daijiang/neondivdata

Cleaned biodiversity data from NEON

neondivdata's Issues

check to see if acceptedTaxonIDs are used in all data products

reminder to look through each of the data tables and make sure we use acceptedTaxonID, or it makes sense to use taxonID in cases where we do that.

family column in data_plant

taxon_id and taxon_name are very useful, but it would be beneficial to have the family column remain in this dataset

Missing field definition: remarks

There is a field named "remarks" in many of the tables but no definition in the metadata. What is the definition?

Issues: data_algae

Units are missing from descriptions of these variables:

• phytoDepth1
• phytoDepth2
• phytoDepth3

Missing field?: release

data_fish metadata lists the field "release" but it is not in the data table. Should it be?

Issues: data_zooplankton

Definitions are missing from these variables:

• towsTrapsVolume

Validation issues

Here are the messages from updating the data:

Validating neon.ecocomdp.20107.001.001:
  Required tables
  Column names
  Required columns
  Column classes
  Datetime formats
  Primary keys
  Composite keys
  Referential integrity
  Latitude and longitude format
  Latitude and longitude range
  Elevation

Validating neon.ecocomdp.10043.001.001:
  Required tables
  Column names
  Required columns
  Column classes
  Datetime formats
  Primary keys
  Composite keys
  Referential integrity
  Latitude and longitude format
  Latitude and longitude range
  Elevation

@sokole do we need to worry about it?

Missing field: reachID?

data_fish has the field "reachID" listed in the metadata but this field is absent from the table. Should it be?

Issues: data_macroinvertebrate

Units are missing from descriptions of these variables:

• ponarDepth
• snagLength
• snagDiameter

Issues: neon_sites

Units are missing from descriptions of these variables:

• Latitude
• Longitude

Missing field?: unique_sample_id

data_fish metadata lists the field "unique_sample_id", but this field is not in the table. Should it be?

Added herp_bycatch

@daijiang I added a pull request for the herp bycatch function and documentation, but not the data. Let me know if you need me to do that too or if you need me to edit anything else to make the herp bycatch code/doc/data work for you.

Issues: data_fish

pointID is in the table but missing from the metadata.

Duplicate fields + definitions listed in metadata

data_small_mammal and data_tick have "elevation" listed twice in their respective metadata .Rd files.

datetime fields contain non-datetime strings

A pipe "|" appears throughout datetime fields of data_fish (and possibly other tables). This will create parsing issues when parsing into an R (or any other language) datetime object. Is there another way to represent these "either-or" values within the neonDivData tables?

Add some details about the data processing workflow

Hi @sokole and @stephparker ,
The reviewer asked us to add some details about the data processing process, like what we have in the data_tick and other groups. (https://daijiang.github.io/neonDivData/reference/data_tick.html)

Can either of you help with this? You can add them after Line 4 here:

neonDivData/R/data_macroinvertebrate.R

Lines 1 to 4 in 155b179

	#' Macroinvertebrate data
	#'
	#' This dataset was derived from [NEON data portal](https://data.neonscience.org) with data product ID 'DP1.20120.001'. Details about this data product can be found at <https://data.neonscience.org/data-products/DP1.20120.001>.
	#'

Thank you!!

Explore taxon lumping

• Get ideas for alternative taxon lumping approaches from folks, categorize as "correct" or "incorrect" -- lump by synonym, by genus, no lumping (incorrect, because it would treat sp and spp as separate taxa, but sp should be considered part of the spp. group)
• Eric make script to lump data in ways that are correct and "incorrect"
• Sydne create script to use iNEXT to make accumulation curves by lumping method

doing this for just beetles? or maybe a few groups?

data_herp_bycatch issues

Fields in table but missing from the metadata:

• neon_trap_id
• observation_datetime
• taxon_id
• taxon_name
• taxon_rank
• variable_name
• value
• unit
• neon_event_id
• release
• latitude
• longitude
• elevation

Fields in metadata but missing from the table:

• trapID
• setDate
• collectDate
• taxonID
• eventID
• taxonRank