Making the package build

.gitignore

@@ -1,2 +1,3 @@
-
 .DS_Store
+.Rproj.user
+fish-tracking.Rproj

scripts/packages/fishtracking/DESCRIPTION

@@ -9,5 +9,8 @@ Description: This package will help you manage fish tracking telemetry data. It
 Depends: R (>= 3.1.0)
 License: GPL
 LazyData: true
-Imports: testthat
-Suggests: testthat
+Imports: 
+  lubridate,
+  DBI
+Suggests: 
+  testthat

scripts/packages/fishtracking/NAMESPACE

@@ -1 +1,10 @@
-exportPattern(".")
+# Generated by roxygen2 (4.1.1): do not edit by hand
+
+export(input2store)
+export(merge_files)
+export(parse_date)
+export(parse_station)
+export(read_input)
+export(validate_data)
+importFrom(DBI,dbWriteTable)
+importFrom(lubridate,parse_date_time)

scripts/packages/fishtracking/R/input2store.R

@@ -16,23 +16,24 @@
 #' following columns: Date.Time, Receiver.id, Receiver.Name, Transmitter.id
 #' @examples
 #' read_input("VR2W_122340_20141010_1.csv")
+#' @export
 read_input <- function (filename) {
   data <- read.csv(filename, sep=",", stringsAsFactors=FALSE)
-  if (length(colnames(data)) == 14) {
+  if (ncol(data) == 14) {
     # inbo format. Date header should be "Date.Time"
     if (colnames(data)[1] == "Date.Time") {
       outdata <- data[, c("Date.Time", "Receiver.Name", "Station.Name")]
       colnames(outdata) <- c("Date.Time", "Receiver.id", "Receiver.Name")
       outdata$Transmitter.id <- paste(data$Code.Space, data$ID, sep="-")
     }
-  } else if (length(colnames(data)) == 10) {
+  } else if (ncol(data) == 10) {
     # vliz format. Field 2 should be "Receiver"
     if (colnames(data)[2] == "Receiver") {
       colnames(data)[1] <- "Date.and.Time"
       outdata <- data[, c("Date.and.Time", "Receiver","Station.Name", "Transmitter")]
       colnames(outdata) <- c("Date.Time", "Receiver.id", "Receiver.Name", "Transmitter.id")
     }
-  } else if (length(colnames(data)) == 11) {
+  } else if (ncol(data) == 11) {
     # VUE export format. Field 1 should be "DateTimeUTC"
     if (colnames(data)[1] == "DateTimeUTC") {
       outdata <- data[, c("DateTimeUTC", "Receiver", "ReceiverCode", "Transmitter")]
@@ -56,13 +57,12 @@ read_input <- function (filename) {
 #' with the columns Date.Time, Receiver.id, Receiver.Name, Transmitter.id
 #' @examples
 #' merge_files("/path/to/directory/")
+#' @export
 merge_files <- function (directory) {
-  if (substr(directory, length(directory), length(directory)) != "/") {
-    directory = paste(directory, "/", sep="")
-  }
-  csvfiles = Sys.glob(paste(directory, "*.csv", sep=""))
-  contents = lapply(csvfiles, read_input)
-  ldply(contents)
+  directory <- normalizePath(directory, winslash = "/", mustWork = TRUE)
+  csvfiles = Sys.glob(paste(directory, "/*.csv", sep=""))
+  contents <- lapply(csvfiles, read_input)
+  do.call(rbind, contents)
 }
 
 
@@ -81,12 +81,14 @@ merge_files <- function (directory) {
 #' @examples
 #' # should return c("2000-03-21 13:21:42", "1952-04-15 09:00:31", NA, NA)
 #' parse_date(c("2000-03-21 13:21:42", "15-04-1952 09:00:31", "03-31-2004 03:49:23", "31-02-2004 04:29:42"))
+#' @export
+#' @importFrom lubridate parse_date_time
 parse_date <- function (dateStr) {
-  # check format "yyyy-mm-dd hh:mm:ss"
-  result1 = strptime(dateStr, "%Y-%m-%d %H:%M:%S")
-   # check format "dd-mm-yyyy hh:mm:ss"
-  result2 = strptime(dateStr, "%d-%m-%Y %H:%M:%S")
-  result1[is.na(result1)] <- result2[is.na(result1)]
+  result1 <- parse_date_time(
+    dateStr, 
+    orders = c("Y-m-d H:M:S", "d-m-Y H:M:S"),
+    tz = ""
+  )
   return(as.character(result1))
 }
 
@@ -98,6 +100,7 @@ parse_date <- function (dateStr) {
 #' 
 #' @param stations Vector containing station names
 #' @return Vector containing valid station names or NA's
+#' @export
 parse_station <- function(stations) {
 	result = grepl(".*-[0-9]*-[0-9]*", stations)
 	stations[!result] <- NA
@@ -112,19 +115,29 @@ parse_station <- function(stations) {
 #' @return TRUE if data is ok
 #' @examples
 #' validate_data(data)
+#' @export
 validate_data <- function(indata) {
   indata$Date.Time <- parse_date(indata$Date.Time)
   indata$Receiver.Name <- parse_station(indata$Receiver.Name)
-  ok = TRUE
-  if (sum(is.na(indata$Date.Time)) > 0) {
-  	print(paste("invalid dates found at rows: ", paste(which(is.na(indata$Date.Time)), collapse=",")))
-  	ok = FALSE
+  if (anyNA(indata$Date.Time)) {
+  	stop(
+      "invalid dates found at rows: ", 
+      paste(
+        which(is.na(indata$Date.Time)), 
+        collapse=","
+      )
+    )
   }
-  if (sum(is.na(indata$Receiver.Name)) > 0) {
-  	print(paste("invalid receiver names found at rows: ", paste(which(is.na(indata$Receiver.Name)), collapse=",")))
-  	ok = FALSE
+  if (anyNA(indata$Receiver.Name)) {
+  	stop(
+      "invalid receiver names found at rows: ", 
+      paste(
+        which(is.na(indata$Receiver.Name)), 
+        collapse=","
+      )
+    )
   }
-  return(ok)
+  return(invisible(TRUE))
 }
 
 #================================
@@ -139,12 +152,10 @@ validate_data <- function(indata) {
 #' @return Nothing
 #' @examples
 #' input2store("/path/to/input/directory/")
+#' @export
+#' @importFrom DBI dbWriteTable
 input2store <- function(dbConnection, directory) {
   data <- merge_files(directory)
   validatedData <- validate_data(data)
-  if (validatedData) {
-  	dbWriteTable(dbConnection, "detections", validatedData, overwrite=FALSE, append=TRUE)
-  } else {
-  	print("errors found during validation. Nothing written to database.")
-  }
-}
+  dbWriteTable(dbConnection, "detections", validatedData, overwrite=FALSE, append=TRUE)
+}

scripts/packages/fishtracking/man/input2store.Rd

@@ -1,10 +1,10 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/input2store.R
 \name{input2store}
 \alias{input2store}
 \title{Migrate input data to data store}
 \usage{
-input2store(directory)
+input2store(dbConnection, directory)
 }
 \arguments{
 \item{directory}{The directory containing the tracking data}

scripts/packages/fishtracking/man/merge_files.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/input2store.R
 \name{merge_files}
 \alias{merge_files}

scripts/packages/fishtracking/man/parse_date.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/input2store.R
 \name{parse_date}
 \alias{parse_date}

scripts/packages/fishtracking/man/parse_station.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/input2store.R
 \name{parse_station}
 \alias{parse_station}

scripts/packages/fishtracking/man/read_input.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/input2store.R
 \name{read_input}
 \alias{read_input}

scripts/packages/fishtracking/man/validate_data.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.0): do not edit by hand
+% Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/input2store.R
 \name{validate_data}
 \alias{validate_data}