From 0af9ba75c787e662b077354c0fff00b3193c04d6 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Mon, 24 Feb 2020 10:46:06 +0100
Subject: [PATCH] Fixed issue in A97 - abs loc uncert
---
code/04_buildHeader.Rmd | 14 +++++++-------
code/A97_ElevationExtract.R | 5 +++--
2 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/code/04_buildHeader.Rmd b/code/04_buildHeader.Rmd
index 6e2a2a7..f65feaf 100644
--- a/code/04_buildHeader.Rmd
+++ b/code/04_buildHeader.Rmd
@@ -448,12 +448,13 @@ Split data into tiles of 1 x 1 degrees, and create sp::SpatialPointsDataFrame fi
```{r create tiles}
header.tiles <- header %>%
dplyr::select(PlotObservationID, Dataset, Longitude, Latitude, `Location uncertainty (m)`) %>%
+ mutate(`Location uncertainty (m)`=abs(`Location uncertainty (m)`)) %>%
filter(`Location uncertainty (m)`<= 50000) %>%
mutate_at(.vars=vars(Longitude, Latitude),
.funs=list(tile=~cut(., breaks = seq(-180,180, by=.2)))) %>%
filter(!is.na(Longitude_tile) & !is.na(Latitude_tile) ) %>%
- mutate(tilenam=factor(paste(Longitude_tile, Latitude_tile))) %>%
- mutate(`Location uncertainty (m)`=abs(`Location uncertainty (m)`))
+ mutate(tilenam=factor(paste(Longitude_tile, Latitude_tile)))
+
```
There are `r nrow(header.tiles)` plots out of `r nrow(header)` plots with Location uncertainty <= 50km (or absent).
@@ -551,16 +552,15 @@ For those tiles that failed, extract elevation of remaining plots one by one
```{r}
#create list of tiles for which dem could not be extracted
myfiles <- list.files("../_derived/elevatr/")
-done <- as.numeric(unlist(regmatches(myfiles, gregexpr("[[:digit:]]+", myfiles))))
-todo <- 1:nlevels(header.tiles$tilenam)
-todo <- todo[-which(todo %in% done)]
+failed <- list.files("../_derived/elevatr/", pattern = "[A-Za-z]*_[0-9]+failed\\.RData$")
+failed <- as.numeric(unlist(regmatches(failed, gregexpr("[[:digit:]]+", failed))))
#create SpatialPointsDataFrame
sp.tile0 <- SpatialPointsDataFrame(coords=header.tiles %>%
- filter(tilenam %in% levels(header.tiles$tilenam)[todo]) %>%
+ filter(tilenam %in% levels(header.tiles$tilenam)[failed]) %>%
dplyr::select(Longitude, Latitude),
data=header.tiles %>%
- filter(tilenam %in% levels(header.tiles$tilenam)[todo]) %>%
+ filter(tilenam %in% levels(header.tiles$tilenam)[failed]) %>%
dplyr::select(-Longitude, -Latitude),
proj4string = CRS("+init=epsg:4326"))
sp.tile0 <- spTransform(sp.tile0, CRSobj = CRS("+init=epsg:3857 +proj=merc +a=6378137 +b=6378137 +lat_ts=0.0
diff --git a/code/A97_ElevationExtract.R b/code/A97_ElevationExtract.R
index 674effc..8bca8f8 100644
--- a/code/A97_ElevationExtract.R
+++ b/code/A97_ElevationExtract.R
@@ -18,11 +18,12 @@ ElevationExtract <- function(header, output, ncores){
header.tiles <- header.shp@data %>%
bind_cols(as.data.frame(header.shp@coords)) %>%
rename(PlotObservationID=PltObID, Longitude=coords.x1, Latitude=coords.x2) %>%
+ mutate(lc_ncrt=abs(lc_ncrt)) %>%
filter(lc_ncrt <= 50000) %>%
mutate_at(.vars=vars(Longitude, Latitude),
.funs=list(tile=~cut(., breaks = seq(-180,180, by=.2)))) %>%
- mutate(tilenam=factor(paste(Longitude_tile, Latitude_tile))) %>%
- mutate(lc_ncrt=abs(lc_ncrt))
+ mutate(tilenam=factor(paste(Longitude_tile, Latitude_tile)))
+
print("Get continent")
sPDF <- rworldmap::getMap(resolution="high")
--
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