diff --git a/docs/articles/A_oce.html b/docs/articles/A_oce.html index 2f539f27d..1718c35f0 100644 --- a/docs/articles/A_oce.html +++ b/docs/articles/A_oce.html @@ -67,7 +67,7 @@

1. Introduction to Oce

Dan Kelley (https://orcid.org/0000-0001-7808-5911) and Clark Richards (https://orcid.org/0000-0002-7833-206X)

-

2025-01-15

+

2025-01-17

Source: vignettes/A_oce.Rmd
A_oce.Rmd
diff --git a/docs/articles/B_ctd.html b/docs/articles/B_ctd.html index 003e1f93b..8555be29a 100644 --- a/docs/articles/B_ctd.html +++ b/docs/articles/B_ctd.html @@ -67,7 +67,7 @@

2. Analysis of CTD data

Dan Kelley (https://orcid.org/0000-0001-7808-5911) and Clark Richards (https://orcid.org/0000-0002-7833-206X)

-

2025-01-15

+

2025-01-17

Source: vignettes/B_ctd.Rmd
B_ctd.Rmd
diff --git a/docs/articles/C_adp.html b/docs/articles/C_adp.html index 4fb9e06a3..72048eda8 100644 --- a/docs/articles/C_adp.html +++ b/docs/articles/C_adp.html @@ -66,7 +66,7 @@

3. Analysis of acoustic-Doppler data

Dan Kelley (https://orcid.org/0000-0001-7808-5911)

-

2025-01-15

+

2025-01-17

Source: vignettes/C_adp.Rmd
C_adp.Rmd
@@ -444,8 +444,8 @@

Solutions to exercises#> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 #> * Processing Log #> -#> - 2025-01-15 15:03:45 UTC: `create 'tidem' object` -#> - 2025-01-15 15:03:45 UTC: `tidem(t = as.sealevel(pressure, time))` +#> - 2025-01-17 14:31:19 UTC: `create 'tidem' object` +#> - 2025-01-17 14:31:19 UTC: `tidem(t = as.sealevel(pressure, time))`

(Note that it fitted for M2, but not S2, because the Rayleigh criterion prevents inferring both, and the conventional tidal analysis favours M2 over S2 if the time series is too short to fit for more than diff --git a/docs/articles/D_map_projections.html b/docs/articles/D_map_projections.html index 8cd4fdfc4..7a988a18f 100644 --- a/docs/articles/D_map_projections.html +++ b/docs/articles/D_map_projections.html @@ -66,7 +66,7 @@

4. Using map projections

Dan Kelley (https://orcid.org/0000-0001-7808-5911)

-

2025-01-15

+

2025-01-17

Source: vignettes/D_map_projections.Rmd
D_map_projections.Rmd
diff --git a/docs/articles/E_flags.html b/docs/articles/E_flags.html index 2d72b52ab..be0f10948 100644 --- a/docs/articles/E_flags.html +++ b/docs/articles/E_flags.html @@ -66,7 +66,7 @@

5. Dealing with data-quality flags

Dan Kelley (https://orcid.org/0000-0001-7808-5911)

-

2025-01-15

+

2025-01-17

Source: vignettes/E_flags.Rmd
E_flags.Rmd
diff --git a/docs/articles/F_subclassing.html b/docs/articles/F_subclassing.html index 0ec1ed597..62e893b82 100644 --- a/docs/articles/F_subclassing.html +++ b/docs/articles/F_subclassing.html @@ -66,7 +66,7 @@

6. Subclassing oce objects

Dan Kelley (https://orcid.org/0000-0001-7808-5911)

-

2025-01-15

+

2025-01-17

Source: vignettes/F_subclassing.Rmd
F_subclassing.Rmd
@@ -135,7 +135,7 @@

Using the base oce classsummary(o) #> * Processing Log #> -#> - 2025-01-15 15:03:54 UTC: `Create oce object` +#> - 2025-01-17 14:31:27 UTC: `Create oce object`

but if we populate the object with some data and metadata

 o <- oceSetData(o, "time", db$t)
@@ -155,11 +155,11 @@ 

Using the base oce class#> #> * Processing Log #> -#> - 2025-01-15 15:03:54 UTC: `Create oce object` -#> - 2025-01-15 15:03:54 UTC: `oceSetData(object = o, name = "time", value = db$t)` -#> - 2025-01-15 15:03:54 UTC: `oceSetData(object = o, name = "longitude", value = db$lon)` -#> - 2025-01-15 15:03:54 UTC: `oceSetData(object = o, name = "latitude", value = db$lat)` -#> - 2025-01-15 15:03:54 UTC: `oceSetMetadata(object = o, name = "ID", value = 4201703)`

+#> - 2025-01-17 14:31:27 UTC: `Create oce object` +#> - 2025-01-17 14:31:27 UTC: `oceSetData(object = o, name = "time", value = db$t)` +#> - 2025-01-17 14:31:27 UTC: `oceSetData(object = o, name = "longitude", value = db$lon)` +#> - 2025-01-17 14:31:27 UTC: `oceSetData(object = o, name = "latitude", value = db$lat)` +#> - 2025-01-17 14:31:27 UTC: `oceSetMetadata(object = o, name = "ID", value = 4201703)`

Note, however, that the ID is not listed by summary(). This is because the general form of that function is set up to focus on the contents of the data @@ -322,7 +322,7 @@

Specializing the summary() function#> #> * Processing Log #> -#> - 2025-01-15 15:03:54 UTC: `create 'drifter' object` +#> - 2025-01-17 14:31:27 UTC: `create 'drifter' object`

Specializing the [[ accessor diff --git a/docs/articles/G_altering_defaults.html b/docs/articles/G_altering_defaults.html index 93efb6b08..441c4e264 100644 --- a/docs/articles/G_altering_defaults.html +++ b/docs/articles/G_altering_defaults.html @@ -66,7 +66,7 @@

7. Altering oce Defaults

Dan Kelley (https://orcid.org/0000-0001-7808-5911)

-

2025-01-15

+

2025-01-17

Source: vignettes/G_altering_defaults.Rmd
G_altering_defaults.Rmd
diff --git a/docs/articles/H_tides.html b/docs/articles/H_tides.html index d12fba79a..ab629eca8 100644 --- a/docs/articles/H_tides.html +++ b/docs/articles/H_tides.html @@ -67,7 +67,7 @@

8. Tidal Analysis

Dan Kelley (https://orcid.org/0000-0001-7808-5911) and Clark Richards (https://orcid.org/0000-0002-7833-206X)

-

2025-01-15

+

2025-01-17

Source: vignettes/H_tides.Rmd
H_tides.Rmd
diff --git a/docs/news/index.html b/docs/news/index.html index c92228491..d228ba38b 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -66,9 +66,9 @@

oce 1.8.4oce.plot.ts() to handle simplify better (issue #2277).
  • Change plot.section() to handle eos="gsw" (issue #2256).
  • Change read.amsr() to handle realtime data files (issue #2230).
  • +
  • Change read.ctd.sbe() to handle files that lack salinity and conductivity (issues #2279 and #2282).
  • +
  • Change read.ctd.sbe() to handle time-related header elements better (issues #2280 and #2281).
  • Change read.ctd.aml() to handle “type 3” format (issue #2247).
  • -
  • Change read.ctd.sbe() to handle cases with no salinity or conductivity data (issue #2279).
  • -
  • Change read.ctd.sbe() to handle some time-related header elements better (issues #2280 and #2281).
  • Change read.netcdf() docs to show how to handle flags (issue #2236).
  • Change read.netcdf() to give a way to rename data (issue #2235).
  • Change read.netcdf() to handle units better.
  • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 0b7ed8111..6a37c4fba 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: F_subclassing: F_subclassing.html G_altering_defaults: G_altering_defaults.html H_tides: H_tides.html -last_built: 2025-01-15T15:01Z +last_built: 2025-01-17T14:29Z urls: reference: https://dankelley.github.io/oce/reference article: https://dankelley.github.io/oce/articles diff --git a/docs/reference/D4902337_219.nc.html b/docs/reference/D4902337_219.nc.html index f20ef13c3..f482bf079 100644 --- a/docs/reference/D4902337_219.nc.html +++ b/docs/reference/D4902337_219.nc.html @@ -100,7 +100,7 @@

    Examples#> Argo Summary #> ------------ #> -#> * Source: "/private/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T/RtmpoabPvy/temp_libpath112ff7303b123/oce/extdata/D4902337_219.nc" +#> * Source: "/private/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T/RtmpTNdCh6/temp_libpath1d205112ffb9/oce/extdata/D4902337_219.nc" #> * ID: "4902337" #> * Feature type: "trajectoryProfile" #> * Profiles: 2 delayed; 0 adjusted; 0 realtime @@ -137,9 +137,9 @@

    Examples#> #> * Processing Log #> -#> - 2025-01-15 15:01:47 UTC: `create 'argo' object` -#> - 2025-01-15 15:01:47 UTC: `initializeFlagScheme(object, name="argo", mapping=list(not_assessed=0,passed_all_tests=1,probably_good=2,probably_bad=3,bad=4,changed=5,not_used_6=6,not_used_7=7,estimated=8,missing=9)), default=c(0,3,4,9))` -#> - 2025-01-15 15:01:47 UTC: `read.argo(file="/private/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T/RtmpoabPvy/temp_libpath112ff7303b123/oce/extdata/D4902337_219.nc")` +#> - 2025-01-17 14:29:24 UTC: `create 'argo' object` +#> - 2025-01-17 14:29:24 UTC: `initializeFlagScheme(object, name="argo", mapping=list(not_assessed=0,passed_all_tests=1,probably_good=2,probably_bad=3,bad=4,changed=5,not_used_6=6,not_used_7=7,estimated=8,missing=9)), default=c(0,3,4,9))` +#> - 2025-01-17 14:29:24 UTC: `read.argo(file="/private/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T/RtmpTNdCh6/temp_libpath1d205112ffb9/oce/extdata/D4902337_219.nc")`

    diff --git a/docs/reference/adp_rdi.000.html b/docs/reference/adp_rdi.000.html index 9726ed7d0..6d89fd27e 100644 --- a/docs/reference/adp_rdi.000.html +++ b/docs/reference/adp_rdi.000.html @@ -112,7 +112,7 @@

    See also

    Examples

    read.oce(system.file("extdata", "adp_rdi.000", package = "oce"))
    -#> adp object, from file "/private/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T/RtmpoabPvy/temp_libpath112ff7303b123/oce/extdata/adp_rdi.000", with data slot containing:
    +#> adp object, from file "/private/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T/RtmpTNdCh6/temp_libpath1d205112ffb9/oce/extdata/adp_rdi.000", with data slot containing:
     #>    distance[1:84]: 2.23, 2.73, ..., 43.23, 43.73
     #>    time[1:9]: 2008-06-25 10:00:00, 2008-06-25 10:00:10, ..., 2008-06-25 10:01:10, 2008-06-25 10:01:20
     #>    pressure[1:9]: -0.244, -0.224, ..., -0.238, -0.266
    diff --git a/docs/reference/as.cm.html b/docs/reference/as.cm.html
    index bb7f9d390..12b0e6408 100644
    --- a/docs/reference/as.cm.html
    +++ b/docs/reference/as.cm.html
    @@ -132,19 +132,19 @@ 

    Examples#> ---------- #> #> * North: magnetic -#> * Time: 2025-01-15 11:01:53 to 2025-01-15 11:02:43 (51 samples, mean increment 1 s) +#> * Time: 2025-01-17 10:29:30 to 2025-01-17 10:30:20 (51 samples, mean increment 1 s) #> * Data Overview #> #> Min. Mean Max. Dim. NAs -#> time 2025-01-15 15:01:53 2025-01-15 15:02:18 2025-01-15 15:02:43 51 0 +#> time 2025-01-17 14:29:30 2025-01-17 14:29:55 2025-01-17 14:30:20 51 0 #> u [m/s] -2.8628 0.0070087 3.2703 51 0 #> v [m/s] -2.5653 0.23561 2.4359 51 0 #> pressure [dbar] 98.1 100.02 101.88 51 0 #> #> * Processing Log #> -#> - 2025-01-15 15:01:53 UTC: `create 'cm' object` -#> - 2025-01-15 15:01:53 UTC: `as.cm(time = t, u = u, v = v, pressure = p)` +#> - 2025-01-17 14:29:30 UTC: `create 'cm' object` +#> - 2025-01-17 14:29:30 UTC: `as.cm(time = t, u = u, v = v, pressure = p)` # Example 2: creation from an adv object data(adv) @@ -173,7 +173,7 @@

    Examples#> - 2015-12-23 17:53:55 UTC: `use aquadoppHR heading; despike own pitch and roll` #> - 2015-12-23 17:54:11 UTC: `beamToXyzAdv(x = x)` #> - 2015-12-23 17:54:34 UTC: `xyzToEnu(x, declination=-18.099, horizontalCase=TRUE, sensorOrientiation=upward, debug=0)` -#> - 2025-01-15 15:01:53 UTC: `as.cm(time = adv)` +#> - 2025-01-17 14:29:30 UTC: `as.cm(time = adv)`

    diff --git a/docs/reference/as.ctd.html b/docs/reference/as.ctd.html index d1b4b5174..c4b35a036 100644 --- a/docs/reference/as.ctd.html +++ b/docs/reference/as.ctd.html @@ -355,9 +355,9 @@

    Examples#> #> * Processing Log #> -#> - 2025-01-15 15:01:53 UTC: `create 'ctd' object` -#> - 2025-01-15 15:01:53 UTC: `as.ctd(salinity = salinity, temperature = temperature, pressure = pressure)` -#> - 2025-01-15 15:01:53 UTC: `oceSetData(object = ctd, name = "fluorescence", value = fluo, unit = list(unit = expression(mg/m^3), scale = ""))` +#> - 2025-01-17 14:29:30 UTC: `create 'ctd' object` +#> - 2025-01-17 14:29:30 UTC: `as.ctd(salinity = salinity, temperature = temperature, pressure = pressure)` +#> - 2025-01-17 14:29:30 UTC: `oceSetData(object = ctd, name = "fluorescence", value = fluo, unit = list(unit = expression(mg/m^3), scale = ""))` # 2. fake data, with supplied units (which are the defaults, actually) ctd <- as.ctd(salinity, temperature, pressure, diff --git a/docs/reference/as.sealevel.html b/docs/reference/as.sealevel.html index dd6b6c5aa..a9fc3ffce 100644 --- a/docs/reference/as.sealevel.html +++ b/docs/reference/as.sealevel.html @@ -211,8 +211,8 @@

    Examples#> #> * Processing Log #> -#> - 2025-01-15 15:01:54 UTC: `create 'sealevel' object` -#> - 2025-01-15 15:01:54 UTC: `as.sealevel(elevation = elevation)` +#> - 2025-01-17 14:29:31 UTC: `create 'sealevel' object` +#> - 2025-01-17 14:29:31 UTC: `as.sealevel(elevation = elevation)` # As above, but start at the Y2K time. time <- as.POSIXct("2000-01-01") + h * 3600 @@ -234,8 +234,8 @@

    Examples#> #> * Processing Log #> -#> - 2025-01-15 15:01:54 UTC: `create 'sealevel' object` -#> - 2025-01-15 15:01:54 UTC: `as.sealevel(elevation = elevation, time = time)` +#> - 2025-01-17 14:29:31 UTC: `create 'sealevel' object` +#> - 2025-01-17 14:29:31 UTC: `as.sealevel(elevation = elevation, time = time)`