,
Meredith Harrison [ctb],
Patrick Lutz [ctb]| Title: | Process and Report 'GreenFeed' Data |
|---|---|
| Description: | Downloading, Processing, and Reporting 'GreenFeed' Data. The 'GreenFeed' system generates substantial amounts of daily data, which can be overwhelming for users. This package facilitates data retrieval and reporting from the 'GreenFeed' system using a streamlined process. Users can retrieve data from the 'C-Lock Inc.' system via an 'API' using the get_gfdata() function. Additionally, the report_gfdata() function allows users to generate both daily and final reports from 'GreenFeed' data. The process_gfdata() function further processes this data for analysis. For pellet intake processing and visit checks, the package also provides the pellin() and viseat() functions, ensuring a comprehensive toolset for managing and analyzing 'GreenFeed' data. |
| Authors: | Guillermo Martinez-Boggio [cre, aut, cph]
,
Meredith Harrison [ctb],
Patrick Lutz [ctb] |
| Maintainer: | Guillermo Martinez-Boggio <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.0.0.9000 |
| Built: | 2024-10-22 07:48:22 UTC |
| Source: | https://github.com/gmbog/greenfeedr |
Downloads daily 'GreenFeed' data from the 'C-Lock Inc.' server via an 'API'. Retrieves data based on specified parameters (login, date range and units), and provides a CSV file with the 'GreenFeed' daily data.
get_gfdata( user, pass, exp = NA, unit, start_date, end_date = Sys.Date(), save_dir = tempdir() )get_gfdata( user, pass, exp = NA, unit, start_date, end_date = Sys.Date(), save_dir = tempdir() )
user |
a character string representing the user name to logging into 'GreenFeed' system |
pass |
a character string representing password to logging into 'GreenFeed' system |
exp |
a character string representing study name or other study identifier. It is used as file name to save the data |
unit |
numeric or character vector, or a list representing one or more 'GreenFeed' unit numbers |
start_date |
a character string representing the start date of the study (format: "mm/dd/yyyy") |
end_date |
a character string representing the end date of the study (format: "mm/dd/yyyy") |
save_dir |
a character string representing the directory to save the output file |
A CSV file with daily 'GreenFeed' data in the specified directory
# Please replace "your_username" and "your_password" with your actual 'GreenFeed' credentials. user <- Sys.getenv("API_USER") pass <- Sys.getenv("API_PASS") exp <- "StudyName" start_date <- "2024-01-01" end_date <- Sys.Date() save_dir <- tempdir() # Example with units as a vector unit <- c(304, 305) get_gfdata(user, pass, exp, unit, start_date, end_date, save_dir)# Please replace "your_username" and "your_password" with your actual 'GreenFeed' credentials. user <- Sys.getenv("API_USER") pass <- Sys.getenv("API_PASS") exp <- "StudyName" start_date <- "2024-01-01" end_date <- Sys.Date() save_dir <- tempdir() # Example with units as a vector unit <- c(304, 305) get_gfdata(user, pass, exp, unit, start_date, end_date, save_dir)
Processes the "feedtimes" file from 'GreenFeed' system, including visits and food drops across a specific period, and it is used to calculate pellet intakes per animal from all units. Aggregates data to provide insights into the feeding behavior and pellet consumption of the animals during a study.
file_path |
a character string or list representing files(s) with "feedtimes" from 'C-Lock Inc.' |
unit |
numeric or character vector or list representing one or more 'GreenFeed' unit numbers. The order should match with "feedtimes" files |
gcup |
a numeric value representing the grams of pellets per cup. |
start_date |
a character string representing the start date of the study (format: "mm/dd/yyyy") |
end_date |
a character string representing the end date of the study (format: "mm/dd/yyyy") |
save_dir |
a character string representing the directory to save the output file |
rfid_file |
a character string representing the file with individual IDs. The order should be Visual ID (col1) and RFID (col2) |
An Excel file with pellet intakes for all animals and days within the specified period is saved to save_dir. The file is named "Pellet_Intakes_YYYY-MM-DD_YYYY-MM-DD.csv".
# You should provide the 'feedtimes' file provided by C-Lock. # it could be a list of files if you have data from multiple units to combine path <- list(system.file("extdata", "feedtimes.csv", package = "greenfeedr")) # You must include the grams of pellets per cup based on the result obtained from the 10-drops test # If the user include an rfid file, the structure should be in col1 AnimalName or Visual ID, and # col2 the RFID or TAG_ID. The file could be save in different formats (.xlsx, .csv, or .txt). RFIDs <- system.file("extdata", "RFID_file.csv", package = "greenfeedr") pellin( file_path = path, unit = 1, gcup = 34, start_date = "2024-05-13", end_date = "2024-05-25", save_dir = tempdir(), rfid_file = RFIDs )# You should provide the 'feedtimes' file provided by C-Lock. # it could be a list of files if you have data from multiple units to combine path <- list(system.file("extdata", "feedtimes.csv", package = "greenfeedr")) # You must include the grams of pellets per cup based on the result obtained from the 10-drops test # If the user include an rfid file, the structure should be in col1 AnimalName or Visual ID, and # col2 the RFID or TAG_ID. The file could be save in different formats (.xlsx, .csv, or .txt). RFIDs <- system.file("extdata", "RFID_file.csv", package = "greenfeedr") pellin( file_path = path, unit = 1, gcup = 34, start_date = "2024-05-13", end_date = "2024-05-25", save_dir = tempdir(), rfid_file = RFIDs )
Processes and calculates daily and weekly averages of 'GreenFeed' data. Handles data filtering, aggregation, and summarization to facilitate further analysis.
data |
a data frame with daily or finalized 'GreenFeed' data |
start_date |
a character string representing the start date of the study (format: "mm/dd/yyyy") |
end_date |
a character string representing the end date of the study (format: "mm/dd/yyyy") |
param1 |
an integer representing the number of records per day to be consider for analysis |
param2 |
an integer representing the number of days with records per week to be consider for analysis |
min_time |
an integer representing the minimum number of minutes for a records to be consider for analysis. By default min_time is 2 |
A list of two data frames:
daily_data |
data frame with daily processed 'GreenFeed' data |
weekly_data |
data frame with weekly processed 'GreenFeed' data |
file <- system.file("extdata", "StudyName_GFdata.csv", package = "greenfeedr") datafile <- readr::read_csv(file) gf_data <- process_gfdata( data = datafile, start_date = "2024-05-13", end_date = "2024-05-25", param1 = 2, param2 = 3, min_time = 2 ) head(gf_data)file <- system.file("extdata", "StudyName_GFdata.csv", package = "greenfeedr") datafile <- readr::read_csv(file) gf_data <- process_gfdata( data = datafile, start_date = "2024-05-13", end_date = "2024-05-25", param1 = 2, param2 = 3, min_time = 2 ) head(gf_data)
Generates PDF reports of daily and final 'GreenFeed' data. If the option daily is used, data is retrieved from 'C-Lock Inc.' server via an 'API' and generates a PDF report to with number of animals, records, and gases production. However, if the option final is used, the finalized data should be provided to generates a PDF report to evaluate all 'GreenFeed' data obtained from the finalized study.
input_type |
a character string representing type of data (options: "daily" and "final") |
exp |
a character string representing study name or other study identifier. It is used as file name to save the data |
unit |
numeric or character vector, or a list representing one or more 'GreenFeed' unit numbers |
start_date |
a character string representing the start date of the study (format: "mm/dd/yyyy") |
end_date |
a character string representing the end date of the study (format: "mm/dd/yyyy") |
save_dir |
a character string representing the directory to save the output file |
plot_opt |
a character string representing the gas(es) to plot (options: "All", "CH4", "CO2", "O2", "H2") |
rfid_file |
a character string representing the file with individual IDs. The order should be Visual ID (col1) and RFID (col2) |
user |
a character string representing the user name to logging into 'GreenFeed' system. If input_type is "final", this parameter is ignored |
pass |
a character string representing password to logging into 'GreenFeed' system. If input_type is "final", this parameter is ignored |
file_path |
A list of file paths containing the final report(s) from the 'GreenFeed' system. If input_type is "final", this parameter is ignored |
A CSV file with daily 'GreenFeed' data and a PDF report with a description of the daily or final records
# Please replace "your_username" and "your_password" with your actual 'GreenFeed' credentials. user <- Sys.getenv("API_USER") pass <- Sys.getenv("API_PASS") # The data range must be fewer than 180 days # Example without rfid_file (by default NA) report_gfdata( input_type = "daily", exp = "StudyName", unit = 1, start_date = "2023-01-01", end_date = Sys.Date(), save_dir = tempdir(), plot_opt = "All" )# Please replace "your_username" and "your_password" with your actual 'GreenFeed' credentials. user <- Sys.getenv("API_USER") pass <- Sys.getenv("API_PASS") # The data range must be fewer than 180 days # Example without rfid_file (by default NA) report_gfdata( input_type = "daily", exp = "StudyName", unit = 1, start_date = "2023-01-01", end_date = Sys.Date(), save_dir = tempdir(), plot_opt = "All" )
Processes 'GreenFeed' visits and food drops for a requested period. Generates a list of animals not visiting the 'GreenFeed' to manage them, and a description of animals visiting the 'GreenFeed'.
file_path |
a character string or list representing files(s) with feedtimes from 'C-Lock Inc.'. |
unit |
numeric or character vector or list representing one or more GreenFeed unit numbers. |
start_date |
a character string representing the start date of the study (format: "mm/dd/yyyy") |
end_date |
a character string representing the end date of the study (format: "mm/dd/yyyy") |
rfid_file |
a character string representing the file with individual RFIDs. The order should be Visual ID (col1) and RFID (col2) |
A list of two data frames:
visits_per_unit |
Data frame with daily processed 'GreenFeed' data, including columns for VisualID, Date, Time, number of drops, and visits. |
visits_per_animal |
Data frame with weekly processed 'GreenFeed' data, including columns for VisualID, total drops, total visits, mean drops, and mean visits. |
# You should provide the feedtimes files. # it could be a list of files if you have data from multiple units to combine path <- list(system.file("extdata", "feedtimes.csv", package = "greenfeedr")) # If the user include an rfid file, the structure should be in col1 AnimalName or VisualID, and # col2 the RFID or TAG_ID. The file could be save in different formats (.xlsx, .csv, or .txt). RFIDs <- system.file("extdata", "RFID_file.csv", package = "greenfeedr") data <- viseat( file_path = path, unit = 1, start_date = "2024-05-13", end_date = "2024-05-25", rfid_file = RFIDs )# You should provide the feedtimes files. # it could be a list of files if you have data from multiple units to combine path <- list(system.file("extdata", "feedtimes.csv", package = "greenfeedr")) # If the user include an rfid file, the structure should be in col1 AnimalName or VisualID, and # col2 the RFID or TAG_ID. The file could be save in different formats (.xlsx, .csv, or .txt). RFIDs <- system.file("extdata", "RFID_file.csv", package = "greenfeedr") data <- viseat( file_path = path, unit = 1, start_date = "2024-05-13", end_date = "2024-05-25", rfid_file = RFIDs )