Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup,echo=FALSE,warning=FALSE,message=FALSE-----------------------------
library(mort)
library(ggplot2)
## ----stnchange_plot_data,echo=FALSE,results=FALSE-----------------------------
stn.change<-stationchange(data=events[events$ID %in% c("G","K"),],type="mort",ID="ID",station="Station.Name")
plot<-mortsplot(data=events[events$ID %in% c("G","K"),],
type="mort",ID="ID",station="Station.Name",
season.start="2004-06-22",season.end="2004-07-01")
## ----stnchange_plot,echo=FALSE,fig.width=7------------------------------------
plot<-plot+
geom_point(data=stn.change,aes(x=ResidenceStart,y=ID))+
scale_colour_discrete(name="Station Name")+
guides(colour=guide_legend(nrow=1,byrow=TRUE))+
theme(legend.position="bottom")
plot
## ----resmax_ex,echo=FALSE,results=FALSE---------------------------------------
stn.change<-stationchange(data=events,type="mort",ID="ID",station="Station.Name")
rm_example<-resmax(data=events,ID="ID",station="Station.Name",
res.start="ResidenceStart",residences="ResidenceLength.days",
stnchange=stn.change)
## ----resmax_table,echo=FALSE--------------------------------------------------
rm_example<-rm_example[order(rm_example$ResidenceLength.days,decreasing=TRUE),]
row.names(rm_example)<-NULL
knitr::kable(head(rm_example),align="c")
## ----morts_last_ex,eval=FALSE-------------------------------------------------
# last_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="last")
## ----morts_last_ex_run,include=FALSE------------------------------------------
last_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="last")
## ----last_ex_plot,echo=FALSE,fig.width=7--------------------------------------
plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name",
morts=last_ex)
plot<-plot+
theme(legend.position="none")
plot
## ----morts_any_ex,eval=FALSE--------------------------------------------------
# any_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="any")
## ----morts_any_ex_run,include=FALSE-------------------------------------------
any_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="any")
## ----morts_any_plot,echo=FALSE,fig.width=7------------------------------------
plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name",morts=any_ex)
plot<-plot+
theme(legend.position="none")
plot
## ----actel_any_ex,eval=FALSE--------------------------------------------------
# actel_ex<-morts(data=data,type="actel",ID="auto",station="auto",method="any")
## ----manual_ex,eval=FALSE-----------------------------------------------------
# manual_ex<-morts(data=data,type="manual",ID="ID",station="Station.Name",
# res.start="ResidenceStart",res.end="ResidenceEnd",
# residences="ResidenceLength.days",units="days",method="any")
## ----sc_cmlres_plot,echo=FALSE,results=FALSE----------------------------------
cml_res<-data.frame(ID=c("C","L"),
Start=as.POSIXct(c("2004-03-26 13:39:43",
"2004-04-20 15:21:35")),
End=as.POSIXct(c("2004-06-08 23:21:49",
"2004-06-09 22:20:20")))
plot<-mortsplot(data=events[events$ID %in% c("C","L"),],
type="mort",ID="ID",station="Station.Name",
season.start="2004-03-26",season.end="2004-06-23")
## ----sc_cmlres_plot_adjust,echo=FALSE,fig.width=7-----------------------------
plot<-plot+
geom_point(data=cml_res,aes(x=Start,y=ID))+
geom_point(data=cml_res,aes(x=End,y=ID))+
scale_colour_discrete(name="Station Name")+
theme(legend.position="bottom")
plot
## ----resmaxcml_ex,echo=FALSE,results=FALSE------------------------------------
stn.change<-stationchange(data=events,type="mort",ID="ID",station="Station.Name")
rmc_example<-resmaxcml(data=events,ID="ID",station="Station.Name",
res.start="ResidenceStart",
res.end="ResidenceEnd",
residences="ResidenceLength.days",
units="days",
stnchange=stn.change)
## ----resmaxcml_ex_table,echo=FALSE--------------------------------------------
rmc_example<-rmc_example[order(rmc_example$ResidenceLength.days,
decreasing=TRUE),]
row.names(rmc_example)<-NULL
knitr::kable(head(rmc_example),align="c")
## ----cumulative_ex,eval=FALSE-------------------------------------------------
# cumulative_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="cumulative")
## ----clm_ex_run,include=FALSE-------------------------------------------------
cumulative_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="cumulative")
## ----clm_ex_plot,echo=FALSE,fig.width=7---------------------------------------
plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name",morts=cumulative_ex)
plot<-plot+
theme(legend.position="none")
plot
## ----all_ex,eval=FALSE--------------------------------------------------------
# all_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="all")
## ----all_ex_run,include=FALSE-------------------------------------------------
all_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",method="all")
## ----all_ex_plot,echo=FALSE,fig.width=7---------------------------------------
plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name",morts=all_ex)
plot<-plot+
theme(legend.position="none")
plot
## ----all_ex_table,echo=FALSE--------------------------------------------------
row.names(all_ex)<-NULL
knitr::kable(head(all_ex),align="c")
## ----inf_plot,echo=FALSE,results=FALSE----------------------------------------
plot<-mortsplot(data=events[events$ID %in% c("M","I"),],
type="mort",ID="ID",station="Station.Name",
season.start="2005-09-25",season.end="2006-09-25")
## ----inf_plot_adjust,echo=FALSE,fig.width=7-----------------------------------
plot<-plot+
theme(legend.position="none")
plot
## ----recent_ex,eval=FALSE-----------------------------------------------------
# recent_ex<-infrequent(data=events,type="mort",ID="ID",station="Station.Name",
# method="recent",threshold=72,threshold.units="hours",
# recent.period=52,recent.units="weeks")
## ----recent_ex_run,include=FALSE----------------------------------------------
recent_ex<-infrequent(data=events,type="mort",ID="ID",station="Station.Name",
method="recent",threshold=72,threshold.units="hours",
recent.period=52,recent.units="weeks")
## ----rec_plot,echo=FALSE,fig.width=7------------------------------------------
plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name",morts=recent_ex)
plot<-plot+
theme(legend.position="none")
plot
## ----defined_ex, eval=FALSE---------------------------------------------------
# defined_ex<-infrequent(data=events,type="mort",ID="ID",station="Station.Name",
# method="defined",threshold=12,threshold.units="hours",
# start="2006-06-15",end="2006-10-15")
## ----defined_ex_run,include=FALSE---------------------------------------------
defined_ex<-infrequent(data=events,type="mort",ID="ID",station="Station.Name",
method="defined",threshold=12,threshold.units="hours",
start="2006-06-15",end="2006-10-15")
## ----def_plot,echo=FALSE,fig.width=7------------------------------------------
plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name",morts=defined_ex)
plot<-plot+
theme(legend.position="none")
plot
## ----datetime_ex--------------------------------------------------------------
start=as.POSIXct("2022-06-15",tz="America/Edmonton")
start
attributes(start)$tzone<-"UTC"
start
## ----mortsprev_ex,eval=FALSE--------------------------------------------------
# prev_ex<-morts(data=events,type="mort",ID="ID",station="Station.Name",morts.prev=recent_ex)
## ----backwards,include=FALSE--------------------------------------------------
morts.all<-morts(data=events,type="mort",ID="ID",station="Station.Name",
method="any")
morts.all.bw<-morts(data=events,type="mort",ID="ID",station="Station.Name",
method="any",backwards=TRUE)
## ----backwards_plot,echo=FALSE,fig.width=7------------------------------------
plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name")
plot<-plot+
geom_point(data=morts.all,aes(x=ResidenceStart,y=ID),colour="black")+
geom_point(data=morts.all.bw,aes(x=ResidenceStart,y=ID),colour="blue")
plot<-plot+
theme(legend.position="none")
plot
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