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Merge pull request #101 from inbo/060_sedimentkenmerken
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060 sedimentkenmerken
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@joost-vanoverbeke
joost-vanoverbeke authored Oct 14, 2024
2 parents 6188038 + 5f06b7d commit f858fff
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77 changes: 74 additions & 3 deletions moneos_2024/060_sedimentkenmerken/10_sediment_data.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,7 @@ dubbel <-data2023 %>%
# subset(data, !(tidaal == "subtidaal" & jaar ==2013 & waterloop == "Zeeschelde I" &
# variabele %in% c("mediaan","slib") ))
data <- data %>%
sediment_data <- data %>%
rbind (data2022, data2023) %>%
na.omit(TRUE)
Expand All @@ -139,14 +139,85 @@ data gecreëerd op `r Sys.time()`

data weggeschreven naar `r paste0(pad_data, "template_data.csv")`

```{r voorbereiding dataset}
table(sediment_data$tidaal)
sediment_data$tidaal[sediment_data$tidaal=="inter"] <- "intertidaal"
sediment_data$tidaal[sediment_data$tidaal=="inter"] <- "Intertidaal"
sediment_data$tidaal[sediment_data$tidaal=="sub"] <- "subtidaal"
unique(sediment_data$tidaal)
table(sediment_data$waterloop)
## tijarm Zwijnaarde en Gentbrugge-Melle afzonderlijk aanleveren
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde_trj_Ml_Gb"] <- "Zeeschelde Ia"
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I trj_Ml_Gb"] <- "Zeeschelde Ia"
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I trj_Ml_Gb\r\n"] <- "Zeeschelde Ia"
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I tijarm Zwijnaarde"] <- "Zeeschelde Ib"
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I tijarm Zwijnaarde\r\n"] <- "Zeeschelde Ib"
sediment_data$waterloop[sediment_data$waterloop=="Beneden_Dijle"] <- "Dijle"
sediment_data <- sediment_data %>%
mutate(waterloop = if_else(startsWith(locatie, "TZ"), "Zeeschelde Ib", waterloop))
sediment_data <- sediment_data %>%
mutate(waterloop = if_else(startsWith(locatie, "GM"), "Zeeschelde Ia", waterloop))
#
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde_trj_Ml_Gb"] <- "Zeeschelde I"
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I trj_Ml_Gb"] <- "Zeeschelde I"
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I trj_Ml_Gb\r\n"] <- "Zeeschelde I"
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I tijarm Zwijnaarde"] <- "Zeeschelde I"
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I tijarm Zwijnaarde\r\n"] <- "Zeeschelde I"
#
table(sediment_data$waterloop)
sediment_data$waterloop <- factor(sediment_data$waterloop,
levels=c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I","Zeeschelde Ia","Zeeschelde Ib", "Rupel","Durme","Nete","Dijle","Zenne"))
# sediment_data$waterloop <- factor(sediment_data$waterloop,
# levels=c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I","Zeeschelde Ia","Zeeschelde Ib", "Rupel","Durme","Nete","Dijle","Zenne"))
table(sediment_data$fysiotoop)
sediment_data$fysiotoop[sediment_data$fysiotoop=="diep subtidaal"] <- "diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoge slikzone"] <- "hoog"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoog slik"] <- "hoog"
sediment_data$fysiotoop[sediment_data$fysiotoop=="lage slikzone"] <- "laag"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laag intertidaal"] <- "laag"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laag slik"] <- "laag"
sediment_data$fysiotoop[sediment_data$fysiotoop=="matig diep subtidaal"] <- "matig diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch matig diep subtidaal"] <- "laagdynamisch matig diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch matig diep subtidaal"] <- "hoogdynamisch matig diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="middelhoge slikzone"] <- "midden"
sediment_data$fysiotoop[sediment_data$fysiotoop=="middelhoog slik"] <- "midden"
sediment_data$fysiotoop[sediment_data$fysiotoop=="nog te bepalen - sub"] <- "sub indet."
sediment_data$fysiotoop[sediment_data$fysiotoop=="subtidaal"] <- "sub indet."
sediment_data$fysiotoop[sediment_data$fysiotoop=="ondiep subtidaal"] <- "ondiep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch ondiep subtidaal"] <- "laagdynamisch ondiep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch ondiep subtidaal"] <- "hoogdynamisch ondiep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="slik onbepaald"] <- "inter indet."
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch diep subtidaal"] <- "laagdynamisch diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch diep subtidaal"] <- "hoogdynamisch diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch zeer diep subtidaal"] <- "hoogdynamisch zeer diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hard antropogeen"] <- "hard substraat"
unique(sediment_data$fysiotoop)
```


```{r wegschrijven-data}
file <- paste0(pad_data, "S_DS_V_004a_sediment_data2008_",(year(Sys.Date())-1),"_rapportage",year(Sys.Date()),".xlsx")
openxlsx::write.xlsx(data, file, rowNames = FALSE, overwrite = TRUE)
openxlsx::write.xlsx(sediment_data, file, rowNames = FALSE, overwrite = TRUE)
data %>%
###voor data analyse 2024 heb ik geen hoog vs laagdynamisch meegenomen
###data wel aangeleverd met opdeling hoog vs laagdynamisch
sediment_data %>%
write_delim(paste0(pad_data, "sediment_data.csv"),
delim = ";")
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88 changes: 33 additions & 55 deletions moneos_2024/060_sedimentkenmerken/20_sediment_analyse.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -122,67 +122,42 @@ meta_data %>%
```

```{r voorbereiding dataset}
table(sediment_data$tidaal)
sediment_data$tidaal[sediment_data$tidaal=="inter"] <- "intertidaal"
sediment_data$tidaal[sediment_data$tidaal=="inter"] <- "Intertidaal"
sediment_data$tidaal[sediment_data$tidaal=="sub"] <- "subtidaal"
table(sediment_data$waterloop)
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde_trj_Ml_Gb"] <- "Zeeschelde I_up"
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I trj_Ml_Gb"] <- "Zeeschelde I_up"
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I trj_Ml_Gb\r\n"] <- "Zeeschelde I_up"
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I tijarm Zwijnaarde"] <- "Zeeschelde I_up"
sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I tijarm Zwijnaarde\r\n"] <- "Zeeschelde I-up"
sediment_data$waterloop[sediment_data$waterloop=="Beneden_Dijle"] <- "Dijle"
#
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde_trj_Ml_Gb"] <- "Zeeschelde I"
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I trj_Ml_Gb"] <- "Zeeschelde I"
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I trj_Ml_Gb\r\n"] <- "Zeeschelde I"
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I tijarm Zwijnaarde"] <- "Zeeschelde I"
# sediment_data$waterloop[sediment_data$waterloop=="Zeeschelde I tijarm Zwijnaarde\r\n"] <- "Zeeschelde I"
#
table(sediment_data$waterloop)
sediment_data$waterloop <- factor(sediment_data$waterloop,
levels=c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I","Zeeschelde I_up","Rupel","Durme","Nete","Dijle","Zenne"))
# sediment_data$waterloop <- factor(sediment_data$waterloop,
# levels=c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I","Zeeschelde I_up","Rupel","Durme","Nete","Dijle","Zenne"))
```{r voorbereiding}
table(sediment_data$waterloop)
##Ruimtelijke indeling
##Zeeschelde Ia = Scheldemeander Melle Gentbrugge
##Zeeschelde Ib = Traject Zwijnaarde - ringvaart
sediment_data$waterloop <- factor(sediment_data$waterloop,
levels=c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I","Zeeschelde Ia","Zeeschelde Ib", "Rupel","Durme","Nete","Dijle","Zenne"))
table(sediment_data$fysiotoop)
sediment_data$fysiotoop[sediment_data$fysiotoop=="diep subtidaal"] <- "diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoge slikzone"] <- "hoog"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoog slik"] <- "hoog"
sediment_data$fysiotoop[sediment_data$fysiotoop=="lage slikzone"] <- "laag"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laag intertidaal"] <- "laag"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laag slik"] <- "laag"
sediment_data$fysiotoop[sediment_data$fysiotoop=="matig diep subtidaal"] <- "matig diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch matig diep subtidaal"] <- "matig diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch matig diep subtidaal"] <- "matig diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="middelhoge slikzone"] <- "midden"
sediment_data$fysiotoop[sediment_data$fysiotoop=="middelhoog slik"] <- "midden"
sediment_data$fysiotoop[sediment_data$fysiotoop=="nog te bepalen - sub"] <- "sub indet."
sediment_data$fysiotoop[sediment_data$fysiotoop=="subtidaal"] <- "sub indet."
sediment_data$fysiotoop[sediment_data$fysiotoop=="ondiep subtidaal"] <- "ondiep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch ondiep subtidaal"] <- "ondiep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch ondiep subtidaal"] <- "ondiep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="slik onbepaald"] <- "inter indet."
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch diep subtidaal"] <- "diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch diep subtidaal"] <- "diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch zeer diep subtidaal"] <- "diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hard antropogeen"] <- "hard substraat"
unique(sediment_data$fysiotoop)
##fysiotopen
##data-analyse 2024 - laag en hoogdynamisch niet meegenomen in analyse
table(sediment_data$fysiotoop)
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch matig diep"] <- "matig diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch matig diep"] <- "matig diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch ondiep"] <- "ondiep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch ondiep"] <- "ondiep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="laagdynamisch diep"] <- "diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch diep"] <- "diep"
sediment_data$fysiotoop[sediment_data$fysiotoop=="hoogdynamisch zeer diep"] <- "diep"
unique(sediment_data$fysiotoop)
fyzzers <- c("hoog","midden","laag",
"hard substraat","inter indet.","ondiep",
"matig diep","diep", "sub indet.","onbepaald")
sediment_data$fysiotoop <- factor(sediment_data$fysiotoop, levels = fyzzers)
hoofd <- c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I","Zeeschelde I_up" )
# hoofd <- c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I")
#hoofd <- c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I","Zeeschelde Ia", "Zeeschelde Ib")
hoofd <- c("Zeeschelde IV","Zeeschelde III","Zeeschelde II","Zeeschelde I")
zij <- c("Rupel","Durme","Nete","Dijle","Zenne")
inter <- c("inter indet.","laag", "hoog", "midden")
sub <- c("diep","matig diep","ondiep","sub indet.")
Expand All @@ -208,10 +183,12 @@ ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1]))
" P =",signif(summary(fit)$coef[2,4], 5)))
}
#data_set regressie
test <- sediment_data %>%
pivot_wider(names_from = variabele, values_from = waarde)
#relaties in dataset verkennen
fit1 <- lm(OM ~ mediaan, data = test)
ggplotRegression(fit1)
Expand All @@ -237,10 +214,11 @@ ggplotRegression(fit6)
fit6 <- lm(mediaan ~ jaar, data = testslib)
ggplotRegression(fit6)
####testjes
####Dataset voor regressie
nested_data <- test %>%
# dplyr::filter(waterloop == "Zeeschelde II") %>%
# dplyr::filter(jaar < 2023) %>%
group_by(waterloop,fysiotoop) %>%
nest()
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