--------------------------------------------------------
# new("Time",TimeDate=c(NA),TimeType=c("day"))
# new("Time",TimeDate=.POSIXct(c(NA,NA)),TimeType=c("day","day"))
# new("Time",TimeType="date",TimeDate="2011-03-27")
# hauldate<-as.POSIXct(strptime("2011-03-27 01:30:03",
# "%Y-%m-%d %H:%M:%S"))
# new("Time",TimeDate=hauldate,TimeType=c("a day"))
# new("Time",TimeDate=hauldate)
## ----time7,eval=T--------------------------------------------------------
#a Time object related to four haul
haultime<-c("2011-03-27 01:30:03",
"2011-03-27 12:00:00",
"2011-03-15 12:00:00",
"2011-02-14 00:00:00")
haultime<-as.POSIXct(strptime(haultime,
"%Y-%m-%d %H:%M:%S"))
haultime<-new("Time",TimeType=c("date","day","month","quarter"),
TimeDate=haultime)
# the value of the total landings of the four hauls
w<-c(10000,3000,2000,10)
#Definition of the Landings class
setClass(Class="Landings",
slots=c("landings"="numeric"),
contains=c("Time"),
prototype=prototype(Landings=numeric(),
Time=new("Time"))
)
#a new Landings object
new("Landings")
#a new Landings object initialized with the previous values
initinherit(new("Landings"),landings=w,Time=haultime)
## ----space1--------------------------------------------------------------
new("Space")
## ----space2--------------------------------------------------------------
print(Spacetype)
## ----space3--------------------------------------------------------------
head(defspace)
## ----space4--------------------------------------------------------------
plot(defspace[1:10,"type"],axes=T)
## ----space5,eval=T-------------------------------------------------------
tripgeo<-new("Space",SpacePlace=c("27.7.f","27.7.g","27.7.h",
"27E8","27F0","28F0",
"GSA07","GSA08",
"FRRTB"),
SpaceType=c("ICESdiv","ICESdiv","ICESdiv",
"ICESrect","ICESrect","ICESrect",
"GSA","GSA",
"harbour"))
print(tripgeo)
## ----space6,eval=T-------------------------------------------------------
map(tripgeo,axes=T)
## ----space7,eval=F-------------------------------------------------------
# new("Space",SpacePlace=c("27.7.h","GSA078"),
# SpaceType=c("ICEdiv","GSA"))
# new("Space",SpacePlace=c("27.7.h","GSA07","FRRTB","DEBRB"),
# SpaceType=c("ICESdiv","GSA","harbour"))
#
## ----space8,eval=T-------------------------------------------------------
#a Time object related to four hauls
haultime<-c("2011-03-27 01:30:03",
"2011-03-27 12:00:00",
"2011-03-15 12:00:00",
"2011-02-14 00:00:00")
haultime<-as.POSIXct(strptime(haultime,
"%Y-%m-%d %H:%M:%S"))
haultime<-new("Time",TimeType=c("date","day","month","quarter"),
TimeDate=haultime)
# the value of the total landings of the four hauls
w<-c(10000,3000,2000,10)
#the area where the hauls were located
haulspace<-new("Space",SpacePlace=c("27.7.f","27.7.g",
"27E8","GSA07"),
SpaceType=c("ICESdiv","ICESdiv",
"ICESrect","GSA"))
#Definition of the Landings class
setClass(Class="Landings",
slots=c("landings"="numeric"),
contains=c("Time","Space"),
prototype=prototype(landings=numeric(),
Time=new("Time"),
Space=new("Space"))
)
#a new Landings object
new("Landings")
#a new Landings object initialized with the previous values
haullanding<-initinherit(new("Landings",landings=w),Time=haultime,Space=haulspace)
print(haullanding)
map(haullanding)
#dimclass(haullanding)
## ----space9,eval=T-------------------------------------------------------
#validity of the landings object
validLandings<-function(object){
if(any(object@landings<0)){print("negative landings !!");FALSE}else{TRUE}
}
#associate the validation function to the landings object
setValidity("Landings",validLandings)
#the original object is still valid
initinherit(new("Landings"),landings=w,Time=haultime,Space=haulspace)
#a negative value in the landings slot will throw an error
## w<-c(10000,3000,-2000,10)
## initinherit(new("Landings",landings=w),Time=haultime,Space=haulspace)
## ----fishframe1----------------------------------------------------------
#Vessel class
setClass(Class="Vessel",
slots=c(VesselId="character",
VesselFlag="character",
VesselType="character",
VesselLength="integer",
VesselPower="integer",
VesselSize="integer"
),
prototype=prototype(VesselId=character(),
VesselFlag=character(),
VesselType=character(),
VesselLength=integer(),
VesselPower=integer(),
VesselSize=integer()),
)
#a fictional vessel
myVessel<-new("Vessel",
VesselId="AAAA123",
VesselFlag="FRA",
VesselType=c("Trawler"),
VesselLength=as.integer(20),
VesselPower=as.integer(5000),
VesselSize=as.integer(1000))
## ----fishframe2----------------------------------------------------------
#Sampling class"
setClass(Class="Sampling",
slots=c(SamplingId="character",
SamplingType="character",
SamplingMethod="character",
SamplingProject="character",
SamplingCountry="character"),
prototype=prototype(SamplingId=character(),
SamplingType=character(),
SamplingMethod=character(),
SamplingProject=character(),
SamplingCountry=character())
)
#a fictionnal sample
mySampling<-new("Sampling",
SamplingId="SAMP2199",
SamplingType="S",
SamplingMethod="Observer",
SamplingProject="SamplingProjectFRA",
SamplingCountry="FRA")
## ----fishframe3----------------------------------------------------------
mySpaceDep<-new("Space",SpacePlace=c("FRCOC"),SpaceType=c("harbour"))
mySpaceArr<-new("Space",SpacePlace=c("FRCOC"),SpaceType=c("harbour"))
myTimeDep<-new("Time",
TimeDate=as.POSIXct(strptime("2011-03-15 12:16:00","%Y-%m-%d %H:%M:%S")),
TimeType="date")
myTimeArr<-new("Time",
TimeDate=as.POSIXct(strptime("2011-03-19 04:00:32","%Y-%m-%d %H:%M:%S")),
TimeType="date")
## ----fishframe4----------------------------------------------------------
# a new Trip class
setClass(Class="Trip",
slots=c(nbhaul="integer",
daysatsea="integer",
TripId="character",
TimeDep="Time",
TimeArr="Time",
SpaceDep="Space",
SpaceArr="Space"
),
contains=c("Vessel",
"Sampling"
),
prototype=prototype(TripId=character(),
nbhaul=integer(),
daysatsea=integer(),
Vessel=new("Vessel"),
Sampling=new("Sampling"),
TimeDep=new("Time"),
TimeArr=new("Time"),
SpaceDep=new("Space"),
SpaceArr=new("Space")
)
)
myTrip<-initinherit(new("Trip",
TripId="FR872",
nbhaul=as.integer(12),
daysatsea=as.integer(5)),
Sampling=mySampling,
Vessel=myVessel,
TimeDep=myTimeDep,
TimeArr=myTimeArr,
SpaceDep=mySpaceDep,
SpaceArr=mySpaceArr)
## ----fishframe5----------------------------------------------------------
FishframeTrip<-data.frame(`Record type`="TR",
`Sampling type`=myTrip@SamplingType,
`Landing country`=myTrip@SamplingCountry,
`Vessel flag country`=myTrip@VesselFlag,
`Year`=substr(myTrip@TimeArr@TimeDate,1,4),
`Project`=myTrip@SamplingProject,
`Trip code`=myTrip@TripId,
`Vessel length`=myTrip@VesselLength,
`Vessel power`=myTrip@VesselPower,
`Vessel size`=myTrip@VesselSize,
`Vessel type`=myTrip@VesselType,
`Harbour`=myTrip@SpaceArr@SpacePlace,
`Number of hauls`=myTrip@nbhaul,
`Days at sea`=myTrip@daysatsea,
`Vessel identifier`=myTrip@VesselId,
`Sampling country`=myTrip@SamplingCountry,
`Sampling method`=myTrip@SamplingMethod)
## ----rdbes1--------------------------------------------------------------
RDBESTrip<-data.frame(`FishingTripID`=myTrip@SamplingId,
`OnShoreEventID`="",
`VesselSelectionID `="",
`VesselDetailsID `=myTrip@VesselId,
`SampleDetailsId`=myTrip@SamplingId,
`Record type`="FT",
`National Fishing trip Code`=myTrip@TripId,
`Stratification`="",
`Trip Stratum`="",
`FishingTripsClustering`="",
`FishingTripsClusterName`="",
`Sampler`="",
`NumberOfHauls`=myTrip@nbhaul,
`Departure location`=myTrip@SpaceDep@SpacePlace,
`Depature date`=substr(myTrip@TimeDep@TimeDate,1,10),
`Depature time`=substr(myTrip@TimeDep@TimeDate,12,19),
`Arrival location`=myTrip@SpaceArr@SpacePlace,
`Arrival date`=substr(myTrip@TimeArr@TimeDate,1,10),
`Arrival time`=substr(myTrip@TimeArr@TimeDate,12,19),
`FishingTrips Total`="",
`FishingTrips Sampled`=1,
`FishingTripSampelProbability`="",
`Selection method`="",
`Selection Method Cluster`="",
`FishingTripsTotClusters`="",
`FishingTripsSampClusters`="",
`FishingTripsClustersProb`="")
ldbk/CLEFRDB documentation built on June 2, 2019, 9:07 p.m.
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## ---- include = FALSE----------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----compilnopack,eval=F,include=F---------------------------------------
# NA
## ----setup---------------------------------------------------------------
library(CLEFRDB)
## ----time1---------------------------------------------------------------
new("Time")
## ----time2---------------------------------------------------------------
print(Timetype)
## ----time3,eval=T--------------------------------------------------------
hauldate<-as.POSIXct(strptime("2011-03-27 01:30:03",
"%Y-%m-%d %H:%M:%S"))
new("Time",TimeType="date",TimeDate=hauldate)
## ----time4---------------------------------------------------------------
haultime<-c("2011-03-27 01:30:03",
"2011-03-27 12:00:00",
"2011-03-15 12:00:00",
"2011-02-14 00:00:00")
haultime<-as.POSIXct(strptime(haultime,
"%Y-%m-%d %H:%M:%S"))
haultime<-new("Time",TimeType=c("date","day","month","quarter"),
TimeDate=haultime)
print(haultime)
## ----time5---------------------------------------------------------------
substr(haultime@TimeDate,1,4)
## ----time6,eval=F--------------------------------------------------------
# new("Time",TimeDate=c(NA),TimeType=c("day"))
# new("Time",TimeDate=.POSIXct(c(NA,NA)),TimeType=c("day","day"))
# new("Time",TimeType="date",TimeDate="2011-03-27")
# hauldate<-as.POSIXct(strptime("2011-03-27 01:30:03",
# "%Y-%m-%d %H:%M:%S"))
# new("Time",TimeDate=hauldate,TimeType=c("a day"))
# new("Time",TimeDate=hauldate)
## ----time7,eval=T--------------------------------------------------------
#a Time object related to four haul
haultime<-c("2011-03-27 01:30:03",
"2011-03-27 12:00:00",
"2011-03-15 12:00:00",
"2011-02-14 00:00:00")
haultime<-as.POSIXct(strptime(haultime,
"%Y-%m-%d %H:%M:%S"))
haultime<-new("Time",TimeType=c("date","day","month","quarter"),
TimeDate=haultime)
# the value of the total landings of the four hauls
w<-c(10000,3000,2000,10)
#Definition of the Landings class
setClass(Class="Landings",
slots=c("landings"="numeric"),
contains=c("Time"),
prototype=prototype(Landings=numeric(),
Time=new("Time"))
)
#a new Landings object
new("Landings")
#a new Landings object initialized with the previous values
initinherit(new("Landings"),landings=w,Time=haultime)
## ----space1--------------------------------------------------------------
new("Space")
## ----space2--------------------------------------------------------------
print(Spacetype)
## ----space3--------------------------------------------------------------
head(defspace)
## ----space4--------------------------------------------------------------
plot(defspace[1:10,"type"],axes=T)
## ----space5,eval=T-------------------------------------------------------
tripgeo<-new("Space",SpacePlace=c("27.7.f","27.7.g","27.7.h",
"27E8","27F0","28F0",
"GSA07","GSA08",
"FRRTB"),
SpaceType=c("ICESdiv","ICESdiv","ICESdiv",
"ICESrect","ICESrect","ICESrect",
"GSA","GSA",
"harbour"))
print(tripgeo)
## ----space6,eval=T-------------------------------------------------------
map(tripgeo,axes=T)
## ----space7,eval=F-------------------------------------------------------
# new("Space",SpacePlace=c("27.7.h","GSA078"),
# SpaceType=c("ICEdiv","GSA"))
# new("Space",SpacePlace=c("27.7.h","GSA07","FRRTB","DEBRB"),
# SpaceType=c("ICESdiv","GSA","harbour"))
#
## ----space8,eval=T-------------------------------------------------------
#a Time object related to four hauls
haultime<-c("2011-03-27 01:30:03",
"2011-03-27 12:00:00",
"2011-03-15 12:00:00",
"2011-02-14 00:00:00")
haultime<-as.POSIXct(strptime(haultime,
"%Y-%m-%d %H:%M:%S"))
haultime<-new("Time",TimeType=c("date","day","month","quarter"),
TimeDate=haultime)
# the value of the total landings of the four hauls
w<-c(10000,3000,2000,10)
#the area where the hauls were located
haulspace<-new("Space",SpacePlace=c("27.7.f","27.7.g",
"27E8","GSA07"),
SpaceType=c("ICESdiv","ICESdiv",
"ICESrect","GSA"))
#Definition of the Landings class
setClass(Class="Landings",
slots=c("landings"="numeric"),
contains=c("Time","Space"),
prototype=prototype(landings=numeric(),
Time=new("Time"),
Space=new("Space"))
)
#a new Landings object
new("Landings")
#a new Landings object initialized with the previous values
haullanding<-initinherit(new("Landings",landings=w),Time=haultime,Space=haulspace)
print(haullanding)
map(haullanding)
#dimclass(haullanding)
## ----space9,eval=T-------------------------------------------------------
#validity of the landings object
validLandings<-function(object){
if(any(object@landings<0)){print("negative landings !!");FALSE}else{TRUE}
}
#associate the validation function to the landings object
setValidity("Landings",validLandings)
#the original object is still valid
initinherit(new("Landings"),landings=w,Time=haultime,Space=haulspace)
#a negative value in the landings slot will throw an error
## w<-c(10000,3000,-2000,10)
## initinherit(new("Landings",landings=w),Time=haultime,Space=haulspace)
## ----fishframe1----------------------------------------------------------
#Vessel class
setClass(Class="Vessel",
slots=c(VesselId="character",
VesselFlag="character",
VesselType="character",
VesselLength="integer",
VesselPower="integer",
VesselSize="integer"
),
prototype=prototype(VesselId=character(),
VesselFlag=character(),
VesselType=character(),
VesselLength=integer(),
VesselPower=integer(),
VesselSize=integer()),
)
#a fictional vessel
myVessel<-new("Vessel",
VesselId="AAAA123",
VesselFlag="FRA",
VesselType=c("Trawler"),
VesselLength=as.integer(20),
VesselPower=as.integer(5000),
VesselSize=as.integer(1000))
## ----fishframe2----------------------------------------------------------
#Sampling class"
setClass(Class="Sampling",
slots=c(SamplingId="character",
SamplingType="character",
SamplingMethod="character",
SamplingProject="character",
SamplingCountry="character"),
prototype=prototype(SamplingId=character(),
SamplingType=character(),
SamplingMethod=character(),
SamplingProject=character(),
SamplingCountry=character())
)
#a fictionnal sample
mySampling<-new("Sampling",
SamplingId="SAMP2199",
SamplingType="S",
SamplingMethod="Observer",
SamplingProject="SamplingProjectFRA",
SamplingCountry="FRA")
## ----fishframe3----------------------------------------------------------
mySpaceDep<-new("Space",SpacePlace=c("FRCOC"),SpaceType=c("harbour"))
mySpaceArr<-new("Space",SpacePlace=c("FRCOC"),SpaceType=c("harbour"))
myTimeDep<-new("Time",
TimeDate=as.POSIXct(strptime("2011-03-15 12:16:00","%Y-%m-%d %H:%M:%S")),
TimeType="date")
myTimeArr<-new("Time",
TimeDate=as.POSIXct(strptime("2011-03-19 04:00:32","%Y-%m-%d %H:%M:%S")),
TimeType="date")
## ----fishframe4----------------------------------------------------------
# a new Trip class
setClass(Class="Trip",
slots=c(nbhaul="integer",
daysatsea="integer",
TripId="character",
TimeDep="Time",
TimeArr="Time",
SpaceDep="Space",
SpaceArr="Space"
),
contains=c("Vessel",
"Sampling"
),
prototype=prototype(TripId=character(),
nbhaul=integer(),
daysatsea=integer(),
Vessel=new("Vessel"),
Sampling=new("Sampling"),
TimeDep=new("Time"),
TimeArr=new("Time"),
SpaceDep=new("Space"),
SpaceArr=new("Space")
)
)
myTrip<-initinherit(new("Trip",
TripId="FR872",
nbhaul=as.integer(12),
daysatsea=as.integer(5)),
Sampling=mySampling,
Vessel=myVessel,
TimeDep=myTimeDep,
TimeArr=myTimeArr,
SpaceDep=mySpaceDep,
SpaceArr=mySpaceArr)
## ----fishframe5----------------------------------------------------------
FishframeTrip<-data.frame(`Record type`="TR",
`Sampling type`=myTrip@SamplingType,
`Landing country`=myTrip@SamplingCountry,
`Vessel flag country`=myTrip@VesselFlag,
`Year`=substr(myTrip@TimeArr@TimeDate,1,4),
`Project`=myTrip@SamplingProject,
`Trip code`=myTrip@TripId,
`Vessel length`=myTrip@VesselLength,
`Vessel power`=myTrip@VesselPower,
`Vessel size`=myTrip@VesselSize,
`Vessel type`=myTrip@VesselType,
`Harbour`=myTrip@SpaceArr@SpacePlace,
`Number of hauls`=myTrip@nbhaul,
`Days at sea`=myTrip@daysatsea,
`Vessel identifier`=myTrip@VesselId,
`Sampling country`=myTrip@SamplingCountry,
`Sampling method`=myTrip@SamplingMethod)
## ----rdbes1--------------------------------------------------------------
RDBESTrip<-data.frame(`FishingTripID`=myTrip@SamplingId,
`OnShoreEventID`="",
`VesselSelectionID `="",
`VesselDetailsID `=myTrip@VesselId,
`SampleDetailsId`=myTrip@SamplingId,
`Record type`="FT",
`National Fishing trip Code`=myTrip@TripId,
`Stratification`="",
`Trip Stratum`="",
`FishingTripsClustering`="",
`FishingTripsClusterName`="",
`Sampler`="",
`NumberOfHauls`=myTrip@nbhaul,
`Departure location`=myTrip@SpaceDep@SpacePlace,
`Depature date`=substr(myTrip@TimeDep@TimeDate,1,10),
`Depature time`=substr(myTrip@TimeDep@TimeDate,12,19),
`Arrival location`=myTrip@SpaceArr@SpacePlace,
`Arrival date`=substr(myTrip@TimeArr@TimeDate,1,10),
`Arrival time`=substr(myTrip@TimeArr@TimeDate,12,19),
`FishingTrips Total`="",
`FishingTrips Sampled`=1,
`FishingTripSampelProbability`="",
`Selection method`="",
`Selection Method Cluster`="",
`FishingTripsTotClusters`="",
`FishingTripsSampClusters`="",
`FishingTripsClustersProb`="")
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