edited title, attribute definition and missing value code, methods

methods.txt

@@ -1,12 +1,12 @@
 # Original event logs
-Events were recorded onboard with Rolling Deck to Repository (R2R) event logger (elog) software described at: https://www.rvdata.us/about/event-log. Prior to each cruise an NES-LTER Information Manager works with shipboard technicians and the R2R elog software team to configure the elog with instruments and actions from a controlled vocabulary. The event log is started when the ship leaves port, and concluded upon arrival. During the cruise the events are added manually by shipboard technicians and science participants. Contents of the event log are reviewed regularly by an on-board Information Manager during a cruise to ensure completeness and accuracy. The elog is often available online during the cruise so that an on-shore Information Manager can review contents as well. The original event logs (elogs) are available per cruise in R2R with Public Domain Mark 1.0 license: https://www.rvdata.us/data.
+Events were recorded onboard with Rolling Deck to Repository (R2R) event logger (elog) software described at: https://www.rvdata.us/about/event-log. Prior to each cruise an NES-LTER Information Manager works with shipboard technicians and the R2R elog software team to configure the elog with instruments and actions from a controlled vocabulary. The event log is started when the ship leaves port, and concluded upon arrival. During the cruise the events are added manually by shipboard technicians and science party. Contents of the event log are reviewed regularly by an on-board Information Manager during a cruise to ensure completeness and accuracy. The elog is often available online during the cruise so that an on-shore Information Manager can review contents as well. The original event logs (elogs) are available per cruise in R2R with Public Domain Mark 1.0 license: https://www.rvdata.us/data.
 
 # Event listings output by NES-LTER REST API
-NES-LTER maintains a RESTful Application Programming Interface (REST API) to provide a set of consistent URLs that, when fetched, returns data in machine-readable form that may be used by application code. For the events product provided by the NES-LTER REST API, a subset of columns is retained from the original elogs, including date, time, ship’s position, instrument, and action (parsing code available at: https://github.com/WHOIGit/nes-lter-ims/blob/master/neslter/parsing/elog.py). For some but not all cruises we corrected and/or added events. Event logs are available per-cruise with the following URL pattern, using cruise en627 as example: https://nes-lter-data.whoi.edu/api/events/en627.csv.
+NES-LTER maintains a RESTful Application Programming Interface (REST API) to provide a set of consistent URLs that, when fetched, returns data in machine-readable form that may be used by application code. For the events product provided by the NES-LTER REST API, a subset of columns is retained from the original elogs, including date, time, ship’s position, instrument, and action (parsing code available at: https://github.com/WHOIGit/nes-lter-ims/blob/master/neslter/parsing/elog.py). For some but not all cruises we corrected and/or added events. Blanks are retained (not filled with missing value code) in the station, cast, and comment columns. Event logs are available per-cruise with the following URL pattern, using cruise en627 as example: https://nes-lter-data.whoi.edu/api/events/en627.csv.
 
 # Data assembly
 The concatenated data product is built from event logs output by the NES-LTER REST API.
-In this first version of this data package, we used a script in Python to acquire all available elogs from the REST API and concatenate into a file “nes_lter_events_raw.csv” that is used in the Data assembly script in R (file and code available at: https://github.com/WHOIGit/nes-lter-events-transect). Cleaning of the concatenated table included formatting datetime, excluding extraneous columns, and excluding instruments specific to Ocean Observatories Initiative (OOI)-led cruises (CPM, CSM, Falcon ROV, Glider, Kraken ROV, REMUS, Slocum Glider, USBL). We did not exclude events listed with instrument “Other” that are pertinent to OOI-led cruises. We added a column project_id to indicate LTER-dedicated or partner cruises.
+In this first version of this data package, we used a script in Python to acquire all available elogs from the REST API and concatenate into a file “nes_lter_events_raw.csv” that is used in the data assembly script in R (file and code available at: https://github.com/WHOIGit/nes-lter-events-transect). Cleaning of the concatenated table included formatting datetime, excluding extraneous columns, and excluding instruments specific to Ocean Observatories Initiative (OOI)-led cruises (CPM, CSM, Falcon ROV, Glider, Kraken ROV, REMUS, Slocum Glider, USBL). We did not exclude events listed with instrument “Other” that are pertinent to OOI-led cruises. We added a column project_id to indicate LTER-dedicated or partner cruises.
 
 # Quality Assurance
-We assured that the geographic and temporal coverage of the concatenated data product were within expected ranges. For corrections made or still needed for the NES-LTER REST API product, see README per-cruise with the following URL pattern, using cruise en627 as example: https://nes-lter-data.whoi.edu/api/events/en627/README. We did not yet regularize the names of LTER-specific instruments, for example “Bongo” and “Bongo net” are equivalent.
+We assured that the geographic and temporal coverage of the concatenated data product were within expected ranges. For corrections made or still needed for the NES-LTER REST API product, see README per-cruise with the following URL pattern, using cruise en627 as example: https://nes-lter-data.whoi.edu/api/events/en627/README. We did not yet regularize the names of LTER-specific instruments, for example “Bongo” and “Bongo net” are equivalent. For cruises prior to ar28a in spring 2018, we had not yet established controlled vocabulary terms related to IFCB, nor had we distinguished the instrument "IFCB continuous" from underway science seawater with action "IFCB discrete". For cruises en608, ar28b, and ar31c, the instrument IFCB refers to IFCB continuous. For cruises ar24a and ar24c, the instrument IFCB109 represents IFCB continuous, and the instrument IFCB102 represents an IFCB analyzing discrete samples.

nes-lter-events-transect.Rmd

@@ -62,7 +62,7 @@ Generate the package and insert the parent project node into the resulting EML
 pkg_id <- 'knb-lter-nes.20.1'
 
 make_eml(here(),
-         dataset.title='Event logs from Northeast U.S. Shelf NES-LTER Transect cruises, ongoing since 2017',
+         dataset.title='Event logs from Northeast U.S. Shelf Long Term Ecological Research (NES-LTER) Transect cruises, ongoing since 2017',
          data.table=product_table_filename,
          data.table.description='Concatenated table of events recorded on seasonal NES-LTER Transect cruises',
          data.table.name = 'nes-lter-events-transect',