From 8b9dd029a75804e6fa0b076acce0ac13016560d5 Mon Sep 17 00:00:00 2001 From: Beni Stocker Date: Thu, 18 Jul 2024 14:59:17 +0200 Subject: [PATCH 1/2] just comments --- R/ingest.R | 3 ++- vignettes/example.Rmd | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/R/ingest.R b/R/ingest.R index 6a93377..dd8c935 100644 --- a/R/ingest.R +++ b/R/ingest.R @@ -868,8 +868,9 @@ ingest <- function( } else if (source == "hwsd"){ - # Get HWSD soil data. year_start and year_end not required + # https://github.com/bluegreen-labs/hwsdr + # Get HWSD soil data. year_start and year_end not required # TODO replace with {hwsdr} call # con <- rhwsd::get_hwsd_con() diff --git a/vignettes/example.Rmd b/vignettes/example.Rmd index d6ab8f5..6fde32b 100644 --- a/vignettes/example.Rmd +++ b/vignettes/example.Rmd @@ -1049,6 +1049,8 @@ Four steps are required before you can use `ingest()` to get HWSD data: ```{r warning=FALSE, eval = FALSE} if(!require(devtools)){install.packages(devtools)} devtools::install_github("stineb/rhwsd") + +# XXX to change to https://github.com/bluegreen-labs/hwsdr ``` 2. Install additionally required packages: DBI and RSQLite. From b24ff93d2c8a561d316da1b9302d0d3b3c9ee71b Mon Sep 17 00:00:00 2001 From: Benjamin Stocker Date: Thu, 18 Jul 2024 15:15:28 +0200 Subject: [PATCH 2/2] revised GSDE data ingest after update to terra --- R/ingest_globalfields.R | 15 ++++++++++----- vignettes/example.Rmd | 2 +- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/R/ingest_globalfields.R b/R/ingest_globalfields.R index 3b3167f..29bd205 100644 --- a/R/ingest_globalfields.R +++ b/R/ingest_globalfields.R @@ -467,8 +467,10 @@ ingest_globalfields <- function( df_out_top <- extract_pointdata_allsites( paste0(dir, "/", filename), df_lonlat, get_time = FALSE ) %>% dplyr::select(-lon, -lat) %>% tidyr::unnest(data) %>% - dplyr::rename(!!layer := V1) %>% - dplyr::select(sitename, !!layer) + tidyr::pivot_longer(cols = starts_with("PBR_depth")) %>% + dplyr::rename(!!layer := value, depth = name) %>% + dplyr::mutate(depth = as.numeric(str_remove(depth, "PBR_depth="))) %>% + dplyr::select(sitename, !!layer, depth) # bottom soil layers filename <- list.files(dir, pattern = paste0(layer, "2.nc")) @@ -477,8 +479,10 @@ ingest_globalfields <- function( df_out_bottom <- extract_pointdata_allsites( paste0(dir, "/", filename), df_lonlat, get_time = FALSE ) %>% dplyr::select(-lon, -lat) %>% tidyr::unnest(data) %>% - dplyr::rename(!!layer := V1) %>% - dplyr::select(sitename, !!layer) + tidyr::pivot_longer(cols = starts_with("PBR_depth")) %>% + dplyr::rename(!!layer := value, depth = name) %>% + dplyr::mutate(depth = as.numeric(str_remove(depth, "PBR_depth="))) %>% + dplyr::select(sitename, !!layer, depth) # combine for layers read from each file df_out <- bind_rows(df_out_top, df_out_bottom) %>% @@ -497,7 +501,8 @@ ingest_globalfields <- function( rename(value = !!layer) %>% # interpret missing values - na_if(-999) %>% + ungroup() %>% + mutate(value = ifelse(value == -999, NA, value)) %>% mutate(value = ifelse(varnam %in% c("PHH2O", "PHK", "PHCA") & value == 100, NA, value)) %>% diff --git a/vignettes/example.Rmd b/vignettes/example.Rmd index 6fde32b..d1ed18b 100644 --- a/vignettes/example.Rmd +++ b/vignettes/example.Rmd @@ -1192,7 +1192,7 @@ df_gsde <- ingest( siteinfo_fluxnet2015 %>% slice(1:2), source = "gsde", settings = settings_gsde, - dir = "~/data/soil/shangguan" + dir = "/data/archive/soil_shangguan_2014/data/" ) ```