tests/run-all.R
In nandadorea/vetsyn: Tools for Syndromic Surveillance Implementation
# manual testing while the right tests are not set up
#data(lab.daily)
#head(lab.weekly)
#data(observed)
#data with only one column
#unnamed columns
#install.packages("devtools")
library(devtools)
install_github("nandadorea/vetsyn")
require(vetsyn)
data(observed)
data(observedW)
data(lab.daily)
data(lab.weekly)
data(lab.daily.update)
data(lab.weekly.update)
#syndromicD(observed,
# dates=data.frame(),
# max.date=NULL,
# date.format="%d/%m/%Y",
# weekends=TRUE,
# baseline=matrix(nrow=0,ncol=0),
# alarms=array(dim=0),
# UCL=array(dim=0),
# LCL=array(dim=0))
my.syndromicD <- syndromicD(observed,min.date="01/01/2011",max.date="26/05/2013")
# syndromicW (observed,
# dates=data.frame(),
# min.week=NULL,
# max.week=NULL,
# min.year=NULL,
# max.year=NULL,
# baseline=matrix(nrow=0,ncol=0),
# alarms=array(dim=0),
# UCL=array(dim=0),
# LCL=array(dim=0))
my.syndromicW <- syndromicW(observedW,min.week=1, min.year=2011,
max.week=22, max.year=2013)
# raw_to_syndromicD(id,
# syndromes.var,
# syndromes.name,
# dates.var,
# date.format="%d/%m/%Y",
# min.date,
# max.date,
# remove.dow=FALSE,
# add.to=0,
# sort=TRUE,
# data=NULL)
my.syndromicD <- raw_to_syndromicD (id=lab.daily$SubmissionID,
syndromes.var=lab.daily$Syndrome,
dates.var=lab.daily$DateofSubmission,
date.format="%d/%m/%Y")
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- raw_to_syndromicD (id=list(HerdID,AnimalID),
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal"),
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal","NonExisting"),
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
min.date="01/01/2011",
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
# raw_to_syndromicW(id,
# syndromes.var,
# syndromes.name,
# dates.var,
# date.format="%d/%m/%Y",
# min.date,
# max.date,
# sort=TRUE,
# data=NULL)
my.syndromicW <- raw_to_syndromicW (id=lab.daily$SubmissionID,
syndromes.var=lab.daily$Syndrome,
dates.var=lab.daily$DateofSubmission,
date.format="%d/%m/%Y")
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- raw_to_syndromicW (id=list(HerdID,AnimalID),
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal"),
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal","NonExisting"),
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- raw_to_syndromicW (id=lab.daily$SubmissionID,
syndromes.var=lab.daily$Syndrome,
dates.var=lab.daily$DateofSubmission,
min.date="01/01/2011",
date.format="%d/%m/%Y")
##
my.syndromicW <- raw_to_syndromicW (id=lab.weekly$SubmissionID,
syndromes.var=lab.weekly$Syndrome,
dates.var=lab.weekly$DateofSubmission,
date.format="ISOweek")
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="ISOweek",
data=lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=list(HerdID,AnimalID),
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="ISOweek",
data=lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal"),
dates.var=DateofSubmission,
date.format="ISOweek",
data=lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal","NonExisting"),
dates.var=DateofSubmission,
date.format="ISOweek",
data=lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="ISOweek",
min.date="2010-W50-1",
data=lab.weekly)
my.syndromicD
my.syndromicW
my.syndromicD[1,10]
my.syndromicW[1,10]
dim(my.syndromicD)
dim(my.syndromicW)
#retro_summary(x,
# object.name="my.syndromic",
# file.name="syndromic.retro.summary",
# frequency=365,
# short=FALSE)
retro_summary(my.syndromicD)
#retro_summary(x,
# object.name="my.syndromic",
# file.name="syndromic.retro.summary",
# frequency=52,
# short=FALSE)
retro_summary(my.syndromicW)
# clean_baseline(x,
# syndromes=NULL,
# family="poisson",
# limit=0.95,
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365,
# plot=TRUE,
# print.model=TRUE)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
my.syndromicD <- clean_baseline(my.syndromicD,
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
formula="dow+month+year",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD, formula="dow+sin+cos+trend",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes="Musculoskeletal",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=c("GIT","Musculoskeletal"),
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=3,
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=c(1,3),
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
family="nbinom",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes="Musculoskeletal",
family="nbinom",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=c("GIT","Musculoskeletal"),
family="nbinom",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=3,
family="nbinom",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=c(1,3),
family="nbinom",
frequency=260)
# clean_baseline(x,
# syndromes=NULL,
# family="poisson",
# limit=0.95,
# formula="year+sin+cos",
# plot=TRUE,
# print.model=TRUE,
# frequency=52)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- clean_baseline(my.syndromicW)
my.syndromicW <- clean_baseline(my.syndromicW, formula="sin+cos")
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes="Musculoskeletal")
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes=c("GIT","Musculoskeletal"))
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes=3)
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes=c(1,3))
my.syndromicW <- clean_baseline(my.syndromicW,
family="nbinom")
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes="Musculoskeletal",family="nbinom")
# clean_baseline_perc(x,
# syndromes=NULL,
# limit=0.95,
# run.window=120,
# plot=TRUE)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- clean_baseline_perc(my.syndromicD)
my.syndromicD <- clean_baseline_perc(my.syndromicD,run.window=90)
my.syndromicD <- clean_baseline_perc(my.syndromicD,
syndromes="Musculoskeletal")
my.syndromicD <- clean_baseline_perc(my.syndromicD,
syndromes=c("GIT","Musculoskeletal"))
my.syndromicD <- clean_baseline_perc(my.syndromicD,
syndromes=3)
my.syndromicD <- clean_baseline_perc(my.syndromicD,
syndromes=c(1,3))
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- clean_baseline_perc(my.syndromicW)
my.syndromicW <- clean_baseline_perc(my.syndromicW,run.window=90)
my.syndromicW <- clean_baseline_perc(my.syndromicW,
syndromes="Musculoskeletal")
my.syndromicW <- clean_baseline_perc(my.syndromicW,
syndromes=c("GIT","Musculoskeletal"))
my.syndromicW <- clean_baseline_perc(my.syndromicW,
syndromes=3)
my.syndromicW <- clean_baseline_perc(my.syndromicW,
syndromes=c(1,3))
# holt_winters_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# frequency=7,
# baseline.window=365,
# limit.sd=c(2.5,3,3.5),
# nahead=7,
# alpha=0.4,
# beta=0,
# gamma=0.15,
# seasonal="additive",
# correct.baseline=1,
# alarm.dim=1,
# UCL=1)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- holt_winters_synd(x=my.syndromicD,
evaluate.window=30,
frequency=7,
baseline.window=365,
limit.sd=c(2.5,3,3.5), #default
nahead=7,
correct.baseline=2,
alarm.dim=1)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
my.syndromicD <- holt_winters_synd(x=my.syndromicD,
syndromes="Musculoskeletal",
evaluate.window=30,
frequency=5,
baseline.window=260,
limit.sd=c(2.5,3,3.5), #default
nahead=5,
correct.baseline=2,
alarm.dim=1,
UCL=2)
# holt_winters_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# frequency=52,
# baseline.window=104,
# limit.sd=c(2.5,3,3.5),
# nahead=2,
# alpha=0.4,
# beta=0,
# gamma=0.15,
# seasonal="additive",
# correct.baseline=1,
# alarm.dim=1,
# UCL=1
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- holt_winters_synd(x=my.syndromicW,
evaluate.window=12,
frequency=52,
baseline.window=104,
limit.sd=c(2.5,3,3.5), #default
nahead=2,
correct.baseline=2,
alarm.dim=1)
# ewma_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=365,
# lambda=0.2,
# limit.sd=c(2.5,3,3.5),
# guard.band=7,
# correct.baseline=FALSE,
# alarm.dim=2,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=7,
# family="poisson",
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
#system.time({
my.syndromicD <- ewma_synd(x=my.syndromicD,
syndrome="Musculoskeletal",
evaluate.window=10,
baseline.window=260,
lambda=0.2,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=2,
pre.process="glm",
family="nbinom",
formula="dow+sin+cos+AR1+AR2+AR3+AR4+AR5",
frequency=260)
#})
#system.time({
my.syndromicD <- ewma_synd(x=my.syndromicD,
#syndrome= c(1,2,4,5),
evaluate.window=60,
baseline.window=260,
lambda=0.2,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=2,
pre.process="diff",
diff.window=5)
})
# ewma_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=52,
# lambda=0.2,
# limit.sd=c(2.5,3,3.5),
# guard.band=2,
# correct.baseline=FALSE,
# alarm.dim=2,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=4,
# family="poisson",
# formula="trend+sin+cos",
# frequency=52)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- ewma_synd(x=my.syndromicW,
syndrome="Musculoskeletal",
evaluate.window=10,
baseline.window=104,
lambda=0.2,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=2,
pre.process="glm",
family="nbinom",
formula="trend+sin+cos",
frequency=52)
my.syndromicW <- ewma_synd(x=my.syndromicW,
syndrome= c(1,2,4,5),
evaluate.window=10,
baseline.window=104,
lambda=0.2,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=2,
pre.process="diff",
diff.window=4)
# pre_process_glm(x,
# slot="observed",
# syndromes=NULL,
# family="poisson",
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365,
# print.model=TRUE,
# plot=TRUE)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
pre_processed_data <- pre_process_glm(my.syndromicD)
pre_processed_data <- pre_process_glm(my.syndromicD,
syndromes="Musculoskeletal")
pre_processed_data <- pre_process_glm(my.syndromicD,
syndromes=c("GIT","Musculoskeletal"))
pre_processed_data <- pre_process_glm(my.syndromicD,
syndromes=3)
pre_processed_data <- pre_process_glm(my.syndromicD,
syndromes=c(1,3))
pre_processed_data <- pre_process_glm(my.syndromicD,
family="nbinom")
# pre_process_glm(x,
# slot="observed",
# syndromes=NULL,
# family="poisson",
# formula="trend+sin+cos",
# frequency=52,
# print.model=TRUE,
# plot=TRUE)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
pre_processed_data <- pre_process_glm(my.syndromicW)
pre_processed_data <- pre_process_glm(my.syndromicW,
syndromes="Musculoskeletal")
pre_processed_data <- pre_process_glm(my.syndromicW,
syndromes=c("GIT","Musculoskeletal"))
pre_processed_data <- pre_process_glm(my.syndromicW,
syndromes=3)
pre_processed_data <- pre_process_glm(my.syndromicW,
syndromes=c(1,3))
pre_processed_data <- pre_process_glm(my.syndromicW,
family="nbinom")
pre_processed_data <- pre_process_glm(my.syndromicW,slot="baseline")
# shew_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=365,
# limit.sd=c(2.5,3,3.5),
# guard.band=7,
# correct.baseline=FALSE,
# alarm.dim=3,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=7,
# family="poisson",
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
my.syndromicD <- shew_synd(x=my.syndromicD,
syndromes="Musculoskeletal",
evaluate.window=1,
baseline.window=365,
limit.sd=c(2.5,3,3.5),
guard.band=7,
correct.baseline=FALSE,
alarm.dim=3,
UCL=1,
LCL=FALSE,
pre.process="glm",
diff.window=7,
family="poisson",
formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
frequency=365)
my.syndromicD <- shew_synd(x=my.syndromicD,
syndromes="Musculoskeletal",
evaluate.window=10,
baseline.window=260,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=3,
pre.process="glm",
family="poisson",
formula="dow+sin+cos+AR1+AR2+AR3+AR4+AR5",
frequency=260)
my.syndromicD <- shew_synd(x=my.syndromicD,
syndrome= c(1,2,4,5),
evaluate.window=30,
baseline.window=260,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=3,
pre.process="diff",
diff.window=5)
# shew_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=52,
# limit.sd=c(2.5,3,3.5),
# guard.band=2,
# correct.baseline=FALSE,
# alarm.dim=3,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=4,
# family="poisson",
# formula="trend+sin+cos",
# frequency=52)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- shew_synd(x=my.syndromicW,
syndrome="Musculoskeletal",
evaluate.window=10,
baseline.window=104,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=3,
pre.process="glm",
family="nbinom",
formula="trend+sin+cos",
frequency=52)
my.syndromicW <- shew_synd(x=my.syndromicW,
syndrome= c(1,2,4,5),
evaluate.window=10,
baseline.window=104,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=3,
pre.process="diff",
diff.window=4)
# cusum_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=365,
# limit.sd=c(2.5,3,3.5),
# guard.band=7,
# correct.baseline=FALSE,
# alarm.dim=4,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=7,
# family="poisson",
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
my.syndromicD <- cusum_synd(x=my.syndromicD,
syndromes="Musculoskeletal",
evaluate.window=30,
baseline.window=260,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=4,
pre.process="glm",
family="poisson",
formula="dow+sin+cos+AR1+AR2+AR3+AR4+AR5",
frequency=260)
my.syndromicD <- cusum_synd(x=my.syndromicD,
syndrome= c(1,2,4,5),
evaluate.window=30,
baseline.window=260,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=4,
pre.process="diff",
diff.window=5)
# cusum_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=52,
# limit.sd=c(2.5,3,3.5),
# guard.band=2,
# correct.baseline=FALSE,
# alarm.dim=4,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=4,
# family="poisson",
# formula="trend+sin+cos",
# frequency=52)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- cusum_synd(x=my.syndromicW,
syndrome="Musculoskeletal",
evaluate.window=10,
baseline.window=104,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=4,
pre.process="glm",
family="nbinom",
formula="trend+sin+cos",
frequency=52)
my.syndromicW <- cusum_synd(x=my.syndromicW,
syndrome= c(1,2,4,5),
evaluate.window=10,
baseline.window=104,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=4,
pre.process="diff",
diff.window=4)
# plot(x, syndromes=NULL,
# window=365,
# baseline=FALSE,
# UCL=1,
# algorithms=NULL,
# limit=NULL)
plot(my.syndromicD)
# plot(x, syndromes=NULL,
# window=52,
# baseline=FALSE,
# UCL=1,
# algorithms=NULL,
# limit=NULL)
plot(my.syndromicW)
# plot_syndromic(x,
# syndromes=NULL,
# window=365,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1)
plot_syndromic(my.syndromicD)
# plot_syndromic(x,
# syndromes=NULL,
# window=52,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1)
plot_syndromic(my.syndromicW)
# syndromic_alarm(x,
# pdf.report=TRUE,
# email.alarm.to=NULL,
# email.noalarm.to=NULL,
# date=NULL,
# plot.all=FALSE,
# window=365,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1,
# email.from=NULL,
# smtpServer=NULL,
# subject= paste((Sys.Date()),"ALARM: There are alarms today",sep=","),
# message=NULL,
# height=7.5,
# width=10.5,
# pdf.dir=TRUE,
# file.name=NULL)
syndromic_alarm(x=my.syndromicD,
plot.all=TRUE,
email.alarm.to="<dorea.meyer@gmail.com>",
email.noalarm.to="<dorea.meyer@gmail.com>")
syndromic_alarm(x=my.syndromicD,
plot.all=TRUE,
date="2013-01-05",
email.alarm.to="<dorea.meyer@gmail.com>",
email.noalarm.to="<dorea.meyer@gmail.com>")
# syndromic_alarm(x,
# pdf.report=TRUE,
# email.alarm.to=NULL,
# email.noalarm.to=NULL,
# date=NULL,
# plot.all=FALSE,
# window=52,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1,
# email.from=NULL,
# smtpServer=NULL,
# subject= paste((Sys.Date()),"ALARM: There are alarms today",sep=","),
# message=NULL,
# height=7.5,
# width=10.5,
# pdf.dir=TRUE,
# file.name=NULL)
syndromic_alarm(x=my.syndromicW,
plot.all=TRUE,
email.alarm.to="<dorea.meyer@gmail.com>",
email.noalarm.to="<dorea.meyer@gmail.com>")
syndromic_alarm(x=my.syndromicW,
plot.all=TRUE,
date="2013-W02-1",
email.alarm.to="<dorea.meyer@gmail.com>",
email.noalarm.to="<dorea.meyer@gmail.com>")
# syndromic.page(x,
# tpoints.display=7,
# window=365,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1,
# file.name="my.syndromic",
# title="My syndromic",
# data.page=FALSE,
# data=NULL,
# date.format="%d/%m/%Y",
# dates.var=NULL,
# syndromes.var=NULL,
# color.null="F8F8FF",
# color.low="F8FF2F",
# color.alarm="FF0000",
# scale=9,
# fill.colors=c("yellow2","orange","tomato"),
# arrow.colors=c("green","orange","tomato","red"))
syndromic_page (x=my.syndromicD,
tpoints.display=5,
file.name="SpeciesX",
title="Lab data daily for Species X",
data.page=TRUE,
data=lab.daily,
date.format="%d/%m/%Y",
dates.var="DateofSubmission",
syndromes.var="Syndrome",
scale=9)
# syndromic_page(x,
# tpoints.display=4,
# window=52,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1,
# file.name="my.syndromic",
# title="My syndromic",
# data.page=FALSE,
# data=NULL,
# date.format="ISOweek",
# dates.var=NULL,
# syndromes.var=NULL,
# color.null="F8F8FF",
# color.low="F8FF2F",
# color.alarm="FF0000",
# scale=9,
# fill.colors=c("yellow2","orange","tomato"),
# arrow.colors=c("green","orange","tomato","red"))
syndromic_page(x=my.syndromicW,
tpoints.display=4,
file.name="SpeciesX",
title="Lab data daily for Species X",
data.page=TRUE,
data=lab.daily,
date.format="%d/%m/%Y",
dates.var="DateofSubmission",
syndromes.var="Syndrome",
scale=9)
# update_syndromic(x,
# id,
# syndromes.var,
# add.syndromes=TRUE,
# dates.var,
# date.format="%d/%m/%Y",
# remove.dow=FALSE,
# add.to=0,
# replace.dates=TRUE,
# data=NULL)
my.syndromicD <- update_syndromic(x=my.syndromicD,
id=SubmissionID,
syndromes.var=Syndrome,
add.syndromes=TRUE,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
replace.dates=TRUE,
data=lab.daily.update)
# update_syndromic(x,
# id,
# syndromes.var,
# add.syndromes=TRUE,
# dates.var,
# date.format="%d/%m/%Y",
# replace.dates=TRUE,
# data=NULL)
my.syndromicW <- update_syndromic(x=my.syndromicW,
id=lSubmissionID,
syndromes.var=Syndrome,
add.syndromes=TRUE,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
replace.dates=TRUE,
data=lab.daily.update)
my.syndromicW <- update_syndromic(x=my.syndromicW,
id=SubmissionID,
syndromes.var=Syndrome,
add.syndromes=TRUE,
dates.var=DateofSubmission,
date.format="ISOweek",
replace.dates=TRUE,
data=lab.weekly.update)
nandadorea/vetsyn documentation built on April 30, 2022, 1:15 a.m.
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# manual testing while the right tests are not set up
#data(lab.daily)
#head(lab.weekly)
#data(observed)
#data with only one column
#unnamed columns
#install.packages("devtools")
library(devtools)
install_github("nandadorea/vetsyn")
require(vetsyn)
data(observed)
data(observedW)
data(lab.daily)
data(lab.weekly)
data(lab.daily.update)
data(lab.weekly.update)
#syndromicD(observed,
# dates=data.frame(),
# max.date=NULL,
# date.format="%d/%m/%Y",
# weekends=TRUE,
# baseline=matrix(nrow=0,ncol=0),
# alarms=array(dim=0),
# UCL=array(dim=0),
# LCL=array(dim=0))
my.syndromicD <- syndromicD(observed,min.date="01/01/2011",max.date="26/05/2013")
# syndromicW (observed,
# dates=data.frame(),
# min.week=NULL,
# max.week=NULL,
# min.year=NULL,
# max.year=NULL,
# baseline=matrix(nrow=0,ncol=0),
# alarms=array(dim=0),
# UCL=array(dim=0),
# LCL=array(dim=0))
my.syndromicW <- syndromicW(observedW,min.week=1, min.year=2011,
max.week=22, max.year=2013)
# raw_to_syndromicD(id,
# syndromes.var,
# syndromes.name,
# dates.var,
# date.format="%d/%m/%Y",
# min.date,
# max.date,
# remove.dow=FALSE,
# add.to=0,
# sort=TRUE,
# data=NULL)
my.syndromicD <- raw_to_syndromicD (id=lab.daily$SubmissionID,
syndromes.var=lab.daily$Syndrome,
dates.var=lab.daily$DateofSubmission,
date.format="%d/%m/%Y")
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- raw_to_syndromicD (id=list(HerdID,AnimalID),
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal"),
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal","NonExisting"),
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
min.date="01/01/2011",
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
# raw_to_syndromicW(id,
# syndromes.var,
# syndromes.name,
# dates.var,
# date.format="%d/%m/%Y",
# min.date,
# max.date,
# sort=TRUE,
# data=NULL)
my.syndromicW <- raw_to_syndromicW (id=lab.daily$SubmissionID,
syndromes.var=lab.daily$Syndrome,
dates.var=lab.daily$DateofSubmission,
date.format="%d/%m/%Y")
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- raw_to_syndromicW (id=list(HerdID,AnimalID),
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal"),
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal","NonExisting"),
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- raw_to_syndromicW (id=lab.daily$SubmissionID,
syndromes.var=lab.daily$Syndrome,
dates.var=lab.daily$DateofSubmission,
min.date="01/01/2011",
date.format="%d/%m/%Y")
##
my.syndromicW <- raw_to_syndromicW (id=lab.weekly$SubmissionID,
syndromes.var=lab.weekly$Syndrome,
dates.var=lab.weekly$DateofSubmission,
date.format="ISOweek")
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="ISOweek",
data=lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=list(HerdID,AnimalID),
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="ISOweek",
data=lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal"),
dates.var=DateofSubmission,
date.format="ISOweek",
data=lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
syndromes.name=c("GIT","Musculoskeletal","NonExisting"),
dates.var=DateofSubmission,
date.format="ISOweek",
data=lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="ISOweek",
min.date="2010-W50-1",
data=lab.weekly)
my.syndromicD
my.syndromicW
my.syndromicD[1,10]
my.syndromicW[1,10]
dim(my.syndromicD)
dim(my.syndromicW)
#retro_summary(x,
# object.name="my.syndromic",
# file.name="syndromic.retro.summary",
# frequency=365,
# short=FALSE)
retro_summary(my.syndromicD)
#retro_summary(x,
# object.name="my.syndromic",
# file.name="syndromic.retro.summary",
# frequency=52,
# short=FALSE)
retro_summary(my.syndromicW)
# clean_baseline(x,
# syndromes=NULL,
# family="poisson",
# limit=0.95,
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365,
# plot=TRUE,
# print.model=TRUE)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
my.syndromicD <- clean_baseline(my.syndromicD,
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
formula="dow+month+year",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD, formula="dow+sin+cos+trend",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes="Musculoskeletal",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=c("GIT","Musculoskeletal"),
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=3,
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=c(1,3),
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
family="nbinom",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes="Musculoskeletal",
family="nbinom",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=c("GIT","Musculoskeletal"),
family="nbinom",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=3,
family="nbinom",
frequency=260)
my.syndromicD <- clean_baseline(my.syndromicD,
syndromes=c(1,3),
family="nbinom",
frequency=260)
# clean_baseline(x,
# syndromes=NULL,
# family="poisson",
# limit=0.95,
# formula="year+sin+cos",
# plot=TRUE,
# print.model=TRUE,
# frequency=52)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- clean_baseline(my.syndromicW)
my.syndromicW <- clean_baseline(my.syndromicW, formula="sin+cos")
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes="Musculoskeletal")
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes=c("GIT","Musculoskeletal"))
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes=3)
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes=c(1,3))
my.syndromicW <- clean_baseline(my.syndromicW,
family="nbinom")
my.syndromicW <- clean_baseline(my.syndromicW,
syndromes="Musculoskeletal",family="nbinom")
# clean_baseline_perc(x,
# syndromes=NULL,
# limit=0.95,
# run.window=120,
# plot=TRUE)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- clean_baseline_perc(my.syndromicD)
my.syndromicD <- clean_baseline_perc(my.syndromicD,run.window=90)
my.syndromicD <- clean_baseline_perc(my.syndromicD,
syndromes="Musculoskeletal")
my.syndromicD <- clean_baseline_perc(my.syndromicD,
syndromes=c("GIT","Musculoskeletal"))
my.syndromicD <- clean_baseline_perc(my.syndromicD,
syndromes=3)
my.syndromicD <- clean_baseline_perc(my.syndromicD,
syndromes=c(1,3))
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- clean_baseline_perc(my.syndromicW)
my.syndromicW <- clean_baseline_perc(my.syndromicW,run.window=90)
my.syndromicW <- clean_baseline_perc(my.syndromicW,
syndromes="Musculoskeletal")
my.syndromicW <- clean_baseline_perc(my.syndromicW,
syndromes=c("GIT","Musculoskeletal"))
my.syndromicW <- clean_baseline_perc(my.syndromicW,
syndromes=3)
my.syndromicW <- clean_baseline_perc(my.syndromicW,
syndromes=c(1,3))
# holt_winters_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# frequency=7,
# baseline.window=365,
# limit.sd=c(2.5,3,3.5),
# nahead=7,
# alpha=0.4,
# beta=0,
# gamma=0.15,
# seasonal="additive",
# correct.baseline=1,
# alarm.dim=1,
# UCL=1)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicD <- holt_winters_synd(x=my.syndromicD,
evaluate.window=30,
frequency=7,
baseline.window=365,
limit.sd=c(2.5,3,3.5), #default
nahead=7,
correct.baseline=2,
alarm.dim=1)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
my.syndromicD <- holt_winters_synd(x=my.syndromicD,
syndromes="Musculoskeletal",
evaluate.window=30,
frequency=5,
baseline.window=260,
limit.sd=c(2.5,3,3.5), #default
nahead=5,
correct.baseline=2,
alarm.dim=1,
UCL=2)
# holt_winters_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# frequency=52,
# baseline.window=104,
# limit.sd=c(2.5,3,3.5),
# nahead=2,
# alpha=0.4,
# beta=0,
# gamma=0.15,
# seasonal="additive",
# correct.baseline=1,
# alarm.dim=1,
# UCL=1
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- holt_winters_synd(x=my.syndromicW,
evaluate.window=12,
frequency=52,
baseline.window=104,
limit.sd=c(2.5,3,3.5), #default
nahead=2,
correct.baseline=2,
alarm.dim=1)
# ewma_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=365,
# lambda=0.2,
# limit.sd=c(2.5,3,3.5),
# guard.band=7,
# correct.baseline=FALSE,
# alarm.dim=2,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=7,
# family="poisson",
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
#system.time({
my.syndromicD <- ewma_synd(x=my.syndromicD,
syndrome="Musculoskeletal",
evaluate.window=10,
baseline.window=260,
lambda=0.2,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=2,
pre.process="glm",
family="nbinom",
formula="dow+sin+cos+AR1+AR2+AR3+AR4+AR5",
frequency=260)
#})
#system.time({
my.syndromicD <- ewma_synd(x=my.syndromicD,
#syndrome= c(1,2,4,5),
evaluate.window=60,
baseline.window=260,
lambda=0.2,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=2,
pre.process="diff",
diff.window=5)
})
# ewma_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=52,
# lambda=0.2,
# limit.sd=c(2.5,3,3.5),
# guard.band=2,
# correct.baseline=FALSE,
# alarm.dim=2,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=4,
# family="poisson",
# formula="trend+sin+cos",
# frequency=52)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- ewma_synd(x=my.syndromicW,
syndrome="Musculoskeletal",
evaluate.window=10,
baseline.window=104,
lambda=0.2,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=2,
pre.process="glm",
family="nbinom",
formula="trend+sin+cos",
frequency=52)
my.syndromicW <- ewma_synd(x=my.syndromicW,
syndrome= c(1,2,4,5),
evaluate.window=10,
baseline.window=104,
lambda=0.2,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=2,
pre.process="diff",
diff.window=4)
# pre_process_glm(x,
# slot="observed",
# syndromes=NULL,
# family="poisson",
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365,
# print.model=TRUE,
# plot=TRUE)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
pre_processed_data <- pre_process_glm(my.syndromicD)
pre_processed_data <- pre_process_glm(my.syndromicD,
syndromes="Musculoskeletal")
pre_processed_data <- pre_process_glm(my.syndromicD,
syndromes=c("GIT","Musculoskeletal"))
pre_processed_data <- pre_process_glm(my.syndromicD,
syndromes=3)
pre_processed_data <- pre_process_glm(my.syndromicD,
syndromes=c(1,3))
pre_processed_data <- pre_process_glm(my.syndromicD,
family="nbinom")
# pre_process_glm(x,
# slot="observed",
# syndromes=NULL,
# family="poisson",
# formula="trend+sin+cos",
# frequency=52,
# print.model=TRUE,
# plot=TRUE)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
pre_processed_data <- pre_process_glm(my.syndromicW)
pre_processed_data <- pre_process_glm(my.syndromicW,
syndromes="Musculoskeletal")
pre_processed_data <- pre_process_glm(my.syndromicW,
syndromes=c("GIT","Musculoskeletal"))
pre_processed_data <- pre_process_glm(my.syndromicW,
syndromes=3)
pre_processed_data <- pre_process_glm(my.syndromicW,
syndromes=c(1,3))
pre_processed_data <- pre_process_glm(my.syndromicW,
family="nbinom")
pre_processed_data <- pre_process_glm(my.syndromicW,slot="baseline")
# shew_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=365,
# limit.sd=c(2.5,3,3.5),
# guard.band=7,
# correct.baseline=FALSE,
# alarm.dim=3,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=7,
# family="poisson",
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
my.syndromicD <- shew_synd(x=my.syndromicD,
syndromes="Musculoskeletal",
evaluate.window=1,
baseline.window=365,
limit.sd=c(2.5,3,3.5),
guard.band=7,
correct.baseline=FALSE,
alarm.dim=3,
UCL=1,
LCL=FALSE,
pre.process="glm",
diff.window=7,
family="poisson",
formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
frequency=365)
my.syndromicD <- shew_synd(x=my.syndromicD,
syndromes="Musculoskeletal",
evaluate.window=10,
baseline.window=260,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=3,
pre.process="glm",
family="poisson",
formula="dow+sin+cos+AR1+AR2+AR3+AR4+AR5",
frequency=260)
my.syndromicD <- shew_synd(x=my.syndromicD,
syndrome= c(1,2,4,5),
evaluate.window=30,
baseline.window=260,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=3,
pre.process="diff",
diff.window=5)
# shew_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=52,
# limit.sd=c(2.5,3,3.5),
# guard.band=2,
# correct.baseline=FALSE,
# alarm.dim=3,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=4,
# family="poisson",
# formula="trend+sin+cos",
# frequency=52)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- shew_synd(x=my.syndromicW,
syndrome="Musculoskeletal",
evaluate.window=10,
baseline.window=104,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=3,
pre.process="glm",
family="nbinom",
formula="trend+sin+cos",
frequency=52)
my.syndromicW <- shew_synd(x=my.syndromicW,
syndrome= c(1,2,4,5),
evaluate.window=10,
baseline.window=104,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=3,
pre.process="diff",
diff.window=4)
# cusum_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=365,
# limit.sd=c(2.5,3,3.5),
# guard.band=7,
# correct.baseline=FALSE,
# alarm.dim=4,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=7,
# family="poisson",
# formula="dow+sin+cos+year+AR1+AR2+AR3+AR4+AR5+AR6+AR7",
# frequency=365)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
data=lab.daily)
my.syndromicD <- cusum_synd(x=my.syndromicD,
syndromes="Musculoskeletal",
evaluate.window=30,
baseline.window=260,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=4,
pre.process="glm",
family="poisson",
formula="dow+sin+cos+AR1+AR2+AR3+AR4+AR5",
frequency=260)
my.syndromicD <- cusum_synd(x=my.syndromicD,
syndrome= c(1,2,4,5),
evaluate.window=30,
baseline.window=260,
limit.sd=c(2.5,3,3.5),
guard.band=5,
correct.baseline=FALSE,
alarm.dim=4,
pre.process="diff",
diff.window=5)
# cusum_synd(x,
# syndromes=NULL,
# evaluate.window=1,
# baseline.window=52,
# limit.sd=c(2.5,3,3.5),
# guard.band=2,
# correct.baseline=FALSE,
# alarm.dim=4,
# UCL=1,
# LCL=FALSE,
# pre.process=FALSE,
# diff.window=4,
# family="poisson",
# formula="trend+sin+cos",
# frequency=52)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
syndromes.var=Syndrome,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
data=lab.daily)
my.syndromicW <- cusum_synd(x=my.syndromicW,
syndrome="Musculoskeletal",
evaluate.window=10,
baseline.window=104,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=4,
pre.process="glm",
family="nbinom",
formula="trend+sin+cos",
frequency=52)
my.syndromicW <- cusum_synd(x=my.syndromicW,
syndrome= c(1,2,4,5),
evaluate.window=10,
baseline.window=104,
limit.sd=c(2.5,3,3.5),
guard.band=2,
correct.baseline=FALSE,
alarm.dim=4,
pre.process="diff",
diff.window=4)
# plot(x, syndromes=NULL,
# window=365,
# baseline=FALSE,
# UCL=1,
# algorithms=NULL,
# limit=NULL)
plot(my.syndromicD)
# plot(x, syndromes=NULL,
# window=52,
# baseline=FALSE,
# UCL=1,
# algorithms=NULL,
# limit=NULL)
plot(my.syndromicW)
# plot_syndromic(x,
# syndromes=NULL,
# window=365,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1)
plot_syndromic(my.syndromicD)
# plot_syndromic(x,
# syndromes=NULL,
# window=52,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1)
plot_syndromic(my.syndromicW)
# syndromic_alarm(x,
# pdf.report=TRUE,
# email.alarm.to=NULL,
# email.noalarm.to=NULL,
# date=NULL,
# plot.all=FALSE,
# window=365,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1,
# email.from=NULL,
# smtpServer=NULL,
# subject= paste((Sys.Date()),"ALARM: There are alarms today",sep=","),
# message=NULL,
# height=7.5,
# width=10.5,
# pdf.dir=TRUE,
# file.name=NULL)
syndromic_alarm(x=my.syndromicD,
plot.all=TRUE,
email.alarm.to="<dorea.meyer@gmail.com>",
email.noalarm.to="<dorea.meyer@gmail.com>")
syndromic_alarm(x=my.syndromicD,
plot.all=TRUE,
date="2013-01-05",
email.alarm.to="<dorea.meyer@gmail.com>",
email.noalarm.to="<dorea.meyer@gmail.com>")
# syndromic_alarm(x,
# pdf.report=TRUE,
# email.alarm.to=NULL,
# email.noalarm.to=NULL,
# date=NULL,
# plot.all=FALSE,
# window=52,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1,
# email.from=NULL,
# smtpServer=NULL,
# subject= paste((Sys.Date()),"ALARM: There are alarms today",sep=","),
# message=NULL,
# height=7.5,
# width=10.5,
# pdf.dir=TRUE,
# file.name=NULL)
syndromic_alarm(x=my.syndromicW,
plot.all=TRUE,
email.alarm.to="<dorea.meyer@gmail.com>",
email.noalarm.to="<dorea.meyer@gmail.com>")
syndromic_alarm(x=my.syndromicW,
plot.all=TRUE,
date="2013-W02-1",
email.alarm.to="<dorea.meyer@gmail.com>",
email.noalarm.to="<dorea.meyer@gmail.com>")
# syndromic.page(x,
# tpoints.display=7,
# window=365,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1,
# file.name="my.syndromic",
# title="My syndromic",
# data.page=FALSE,
# data=NULL,
# date.format="%d/%m/%Y",
# dates.var=NULL,
# syndromes.var=NULL,
# color.null="F8F8FF",
# color.low="F8FF2F",
# color.alarm="FF0000",
# scale=9,
# fill.colors=c("yellow2","orange","tomato"),
# arrow.colors=c("green","orange","tomato","red"))
syndromic_page (x=my.syndromicD,
tpoints.display=5,
file.name="SpeciesX",
title="Lab data daily for Species X",
data.page=TRUE,
data=lab.daily,
date.format="%d/%m/%Y",
dates.var="DateofSubmission",
syndromes.var="Syndrome",
scale=9)
# syndromic_page(x,
# tpoints.display=4,
# window=52,
# baseline=TRUE,
# UCL=1,
# algorithms=NULL,
# limit=1,
# file.name="my.syndromic",
# title="My syndromic",
# data.page=FALSE,
# data=NULL,
# date.format="ISOweek",
# dates.var=NULL,
# syndromes.var=NULL,
# color.null="F8F8FF",
# color.low="F8FF2F",
# color.alarm="FF0000",
# scale=9,
# fill.colors=c("yellow2","orange","tomato"),
# arrow.colors=c("green","orange","tomato","red"))
syndromic_page(x=my.syndromicW,
tpoints.display=4,
file.name="SpeciesX",
title="Lab data daily for Species X",
data.page=TRUE,
data=lab.daily,
date.format="%d/%m/%Y",
dates.var="DateofSubmission",
syndromes.var="Syndrome",
scale=9)
# update_syndromic(x,
# id,
# syndromes.var,
# add.syndromes=TRUE,
# dates.var,
# date.format="%d/%m/%Y",
# remove.dow=FALSE,
# add.to=0,
# replace.dates=TRUE,
# data=NULL)
my.syndromicD <- update_syndromic(x=my.syndromicD,
id=SubmissionID,
syndromes.var=Syndrome,
add.syndromes=TRUE,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
remove.dow=c(6,0),
add.to=c(2,1),
replace.dates=TRUE,
data=lab.daily.update)
# update_syndromic(x,
# id,
# syndromes.var,
# add.syndromes=TRUE,
# dates.var,
# date.format="%d/%m/%Y",
# replace.dates=TRUE,
# data=NULL)
my.syndromicW <- update_syndromic(x=my.syndromicW,
id=lSubmissionID,
syndromes.var=Syndrome,
add.syndromes=TRUE,
dates.var=DateofSubmission,
date.format="%d/%m/%Y",
replace.dates=TRUE,
data=lab.daily.update)
my.syndromicW <- update_syndromic(x=my.syndromicW,
id=SubmissionID,
syndromes.var=Syndrome,
add.syndromes=TRUE,
dates.var=DateofSubmission,
date.format="ISOweek",
replace.dates=TRUE,
data=lab.weekly.update)
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