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updates to use neon_cloud
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@rqthomas
rqthomas committed Jan 4, 2024
1 parent 2260d1c commit 416b44a
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Showing 3 changed files with 45 additions and 106 deletions.
14 changes: 7 additions & 7 deletions data/site_carbon_data.csv
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Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
datetime,variable,observation,site_id
2015-10-12,wood,113.81052385799126,TALL
2015-10-12,wood,113.81058165884993,TALL
2015-10-12,som,NA,TALL
2016-11-01,wood,110.42574322503671,TALL
2016-11-01,wood,110.42579516994523,TALL
2016-11-01,som,NA,TALL
2017-12-21,wood,111.35459000221715,TALL
2017-12-21,wood,111.35456653564788,TALL
2017-12-21,som,NA,TALL
2018-12-19,wood,115.19570145506081,TALL
2018-12-19,wood,115.19575923898176,TALL
2018-12-19,som,NA,TALL
2021-12-23,wood,121.2803046036263,TALL
2021-12-23,wood,121.28035655848089,TALL
2021-12-23,som,NA,TALL
2023-01-17,wood,122.54987707238284,TALL
2023-01-17,wood,122.54992560106908,TALL
2023-01-17,som,NA,TALL
2019-12-19,wood,NA,TALL
2019-12-19,som,NA,TALL
Expand All @@ -26,7 +26,7 @@ datetime,variable,observation,site_id
2021-01-01,wood,NA,TALL
2021-01-01,som,NA,TALL
2014-01-01,wood,NA,TALL
2014-01-01,som,103.54546846153306,TALL
2014-01-01,som,103.54546847931915,TALL
2014-01-09,lai,1.7000000000000002,TALL
2014-01-17,lai,1.7000000000000002,TALL
2014-02-18,lai,1.8,TALL
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3 changes: 2 additions & 1 deletion install.R
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
install.packages("neonstore")
#install.packages("neonstore")
install.packages("MODISTools")
install.packages("scoringRules")
install.packages("patchwork")
install.packages("daymetr")
remotes::install_github("ropensci/allodb")
remotes::install_github("cboettig/neonstore")
install.packages("duckdbfs")
134 changes: 36 additions & 98 deletions neon-data.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -41,74 +41,33 @@ The code below read the data directly from NEON's cloud storage. Since the colum
```{r}
#| message: false
index <- neonstore:::neon_data(product = "DP1.10098.001",
site = site,
type="basic")
## Mapping and tagging table
df1 <-index |>
filter(grepl("mappingandtagging", name)) |>
filter(grepl("RELEASE", release)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
map_tag_table <- neon_cloud("mappingandtagging",
product = "DP1.10098.001",
site = site) |>
select(individualID, scientificName) |>
collect()
df2 <- index |>
filter(grepl("mappingandtagging", name)) |>
filter(!grepl("RELEASE", release)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
select(individualID, scientificName) |>
collect()
map_tag_table <- bind_rows(df1,df2) |>
collect() |>
group_by(individualID) |>
slice(1) |> #This is needed because some individuals change species IDs
ungroup()
## Individual table
df1 <- index |>
filter(grepl("apparentindividual", name)) |>
filter(grepl("RELEASE", release)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
select(individualID, eventID, plotID, date, stemDiameter,plantStatus, measurementHeight) |>
collect()
df2 <- index |>
filter(grepl("apparentindividual", name)) |>
filter(!grepl("RELEASE", release)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
ind_table <- neon_cloud("apparentindividual",
product = "DP1.10098.001",
site = site) |>
select(individualID, eventID, plotID, date, stemDiameter,plantStatus, measurementHeight) |>
distinct() |>
collect()
ind_table <- bind_rows(df1,df2) |>
distinct()
## Plot table
df1 <-index |>
filter(grepl("perplotperyear", name)) |>
filter(grepl("RELEASE", release)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
plot_table <- neon_cloud("perplotperyear",
product = "DP1.10098.001",
site = site) |>
select(plotID,totalSampledAreaTrees,plotType) |>
distinct(plotID, .keep_all = TRUE) |>
collect()
df2 <- index |>
filter(grepl("perplotperyear", name)) |>
filter(!grepl("RELEASE", release)) |>
pull(url) |>
duckdbfs::open_dataset(perplotperyear$url, format="csv", filename = TRUE) |>
select(plotID,totalSampledAreaTrees,plotType) |>
collect()
plot_table <- bind_rows(df1,df2) |>
distinct(plotID, .keep_all = TRUE)
```

The species names in the mapping and tagging table need to be separated into the genus and species so that we can calculate the biomass.
Expand Down Expand Up @@ -294,31 +253,21 @@ The data needed to calculate carbon in trees that are laying on the ground are i
```{r}
#| message: false
index <- neonstore:::neon_data(product = "DP1.10014.001",
site = site,
type="basic")
cdw_density <- index |>
filter(grepl("cdw_densitydisk", name)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
cdw_density <- neon_cloud("cdw_densitydisk",
product = "DP1.10014.001",
site = site) |>
collect()
log_table <- index |>
filter(grepl("cdw_densitylog", name)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
log_table <- neon_cloud("cdw_densitylog",
product = "DP1.10014.001",
site = site) |>
collect()
cdw_tally <- neon_cloud("cdw_fieldtally",
product = "DP1.10010.001",
site = site) |>
collect()
index <- neonstore:::neon_data(product = "DP1.10010.001",
site = site,
type="basic")
cdw_tally <- index |>
filter(grepl("cdw_fieldtally", name)) |>
pull(url) |>
#duckdbfs::open_dataset(format="csv", filename = TRUE) |>
read_csv(show_col_types = FALSE)
```

```{r}
Expand Down Expand Up @@ -359,20 +308,14 @@ Here we are going to calculate the carbon stored in fine roots using the root ch
#| message: false
## root chemistry data product
index <- neonstore:::neon_data(product = "DP1.10067.001",
site = site,
type="basic")
bbc_percore <- index |>
filter(grepl("bbc_percore", name)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
bbc_percore <- neon_cloud("bbc_percore",
product = "DP1.10067.001",
site = site) |>
collect()
rootmass <- index |>
filter(grepl("bbc_rootmass", name)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
rootmass <- neon_cloud("bbc_rootmass",
product = "DP1.10067.001",
site = site) |>
collect()
```

Expand Down Expand Up @@ -429,20 +372,15 @@ site_roots <- rootmass %>%
#Download bieogeochemistry soil data to get carbon concentration
#data_product1 <- "DP1.00097.001"
#Download physical soil data to get bulk density
index <- neonstore:::neon_data(product = "DP1.00096.001",
site = site,
type="basic")
mgc_perbiogeosample <- index |>
filter(grepl("mgp_perbiogeosample", name)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
mgc_perbiogeosample <- neon_cloud("mgp_perbiogeosample",
product = "DP1.00096.001",
site = site) |>
collect()
mgp_perbulksample <- index |>
filter(grepl("mgp_perbulksample", name)) |>
pull(url) |>
duckdbfs::open_dataset(format="csv", filename = TRUE) |>
mgp_perbulksample <- neon_cloud("mgp_perbulksample",
product = "DP1.00096.001",
site = site) |>
collect()
```

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