RchivalTag (version 0.1.9)

resample_PDT: resample temperature at depth data from interpolated daily temperature at depth profiles or time series data

Description

interpolates depth-temperature data from a provided source (depth-temperature time series data or PDT data) and resamples the interpolated data by the depth time series data provided, to faciliate plot_DepthTempTS-plots even for tags with no temperature time series data or to improve interpolation results of the plot_DepthTempTS-plots from low-resolution depth-temperature time series data.

Usage

resample_PDT(ts_df, PDT, ...)
resample_DepthTempTS(ts_df, ...)

Value

a data.frame with depth-temperature time series data.

Arguments

ts_df

ts_df is a data.frame with depth-temperature time series data data or only depth time series data. Required columns are Depth for the depth data and a column containing temperature data, whose name is defined by Temp_field, by default Temperature.

PDT

an optional data.frame containing PDT-data from read_PDT.

...

additional arguments to be passed to interpolate_TempDepthProfiles, or interpolate_PDTs.

Author

Robert K. Bauer

References

Bauer, R., F. Forget and JM. Fromentin (2015) Optimizing PAT data transmission: assessing the accuracy of temperature summary data to estimate environmental conditions. Fisheries Oceanography, 24(6): 533-539, tools:::Rd_expr_doi("10.1111/fog.12127")

See Also

read_PDT, interpolate_TempDepthProfiles, get_thermalstrat, image_TempDepthProfiles

Examples

## read in depth temperature time series data (sampling rate 5min)
ts_file <- system.file("example_files/104659-Series.csv",package="RchivalTag")
ts_df <- read_TS(ts_file)
head(ts_df)

## run daily interpolation of depth temperature time series data
m <- interpolate_TempDepthProfiles(ts_df)
image_TempDepthProfiles(m$station.1)
ts_df2 <- resample_DepthTempTS(ts_df) ## reassign temperature at depth values

## read PDT data from same tag 
## (= low resolution depth temperature data (8 Depth and Temperature records per day))
path <- system.file("example_files",package="RchivalTag")
PDT <- read_PDT("104659-PDTs.csv",folder=path)
head(PDT)

m <- interpolate_PDTs(PDT) ## interpolate PDTs
image_TempDepthProfiles(m$station.1)
ts_df3 <- resample_PDT(ts_df, PDT) ## reassign temperature at depth values



#### plot results:
## 1) dot plots:

## dot plot of RECORDED depth temperature time series data
## plot_DepthTempTS(ts_df, do_interp = FALSE) 

## dot plot of RESAMPLED depth temperature time series data 
## from previously daily interpolated depth temperature time series data
# plot_DepthTempTS(ts_df2, do_interp = FALSE) 

## dot plot of RESAMPLED depth temperature time series data 
## from daily interpolated PDT data (external resampling)
# plot_DepthTempTS(ts_df3, do_interp = FALSE) 

## dot plot of RESAMPLED depth temperature time series data 
## from daily interpolated PDT data (internal resampling)
# plot_DepthTempTS_resampled_PDT(ts_df, PDT, do_interp = FALSE) 


## 2) line plots:

## line plot of depth temperature time series data
## (internal interpolation between neighboring temperature records)
## not recommended for low resolution time series data
# plot_DepthTempTS(ts_df, do_interp = TRUE) 

## line plot of depth temperature time series data 
## (based on internal daily interpolated depth temperature time series data)
# plot_DepthTempTS_resampled(ts_df, do_interp = TRUE) 

## line plot of depth temperature time series data 
## from daily interpolated PDT data (external resampling)
# plot_DepthTempTS(ts_df3, do_interp = TRUE) 

## line plot of depth temperature time series data
## from daily interpolated PDT data (internal resampling)
# plot_DepthTempTS_resampled_PDT(ts_df, PDT, do_interp = TRUE)