bbest commented 2 years ago

From: Shonna Dovel sdovel@ucsd.edu Date: Thu, Mar 17, 2022 at 2:39 PM Subject: Re: [CalCOFI] Question regarding station data from our server To: Erin Satterthwaite esatterthwaite@ucsd.edu, Ben ben@ecoquants.com Cc: Renae Logston rlogston@ucsd.edu, Kelsey Vogel kdvogel@ucsd.edu

Hi Ben and Erin,

While the CalCOFI website is being updated, the CCE-LTER site has a few ways to map the CalCOFI grid.

http://cce.lternet.edu/data/gmt-mapper

Please see the attachment for the desired Lat/Longs for the 66 station cast. Please let me know if you need the SCCOOS and northern lines as well. Cheers, Shonna

GMT Map

More Links

This interface uses GMT v4.1.1 with the following data files:

Bathymetry and Coastline Files

cce2min.grd - 2-minute resolution Long/Lat/Elevation data for the CCE region, in the GMT-compatible grid format. Originally obtained from the National Geophysical Data Center's Global Relief page.
coastline.txt - CCE region coastline and islands as a series of decimal Long/Lat points. Islands and coastline are separated with a comment (#) character. Originally obtained from the National Geophysical Data Center's Global Coastline Extractor page.

Station and Feature Files

Cruise Data - Cruise specific points can be found on their respective cruise pages.

bbest commented 2 years ago

CalCOFI staion LatLong.xlsx - Google Sheets

Order	Line	Sta	Lat deg	Lat mins	Lon deg	Lon mins	Lon Dec	Lat Dec
1	93.3	26.7	32	57.4	117	18.3	-117.31	32.96
2	93.3	28	32	54.8	117	23.7	-117.4	32.91
3	93.3	30	32	50.8	117	31.9	-117.53	32.85
4	93.3	35	32	40.8	117	52.4	-117.87	32.68
5	93.3	40	32	30.8	118	12.8	-118.21	32.51
6	93.3	45	32	20.8	118	33.3	-118.56	32.35
7	93.3	50	32	10.8	118	53.6	-118.89	32.18
8	93.3	55	32	0.8	119	14	-119.23	32.01
9	93.3	60	31	50.8	119	34.3	-119.57	31.85
10	93.3	70	31	30.8	120	14.8	-120.25	31.51
11	93.3	80	31	10.8	120	55.2	-120.92	31.18
12	93.3	90	30	50.8	121	35.4	-121.59	30.85
13	93.3	100	30	30.8	122	15.5	-122.26	30.51
14	93.3	110	30	10.8	122	55.4	-122.92	30.18
15	93.3	120	29	50.8	123	35.2	-123.59	29.85
16	90	120	30	25.1	123	59.9	-124	30.42
17	90	110	30	45.1	123	19.9	-123.33	30.75
18	90	100	31	5.1	122	39.7	-122.66	31.09
19	90	90	31	25.1	121	59.4	-121.99	31.42
20	90	80	31	45.1	121	18.9	-121.32	31.75
21	90	70	32	5.1	120	38.3	-120.64	32.09
22	90	60	32	25.1	119	57.6	-119.96	32.42
23	90	53	32	39.1	119	28.9	-119.48	32.65
24	90	45	32	55.1	118	56.1	-118.94	32.92
25	90	37	33	11.1	118	23.2	-118.39	33.19
26	90	35	33	15.1	118	15	-118.25	33.25
27	90	30	33	25.1	117	54.3	-117.91	33.42
28	90	28	33	29.1	117	46.1	-117.77	33.49
29	86.7	33	33	53.4	118	29.4	-118.49	33.89
30	86.7	35	33	49.4	118	37.7	-118.63	33.82
31	86.7	40	33	39.4	118	58.5	-118.98	33.66
32	86.7	45	33	29.4	119	19.1	-119.32	33.49
33	86.7	50	33	19.4	119	39.8	-119.66	33.32
34	86.7	55	33	9.4	120	0.4	-120.01	33.16
35	86.7	60	32	59.4	120	21	-120.35	32.99
36	86.7	70	32	39.4	121	2	-121.03	32.66
37	86.7	80	32	19.4	121	42.9	-121.72	32.32
38	86.7	90	31	59.4	122	23.6	-122.39	31.99
39	86.7	100	31	39.4	123	4.2	-123.07	31.66
40	86.7	110	31	19.4	123	44.6	-123.74	31.32
41	83.3	110	31	54.7	124	10.2	-124.17	31.91
42	83.3	100	32	14.7	123	29.5	-123.49	32.25
43	83.3	90	32	34.7	122	48.7	-122.81	32.58
44	83.3	80	32	54.7	122	7.7	-122.13	32.91
45	83.3	70	33	14.7	121	26.6	-121.44	33.25
46	83.3	60	33	34.7	120	45.3	-120.76	33.58
47	83.3	55	33	44.7	120	24.6	-120.41	33.75
48	83.3	51	33	52.7	120	8	-120.13	33.88
49	83.3	42	34	10.7	119	30.5	-119.51	34.18
50	83.3	40.6	34	13.5	119	24.7	-119.41	34.23
51	81.8	46.9	34	16.5	120	1.5	-120.03	34.28
52	80	51	34	27	120	31.4	-120.52	34.45
53	80	55	34	19	120	48.1	-120.8	34.32
54	80	60	34	9	121	9	-121.15	34.15
55	80	70	33	49	121	50.6	-121.84	33.82
56	80	80	33	29	122	32	-122.53	33.48
57	80	90	33	9	123	13.3	-123.22	33.15
58	80	100	32	49	123	54.4	-123.91	32.82
59	76.7	100	33	23.3	124	19.4	-124.32	33.39
60	76.7	90	33	43.3	123	38	-123.63	33.72
61	76.7	80	34	3.3	122	56.5	-122.94	34.06
62	76.7	70	34	23.3	122	14.8	-122.25	34.39
63	76.7	60	34	43.3	121	32.9	-121.55	34.72
64	76.7	55	34	53.3	121	11.9	-121.2	34.89
65	76.7	51	35	1.3	120	55.1	-120.92	35.02
66	76.7	49	35	5.3	120	46.6	-120.78	35.09

bbest commented 2 years ago

From: @evsatt Date: Mon, Mar 21, 2022 at 2:35 PM Subject: lat lon & line station transformation info from Ed

Hey Ben, Got this from Ed in another email but made me think of our call last week: "The CalCOFI line/station transform has been incorporated into the Proj C library years ago. This means that you can do line/station <--> lat/lon transformations (or any other geographic projection) in just about any language that calls the library (R, Python, Matlab, ...) including PostGIS, I think. This may come in handy for front-end tools or queries."

CalCOFI in `proj` library

PROJ/calcofi.rst at e3d7e18f988230973ced5163fa2581b6671c8755 · OSGeo/PROJ:

Cal Coop Ocean Fish Invest Lines/Stations

The CalCOFI pseudo-projection is the line and station coordinate system of the California Cooperative Oceanic Fisheries Investigations program, known as CalCOFI, for sampling offshore of the west coast of the U.S. and Mexico.

Cal Coop Ocean Fish Invest Lines/Stations The CalCOFI pseudo-projection is the line and station coordinate system of the California Cooperative Oceanic Fisheries Investigations program, known as CalCOFI, for sampling offshore of the west coast of the U.S. and Mexico.

bbest commented 2 years ago

small set

Starting with CalCOFI staion LatLong.xlsx - Google Sheets

librarian::shelf(
  glue, here, dplyr, mapview, readr, sf)

stations_csv <- here("data-raw/CalCOFI station LatLong.csv")

stations <- read_csv(stations_csv) %>%
  rename_with(tolower) %>%
  select(order, line, sta, lon = `lon dec`, lat = `lat dec`) %>%
  mutate(
    line_sta = glue("{line} {sta}") %>% as.character(),
    offshore = ifelse(sta > 60, T, F)) %>%
  st_as_sf(
    coords = c("lon", "lat"), crs=4326, remove = F)

mapviewOptions(fgb = FALSE)
mapview(stations, zcol = "offshore")

usethis::use_data(stations, overwrite = TRUE)

bbest commented 2 years ago

See:

Weber, E. D., & Moore, T. J. (2013). Corrected conversion algorithms for the CalCOFI station grid and their implementation in several computer languages. Calif. Coop. Oceanic Fish. Invest. Rep, 54, 97-106.

bbest commented 2 years ago

https://proj.org/operations/projections/calcofi.html?highlight=calcofi

bbest commented 2 years ago

Noticing at http://cce.lternet.edu/data/gmt-mapper, other station identifier columns to include besides California Current Ecosystem (CCE):

bbest commented 2 years ago

Hi @superjai,

The stations data are ready for documentation. Please see stations column descriptions below

After git pull latest https://github.com/CalCOFI/calcofi4r and in that RStudio project...

devtools::load_all()
stations

Simple feature collection with 2634 features and 10 fields
Geometry type: POINT
Dimension:     XY
Bounding box:  xmin: -153.165 ymin: 17.40827 xmax: -107.1261 ymax: 47.94102
Geodetic CRS:  WGS 84
# A tibble: 2,634 × 11
   Sta_ID  Sta_ID_line Sta_ID_station is_cast   lon   lat offshore             geometry is_calcofi66 is_cce is_sccoos
   <glue>        <dbl>          <dbl> <lgl>   <dbl> <dbl> <lgl>             <POINT [°]> <lgl>        <lgl>  <lgl>    
 1 001.0 …           1          168   TRUE    -141.  44.2 TRUE      (-140.5967 44.2332) NA           NA     NA       
 2 001.0 …           1          264.  TRUE    -148.  41.0 TRUE     (-148.0675 41.04987) NA           NA     NA       
 3 002.0 …           2           65.7 TRUE    -132.  47.5 TRUE        (-131.9775 47.47) NA           NA     NA       
 4 004.0 …           4           86   TRUE    -133.  46.4 TRUE     (-133.3855 46.44692) NA           NA     NA       
 5 004.0 …           4           88   TRUE    -134.  46.4 TRUE     (-133.5524 46.38025) NA           NA     NA       
 6 004.0 …           4           99   TRUE    -134.  46.0 TRUE      (-134.467 46.01359) NA           NA     NA       
 7 004.0 …           4          104   TRUE    -135.  45.8 TRUE     (-134.8807 45.84692) NA           NA     NA       
 8 004.0 …           4          121   TRUE    -136.  45.3 TRUE      (-136.278 45.28025) NA           NA     NA       
 9 004.0 …           4          138.  TRUE    -138.  44.7 TRUE     (-137.7018 44.69692) NA           NA     NA       
10 004.0 …           4          156.  TRUE    -139.  44.1 TRUE     (-139.0872 44.12359) NA           NA     NA

names(stations) %>% paste(collapse = "\n- ") %>% cat()

`stations` column descriptions

Sta_ID: Station ID
Sta_ID_line: line component of the Station ID
Sta_ID_station: station component of the Station ID
lon: longitude, decimal degrees
lat: latitude, decimal degrees
offshore: Sta_ID_station > 60
geometry: geographic projection (SIRD 4326)
is_cast: in the bottle cast database as of 2022-04-01
is_cce: in the California Coastal Ecosystem (CCE) set of stations
is_ccelter: in the California Coastal Ecosystem (CCE) Long-Term Ecological Research (LTER) set of stations
is_sccoos: in the Southern California Coastal Ocean Observing (SCOOS) set of stations

bbest commented 2 years ago

TODO for @bbest:

Ask Shonna about station ids for "northern lines"?

CalCOFI / workflows

get generalized line stations #12

GMT Map

More Links

Bathymetry and Coastline Files

Station and Feature Files

CalCOFI in `proj` library

Cal Coop Ocean Fish Invest Lines/Stations

small set

`stations` column descriptions

CalCOFI / workflows

get generalized line stations #12

GMT Map

More Links

Bathymetry and Coastline Files

Station and Feature Files

CalCOFI in proj library

Cal Coop Ocean Fish Invest Lines/Stations

small set

stations column descriptions

CalCOFI in `proj` library

`stations` column descriptions