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WildCoLab / WildCo_Single_Site_Exploration

R code to explore the standardised data with the Wild3 database for a single site.
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WildCo standards #6

Open ChrisBeirne opened 2 years ago

ChrisBeirne commented 2 years ago

@mitch-fen @wildcole @catherinecsun @ccheng91 I am contemplating whether we change the heading titles in the wildco standards from periods ( . ) spaces, to undescores ( _ ).

In the Covid synthesis "Project.ID" was something interpreted as a hyperlink by excel (or google drive... I am not sure which), which made for some odd behaviour when reading in the .csv

Any thoughts? It might be a lot of work for minimal benefit?

Other options would be no space... but I like having a delimiter in there as the wildlife insights standards uses spaces.

mitch-fen commented 2 years ago

I'm big on team underscore! Might not be tooooo bad if we just find&replace throughout the script (but I can already feel that we may end up wth chaos from different folks whose data used to work, and suddenly doesn't!)

ChrisBeirne commented 2 years ago

Thats my fear! Maybe it isnt an issue worth messing with!

On Thu, 13 Jan 2022 at 09:37, Mitch Fennell @.***> wrote:

I'm big on team underscore! Might not be tooooo bad if we just find&replace throughout the script (but I can already feel that we may end up wth chaos from different folks who's data used to work, and suddenly doesn't!)

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catherinecsun commented 2 years ago

I am also a fan of the underscore! I agree it would require a pretty systematic and daunting review of all scripts though, to add in code that says look for files with patterns containing "." or "_".... If we decide to move away from the ".", it may have to just be a note in ReadMe's that file names transitioned to a different format on date XX/XX/2022....? Thoughts?

On Thu, Jan 13, 2022 at 10:29 AM Chris Beirne @.***> wrote:

Thats my fear! Maybe it isnt an issue worth messing with!

On Thu, 13 Jan 2022 at 09:37, Mitch Fennell @.***> wrote:

I'm big on team underscore! Might not be tooooo bad if we just find&replace throughout the script (but I can already feel that we may end up wth chaos from different folks who's data used to work, and suddenly doesn't!)

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ChrisBeirne commented 2 years ago

Thats a good idea! The output from wildlife insights is all lowercase too! e.g. "project_id" and "deployment_id"

lastew commented 2 years ago

Wildtrax also has collumn names with lowercase, underscores:

project | organization | location | latitude | longitude | buffer_radius_m | date_detected | field_of_view | scientific_name | common_name | species_rank | species_class | age_class | sex | number_individuals | id_by | camera_make | camera_model | serial_number | image_comments | tag_comments

ChrisBeirne commented 2 years ago

Raw Wildlife Insights output projects.csv: <html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

project_id | project_name | project_short_name | project_objectives | project_species | project_species_individual | project_sensor_layout | project_sensor_layout_targeted_type | project_bait_use | project_bait_type | project_stratification | project_stratification_type | project_sensor_method | project_individual_animals | project_blank_images | project_sensor_cluster | project_admin | project_admin_email | project_admin_organization | country_code | embargo | initiative_id | metadata_license | image_license | data_citation | count_optional | project_type -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | --

images.csv:

<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

project_id | deployment_id | image_id | filename | location | is_blank | identified_by | wi_taxon_id | class | order | family | genus | species | common_name | uncertainty | timestamp | number_of_objects | age | sex | animal_recognizable | individual_id | individual_animal_notes | highlighted | markings | cv_confidence | license -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | --

deployments.csv:

<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

project_id | deployment_id | placename | longitude | latitude | start_date | end_date | bait_type | bait_description | feature_type | feature_type_methodology | camera_id | quiet_period | camera_functioning | sensor_height | height_other | sensor_orientation | orientation_other | plot_treatment | plot_treatment_description | detection_distance | subproject_name | subproject_design | event_name | event_description | event_type | recorded_by -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | --

ChrisBeirne commented 2 years ago

Reflagging this: I have realise wildlife insights have changed their standards to underscores now too (when we originally looked at the they had spaces and capitols).

I think making this change would be a good idea and bring us in line with a massively expanding data portal...

I forgot to put the link in https://docs.google.com/spreadsheets/d/1Jg-WybmVeGlWGrbPpwuwJCgranOV1r3M_LrzELttfK0/edit#gid=412365965

mitch-fen commented 2 years ago

I agree, and think we should do it! We can have an archived (internal?) version for use by older projects finishing up, and move to the accepted standards moving forward to prevent future headache.