read_TS: reads Time Series Data from Archival Tags

In RchivalTag: Analyzing and Interactive Visualization of Archival Tagging Data

reads Time Series Data from Archival Tags

Description

reads Time Series Data (e.g. Depth and Temperature) from Archival Tags (Supported Models: MiniPAT, sPAT, recovered mk10, mk9 from Wildlife Computers as well as LOTEK PSAT Models LOTEK. Models from other Manufactorers might be supported as well.

Usage

read_TS(ts_file, header=TRUE, sep=",", skip = 0, 
        date_format, lang_format = "en", tz = "UTC")

Arguments

ts_file	character string indicating the name of a standard Wildlife Computers file to read or the data.frame of a manually loaded histogram data file. The file is assumed to include the columns Day, Time (or a preformatted date-time vector termed datetime in "UTC" format.) as well as at one of the subsequent columns DeployID, Ptt and Serial to distinguish data from indiviudal tags.
header	a logical value indicating whether the file contains the names of the variables as its first line. If missing, the value is determined from the file format: header is set to TRUE if and only if the first row contains one fewer field than the number of columns.
sep	the field separator character. Values on each line of the file are separated by this character. If sep = "" the separator is 'white space', that is one or more spaces, tabs, newlines or carriage returns.
skip	integer: the number of lines of the data file to skip before beginning to read data.
date_format, lang_format, tz	character strings indicating the date format, language format and the corresponding time zone, defined by the vectors Date and Time (by default: date_format="%d-%b-%Y %H:%M:%S", lang_format="en", tz='UTC') If formatting fails, please check as well the input language format, defined by lang_format (and use abbrviations such as "en" for English,"es" for Spanish, "fr" for French, etc.) as well.

Details

This function reads a time series data file from archival tags. Data sets are "completed" to facilitate an assessment of the data coverage (i.e. by ts2histos or hist_tad).

Value

A data frame (data.frame) containing a representation of the data in the file.

Author(s)

Robert K. Bauer

See Also

ts2histos, hist_tad, plot_TS

Examples

### load sample depth and temperature time series data from miniPAT:
ts_file <- system.file("example_files/104659-Series.csv",package="RchivalTag")
ts_df <- read_TS(ts_file)
head(ts_df)

## other date_format:
ts_file2 <- system.file("example_files/104659-Series_date_format2.csv",package="RchivalTag")
# ts_miniPAT2 <- read_TS(ts_file2) # run to see error message
ts_miniPAT2 <- read_TS(ts_file2,date_format = "%d-%m-%Y %H:%M:%S")
head(ts_miniPAT2)

## other date_format and lang_format:
ts_file_ES <- system.file("example_files/104659-Series_date_format_ES.csv",package="RchivalTag")
# ts_miniPAT_ES <- read_TS(ts_file_ES) # run to see error message
ts_miniPAT_ES <- read_TS(ts_file_ES,skip=1,sep=";",header = TRUE, 
                         date_format = "%d/%b/%y %H:%M:%S",lang_format = "es")
head(ts_miniPAT_ES)


## load same data in LOTEK format
ts_file <- system.file("example_files/104659_PSAT_Dive_Log.csv",package="RchivalTag")
ts_df <- read_TS(ts_file,date_format="%m/%d/%Y %H:%M:%S")
head(ts_df) ## attention no identifier (Ptt, Serial, DeployID) included!
ts_df$DeployID <- ts_df$Ptt <- "104659"

## example 1) convert only DepthTS data to daily TaD frequencies:
tad_breaks <- c(0, 2, 5, 10, 20, 50, 100, 200, 300, 400, 600, 2000)
tat_breaks <- c(10,12,15,17,18,19,20,21,22,23,24,27)

histos <- ts2histos(ts_df, tad_breaks = tad_breaks, tat_breaks = tat_breaks)
histos$TAD$merged$df$nperc ## check completeness of TAD data sets
histos$TAT$merged$df$nperc ## check completeness of TAT data sets
# histos <- ts2histos(ts_df, tad_breaks = tad_breaks, tat_breaks = tat_breaks,min_perc = 90)


### example 2) add daytime (Day vs Night) information and plot results
# add daytime periods during plot-function call and return extended data set
# ts_df$Lon <- 5; ts_df$Lat <- 43
# plot_DepthTS(ts_df, plot_DayTimePeriods = TRUE, xlim = unique(ts_df$date)[2:3])
# ts_df2 <- plot_DepthTS(ts_df, plot_DayTimePeriods = TRUE, Return = TRUE) 
# names(ts_df)
# names(ts_df2)

### add daytime periods before function call
# ts_df_extended <- get_DayTimeLimits(ts_df)
# plot_DepthTS(ts_df_extended, plot_DayTimePeriods = TRUE)
# plot_DepthTS(ts_df_extended, plot_DayTimePeriods = TRUE, twilight.set = "naut")

RchivalTag documentation built on Nov. 10, 2023, 5:06 p.m.