Difference between revisions of "Wikisym 2012 Demo"

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(→‎Large quantity of points on a static Google Maps)
(→‎Water model)
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</rcode>
 
</rcode>
  
−
==Water model==
+
<rcode
 +
            name="answer"
 +
    variables="
 +
        name:i.raw.class|description:Water resource|type:selection|
 +
            options:
 +
                'Ground water - Clean';Ground water - Clean;
 +
                'Ground water - Surface water stress';Ground water - Surface water stress;
 +
                'Surface water - Vähäinen kuormitus';Surface water - Vähäinen kuormitus;
 +
                'Surface water - Keskisuuri kuormitus';Surface water - Keskisuuri kuormitus;
 +
                'Surface water - Suuri kuormitus';Surface water - Suuri kuormitus|
 +
            category:Raakavesi: Patogeenien pitoisuudet|
 +
                name:Kampylo|description:Kampylobakteeri-pitoisuus arvio (mikrobia/l)|default:'Luokituksen mukainen'|
 +
                name:Ecoli|description:E.coli O157:H7 -pitoisuus arvio (mikrobia/l)|default:'Luokituksen mukainen'|
 +
                name:Rota|description:Rotavirus-pitoisuus arvio (mikrobia/l)|default:'Luokituksen mukainen'|
 +
                name:Noro|description:Norovirus-pitoisuus arvio (mikrobia/l)|default:'Luokituksen mukainen'|
 +
                name:Crypto|description:Cryptosporidium-pitoisuus arvio (mikrobia/l)|default:'Luokituksen mukainen'|
 +
                name:Giardia|description:Giardia-pitoisuus arvio (mikrobia/l)|default:'Luokituksen mukainen'|
 +
               
 +
               
 +
            name:Kaupunni|description:Kaupungin oletusarvot|default:'Custom'|type:selection|
 +
            options:
 +
                'Custom';Käytä yllä määriteltyjä arvoja;
 +
                'Op_fi2603';Kuopio|
 +
            name:Puhdistus|description:Käytössä olevat puhdistusmenetelmät|type:checkbox|
 +
            options:
 +
                1;Perinteinen puhdistus;
 +
                2;Hyvin toimva puhdistus;
 +
                3;Tehostettu puhdistus;
 +
                4;Hidas hiekkasuodatus;
 +
                5;Kalkkikivisuodatus;
 +
                6;Aktiivihiilisuodatus;
 +
                7;UV suodatus;
 +
                8;Otsonointi;|
 +
            default:1;4;5;6|category:Vedenpuhdistus: Puhdistusprosessi ja klooraus|
 +
        name:KlooriAnnos|default:1.5|description:Klooriannos (mg/l)|
 +
   
 +
        name:VedeKulu|default:1153|description:veden kulutus (ml)|category:Verkosto ja kuluttajat|
 +
        name:Vaestonkoko|default:100000|description:Altistuvan väestön koko
 +
    "
 +
>
 +
library(OpasnetUtils)
 +
library(xtable)
 +
library(reshape2)
 +
    i.raw.pat.conc.val <- list(Kampylo, Ecoli, Rota, Noro, Crypto, Giardia)
 +
 
 +
    #vedenkulutus
 +
   
 +
    VedeKulu = data.frame(VedkulResult = VedeKulu)
 +
    InpVedkul = new("ovariable",name = "InpVedkul" , output = VedeKulu)
 +
 
 +
   
 +
    #Patogeenien pitoisuudet
 +
   
 +
    Fetch2(data.frame(Name = "RaaPatPitLuo", Key = "AEmnj6ZNfhIHAt2X"), evaluate = TRUE)
 +
   
 +
    RaaPatPitLuo@output <- RaaPatPitLuo@output[RaaPatPitLuo@output$Raakavesilähde == i.raw.class, ]
 +
    RaaPatPitLuo@output <- merge(
 +
        RaaPatPitLuo@output,
 +
        data.frame(
 +
            Patogeeni = c("Kampylobakteeri","E.coli O157:H7","Rotavirus","Norovirus","Cryptosporidium","Giardia"),
 +
            TempResult = suppressWarnings(as.numeric(i.raw.pat.conc.val))
 +
        )
 +
    )
 +
    RaaPatPitLuo@output$RaaPatPitLuoResult <- ifelse(
 +
        is.na(RaaPatPitLuo@output$TempResult),
 +
        RaaPatPitLuo@output$RaaPatPitLuoResult,
 +
        RaaPatPitLuo@output$TempResult
 +
    )
 +
    RaaPatPitLuo@output <- RaaPatPitLuo@output[,!colnames(RaaPatPitLuo@output)%in%"TempResult"]
 +
 
 +
 
 +
    Temp = rep(FALSE,8)
 +
    Temp[Puhdistus] = TRUE
 +
    Puhdistus = Temp
 +
   
 +
 
 +
    InpKloori = new("ovariable", output = data.frame(KlooriResult = KlooriAnnos))
 +
   
 +
    #tehdaan InpVedKasTeh ovariable paalla olevista puhdistuksista
 +
    Fetch2(data.frame(Name = c("VedKasTeh","VedDesTeh"), Key = c("J8AofoHKjKEOuPWK","iFnLQFpUAH3QfwGz")))
 +
        VedKasTeh <- EvalOutput(VedKasTeh)
 +
    VedDesTeh <- EvalOutput(VedDesTeh, substitute = TRUE)
 +
 
 +
    Puhdistus = c(Puhdistus,TRUE)
 +
    Puhdistus = data.frame(tottavaitarua = Puhdistus, Vedenpuhdistusmenetelmä = c("Perinteinen puhdistus"
 +
    ,"Hyvin toimva puhdistus" , "Tehostettu puhdistus" ,"Hidas hiekkasuodatus"
 +
    ,"Kalkkikivisuodatus","Aktiivihiilisuodatus" ,"UV" ,"Otsonointi","Klooraus"))
 +
    PuhdistusKasTeh = Puhdistus[1:6,]
 +
    PuhdistusDesTeh = Puhdistus[7:9,]
 +
   
 +
    VedKasTeh@output = merge(VedKasTeh@output, PuhdistusKasTeh)
 +
    colnames(PuhdistusDesTeh)[colnames(PuhdistusDesTeh) == "Vedenpuhdistusmenetelmä"] = "Menetelmä"
 +
    VedDesTeh@output = merge(VedDesTeh@output, PuhdistusDesTeh)
 +
   
 +
    VedKasTeh@output[,"VedKasTehResult"] = ifelse(
 +
        VedKasTeh@output[,"tottavaitarua"] == FALSE,
 +
        0,
 +
        VedKasTeh@output[,"VedKasTehResult"]
 +
    )
 +
    VedDesTeh@output[,"VedDesTehResult"] = ifelse(
 +
        VedDesTeh@output[,"tottavaitarua"] == FALSE,
 +
        0,
 +
        VedDesTeh@output[,"VedDesTehResult"]
 +
    )
 +
   
 +
    VedKasTeh@output <- VedKasTeh@output[,!colnames(VedKasTeh@output) %in%c("tottavaitarua")]
 +
    VedDesTeh@output <- VedDesTeh@output[,!colnames(VedDesTeh@output) %in%c("tottavaitarua")]
 +
 
 +
    Fetch2(data.frame(Name = "ExpoPatAnn", Key = "PPdMOCJzOZikWlKW"))
 +
   
 +
    #Fetch2(data.frame(Name = "Exposure", Key = "YpqDCiPvtTUDUGMO"))
 +
   
 +
    Fetch2(data.frame(Name = "PatPitPuhVed", Key = "hjUP8y5Rc2laF45F"))
 +
   
 +
    PatPitPuhVed <- EvalOutput(PatPitPuhVed)
 +
   
 +
    #print(xtable(VedKasTeh@output), type = "html")
 +
    #print(xtable(VedDesTeh@output), type = "html")
 +
    #print(xtable(PatPitPuhVed@output), type = "html")
 +
   
 +
    #Exposure <- EvalOutput(Exposure, substitute = TRUE)
 +
   
 +
    #Exposure
 +
   
 +
    #print(xtable(Exposure@output), type = "html")
 +
   
 +
    ExpoPatAnn <- EvalOutput(ExpoPatAnn, substitute = TRUE)
 +
    #print(xtable(ExpoPatAnn@output), type = "html")
 +
 
 +
#################################################################################
 +
 
 +
dose.response = ExpoPatAnn@output
 +
 
 +
Pathogen <- c("Kampylobakteeri","E.coli O157:H7","Rotavirus","Norovirus","Cryptosporidium","Giardia")
 +
 
 +
vaesto <- op_baseGetData("opasnet_base", "Op_fi2652")[,c("Ikä","Result")]
 +
colnames(vaesto) <- c("Age", "Osuus")
 +
 
 +
vaesto$Populaatio <- vaesto$Osuus * Vaestonkoko
 +
 
 +
odotettu.elinika <- 81
 +
 
 +
colnames(dose.response)[colnames(dose.response) == "Patogeeni"] <- "Pathogen"
 +
colnames(dose.response)[colnames(dose.response) == "ExpoPatAnnResult"] <- "P.inf"
 +
colnames(dose.response)[colnames(dose.response) == "ExposureResult"] <- "Exp.pat"
 +
#dose.response = data.frame(Pathogen = ExpoPatAnn@output[,"Patogeeni"],P.inf = ExpoPatAnn@output[,"ExpoPatAnnResult"])
 +
P.ill.g.inf <- data.frame(Pathogen, P.ill.g.inf = c(0.33, 1 - (270 / 1540), 0.9, 0.7, 0.71, 1)) # todennäköisyys sairastua kun saa infektion
 +
 
 +
# Kampylobakteeri, DALYt per infektio
 +
 
 +
P.treat.g.ill.Kamp.Gastr <- data.frame(Pathogen = Pathogen[c(1,1,1)], Outcome = "Gastroenteritis", ill.treat = c("Untreated",
 +
    "General practitioner", "Hospitalised", "Unspecified")[c(1,2,3)], P.treat.g.ill = c(0.7627, 0.2373, 0.0097))
 +
 
 +
P.treat.ill.g.inf.Kamp.Gastr <- merge(P.treat.g.ill.Kamp.Gastr, P.ill.g.inf)
 +
P.treat.ill.g.inf.Kamp.Gastr$P.treat.ill.g.inf <- P.treat.ill.g.inf.Kamp.Gastr$P.ill.g.inf *
 +
    P.treat.ill.g.inf.Kamp.Gastr$P.treat.g.ill
 +
 
 +
duration.ill.treat.Kamp.Gastr <- data.frame(Outcome = c("Gastroenteritis"), ill.treat = c("Untreated", "General practitioner",
 +
    "Hospitalised", "Unspecified")[c(1,2,3)], dur.ill = c(5.1 / 365, 8.4 / 365, 14.39 / 365))
 +
 
 +
severity.ill.treat.Kamp.Gastr <- data.frame(Outcome = c("Gastroenteritis"), ill.treat = c("Untreated", "General practitioner",
 +
    "Hospitalised", "Unspecified")[c(1,2,3)], sev.ill = c(0.067, 0.393, 0.393))
 +
 
 +
daly.ill.treat.Kamp.Gastr <- merge(P.treat.ill.g.inf.Kamp.Gastr, duration.ill.treat.Kamp.Gastr)
 +
daly.ill.treat.Kamp.Gastr <- merge(daly.ill.treat.Kamp.Gastr, severity.ill.treat.Kamp.Gastr)
 +
daly.ill.treat.Kamp.Gastr$dalys <- daly.ill.treat.Kamp.Gastr$P.treat.ill.g.inf * daly.ill.treat.Kamp.Gastr$dur.ill *
 +
    daly.ill.treat.Kamp.Gastr$sev.ill
 +
 
 +
 
 +
P.death.g.ill.Gastr <- 0.0004
 +
P.death.g.inf.Gastr <- P.death.g.ill.Gastr * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "Kampylobakteeri"]
 +
death.Gastr.life.lost <- 13.2
 +
daly.death.Kamp.Gastr <- P.death.g.inf.Gastr * death.Gastr.life.lost
 +
 
 +
## GBS Kamp.
 +
 
 +
P.gbs.g.ill <- 2e-004
 +
P.gbs.g.inf <- P.gbs.g.ill * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "Kampylobakteeri"]
 +
dur.sev.factor.gbs <- data.frame(Outcome = c("Clinical GBS", "Residual GBS"), dur.sev.factor = c(0.29, 5.8)) # duration * severity * fraction?
 +
daly.Kamp.gbs <- data.frame(dur.sev.factor.gbs$Outcome, dalys = dur.sev.factor.gbs$dur.sev.factor * P.gbs.g.inf)
 +
 
 +
P.death.g.gbs <- 0.08 / 3 # triangular 0.01, 0.02, 0.05
 +
P.death.g.inf.gbs <- P.death.g.gbs * P.gbs.g.inf
 +
death.gbs.life.lost <- 18.7
 +
daly.death.Kamp.gbs <- P.death.g.inf.gbs * death.gbs.life.lost
 +
 
 +
## reactive arthritis Kamp.
 +
 
 +
P.arth.g.ill <- 0.02 # triangluar 0.01, 0.02, 0.03
 +
P.arth.g.inf <- P.arth.g.ill * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "Kampylobakteeri"]
 +
duration.arth <- 6 / 52
 +
severity.arth <- 0.21
 +
daly.Kamp.arth <- P.arth.g.inf * duration.arth * severity.arth
 +
 
 +
# E.coli
 +
 
 +
P.wd.g.ill <- 0.53 # watery diarrhea
 +
P.wd.g.inf <- P.wd.g.ill * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "E.coli O157:H7"]
 +
severity.wd <- 0.067
 +
duration.wd <- 3.4 / 365
 +
daly.wd.Ecoli <- P.wd.g.inf * severity.wd * duration.wd
 +
 
 +
P.hc.g.ill <- 0.47
 +
P.hc.g.inf <- P.hc.g.ill * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "E.coli O157:H7"]
 +
severity.hc <- 0.39
 +
duration.hc <- 5.6 / 365
 +
daly.hc.Ecoli <- P.hc.g.inf * severity.hc * duration.hc
 +
 
 +
P.death.g.ill.Ecoli <- 0.00027
 +
P.death.g.inf.Ecoli <- P.death.g.ill.Ecoli * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "E.coli O157:H7"]
 +
age.death.Ecoli <- 81 - 13.2
 +
daly.death.Ecoli <- P.death.g.inf.Ecoli * (odotettu.elinika - age.death.Ecoli)
 +
 
 +
## Haemolytic uraemic syndrome (HUS)
 +
 
 +
P.hus.g.ill <- 0.01
 +
P.hus.g.inf <- P.hus.g.ill * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "E.coli O157:H7"]
 +
severity.hus <- 0.93
 +
duration.hus <- 21 / 365
 +
daly.hus.Ecoli <- P.hus.g.inf * severity.hus * duration.hus
 +
 
 +
P.death.g.hus <- 0.04
 +
P.death.hus.g.inf <- P.death.g.hus * P.hus.g.inf
 +
age.death.hus.Ecoli <- 81 - 26.2
 +
daly.death.hus.Ecoli <- P.death.hus.g.inf * (odotettu.elinika - age.death.hus.Ecoli)
 +
 
 +
## End Stage Renal Disease (ESRD)
 +
 
 +
P.esrd.g.hus <- 0.118
 +
P.esrd.g.inf <- P.hus.g.inf * P.esrd.g.hus
 +
severity.duration.hus <- 8.7 # severity * duration
 +
daly.esrd.Ecoli <- P.esrd.g.inf * severity.duration.hus
 +
 
 +
P.death.g.esrd <- 0.0252
 +
P.death.esrd.g.inf <- P.esrd.g.inf * P.death.g.esrd
 +
age.death.esrd.Ecoli <- 81 - 34
 +
daly.death.esrd.Ecoli <- P.death.esrd.g.inf * (odotettu.elinika - age.death.esrd.Ecoli)
 +
 
 +
# Rotavirus
 +
 
 +
P.treat.g.ill.Rotavirus <- data.frame(Pathogen = "Rotavirus", ill.treat = c("Untreated",
 +
    "General practitioner", "Hospitalised")[rep(1:3, each = 82)], Age = rep(0:81, 3), P.treat.g.ill = c(rep(0.82,5),
 +
    rep(0.95, 10), rep(0.99, 50), rep(0.97, 17), rep(0.137, 5), rep(0.0244, 5), rep(0.0511, 5), rep(0.0127, 50),
 +
    rep(0.0299, 17), rep(0.0416, 5), rep(0.0213, 5), rep(0, 72)))
 +
 
 +
P.treat.ill.g.inf.Rotavirus <- merge(P.treat.g.ill.Rotavirus, P.ill.g.inf)
 +
P.treat.ill.g.inf.Rotavirus$P.treat.g.inf <- P.treat.ill.g.inf.Rotavirus$P.ill.g.inf * P.treat.ill.g.inf.Rotavirus$P.treat.g.ill
 +
 
 +
duration.ill.treat.Rotavirus <- data.frame(ill.treat = c("Untreated", "General practitioner","Hospitalised"), dur.ill = c(4.9 / 365,
 +
    7.1 / 365, 7.7 / 365))
 +
 
 +
severity.ill.treat.Rotavirus <- data.frame(ill.treat = c("Untreated", "General practitioner", "Hospitalised"), sev.ill = c(0.067,
 +
    0.393, 0.393))
 +
 
 +
daly.ill.treat.Rotavirus <- merge(P.treat.ill.g.inf.Rotavirus, duration.ill.treat.Rotavirus)
 +
daly.ill.treat.Rotavirus <- merge(daly.ill.treat.Rotavirus, severity.ill.treat.Rotavirus)
 +
daly.ill.treat.Rotavirus$dalys <- daly.ill.treat.Rotavirus$P.treat.g.inf * daly.ill.treat.Rotavirus$dur.ill *
 +
    daly.ill.treat.Rotavirus$sev.ill
 +
 
 +
 
 +
P.death.Rotavirus <- data.frame(Age = 0:81, P.death.g.ill = c(rep(2.13e-005, 5), rep(0, 77)))
 +
P.death.Rotavirus$P.death.g.inf <- P.death.Rotavirus$P.death.g.ill * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "Rotavirus"]
 +
P.death.Rotavirus$Life.lost <- odotettu.elinika - P.death.Rotavirus$Age
 +
daly.death.Rotavirus <- data.frame(Age = P.death.Rotavirus$Age, dalys = P.death.Rotavirus$P.death.g.inf * P.death.Rotavirus$Life.lost)
 +
 
 +
# Norovirus
 +
 
 +
P.treat.g.ill.Norovirus <- data.frame(Pathogen = "Norovirus", ill.treat = c("Untreated",
 +
    "General practitioner", "Hospitalised")[rep(1:3, each = 82)], Age = rep(0:81, 3), P.treat.g.ill = c(rep(0.94876706,5),
 +
    rep(0.9902, 5), rep(0.98239, 5), rep(0.98434, 51), rep(0.992741, 16), rep(0.0448,5), rep(8.6e-003, 5), rep(0.0154, 5),
 +
    rep(0.0137, 51), rep(6.17e-003, 16), rep(6.43e-003,5), rep(1.2e-003, 5), rep(2.21e-003, 5), rep(1.96e-003, 51),
 +
    rep(8.85e-004, 16)))
 +
 
 +
P.treat.ill.g.inf.Norovirus <- merge(P.treat.g.ill.Norovirus, P.ill.g.inf)
 +
P.treat.ill.g.inf.Norovirus$P.treat.g.inf <- P.treat.ill.g.inf.Norovirus$P.ill.g.inf * P.treat.ill.g.inf.Norovirus$P.treat.g.ill
 +
 
 +
duration.ill.treat.Norovirus <- data.frame(ill.treat = c("Untreated", "General practitioner","Hospitalised"), dur.ill = c(3.8 / 365,
 +
    5.73 / 365, 7.23 / 365))
 +
 
 +
severity.ill.treat.Norovirus <- data.frame(ill.treat = c("Untreated", "General practitioner", "Hospitalised"), sev.ill = c(0.067,
 +
    0.393, 0.393))
 +
 
 +
daly.ill.treat.Norovirus <- merge(P.treat.ill.g.inf.Norovirus, duration.ill.treat.Norovirus)
 +
daly.ill.treat.Norovirus <- merge(daly.ill.treat.Norovirus, severity.ill.treat.Norovirus)
 +
daly.ill.treat.Norovirus$dalys <- daly.ill.treat.Norovirus$P.treat.g.inf * daly.ill.treat.Norovirus$dur.ill *
 +
    daly.ill.treat.Norovirus$sev.ill
 +
 
 +
P.death.Norovirus <- data.frame(Age = 0:81, P.death.g.ill = c(rep(2.94e-006, 5), rep(0, 61), rep(2.04e-004, 16)))
 +
P.death.Norovirus$P.death.g.inf <- P.death.Norovirus$P.death.g.ill * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "Norovirus"]
 +
P.death.Norovirus$Life.lost <- odotettu.elinika - P.death.Norovirus$Age
 +
daly.death.Norovirus <- data.frame(Age = P.death.Norovirus$Age, dalys = P.death.Norovirus$P.death.g.inf * P.death.Norovirus$Life.lost)
 +
 
 +
# Cryptosporidium
 +
 
 +
P.treat.g.ill.Crypt <- data.frame(Pathogen = "Cryptosporidium", ill.treat = c("Untreated",
 +
    "General practitioner", "Hospitalised")[rep(1:3, each = 82)], Age = rep(0:81, 3), P.treat.g.ill = c(rep(0.9175730049999999,5),
 +
    rep(0.80937, 5), rep(0.6810499999999999, 5), rep(0.9774191, 50), rep(0.94706, 17), rep(0.082,5), rep(0.188, 5), rep(0.316, 5),
 +
    rep(0.0209, 50), rep(0.0367, 17), rep(4.26e-004,5), rep(2.63e-003, 5), rep(2.95e-003, 5), rep(1.66e-003, 50), rep(0.0146, 17)))
 +
 
 +
P.treat.ill.g.inf.Crypt <- merge(P.treat.g.ill.Crypt, P.ill.g.inf)
 +
P.treat.ill.g.inf.Crypt$P.treat.g.inf <- P.treat.ill.g.inf.Crypt$P.ill.g.inf * P.treat.ill.g.inf.Crypt$P.treat.g.ill
 +
 
 +
duration.ill.treat.Crypt <- data.frame(ill.treat = c("Untreated", "General practitioner","Hospitalised"), dur.ill = c(3.5 / 365,
 +
    7 /365, 18.4 / 365))
 +
 
 +
severity.ill.treat.Crypt <- data.frame(ill.treat = c("Untreated", "General practitioner", "Hospitalised"), sev.ill = c(0.067,
 +
    0.393, 0.393))
 +
 
 +
daly.ill.treat.Crypt <- merge(P.treat.ill.g.inf.Crypt, duration.ill.treat.Crypt)
 +
daly.ill.treat.Crypt <- merge(daly.ill.treat.Crypt, severity.ill.treat.Crypt)
 +
daly.ill.treat.Crypt$dalys <- daly.ill.treat.Crypt$P.treat.g.inf * daly.ill.treat.Crypt$dur.ill *
 +
    daly.ill.treat.Crypt$sev.ill
 +
 
 +
P.death.Crypt <- data.frame(Age = 0:81, P.death.g.ill = c(rep(9.95e-007, 5), rep(0, 10), rep(2.09e-005, 50), rep(1.64e-003, 17)))
 +
P.death.Crypt$P.death.g.inf <- P.death.Crypt$P.death.g.ill * P.ill.g.inf$P.ill.g.inf[P.ill.g.inf$Pathogen == "Cryptosporidium"]
 +
P.death.Crypt$Life.lost <- odotettu.elinika - P.death.Crypt$Age
 +
daly.death.Crypt <- data.frame(Age = P.death.Crypt$Age, dalys = P.death.Crypt$P.death.g.inf * P.death.Crypt$Life.lost)
 +
 
 +
# Giardia
 +
 
 +
P.treat.g.ill.Giardia <- data.frame(Pathogen = "Giardia", ill.treat = c("Untreated",
 +
    "General practitioner", "Hospitalised")[rep(1:3, each = 82)], Age = rep(0:81, 3), P.treat.g.ill = c(rep(0.9376,5),
 +
    rep(0.91034, 5), rep(0.72642, 5), rep(0.92486, 50), 0.54596, rep(0.5365, 16), rep(0.0609,5), rep(0.0852, 5), rep(0.272, 5),
 +
    rep(0.0721, 50), rep(0.451, 17), rep(1.5e-003,5), rep(4.46e-003, 5), rep(1.58e-003, 5), rep(3.04e-003, 51), rep(0.0125, 16)))
 +
 
 +
P.treat.ill.g.inf.Giardia <- merge(P.treat.g.ill.Giardia, P.ill.g.inf)
 +
P.treat.ill.g.inf.Giardia$P.treat.g.inf <- P.treat.ill.g.inf.Giardia$P.ill.g.inf * P.treat.ill.g.inf.Giardia$P.treat.g.ill
 +
 
 +
duration.ill.treat.Giardia <- data.frame(ill.treat = c("Untreated", "General practitioner","Hospitalised"), dur.ill = c(10 / 365,
 +
    10 /365, 30 / 365))
 +
 
 +
severity.ill.treat.Giardia <- data.frame(ill.treat = c("Untreated", "General practitioner", "Hospitalised"), sev.ill = c(0.067,
 +
    0.393, 0.393))
 +
 
 +
daly.ill.treat.Giardia <- merge(P.treat.ill.g.inf.Giardia, duration.ill.treat.Giardia)
 +
daly.ill.treat.Giardia <- merge(daly.ill.treat.Giardia, severity.ill.treat.Giardia)
 +
daly.ill.treat.Giardia$dalys <- daly.ill.treat.Giardia$P.treat.g.inf * daly.ill.treat.Giardia$dur.ill *
 +
    daly.ill.treat.Giardia$sev.ill
 +
 
 +
# yhteenveto DALYistä
 +
 
 +
Health.effects <- vaesto[,c("Age","Populaatio")]
 +
 
 +
Health.effects$Untreated.Gastr.Kamp <- daly.ill.treat.Kamp.Gastr[daly.ill.treat.Kamp.Gastr$ill.treat == "Untreated", c("dalys")]
 +
Health.effects$GP.Gastr.Kamp <- daly.ill.treat.Kamp.Gastr[daly.ill.treat.Kamp.Gastr$ill.treat == "General practitioner", c("dalys")]
 +
Health.effects$Hospitalised.Gastr.Kamp <- daly.ill.treat.Kamp.Gastr[daly.ill.treat.Kamp.Gastr$ill.treat == "Hospitalised", c("dalys")]
 +
Health.effects$Death.Gastr.Kamp <- daly.death.Kamp.Gastr
 +
 
 +
Health.effects$Clinical.GBS.Kamp <- daly.Kamp.gbs$dalys[1]
 +
Health.effects$Residual.GBS.Kamp <- daly.Kamp.gbs$dalys[2]
 +
Health.effects$Death.GBS.Kamp <- daly.death.Kamp.gbs
 +
 
 +
Health.effects$Arth.Kamp <- daly.Kamp.arth
 +
 
 +
Health.effects$WD.Ecoli <- daly.wd.Ecoli
 +
Health.effects$HC.Ecoli <- daly.hc.Ecoli
 +
Health.effects$Death.Ecoli <- daly.death.Ecoli
 +
 
 +
Health.effects$HUS.Ecoli <- daly.hus.Ecoli
 +
Health.effects$Death.HUS.Ecoli <- daly.death.hus.Ecoli
 +
 
 +
Health.effects$ESRD.Ecoli <- daly.esrd.Ecoli
 +
Health.effects$Death.ESRD.Ecoli <- daly.death.esrd.Ecoli
 +
 
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Rotavirus[daly.ill.treat.Rotavirus$ill.treat == "Untreated", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Untreated.Rotavirus"
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Rotavirus[daly.ill.treat.Rotavirus$ill.treat == "General practitioner", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "GP.Rotavirus"
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Rotavirus[daly.ill.treat.Rotavirus$ill.treat == "Hospitalised", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Hospitalised.Rotavirus"
 +
Health.effects <- merge(Health.effects, daly.death.Rotavirus)
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Death.Rotavirus"
 +
 
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Norovirus[daly.ill.treat.Norovirus$ill.treat == "Untreated", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Untreated.Norovirus"
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Norovirus[daly.ill.treat.Norovirus$ill.treat == "General practitioner", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "GP.Norovirus"
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Norovirus[daly.ill.treat.Norovirus$ill.treat == "Hospitalised", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Hospitalised.Norovirus"
 +
Health.effects <- merge(Health.effects, daly.death.Norovirus)
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Death.Norovirus"
 +
 
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Crypt[daly.ill.treat.Crypt$ill.treat == "Untreated", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Untreated.Crypt"
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Crypt[daly.ill.treat.Crypt$ill.treat == "General practitioner", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "GP.Crypt"
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Crypt[daly.ill.treat.Crypt$ill.treat == "Hospitalised", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Hospitalised.Crypt"
 +
Health.effects <- merge(Health.effects, daly.death.Crypt)
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Death.Crypt"
 +
 
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Giardia[daly.ill.treat.Giardia$ill.treat == "Untreated", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Untreated.Giardia"
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Giardia[daly.ill.treat.Giardia$ill.treat == "General practitioner", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "GP.Giardia"
 +
Health.effects <- merge(Health.effects, daly.ill.treat.Giardia[daly.ill.treat.Giardia$ill.treat == "Hospitalised", c("Age", "dalys")])
 +
colnames(Health.effects)[ncol(Health.effects)] <- "Hospitalised.Giardia"
 +
 
 +
Health.effects <- reshape(Health.effects, idvar = c("Age"), times = colnames(Health.effects)[-c(1,2)], timevar = "Outcome",
 +
    varying = list(colnames(Health.effects)[-c(1,2)]), direction = "long")
 +
colnames(Health.effects)[4] <- "P.daly.g.inf"
 +
   
 +
Health.effects$Pathogen <- NA
 +
Health.effects$Pathogen[grep(".Kamp", Health.effects$Outcome)] <- Pathogen[1]
 +
Health.effects$Pathogen[grep(".Ecoli", Health.effects$Outcome)] <- Pathogen[2]
 +
Health.effects$Pathogen[grep(".Rotavirus", Health.effects$Outcome)] <- Pathogen[3]
 +
Health.effects$Pathogen[grep(".Norovirus", Health.effects$Outcome)] <- Pathogen[4]
 +
Health.effects$Pathogen[grep(".Crypt", Health.effects$Outcome)] <- Pathogen[5]
 +
Health.effects$Pathogen[grep(".Giardia", Health.effects$Outcome)] <- Pathogen[6]
 +
 
 +
Health.effects <- merge(Health.effects, dose.response[,c("Pathogen", "P.inf")])
 +
Health.effects$DALYs <- (1 - (1 - Health.effects$P.inf * Health.effects$P.daly.g.inf)^365) * Health.effects$Populaatio
 +
 
 +
 
 +
 
 +
temp <- merge(dose.response, P.ill.g.inf)
 +
 
 +
############# TULOKSET #########################################################################################################
 +
 
 +
cat("<span style='font-size: 1.2em;font-weight:bold;'>Patogeenien konsentraatio raakavedessä</span>\n")
 +
print(xtable(RaaPatPitLuo@output), type='html') # Patogeenien konsentraatio raakavedessä
 +
cat("<span style='font-size: 1.2em;font-weight:bold;'>Patogeenien log vähenemä puhdistuksessa</span>\n")
 +
print(xtable(VedKasTeh@output), type='html') # Patogeenien log vähenemä puhdistuksessa
 +
print(xtable(VedDesTeh@output), type='html') # Patogeenien log vähenemä desinfioinnissa
 +
cat("<span style='font-size: 1.2em;font-weight:bold;'>Patogeeneille altistuminen ja infektion todennäköisyys</span>\n")
 +
cat(colnames(dose.response), "\n")
 +
#cat(colnames(ExpoPatAnn@output), "\n")
 +
print(xtable(dose.response[,c("Pathogen", "Exp.pat", "P.inf", "VedDesTehSource")]), type="html") # Patogeeneille altistuminen ja infektion todennäköisyys
 +
 
 +
cat("<span style='font-size: 1.2em;font-weight:bold;'>Arvioitu terveysvaikutus</span>\n")
 +
 
 +
cat(sum((1 - (1 - temp$P.ill.g.inf * temp$P.inf)^365) * Vaestonkoko, na.rm = TRUE), " vatsatautia vuodessa \n")
 +
 
 +
cat(sum(Health.effects$DALYs, na.rm = TRUE), " DALY:ä vatsataudeista \n")   
 +
</rcode>

Revision as of 09:49, 23 August 2012

Polygons on dynamic Google Maps

This example plots municipalities of Finland on Google Maps using data from National Land Survey of Finland.

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Points on dynamic Google Maps

This examples plots buildings of Kuopio on Google Maps. User can give the minimum age of buildings to plot as an input parameter.


Building minimum age:

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Large quantity of points on a static Google Maps

This example plots large number of point data on static Google Maps. The map produced in this example shows the age (in years) distribution of buildings within Kuopio. User can select the number of age classes (4,6 or 8) and the type of classification.

Number of classes:

Type of classification:

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Raakavesi: Patogeenien pitoisuudet

Water resource:

Kampylobakteeri-pitoisuus arvio (mikrobia/l):

E.coli O157:H7 -pitoisuus arvio (mikrobia/l):

Rotavirus-pitoisuus arvio (mikrobia/l):

Norovirus-pitoisuus arvio (mikrobia/l):

Cryptosporidium-pitoisuus arvio (mikrobia/l):

Giardia-pitoisuus arvio (mikrobia/l):

Kaupungin oletusarvot:

Vedenpuhdistus: Puhdistusprosessi ja klooraus

Käytössä olevat puhdistusmenetelmät:
Perinteinen puhdistus
Hyvin toimva puhdistus
Tehostettu puhdistus
Hidas hiekkasuodatus
Kalkkikivisuodatus
Aktiivihiilisuodatus
UV suodatus
Otsonointi

Klooriannos (mg/l):

Verkosto ja kuluttajat

veden kulutus (ml):

Altistuvan väestön koko:

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