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R package to interface with neon terms database.

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R
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inst
inst
 
 
man
man
 
 
testdata
testdata
 
 
.Rbuildignore
.Rbuildignore
 
 
.gitignore
.gitignore
 
 
DB_commands_other_useful.R
DB_commands_other_useful.R
 
 
DB_generation_commands.R
DB_generation_commands.R
 
 
DESCRIPTION
DESCRIPTION
 
 
DP_number_generation_commands.R
DP_number_generation_commands.R
 
 
NAMESPACE
NAMESPACE
 
 
README.Rmd
README.Rmd
 
 
README.md
README.md
 
 
controlled terms not in database.csv
controlled terms not in database.csv
 
 
database terms not in controlled fields.csv
database terms not in controlled fields.csv
 
 
demo.R
demo.R
 
 
fake.sqlite
fake.sqlite
 
 
index.sqlite
index.sqlite
 
 
november copy.sqlite
november copy.sqlite
 
 
november.sqlite
november.sqlite
 
 
term compare.csv
term compare.csv
 
 

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neonTerms

This is a package that will manage data about NEON's internal data product structures

This readme and its instructions are out of date. Until I get around to updating it, use the scripts in DB_generation_commands.R and DP_number_generation_commands.R

And if you make a "new" database, always use the term definition table from the old database! Always!

The current version of the database is november.sqlite

Quick start

#install.packages("devtools")
#library(devtools)
#install_github("NEONdps/neonTerms")
library(neonTerms)
library(RSQLite)
## Loading required package: DBI

options(stringsAsFactors = F)

Create and set a database in options

First thing you can do is create a database. Setting it in options makes your life a bit easier.

createDB("test.sqlite")
db <- "test.sqlite"
options(termDB = "test.sqlite")

Load in data from csv's

Next load data into CSV's

dpd <- read.csv("testdata/dpd.csv")
space <- read.csv("testdata/spatial.csv")
temporal <- read.csv("testdata/temporal.csv")
datapub <- read.csv("testdata/mam_datain_test.csv")
genIS <- read.csv("testdata/genericIS_L1.csv")

## Add rev numbers

dpd$rev <- 1

Finally you can add data to the the database. We'll input the data publication workooks to create table definitions.

addDPD(dpd)
## [1] "Successfully wrote 7 rows to the DataProductDescription table in your database test.sqlite"

addTempRes(temporal)
## [1] "Successfully wrote 10 rows to the TemporalResolution table in your database test.sqlite"

addSpRes(space)
## [1] "Successfully wrote 26 rows to the SpatialResolution table in your database test.sqlite"

inputDataPub(datapub,db)
## [1] "Successfully wrote 38 rows to the TermDefinition table in your database test.sqlite"

## Warning: RS-DBI driver warning: (closing pending result sets before closing this connection)
## Warning: RS-DBI driver warning: (closing pending result sets before closing this connection)
## Warning: RS-DBI driver warning: (closing pending result sets before closing this connection)

## [1] "Successfully wrote 2 rows to the TableDescription table in your database test.sqlite"
## [1] "Successfully wrote 2 rows to the TableDPLink table in your database test.sqlite"

## Warning: RS-DBI driver warning: (closing pending result sets before closing this connection)
## Warning: RS-DBI driver warning: (closing pending result sets before closing this connection)

## [1] "Successfully wrote 44 rows to the TableDefinition table in your database test.sqlite"

inputDataPub(genIS,db)
## [1] "Successfully wrote 6 rows to the TermDefinition table in your database test.sqlite"
## [1] "Successfully wrote 1 rows to the TableDescription table in your database test.sqlite"
## [1] "Successfully wrote 1 rows to the TableDPLink table in your database test.sqlite"
## [1] "Successfully wrote 10 rows to the TableDefinition table in your database test.sqlite"

## I input a generic table, so we can make extra linkages by adding a new entry to the table description table
toAdd <- data.frame(c("NEON.DOM.SIT.DP1.00002","NEON.DOM.SIT.DP1.00003"))
toAdd <- cbind(c(3,3),toAdd)
colnames(toAdd) <- c("tableID","dpID")
addTDPL(toAdd)
## [1] "Successfully wrote 2 rows to the TableDPLink table in your database test.sqlite"

Retrieve data

Data can be accessed via data product numbers, Once data product numbers have been fully extracted you can easily generate a full suite of unique field numbers

out <- qFull("NEON.DOM.SIT.DP1.00002",db)
### Generate full numbers
genFieldUID(out,db)
##   [1] "NEON.DOM.SIT.DP1.00002.001.001.001.00001.003"
##   [2] "NEON.DOM.SIT.DP1.00002.001.001.001.00002.003"
##   [3] "NEON.DOM.SIT.DP1.00002.001.001.001.00003.003"
##   [4] "NEON.DOM.SIT.DP1.00002.001.001.001.00005.003"
##   [5] "NEON.DOM.SIT.DP1.00002.001.001.001.00039.003"
##   [6] "NEON.DOM.SIT.DP1.00002.001.001.001.00040.003"
##   [7] "NEON.DOM.SIT.DP1.00002.001.001.001.00041.003"
##   [8] "NEON.DOM.SIT.DP1.00002.001.001.001.00042.003"
##   [9] "NEON.DOM.SIT.DP1.00002.001.001.001.00043.003"
##  [10] "NEON.DOM.SIT.DP1.00002.001.001.001.00044.003"
##  [11] "NEON.DOM.SIT.DP1.00002.002.001.001.00001.003"
##  [12] "NEON.DOM.SIT.DP1.00002.002.001.001.00002.003"
##  [13] "NEON.DOM.SIT.DP1.00002.002.001.001.00003.003"
##  [14] "NEON.DOM.SIT.DP1.00002.002.001.001.00005.003"
##  [15] "NEON.DOM.SIT.DP1.00002.002.001.001.00039.003"
##  [16] "NEON.DOM.SIT.DP1.00002.002.001.001.00040.003"
##  [17] "NEON.DOM.SIT.DP1.00002.002.001.001.00041.003"
##  [18] "NEON.DOM.SIT.DP1.00002.002.001.001.00042.003"
##  [19] "NEON.DOM.SIT.DP1.00002.002.001.001.00043.003"
##  [20] "NEON.DOM.SIT.DP1.00002.002.001.001.00044.003"
##  [21] "NEON.DOM.SIT.DP1.00002.001.002.001.00001.003"
##  [22] "NEON.DOM.SIT.DP1.00002.001.002.001.00002.003"
##  [23] "NEON.DOM.SIT.DP1.00002.001.002.001.00003.003"
##  [24] "NEON.DOM.SIT.DP1.00002.001.002.001.00005.003"
##  [25] "NEON.DOM.SIT.DP1.00002.001.002.001.00039.003"
##  [26] "NEON.DOM.SIT.DP1.00002.001.002.001.00040.003"
##  [27] "NEON.DOM.SIT.DP1.00002.001.002.001.00041.003"
##  [28] "NEON.DOM.SIT.DP1.00002.001.002.001.00042.003"
##  [29] "NEON.DOM.SIT.DP1.00002.001.002.001.00043.003"
##  [30] "NEON.DOM.SIT.DP1.00002.001.002.001.00044.003"
##  [31] "NEON.DOM.SIT.DP1.00002.002.002.001.00001.003"
##  [32] "NEON.DOM.SIT.DP1.00002.002.002.001.00002.003"
##  [33] "NEON.DOM.SIT.DP1.00002.002.002.001.00003.003"
##  [34] "NEON.DOM.SIT.DP1.00002.002.002.001.00005.003"
##  [35] "NEON.DOM.SIT.DP1.00002.002.002.001.00039.003"
##  [36] "NEON.DOM.SIT.DP1.00002.002.002.001.00040.003"
##  [37] "NEON.DOM.SIT.DP1.00002.002.002.001.00041.003"
##  [38] "NEON.DOM.SIT.DP1.00002.002.002.001.00042.003"
##  [39] "NEON.DOM.SIT.DP1.00002.002.002.001.00043.003"
##  [40] "NEON.DOM.SIT.DP1.00002.002.002.001.00044.003"
##  [41] "NEON.DOM.SIT.DP1.00002.001.003.001.00001.003"
##  [42] "NEON.DOM.SIT.DP1.00002.001.003.001.00002.003"
##  [43] "NEON.DOM.SIT.DP1.00002.001.003.001.00003.003"
##  [44] "NEON.DOM.SIT.DP1.00002.001.003.001.00005.003"
##  [45] "NEON.DOM.SIT.DP1.00002.001.003.001.00039.003"
##  [46] "NEON.DOM.SIT.DP1.00002.001.003.001.00040.003"
##  [47] "NEON.DOM.SIT.DP1.00002.001.003.001.00041.003"
##  [48] "NEON.DOM.SIT.DP1.00002.001.003.001.00042.003"
##  [49] "NEON.DOM.SIT.DP1.00002.001.003.001.00043.003"
##  [50] "NEON.DOM.SIT.DP1.00002.001.003.001.00044.003"
##  [51] "NEON.DOM.SIT.DP1.00002.002.003.001.00001.003"
##  [52] "NEON.DOM.SIT.DP1.00002.002.003.001.00002.003"
##  [53] "NEON.DOM.SIT.DP1.00002.002.003.001.00003.003"
##  [54] "NEON.DOM.SIT.DP1.00002.002.003.001.00005.003"
##  [55] "NEON.DOM.SIT.DP1.00002.002.003.001.00039.003"
##  [56] "NEON.DOM.SIT.DP1.00002.002.003.001.00040.003"
##  [57] "NEON.DOM.SIT.DP1.00002.002.003.001.00041.003"
##  [58] "NEON.DOM.SIT.DP1.00002.002.003.001.00042.003"
##  [59] "NEON.DOM.SIT.DP1.00002.002.003.001.00043.003"
##  [60] "NEON.DOM.SIT.DP1.00002.002.003.001.00044.003"
##  [61] "NEON.DOM.SIT.DP1.00002.001.004.001.00001.003"
##  [62] "NEON.DOM.SIT.DP1.00002.001.004.001.00002.003"
##  [63] "NEON.DOM.SIT.DP1.00002.001.004.001.00003.003"
##  [64] "NEON.DOM.SIT.DP1.00002.001.004.001.00005.003"
##  [65] "NEON.DOM.SIT.DP1.00002.001.004.001.00039.003"
##  [66] "NEON.DOM.SIT.DP1.00002.001.004.001.00040.003"
##  [67] "NEON.DOM.SIT.DP1.00002.001.004.001.00041.003"
##  [68] "NEON.DOM.SIT.DP1.00002.001.004.001.00042.003"
##  [69] "NEON.DOM.SIT.DP1.00002.001.004.001.00043.003"
##  [70] "NEON.DOM.SIT.DP1.00002.001.004.001.00044.003"
##  [71] "NEON.DOM.SIT.DP1.00002.002.004.001.00001.003"
##  [72] "NEON.DOM.SIT.DP1.00002.002.004.001.00002.003"
##  [73] "NEON.DOM.SIT.DP1.00002.002.004.001.00003.003"
##  [74] "NEON.DOM.SIT.DP1.00002.002.004.001.00005.003"
##  [75] "NEON.DOM.SIT.DP1.00002.002.004.001.00039.003"
##  [76] "NEON.DOM.SIT.DP1.00002.002.004.001.00040.003"
##  [77] "NEON.DOM.SIT.DP1.00002.002.004.001.00041.003"
##  [78] "NEON.DOM.SIT.DP1.00002.002.004.001.00042.003"
##  [79] "NEON.DOM.SIT.DP1.00002.002.004.001.00043.003"
##  [80] "NEON.DOM.SIT.DP1.00002.002.004.001.00044.003"
##  [81] "NEON.DOM.SIT.DP1.00002.001.005.001.00001.003"
##  [82] "NEON.DOM.SIT.DP1.00002.001.005.001.00002.003"
##  [83] "NEON.DOM.SIT.DP1.00002.001.005.001.00003.003"
##  [84] "NEON.DOM.SIT.DP1.00002.001.005.001.00005.003"
##  [85] "NEON.DOM.SIT.DP1.00002.001.005.001.00039.003"
##  [86] "NEON.DOM.SIT.DP1.00002.001.005.001.00040.003"
##  [87] "NEON.DOM.SIT.DP1.00002.001.005.001.00041.003"
##  [88] "NEON.DOM.SIT.DP1.00002.001.005.001.00042.003"
##  [89] "NEON.DOM.SIT.DP1.00002.001.005.001.00043.003"
##  [90] "NEON.DOM.SIT.DP1.00002.001.005.001.00044.003"
##  [91] "NEON.DOM.SIT.DP1.00002.002.005.001.00001.003"
##  [92] "NEON.DOM.SIT.DP1.00002.002.005.001.00002.003"
##  [93] "NEON.DOM.SIT.DP1.00002.002.005.001.00003.003"
##  [94] "NEON.DOM.SIT.DP1.00002.002.005.001.00005.003"
##  [95] "NEON.DOM.SIT.DP1.00002.002.005.001.00039.003"
##  [96] "NEON.DOM.SIT.DP1.00002.002.005.001.00040.003"
##  [97] "NEON.DOM.SIT.DP1.00002.002.005.001.00041.003"
##  [98] "NEON.DOM.SIT.DP1.00002.002.005.001.00042.003"
##  [99] "NEON.DOM.SIT.DP1.00002.002.005.001.00043.003"
## [100] "NEON.DOM.SIT.DP1.00002.002.005.001.00044.003"

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R package to interface with neon terms database.

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