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Vincyane Badouard
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Aug 16, 2021
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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| title: "Crowns_draft" | ||
| author: "Vincyane Badouard" | ||
| date: "16/08/2021" | ||
| output: html_document | ||
| --- | ||
|
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| ```{r} | ||
| inventory <- addtreedim(inventorycheckformat(Paracou6_2016)) | ||
| dat <- inventory[679,] | ||
| ``` | ||
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| ```{r} | ||
| # The crown | ||
| treefromthesky <- function(dat){ | ||
| Crown <- dat %>% | ||
| mutate(xCrown = Xutm, # X centroid | ||
| yCrown = Yutm, # Y ventroid | ||
| exCrown = CrownDiameter/2, | ||
| eyCrown = CrownHeight/2) %>% | ||
| st_as_sf(coords = c("xCrown", "yCrown")) # ellipse centroid coordinates | ||
| Crown <- st_ellipse(Crown, Crown$exCrown, Crown$eyCrown) # create the ellipse | ||
| } | ||
| ``` | ||
|
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| ```{r} | ||
| library(ggplot2) | ||
| g <- ggplot() + | ||
| geom_sf(data = st_as_sf(inventory, coords = c("Xutm", "Yutm")), aes(label = ScientificName)) + | ||
| geom_sf(data = Crown, fill = "forestgreen") # trees polygons | ||
| plotly::ggplotly(g) | ||
| ``` | ||
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| ```{r} | ||
| Canopy <- inventory %>% | ||
| group_by(idTree) %>% # for each tree | ||
| do(Crowns = # inform geometry. # Filling a column from a function whose input is a table | ||
| treefromthesky(.) %>% | ||
| st_as_text()) %>% # as text to easy join with a non spacial table | ||
| tidyr::unnest(Crowns) # here to pass from list to character | ||
| inventory <- left_join(inventory, Canopy, by = "idTree") # join spatial filtered inventory and non spatial complete inventory | ||
| ``` | ||
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| ```{r} | ||
| #The small ones first so that they are behind the big ones on the plot | ||
| inventory <- arrange(inventory, TreeHeight) | ||
| ggplot() + | ||
| geom_sf(data = getgeometry(inventory, Crowns), | ||
| aes(alpha = TreeHeight), # label = paste(idTree, Species), | ||
| fill = "forestgreen") | ||
| ``` | ||
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| # Plotly version | ||
| ```{r} | ||
| #The small ones first so that they are behind the big ones on the plot | ||
| inventory <- arrange(inventory, TreeHeight) %>% | ||
| filter(TreeHeight >30) | ||
| g <- ggplot() + | ||
| geom_sf(data = getgeometry(inventory, Crowns), | ||
| aes(label = paste(idTree, Species), alpha = 1/2), | ||
| fill = "forestgreen") # trees polygons | ||
| plotly::ggplotly(g) | ||
| ``` | ||
|
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| #' createcanopy | ||
| #' | ||
| #' @param inventory (data.frame) | ||
| #' | ||
| #' @return a dataframe with a column 'Crowns' containing the ellipses | ||
| #' (sfc_POLYGON) as trees crown, with their diameter and height filled in, | ||
| #' representing trees from the sky. | ||
| #' @export | ||
| #' | ||
| #' @importFrom dplyr group_by do left_join | ||
| #' @importFrom sf st_as_text | ||
| #' @importFrom tidyr unnest | ||
| #' | ||
| #' @examples | ||
| #' data(Paracou6_2016) | ||
| #' Paracou6_2016 <- dplyr::slice(Paracou6_2016, 1:10) | ||
| #' | ||
| #' inventory <- addtreedim(inventorycheckformat(Paracou6_2016)) | ||
| #' | ||
| #' inventory <- createcanopy(inventory) | ||
| #' | ||
| #' # The small ones first so that they are behind the big ones on the plot | ||
| #' inventory <- dplyr::arrange(inventory, TreeHeight) | ||
| #' library(ggplot2) | ||
| #' ggplot() + | ||
| #' geom_sf(data = getgeometry(inventory, Crowns), | ||
| #' aes(alpha = TreeHeight), | ||
| #' fill = "forestgreen") | ||
| #' | ||
| createcanopy <- function(inventory){ | ||
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| # Arguments check | ||
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| if(!inherits(inventory, "data.frame")) | ||
| stop("The 'inventory' argument of the 'createcanopy' function must be a data.frame") | ||
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| # Global variables | ||
| idTree <- Crowns <- . <- NULL | ||
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| # Function | ||
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| Canopy <- inventory %>% | ||
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| group_by(idTree) %>% # for each tree | ||
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| do(Crowns = # inform geometry. # do: filling a column from a function whose input is a table | ||
| treefromthesky(.) %>% | ||
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| st_as_text()) %>% # as text to easy join with a non spacial table | ||
| tidyr::unnest(Crowns) # here to pass from list to character | ||
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| inventory <- left_join(inventory, Canopy, by = "idTree") # join the column 'Crowns' to the inventory | ||
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| } | ||
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| #' treefromthesky | ||
| #' | ||
| #' @param dat 1 row data.frame with columns: | ||
| #' Xutm, Yutm (Tree coordinates), CrownDiameter, CrownHeight | ||
| #' | ||
| #' @return an ellipse (sfc_POLYGON) as a crown, with its diameter and height | ||
| #' filled in, representing the tree from the sky. | ||
| #' @export | ||
| #' | ||
| #' @importFrom dplyr mutate | ||
| #' @importFrom sf st_as_sf | ||
| #' @importFrom nngeo st_ellipse | ||
| #' | ||
| #' @examples | ||
| #' inventory <- addtreedim(inventorycheckformat(Paracou6_2016)) | ||
| #' dat <- inventory[679,] | ||
| #' | ||
| #' Crown <- treefromthesky(dat) | ||
| #' | ||
| #' library(ggplot2) | ||
| #' ggplot() + | ||
| #' geom_sf(data = st_as_sf(inventory, coords = c("Xutm", "Yutm"))) + | ||
| #' geom_sf(data = Crown, fill = "forestgreen") # trees polygons | ||
| #' | ||
| treefromthesky <- function(dat){ | ||
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| # Arguments check | ||
|
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| if(!inherits(dat, "data.frame")) | ||
| stop("The 'dat' argument of the 'treefromthesky' function must be a data.frame") | ||
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| if(nrow(dat)!=1) | ||
| stop("the data.frame given in the 'dat' argument | ||
| of the 'treefromthesky' function must contain only 1 row") | ||
|
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| # Global variables | ||
| Xutm <- Yutm <- CrownDiameter <- CrownHeight <- NULL | ||
|
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| # Function | ||
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| Crown <- dat %>% | ||
| mutate(xCrown = Xutm, # X centroid | ||
| yCrown = Yutm, # Y ventroid | ||
| exCrown = CrownDiameter/2, # crown radius | ||
| eyCrown = CrownHeight/2) %>% # half crown height | ||
| st_as_sf(coords = c("xCrown", "yCrown")) # ellipse centroid coordinates | ||
|
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| Crown <- st_ellipse(Crown, Crown$exCrown, Crown$eyCrown) # create the ellipse | ||
|
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| } |
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