Read SBE bottle file

David Kaiser 2018/01/19

Description

This function reads bottle files produced during Seabird Electronics CTD casts. It was written for data recorded during various cruises by the IOW and some adjustments might be necessary before application to data recorded elsewhere. However, the function offers optional input of identifiers for geographic position, cruise name, station name, and the station's bottom depth. The idea is that the user knows any character string that identifies these meta variables in the header of the .btl file and the function finds the corresponding position in the file using grep() and extracts the values using sub().

Arguments

filename -- the file to be imported

position.identifer -- any string identifying the GPS position in the header, defaults to "GPS_Posn",

cruise.identifier -- any string identifying the curise name in the header, defaults to "ReiseNr",

station.identifier -- any string identifying the station name in the header, defaults to "StationNr",

bottom.identifier -- any string identifying the station depth in the header, defaults to "Echolote"

Format requirements

Currently the identifiers must have a format of ".*= (.*)" where "(.*)" contains the value.

Examples

Ex1 <- read_btl_DK("example_data/EMB.btl")
Ex2 <- read_btl_DK("example_data/POS.btl")

Full data frame

Each record is represented by 4 lines in the table:

• average,
• standard deviation,
• minimum,
• maximum (see column statistic)

library(pander)

pander(Ex1$data, emphasize.strong.rows = which(Ex1$data$statistic == "(avg)"))

Table continues below

Btl_Posn	Date	DepSM	PrDM	C0mS.cm
10	Dec 06 2014 09:11:53	6.444	6.502	8.629
10	Dec 06 2014 09:11:53	0.054	0.055	0.000143
10	Dec 06 2014 09:11:53	6.363	6.42	8.628
10	Dec 06 2014 09:11:53	6.547	6.606	8.629
11	Dec 06 2014 09:12:01	6.539	6.598	8.63
11	Dec 06 2014 09:12:01	0.089	0.09	0.001851
11	Dec 06 2014 09:12:01	6.418	6.476	8.628
11	Dec 06 2014 09:12:01	6.712	6.772	8.634

Table continues below

C1mS.cm	T090C	T190C	Sal00	Sal11	Sbeox0ML.L
8.629	8.035	8.034	7.321	7.321	7.666
0.000147	7e-04	7e-04	1e-04	1e-04	0.0058
8.629	8.034	8.033	7.321	7.321	7.654
8.629	8.036	8.036	7.321	7.321	7.671
8.629	8.041	8.033	7.321	7.321	7.662
0.000368	0.0088	0.002	2e-04	1e-04	0.0055
8.628	8.034	8.028	7.32	7.321	7.653
8.629	8.061	8.035	7.321	7.322	7.669

Sbeox1ML.L	Par	Spar	FlECO.AFL	TurbWETntu0	statistic	Btl_ID
7.643	3.78	28.93	0.8226	0.1008	(avg)	61
0.0046	0.1193	1.349e-06	0.0428	0.0081	(sdev)	61
7.631	3.579	28.93	0.7176	0.0889	(min)	61
7.646	3.969	28.93	0.908	0.1182	(max)	61
7.646	3.775	28.93	0.7726	0.0928	(avg)	62
5e-04	0.1762	1.349e-06	0.0207	0.0099	(sdev)	62
7.646	3.497	28.93	0.7469	0.0742	(min)	62
7.647	4.015	28.93	0.8201	0.1084	(max)	62

pander(Ex1$meta)

• filename: example_data/EMB.btl
• cruise: EMB-91
• station: 0001
• bottom: 56.34
• position: ** GPS_Posn = 55 43.6488N 17 43.7241E
• longitude decdeg: 17.73
• longitude decdir: E
• latitude decdeg: 55.73
• latitude decdir: N

Only averages

pander(subset(Ex2$data, statistic == "(avg)"))

Table continues below

	Btl_Posn	Date	DepSM	PrDM	C0mS.cm	T090C
1	1	May 28 2014 12:46:59	519.2	523.7	40.52	11.62
5	2	May 28 2014 12:47:04	519.2	523.7	40.52	11.63
9	3	May 28 2014 12:47:07	518.6	523.1	40.52	11.63
13	4	May 28 2014 12:47:14	518.5	523	40.52	11.63
17	5	May 28 2014 12:47:16	518.6	523.1	40.52	11.63
21	6	May 28 2014 12:47:19	519.1	523.6	40.52	11.63
25	7	May 28 2014 12:47:21	519.4	523.9	40.52	11.63
29	8	May 28 2014 12:47:23	519.4	523.9	40.52	11.63
33	10	May 28 2014 12:47:29	518.6	523.1	40.52	11.63
37	11	May 28 2014 12:47:32	519.2	523.7	40.52	11.63
41	12	May 28 2014 12:47:35	519	523.5	40.52	11.63
45	13	May 28 2014 12:47:37	518.4	522.9	40.52	11.63
49	14	May 28 2014 12:47:39	518.6	523.1	40.52	11.63

Table continues below

	T190C	Sal00	Sbeox0ML.L	SvCM	OxsatML.L	FlECO.AFL
1	11.63	35.63	4.389	1505	6.076	0.0198
5	11.63	35.63	4.389	1505	6.075	0.0225
9	11.63	35.63	4.394	1505	6.075	0.026
13	11.63	35.63	4.392	1505	6.075	0.0075
17	11.63	35.63	4.392	1505	6.075	0.0162
21	11.63	35.63	4.395	1505	6.075	0.0133
25	11.63	35.63	4.406	1505	6.075	0.0112
29	11.63	35.63	4.394	1505	6.075	0.0144
33	11.63	35.63	4.391	1505	6.075	0.0112
37	11.63	35.63	4.403	1505	6.075	0.0223
41	11.63	35.63	4.397	1505	6.075	0.0173
45	11.63	35.63	4.396	1505	6.075	0.0144
49	11.63	35.63	4.399	1505	6.075	0.0227

	TurbWETntu0	Latitude	Longitude	statistic	Btl_ID
1	0.038	36.67	-16.23	(avg)	27
5	0.0404	36.67	-16.23	(avg)	28
9	0.0339	36.67	-16.23	(avg)	29
13	0.0353	36.67	-16.23	(avg)	30
17	0.0343	36.67	-16.23	(avg)	31
21	0.0362	36.67	-16.23	(avg)	32
25	0.0362	36.67	-16.23	(avg)	33
29	0.0351	36.67	-16.23	(avg)	34
33	0.0405	36.67	-16.23	(avg)	36
37	0.0378	36.67	-16.23	(avg)	37
41	0.0337	36.67	-16.23	(avg)	38
45	0.0386	36.67	-16.23	(avg)	39
49	0.0394	36.67	-16.23	(avg)	40

pander(Ex2$meta)

• filename: example_data/POS.btl
• cruise: POS-470
• station: 0001
• bottom: 4027.41 m
• position: ** GPS_Posn = 36 40.2677N 16 14.0217W
• longitude decdeg: 16.23
• longitude decdir: W
• latitude decdeg: 36.67
• latitude decdir: N

Issues / ToDo's

Time: date and time are currently class character, need to be changed to strptime, but the user can of course do that in post Generalization: as described above, the function was build for a specific data set and should become more generally useable with time