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R function to read SBE CTD cnv-files into data.frame

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read and plot SBE CTD cnv-files

Marko Lipka, David Kaiser 2021-05-05

read.cnv.file() function takes a filename of a .cnv file as argument and returns a data.frame.

plot.CTD.data() function

  • takes the output of read.cnv.file() and returns a facetted ggplot.
  • optional arguments:
    • depvar: character (vector) of parameter(s) that should be used as depth axis. First match in parameter names will be used if multiple parameters are defined.
    • not2plot: character (vector) of parameter(s) that should not be plotted. default is a list of common metadata parameters like “scan”, “nbin”, “flag”, “latitude”, …

extract.stats() function takes a filename of a .cnv file or the output of read.cnv.file() as argument and returns summary statistics of each parameter.

extract.stats.dir() function takes a directory as argument and returns summary statistics of each parameter in each .cnv file in the given directory.

map.CTD.data() function

  • takes a directory as argument
  • finds and read.cnv.file() all cnv files in this directory
  • creates a dynamic point map which popups the plot.CTD.data()-plot on click

Examples

V0001F01.cnv

Ex1 <- read.cnv.file("example data/IOW/V0001F01.cnv")

knitr::kable(head(Ex1$data))
depSM prDM c0mS.cm c1mS.cm t090C t190C sal00 sal11 sbeox0ML.L sbeox1ML.L svCM oxsatML.L altM par spar flECO.AFL turbWETntu0 nbf upoly0 upoly1 timeS scan sigma.é00 flag nbin
1.50 1.36001 14.16115 14.16036 6.1272 6.1251 13.2087 13.2088 8.65394 8.74601 1447.91 7.95670 17.55465 402.87 1012.2 1.4015 0.29254 0 0.04206 0.04201 -3.638 -86 10.3704 0 92
1.75 1.61264 14.16280 14.16364 6.1245 6.1219 13.2115 13.2133 8.65493 8.72731 1447.90 7.95708 16.83636 386.34 1241.7 1.2540 0.29134 0 0.04205 0.04213 14.117 340 10.3727 0 95
2.00 1.86478 14.16379 14.16305 6.1236 6.1211 13.2128 13.2130 8.65435 8.73503 1447.91 7.95719 16.97811 365.78 1247.6 1.3204 0.29062 0 0.04192 0.04212 17.178 413 10.3738 0 68
2.25 2.11683 14.16334 14.16383 6.1227 6.1207 13.2126 13.2138 8.65487 8.74630 1447.91 7.95737 16.75866 336.83 1246.8 1.3079 0.29237 0 0.04172 0.04213 18.940 456 10.3737 0 34
2.50 2.36962 14.16532 14.16366 6.1229 6.1206 13.2145 13.2137 8.65615 8.72256 1447.91 7.95724 16.53253 306.92 1250.1 1.3161 0.29388 0 0.04189 0.04196 20.410 491 10.3752 0 31
2.75 2.62119 14.16302 14.16275 6.1224 6.1208 13.2122 13.2126 8.65235 8.73113 1447.91 7.95746 16.25545 282.55 1245.4 1.3918 0.28734 0 0.04177 0.04188 21.853 525 10.3735 0 41 
pander(Ex1$meta)

ReiseNr = EMB-100, StationNr= 0001, EinsatzNr= 0001, SerieNr = 01 Operator= Kiki, StatBez = STOL aus .eMission., Startzeit= 09:18:13 09-APR-15, GPS_Posn = 54 15.3678N 11 56.7485E, Echolote = 18.54 m, Luftdruck= 1028.6 hPa, ThermoSal= 6.274 grdC 13.02 ppth and WsStartID= 1

pander(Ex1$coords)
  • Lat: 54 15.3678N
  • Lon: 11 56.7485E
plot.CTD.data(Ex1)

knitr::kable(extract.stats(Ex1))
parameter Min. 1st Qu. Median Mean 3rd Qu. Max.
depSM 1.50000 5.50000 9.50000 9.500000e+00 13.50000 17.50000
prDM 1.36001 5.39597 9.43236 9.432500e+00 13.46876 17.50504
c0mS.cm 14.16115 14.18255 14.43783 1.469591e+01 14.80368 16.65272
c1mS.cm 14.16036 14.17993 14.43694 1.469836e+01 14.80367 16.65273
t090C 5.11450 5.73350 5.85950 5.843791e+00 6.10280 6.12720
t190C 5.11340 5.73160 5.85680 5.840982e+00 6.10160 6.12510
sal00 13.20870 13.23940 13.58380 1.387377e+01 14.02030 16.22560
sal11 13.20880 13.23730 13.58560 1.387746e+01 14.02080 16.22670
sbeox0ML.L 7.93073 8.51706 8.63803 8.550225e+00 8.66173 8.69804
sbeox1ML.L 7.99170 8.59136 8.71539 8.619413e+00 8.74519 8.77727
svCM 1447.26000 1447.39000 1447.68000 1.447675e+03 1447.91000 1448.21000
oxsatML.L 7.94831 7.95861 7.97670 7.977887e+00 7.99410 8.01248
altM 1.14989 4.99694 9.26731 9.270412e+00 13.43070 17.55465
par 3.24560 10.45500 36.60100 8.514989e+01 115.30000 402.87000
spar 1012.20000 1181.20000 1219.40000 1.223674e+03 1260.10000 1320.50000
flECO.AFL 1.25400 1.70370 4.70550 4.226457e+00 6.25550 8.14330
turbWETntu0 0.23239 0.29955 0.33523 3.362509e-01 0.37339 0.41291
nbf 0.00000 2.00000 3.00000 2.769231e+00 4.00000 5.00000
upoly0 0.04151 0.04194 0.04214 4.214062e-02 0.04236 0.04270
upoly1 0.04154 0.04196 0.04219 4.217492e-02 0.04238 0.04266
timeS -3.63800 36.06700 56.78000 5.660052e+01 77.34400 112.32000
scan -86.00000 867.00000 1364.00000 1.359477e+03 1857.00000 2697.00000
sigma.é00 10.37040 10.39620 10.68220 1.091262e+01 11.03640 12.81770
flag 0.00000 0.00000 0.00000 0.000000e+00 0.00000 0.00000
nbin 27.00000 30.00000 31.00000 4.261538e+01 32.00000 618.00000

P0009F01.cnv

Ex2 <- read.cnv.file("example data/IOW/P0009F01.cnv")

knitr::kable(head(Ex2$data))
depSM prDM c0mS.cm t090C sal00 sbeox0ML.L svCM oxsatML.L altM spar flECO.AFL turbWETntu0 nbf latitude longitude timeS scan sigma.é00 flag nbin
6.00 5.94454 23.47002 14.4042 18.2368 6.44049 1485.34 6.38187 120.4128 0 0.28637 0.46429 0 44.697 31.4564 15.945 384 13.2020 0 710
6.25 6.19658 23.47004 14.4042 18.2368 6.44113 1485.34 6.38188 123.2926 0 0.28241 0.46385 0 44.697 31.4564 29.884 718 13.2019 0 17
6.50 6.44872 23.47012 14.4042 18.2368 6.44125 1485.35 6.38188 131.2332 0 0.27295 0.46274 0 44.697 31.4564 30.678 737 13.2020 0 19
6.75 6.70098 23.47121 14.4062 18.2367 6.44137 1485.36 6.38161 129.1096 0 0.27584 0.46556 0 44.697 31.4564 31.517 757 13.2016 0 23
7.00 6.95274 23.47125 14.4059 18.2369 6.44155 1485.36 6.38165 126.9133 0 0.28945 0.46188 0 44.697 31.4564 32.671 785 13.2017 0 34
7.25 7.20464 23.47110 14.4056 18.2368 6.44189 1485.36 6.38171 135.6922 0 0.28379 0.47353 0 44.697 31.4564 34.233 823 13.2018 0 36 
pander(Ex2$meta)

StationNr= 0009, EinsatzNr= 0009, SerieNr = 01 Operator= Krueger, StatBez = MSM33/28 aus .eMission., Startzeit= 03:41:07 12-Nov-13, GPS_Posn = 44 41.8229N 031 27.3851E, Echolote = m 153.2 m, Luftdruck= 1023.7 hPa, ThermoSal= 14.408 grdC 18.254 ppth and WsStartID= 76

pander(Ex2$coords)
  • Lat: 44 41.82 N
  • Lon: 031 27.38 E
plot.CTD.data(Ex2)

plot.CTD.data(Ex2, depvar = "prDM")

plot.CTD.data(Ex2, depvar = "sigma.é00", not2plot = c("flag", "nbin", "nbf", "upoly0", "upoly1"))

plot.CTD.data(Ex2, not2plot = "par")

knitr::kable(extract.stats(Ex2))
parameter Min. 1st Qu. Median Mean 3rd Qu. Max.
depSM 6.000000 44.3750000 82.750000 82.7500000 121.125000 159.50000
prDM 5.944540 44.6371600 83.337350 83.3422434 122.045085 160.76025
c0mS.cm 20.477365 20.8868860 21.332397 21.8644415 23.054894 23.47625
t090C 7.861800 7.8905000 8.313400 9.1691005 8.574650 14.41040
sal00 18.233800 18.6450500 19.223500 19.4156091 20.485600 21.07180
sbeox0ML.L -0.011130 0.2700600 2.807190 2.9985646 5.210405 6.64871
svCM 1462.900000 1463.8200000 1465.300000 1468.9153171 1469.785000 1485.61000
oxsatML.L 6.381040 7.1362900 7.257620 7.1239137 7.335025 7.35166
altM 0.183810 40.2139050 79.066310 76.5849562 114.381920 151.16043
spar 0.000000 0.0000000 0.000000 0.0000000 0.000000 0.00000
flECO.AFL 0.016421 0.0341325 0.048649 0.1080484 0.187315 0.42177
turbWETntu0 0.412690 0.4210050 0.454410 0.5643113 0.515245 1.36128
nbf 0.000000 0.0000000 0.000000 0.0000000 0.000000 0.00000
latitude 44.697000 44.6970000 44.697000 44.6970000 44.697000 44.69700
longitude 31.456400 31.4564000 31.456400 31.4564000 31.456400 31.45640
timeS 15.945000 221.5885000 413.403000 415.4409593 605.760500 1147.09500
scan 384.000000 5319.0000000 9923.000000 9971.5772358 14539.500000 27531.00000
sigma.é00 13.201100 14.4521500 14.928000 14.8975966 15.855100 16.28920
flag 0.000000 0.0000000 0.000000 0.0000000 0.000000 0.00000
nbin 7.000000 27.0000000 30.000000 40.9170732 34.000000 3800.00000

Summary statistics of both files

extract.stats.dir("example data/IOW/")
## # A tibble: 45 x 8
##    source         parameter  Min.    `1st Qu.`  Median  Mean    `3rd Qu.` Max.  
##    <chr>          <chr>      <table> <table>    <table> <table> <table>   <tabl>
##  1 example data/… depSM         6.0…   44.37500   82.7…   82.7…  121.125…  159.…
##  2 example data/… prDM          5.9…   44.63716   83.3…   83.3…  122.045…  160.…
##  3 example data/… c0mS.cm      20.4…   20.88689   21.3…   21.8…   23.054…   23.…
##  4 example data/… t090C         7.8…    7.89050    8.3…    9.1…    8.574…   14.…
##  5 example data/… sal00        18.2…   18.64505   19.2…   19.4…   20.485…   21.…
##  6 example data/… sbeox0ML.L   -0.0…    0.27006    2.8…    2.9…    5.210…    6.…
##  7 example data/… svCM       1462.9… 1463.82000 1465.3… 1468.9… 1469.785… 1485.…
##  8 example data/… oxsatML.L     6.3…    7.13629    7.2…    7.1…    7.335…    7.…
##  9 example data/… altM          0.1…   40.21390   79.0…   76.5…  114.381…  151.…
## 10 example data/… spar          0.0…    0.00000    0.0…    0.0…    0.000…    0.…
## # … with 35 more rows

Example CNV-files from other sources

Savannah

via mail and with kind permission from SimplySav101

Sav <- read.cnv.file("example data/Savannah/2017-03-10T075604 SBE02501006.cnv")

knitr::kable(head(Sav$data))
prdM t090C c0uS.cm sbox0Mm.Kg flECO.AFL turbWETntu0 upoly0 upoly1 flag
0.124 5.1496 9.369485 -100.279 -0.3196 -0.2622 0.0475319 0.0485237 0
0.118 5.1406 9.369485 508.636 -0.3188 -0.2619 0.0476081 0.0486000 0
0.115 5.1311 9.540741 1010.594 -0.3196 -0.2619 0.0475319 0.0485237 0
0.121 5.1225 9.637391 549.142 -0.3203 -0.2622 0.0476081 0.0485237 0
0.109 5.1139 9.564480 717.860 -0.3196 -0.2622 0.0475319 0.0485237 0
0.111 5.1053 9.954473 841.882 -0.3196 -0.2622 0.0476081 0.0486000 0 
pander(Sav$meta)

Station: SH, Depth: 50.0 m, Latitude: 60 40.277 N, Longitude: 145 52.522 W, AKST (time): 10 Mar 2017 07:56, Cruise: LTM2017-01 and Comment: Touched bottom

pander(Sav$coords)
  • Lat: 60 40.277 N
  • Lon: 145 52.522 W
plot.CTD.data(Sav)

knitr::kable(extract.stats(Sav))
parameter Min. 1st Qu. Median Mean 3rd Qu. Max.
prdM 0.0420000 1.839000e+00 1.852000e+00 8.363139e+00 2.415500e+00 51.934000
t090C 0.0309000 4.580100e+00 4.753800e+00 4.739716e+00 5.225400e+00 5.365300
c0uS.cm 5.4633120 3.035425e+04 3.051600e+04 2.964673e+04 3.109000e+04 31183.000000
sbox0Mm.Kg -100.2790000 2.749352e+02 2.775220e+02 2.698899e+02 2.803083e+02 1334.778000
flECO.AFL -0.8300000 1.908000e-01 2.038000e-01 2.423933e-01 2.168000e-01 4.422900
turbWETntu0 -0.4457000 7.738000e-01 8.041000e-01 1.456253e+00 8.581000e-01 19.540000
upoly0 0.0302129 1.149615e+00 1.519493e+00 1.488448e+00 1.895171e+00 3.267491
upoly1 0.0309758 2.976272e-01 3.242542e-01 3.374228e-01 3.485161e-01 1.230106
flag 0.0000000 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000

Github

path_CNVs <- "example data/fromGithub"

files <- list.files(path = path_CNVs, 
                    pattern = "\\.cnv$",
                    full.names = TRUE,
                    recursive = T, ignore.case = T)

for(file in files){
    print(file)
    import <- read.cnv.file(file)
    print(plot.CTD.data(import))
}
## [1] "example data/fromGithub/from castelao_seabird/dPIRX003.cnv"

## Warning: Removed 2 row(s) containing missing values (geom_path).


## [1] "example data/fromGithub/from castelao_seabird/dPIRX010.cnv"


## [1] "example data/fromGithub/from castelao_seabird/Hotin.cnv"


## [1] "example data/fromGithub/from castelao_seabird/PIRA001.cnv"


## [1] "example data/fromGithub/from castelao_seabird/sta0860.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_01.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_02.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_03.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_04.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_05.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_06.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_07.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_08.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_09.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/dradmed_10.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/ds2_02.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/ds2_03.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/ds2_04.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/ds2_05.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/ds2_06.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/ds2_07.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/ds2_08.cnv"


## [1] "example data/fromGithub/from cmunozmas_plot_raw_ctd/ds2_085.cnv"


## [1] "example data/fromGithub/from labons_cnv_reader/PIRA001.cnv"


## [1] "example data/fromGithub/from NatalyaEvans_cnv_concatenator/Station00_test_cast1.cnv"


## [1] "example data/fromGithub/from NatalyaEvans_cnv_concatenator/Station01_test_cast2.cnv"

Dynamic map

only a screenshot of the dynamic map can be shown on github

map.CTD.data("example data/IOW/")

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R function to read SBE CTD cnv-files into data.frame

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