README.md

In scoyoc/dataprocessR: Import Data into the SEUG LTVMP Database

dataprocessR

This package processes plant and ground cover data collected in the field and imports them to the Southeast Utah Group (SEUG) Long-term Vegetation Monitoring Program (LTVMP) database. Plant cover and frequency and ground cover data are collected in the field using paper datasheets, then transcribed into Excel workbooks. This package imports the workbook files into R, restructures the data, then exports them to the database. Onset data loggers collect temperature, relative humidity, and precipitation data that are exported to comma delimited files (*.csv) using the HOBOware application from Onset. The raindancer package is used to import these data into R and summarize them; this package then exports the processed data to the SEUG LTVMP database.

Version: 1.0.0

Depends: R (>= 4.0)

Imports: dplyr, glue, lubridate, raindancer, RODBC, stringr, tibble, tidyr

Author: Matthew Van Scoyoc

Maintainer: Matthew Van Scoyoc

Issues: https://github.com/scoyoc/dataprocessR/issues

License: MIT + file LICENSE

URL: https://github.com/scoyoc/dataprocessR

Documentation: Vignette and man pages.

Installation

devtools::install_github("scoyoc/dataprocessR", build_vignettes = TRUE)

Examples

library("dataprocessR")

# Connect to DB ----
my_db <- RODBC::odbcConnectAccess2007("C:/path/to/database.accdb")

# Process weather data ----
#-- List files
wx_dir <- "C:/path/to/data"
wx_files <- list.files(wx_dir, pattern = ".csv", full.names = TRUE,
                       recursive = FALSE)
#-- Process a single file
export_hobo(my_file = wx_files[1], my_db = my_db,
            import_table = "tblWxImportLog",
            raw_data_table = "tblWxData_raw",
            prcp_data_table = "tblWxData_PRCP",
            temp_rh_data_table = "tblWxData_TEMP_RH",
            details_table = "tblWxLoggerDetails")

#-- Batch process several files
lapply(wx_files[2:10], function(this_file){
  export_hobo(my_file = this_file, my_db = my_db,
              import_table = "tblWxImportLog",
              raw_data_table = "tblWxData_raw",
              prcp_data_table = "tblWxData_PRCP",
              temp_rh_data_table = "tblWxData_TEMP_RH",
              details_table = "tblWxLoggerDetails",
              view = FALSE)
})

# Process plant and ground cover data ----
#-- List files
veg_dir <- "C:/pate/to/data"
veg_files <- list.files(veg_dir, pattern = ".xls", full.names = TRUE, 
                        recursive = FALSE)

#-- Process a single file
export_xls(my_xls = veg_files[1], my_db = my_db,
           data_table = tblData_FreqCov,
           sampling_event_table = tblSamplingEvent,
           import_table = tblImportRecord)

#-- Batch process several files
lapply(veg_files[2:10], function(this_xls){
  export_xls(my_xls = this_xls, my_db = my_db,
             data_table = tblData_FreqCov,
             sampling_event_table = tblSamplingEvent,
             import_table = tblImportRecord,
             view = FALSE)
})

# Close database ----
RODBC::odbcClose(my_db); rm(my_db)

scoyoc/dataprocessR documentation built on March 11, 2023, 6:02 a.m.