Metadata Correction

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 1.0.0
-Date: 2024-10-16 14:11:39 UTC
-SHA: b738b472e7bfe04747898a65e8d48087fd328caa
+Date: 2024-10-16 15:48:00 UTC
+SHA: 06aa2c9af8d8b20b0846068ab9528f46a691e462

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: greenfeedr
 Type: Package
-Title: Process and Report GreenFeed Data
+Title: Process and Report 'GreenFeed' Data
 Version: 1.0.0
 Authors@R: 
   c(
@@ -16,12 +16,14 @@ Authors@R:
            role = c("ctb"))
     )
 Maintainer: Guillermo Martinez-Boggio <[email protected]>
-Description: Functions for downloading, processing, and reporting GreenFeed data. The
-    GreenFeed system generates large amount of daily data that could be overwhelming for users.
-    So, the first step is to retrieve data from C-Lock system so use `get_gfdata()` to download via API.
-    Also, other function such as `report_gfdata()` allows to download and report daily and final data from GreenFeed.
-    The function `process_gfdata()` process daily or final data for further analysis. Two more functions as
-    `pellin()` and `viseat()` helps for processing and checking pellet intakes and visits to the GreenFeed.
+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' 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.
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true

R/get_gfdata.R

@@ -1,23 +1,22 @@
 #' @name get_gfdata
-#' @title Download Daily GreenFeed Data via API
+#' @title Download Daily 'GreenFeed' Data via 'API'
 #'
-#' @description Downloads daily GreenFeed data from the C-Lock Inc. server
-#'     via an application programming interface (API). Retrieves data
-#'     based on specified parameters such as login information, date range and units,
-#'     and provides an Excel file with the GreenFeed data.
+#' @description 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.
 #'
-#' @param user a character string representing the user name to logging into GreenFeed system
-#' @param pass a character string representing password to logging into GreenFeed system
+#' @param user a character string representing the user name to logging into 'GreenFeed' system
+#' @param pass a character string representing password to logging into 'GreenFeed' system
 #' @param exp a character string representing study name or other study identifier. It is used as file name to save the data
-#' @param unit numeric or character vector, or a list representing one or more GreenFeed unit numbers
+#' @param unit numeric or character vector, or a list representing one or more 'GreenFeed' unit numbers
 #' @param start_date a character string representing the start date of the study (format: "mm/dd/yyyy")
 #' @param end_date a character string representing the end date of the study (format: "mm/dd/yyyy")
 #' @param save_dir a character string representing the directory to save the output file
 #'
-#' @return A CSV file with daily GreenFeed data in the specified directory
+#' @return A CSV file with daily 'GreenFeed' data in the specified directory
 #'
 #' @examplesIf has_credentials()
-#' # Please replace "your_username" and "your_password" with your actual GreenFeed credentials.
+#' # Please replace "your_username" and "your_password" with your actual 'GreenFeed' credentials.
 #' user <- Sys.getenv("API_USER")
 #' pass <- Sys.getenv("API_PASS")
 #' exp <- "StudyName"
@@ -36,7 +35,7 @@
 #' @import stringr
 
 get_gfdata <- function(user, pass, exp = NA, unit,
-                       start_date, end_date = Sys.Date(), save_dir = getwd()) {
+                       start_date, end_date = Sys.Date(), save_dir = tempdir()) {
   # Ensure unit is a comma-separated string
   unit <- convert_unit(unit)
 
@@ -54,7 +53,7 @@ get_gfdata <- function(user, pass, exp = NA, unit,
     "https://portal.c-lockinc.com/api/getemissions?d=visits&fids=", unit,
     "&st=", start_date, "&et=", end_date, "%2012:00:00"
   )
-  print(URL)
+  message(URL)
 
   req <- httr::POST(URL, body = list(token = TOK))
   httr::stop_for_status(req)

R/pellin.R

@@ -1,21 +1,21 @@
 #' @name pellin
-#' @title Process GreenFeed Pellet Intakes
+#' @title Process 'GreenFeed' Pellet Intakes
 #'
-#' @description Processes the feedtimes file from GreenFeed system,
+#' @description 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.
 #'
-#' @param file_path a character string or list representing files(s) with feedtimes from C-Lock
-#' @param unit numeric or character vector or list representing one or more GreenFeed unit numbers. The order should match with feedtimes files
+#' @param file_path a character string or list representing files(s) with "feedtimes" from 'C-Lock Inc.'
+#' @param unit numeric or character vector or list representing one or more 'GreenFeed' unit numbers. The order should match with "feedtimes" files
 #' @param gcup a numeric value representing the grams of pellets per cup.
 #' @param start_date a character string representing the start date of the study (format: "mm/dd/yyyy")
 #' @param end_date a character string representing the end date of the study (format: "mm/dd/yyyy")
 #' @param save_dir a character string representing the directory to save the output file
-#' @param rfid_file a character string representing the file with individual IDs. The order should be AnimalName (col1) and RFID (col2)
+#' @param rfid_file a character string representing the file with individual IDs. The order should be Visual ID (col1) and RFID (col2)
 #'
-#' @return An Excel file with pellet intakes for all animals and days within the specified period is saved to `save_dir`.
+#' @return 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".
 #'
 #' @examples
@@ -25,7 +25,7 @@
 #'
 #' # 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 VisualID, and
+#' # 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")
 #'
@@ -56,7 +56,7 @@ utils::globalVariables(c(
 ))
 
 pellin <- function(file_path, unit, gcup, start_date, end_date,
-                   save_dir = getwd(), rfid_file = NULL) {
+                   save_dir = tempdir(), rfid_file = NULL) {
   message("Please set the 'gcup' parameter based on the 10-drops test.
            If units have different gram values, define 'gcup' as a vector with an element for each unit.")
 
@@ -88,7 +88,7 @@ pellin <- function(file_path, unit, gcup, start_date, end_date,
 
 
 
-  # If rfid_file provided, filter and get animal ID not visiting the GreenFeed units
+  # If rfid_file provided, filter and get animal ID not visiting the 'GreenFeed' units
   if (!is.null(rfid_file) && is.data.frame(rfid_file) && nrow(rfid_file) > 0) {
     df <- df[df$CowTag %in% rfid_file$RFID, ]
     noGFvisits <- rfid_file$FarmName[!(rfid_file$RFID %in% df$CowTag)]

R/process_gfdata.R

@@ -1,20 +1,19 @@
 #' @name process_gfdata
-#' @title Process Daily and Final GreenFeed Data
+#' @title Process Daily and Final 'GreenFeed' Data
 #'
-#' @description Processes and calculates daily and weekly averages of GreenFeed data.
-#'     Handles data filtering, aggregation, and summarization to facilitate
-#'     further analysis and reporting.
+#' @description Processes and calculates daily and weekly averages of 'GreenFeed' data.
+#'     Handles data filtering, aggregation, and summarization to facilitate further analysis.
 #'
-#' @param data a data frame with daily or finalized GreenFeed data
+#' @param data a data frame with daily or finalized 'GreenFeed' data
 #' @param start_date a character string representing the start date of the study (format: "mm/dd/yyyy")
 #' @param end_date a character string representing the end date of the study (format: "mm/dd/yyyy")
 #' @param param1 an integer representing the number of records per day to be consider for analysis
 #' @param param2 an integer representing the number of days with records per week to be consider for analysis
 #' @param min_time an integer representing the minimum number of minutes for a records to be consider for analysis. By default min_time is 2
 #'
 #' @return A list of two data frames:
-#'   \item{daily_data }{data frame with daily processed GreenFeed data}
-#'   \item{weekly_data }{data frame with weekly processed GreenFeed data}
+#'   \item{daily_data }{data frame with daily processed 'GreenFeed' data}
+#'   \item{weekly_data }{data frame with weekly processed 'GreenFeed' data}
 #'
 #' @examples
 #' file <- system.file("extdata", "StudyName_GFdata.csv", package = "greenfeedr")
@@ -25,7 +24,8 @@
 #'   start_date = "2024-05-13",
 #'   end_date = "2024-05-25",
 #'   param1 = 2,
-#'   param2 = 3
+#'   param2 = 3,
+#'   min_time = 2
 #' )
 #' head(gf_data)
 #'
@@ -229,17 +229,17 @@ process_gfdata <- function(data, start_date, end_date,
 
 
   # Description of mean, sd, and CV for weekly gases
-  print(paste0("CH4: ", round(mean(weekly_df$CH4GramsPerDay, na.rm = TRUE), 2), " +- ", round(stats::sd(weekly_df$CH4GramsPerDay, na.rm = TRUE), 2)))
-  print(paste0("CH4 CV = ", round(stats::sd(weekly_df$CH4GramsPerDay, na.rm = TRUE) / mean(weekly_df$CH4GramsPerDay, na.rm = TRUE) * 100, 1), "%"))
+  message(paste0("CH4: ", round(mean(weekly_df$CH4GramsPerDay, na.rm = TRUE), 2), " +- ", round(stats::sd(weekly_df$CH4GramsPerDay, na.rm = TRUE), 2)))
+  message(paste0("CH4 CV = ", round(stats::sd(weekly_df$CH4GramsPerDay, na.rm = TRUE) / mean(weekly_df$CH4GramsPerDay, na.rm = TRUE) * 100, 1), "%"))
 
-  print(paste0("CO2: ", round(mean(weekly_df$CO2GramsPerDay, na.rm = TRUE), 2), " +- ", round(stats::sd(weekly_df$CO2GramsPerDay, na.rm = TRUE), 2)))
-  print(paste0("CO2 CV = ", round(stats::sd(weekly_df$CO2GramsPerDay, na.rm = TRUE) / mean(weekly_df$CO2GramsPerDay, na.rm = TRUE) * 100, 1), "%"))
+  message(paste0("CO2: ", round(mean(weekly_df$CO2GramsPerDay, na.rm = TRUE), 2), " +- ", round(stats::sd(weekly_df$CO2GramsPerDay, na.rm = TRUE), 2)))
+  message(paste0("CO2 CV = ", round(stats::sd(weekly_df$CO2GramsPerDay, na.rm = TRUE) / mean(weekly_df$CO2GramsPerDay, na.rm = TRUE) * 100, 1), "%"))
 
-  print(paste0("O2: ", round(mean(weekly_df$O2GramsPerDay, na.rm = TRUE), 2), " +- ", round(stats::sd(weekly_df$O2GramsPerDay, na.rm = TRUE), 2)))
-  print(paste0("O2 CV = ", round(stats::sd(weekly_df$O2GramsPerDay, na.rm = TRUE) / mean(weekly_df$O2GramsPerDay, na.rm = TRUE) * 100, 1), "%"))
+  message(paste0("O2: ", round(mean(weekly_df$O2GramsPerDay, na.rm = TRUE), 2), " +- ", round(stats::sd(weekly_df$O2GramsPerDay, na.rm = TRUE), 2)))
+  message(paste0("O2 CV = ", round(stats::sd(weekly_df$O2GramsPerDay, na.rm = TRUE) / mean(weekly_df$O2GramsPerDay, na.rm = TRUE) * 100, 1), "%"))
 
-  print(paste0("H2: ", round(mean(weekly_df$H2GramsPerDay, na.rm = TRUE), 2), " +- ", round(stats::sd(weekly_df$H2GramsPerDay, na.rm = TRUE), 2)))
-  print(paste0("H2 CV = ", round(stats::sd(weekly_df$H2GramsPerDay, na.rm = TRUE) / mean(weekly_df$H2GramsPerDay, na.rm = TRUE) * 100, 1), "%"))
+  message(paste0("H2: ", round(mean(weekly_df$H2GramsPerDay, na.rm = TRUE), 2), " +- ", round(stats::sd(weekly_df$H2GramsPerDay, na.rm = TRUE), 2)))
+  message(paste0("H2 CV = ", round(stats::sd(weekly_df$H2GramsPerDay, na.rm = TRUE) / mean(weekly_df$H2GramsPerDay, na.rm = TRUE) * 100, 1), "%"))
 
 
   # Return a list of data frames

R/report_gfdata.R

@@ -1,28 +1,28 @@
 #' @name report_gfdata
-#' @title Download and Report GreenFeed Data
+#' @title Download and Report 'GreenFeed' Data
 #'
-#' @description Generates PDF reports of daily and final GreenFeed data.
-#'     If option "daily" is used, data is retrieved from C-Lock server via an application programming interface (API)
-#'     and generates a PDF report to with number of animals, records, and gas production of the ongoing study.
-#'     But, if option "final" is used, final data should be provided to generates a PDF report
-#'     to evaluate all GreenFeed data obtained from the finalized study.
+#' @description 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.
 #'
-#' @param input_type a character string representing type of data (options: "daily" or "final")
+#' @param input_type a character string representing type of data (options: "daily" and "final")
 #' @param exp a character string representing study name or other study identifier. It is used as file name to save the data
-#' @param unit numeric or character vector, or a list representing one or more GreenFeed unit numbers
+#' @param unit numeric or character vector, or a list representing one or more 'GreenFeed' unit numbers
 #' @param start_date a character string representing the start date of the study (format: "mm/dd/yyyy")
 #' @param end_date a character string representing the end date of the study (format: "mm/dd/yyyy")
 #' @param save_dir a character string representing the directory to save the output file
-#' @param plot_opt a character string representing the gas(es) to plot (options: 'All', 'CH4', 'CO2', 'O2', 'H2')
-#' @param rfid_file a character string representing the file with individual IDs. The order should be AnimalName (col1) and RFID (col2)
-#' @param user a character string representing the user name to logging into GreenFeed system. If `input_type` is "final", this parameter is ignored
-#' @param pass a character string representing password to logging into GreenFeed system. If `input_type` is "final", this parameter is ignored
-#' @param 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
+#' @param plot_opt a character string representing the gas(es) to plot (options: "All", "CH4", "CO2", "O2", "H2")
+#' @param rfid_file a character string representing the file with individual IDs. The order should be Visual ID (col1) and RFID (col2)
+#' @param user a character string representing the user name to logging into 'GreenFeed' system. If input_type is "final", this parameter is ignored
+#' @param pass a character string representing password to logging into 'GreenFeed' system. If input_type is "final", this parameter is ignored
+#' @param 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
 #'
-#' @return A CSV file with daily GreenFeed data and a PDF report with a description of the daily or final records
+#' @return A CSV file with daily 'GreenFeed' data and a PDF report with a description of the daily or final records
 #'
 #' @examplesIf has_credentials()
-#' # Please replace "your_username" and "your_password" with your actual GreenFeed credentials.
+#' # Please replace "your_username" and "your_password" with your actual 'GreenFeed' credentials.
 #' user <- Sys.getenv("API_USER")
 #' pass <- Sys.getenv("API_PASS")
 #'
@@ -54,7 +54,7 @@
 utils::globalVariables(c("GoodDataDuration", "StartTime", "AirflowLitersPerSec", "Gas_Data"))
 
 report_gfdata <- function(input_type, exp = NA, unit, start_date, end_date = Sys.Date(),
-                          save_dir = getwd(), plot_opt = "CH4", rfid_file = NULL,
+                          save_dir = tempdir(), plot_opt = "CH4", rfid_file = NULL,
                           user = NA, pass = NA, file_path) {
   # Ensure unit is a comma-separated string
   unit <- convert_unit(unit)
@@ -84,12 +84,12 @@ report_gfdata <- function(input_type, exp = NA, unit, start_date, end_date = Sys
       "https://portal.c-lockinc.com/api/getemissions?d=visits&fids=", unit,
       "&st=", start_date, "&et=", end_date, "%2012:00:00"
     )
-    print(URL)
+    message(URL)
 
     req <- httr::POST(URL, body = list(token = TOK))
     httr::stop_for_status(req)
     a <- httr::content(req, as = "text")
-    print(a)
+    message(a)
 
     # Split the lines
     perline <- stringr::str_split(a, "\\n")[[1]]
@@ -126,7 +126,7 @@ report_gfdata <- function(input_type, exp = NA, unit, start_date, end_date = Sys
       dir.create(save_dir, recursive = TRUE)
     }
 
-    # Save GreenFeed data as a csv file in the specified directory
+    # Save 'GreenFeed' data as a csv file in the specified directory
     readr::write_excel_csv(df, file = paste0(save_dir, "/", exp, "_GFdata.csv"))
 
 
@@ -142,7 +142,7 @@ report_gfdata <- function(input_type, exp = NA, unit, start_date, end_date = Sys
       }
     }
 
-    # Dataframe (df) contains daily GreenFeed data
+    # Dataframe (df) contains daily 'GreenFeed' data
     df <- df %>%
       ## Remove "unknown IDs" and leading zeros from RFID col
       dplyr::filter(RFID != "unknown") %>%
@@ -205,7 +205,7 @@ report_gfdata <- function(input_type, exp = NA, unit, start_date, end_date = Sys
         "AirflowCf"
       )
 
-      # df contains finalized GreenFeed data
+      # df contains finalized 'GreenFeed' data
       df <- df %>%
         ## Remove "unknown IDs" and leading zeros from RFID col
         dplyr::filter(RFID != "unknown") %>%