future Remora lesson

[CaitlinBate]

Name of lesson:

intro to Remora

Brief description of lesson content:

• QC flags
• pairing env data w acoustic detections
• lots of fun plots

To whom should we talk to help develop lesson content?

• Bruce (lead)
• Caitlin (backup code tester)
• Jon (ideas guy)

About how many chapters will constitute this lesson?

• one lesson

Has anyone in our network specifically requested this lesson?

• not yet :) but lots of requests for "novel packages"

[CaitlinBate]

when we're ready, the shorter-timescale scope of this workshop is:

Lesson plan: Show them the package (readme style), show them how to import their data, leave them on their own (for now)

then expand in the future to include the other topics. need to ensure the setup instructions include install instructions for @jackVanish 's branch

[CaitlinBate]

this is being started for the ACT workshop https://github.com/ocean-tracking-network/otn-workshop-base/tree/remora_lesson

[naomitress]

@diniangela is reviewing the content bruce has pushed up

[diniangela]

Reviewed the material and found 2 things:

• read_csv should be read.csv
• otn_test_tag_qc <- remora::runQC(otn_files, data_format = "otn", tests_vector = tests_vector, .parallel = FALSE, .progress = TRUE) gives the following error:

Reading data...
Error in base::nchar(wide_chars$test, type = "width") :                                  
  read failed on /Library/Frameworks/R.framework/Versions/3.6/Resources/library/cli/R/sysdata.rdb
In addition: Warning message:
In base::nchar(wide_chars$test, type = "width") :
  restarting interrupted promise evaluation

when looking at otn_files that only contains one file in the list (["./testDataOTN/qc_princess.csv"])

[jackVanish]

@diniangela Elsewhere in the lesson code we use read_csv rather than read.csv, so I think we should leave that as it is. read_csv is the tidyverse/readr version, while read.csv is base R.

Regarding the error, I've never seen that happen before and a quick google suggests that it may be an environment problem (or to do with a package installation). Can you restart your R session and try again?

[CaitlinBate]

first taste of the remora lesson (remora QC) is in gh-pages, will be in master ASAP.

[diniangela]

After figuring out my imports, those errors went away thankfully!

However, I got another error on the last step:

> otn_test_tag_qc <- remora::runQC(otn_files, data_format = "otn", tests_vector = tests_vector, .parallel = FALSE, .progress = TRUE)
Reading data...
New names:                                                                                              
• `` -> `...1`
Rows: 72 Columns: 35
── Column specification ─────────────────────────────────────────────
Delimiter: ","
chr  (20): collectioncode, catalognumber, scientificname, commonn...
dbl  (12): ...1, bottom_depth, receiver_depth, sensorraw, sensorv...
lgl   (1): notes
dttm  (1): datecollected
date  (1): datelastmodified

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Deriving receiver dataframe...
Deriving tag dataframe...
rec_meta is not null
tag meta is not null
Starting sequential QC...
file: A69-9002-6146_A69-9002-6145_NSBS-Princess-2019-08-12_NSBS-Princess-2019-08-12, 1 of 1    StartingQC
Configuring temporal outcome vector
Temporal outcome vector configured
shapefile not null, starting lat/lon conversion to SpatialPoints


 Please see QC_logfile.txt for potential data and/or metadata issues

Error in eval(predvars, data, env) : object 'x.longitude' not found

Error in `bind_rows()`:
! Argument 1 must have names.
Run `rlang::last_error()` to see where the error occurred.
Warning message:
1 tag detection file(s) could not be QC'd 

[CaitlinBate]

i got a very similar error:

otn_test_tag_qc <- remora::runQC(imos_files, data_format = "imos", tests_vector = tests_vector, .parallel = FALSE, .progress = TRUE)
Reading data...
Rows: 597 Columns: 31                                                                                                                             
── Column specification ───────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr  (13): transmitter_id, tagging_project_name, species_common_name, species_scientific_name, animal_sex, ...
dbl  (15): tag_id, transmitter_deployment_id, CAAB_species_id, WORMS_species_aphia_id, receiver_id, receive...
lgl   (1): transmitter_dual_sensor
dttm  (2): detection_datetime, transmitter_deployment_datetime

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 352 Columns: 14                                                                                                                             
── Column specification ───────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr  (6): receiver_name, purchasing_organisation, receiver_project_name, receiver_status, installation_name...
dbl  (6): receiver_deployment_id, receiver_deployment_longitude, receiver_deployment_latitude, depth_below_...
dttm (2): receiver_deployment_datetime, receiver_recovery_datetime

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 5 Columns: 24                                                                                                                               
── Column specification ───────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr  (12): transmitter_id, tagging_project_name, transmitter_type, transmitter_sensor_type, transmitter_sen...
dbl   (7): transmitter_serial_number, transmitter_sensor_slope, transmitter_sensor_intercept, transmitter_e...
lgl   (3): transmitter_recovery_datetime, transmitter_recovery_latitude, transmitter_recovery_longitude
dttm  (2): transmitter_deployment_datetime, embargo_date

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 5 Columns: 6                                                                                                                                
── Column specification ───────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr (3): transmitter_id, measurement_type, measurement_unit
dbl (2): transmitter_deployment_id, measurement_value
lgl (1): comments

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
rec_meta is not null
tag meta is not null
Starting sequential QC...
file: A69-9002-14762_43669513_43669944, 1 of 5    StartingQC
Configuring temporal outcome vector
Temporal outcome vector configured
shapefile not null, starting lat/lon conversion to SpatialPoints
Step one
Step two
Step three
Conversion done.
Starting false detections test
False detection test done.
position set
Error in .local(x, y, ...) : extents do not overlap
file: A69-9002-14765_43669525_43669972, 2 of 5    StartingQC
Configuring temporal outcome vector
Temporal outcome vector configured
shapefile not null, starting lat/lon conversion to SpatialPoints
Step one
Step two
Step three
Conversion done.
Starting false detections test
False detection test done.
position set
Error in .local(x, y, ...) : extents do not overlap
file: A69-9002-13807_69918686_69918684, 3 of 5    StartingQC
Configuring temporal outcome vector
Temporal outcome vector configured
shapefile not null, starting lat/lon conversion to SpatialPoints
Step one
Step two
Step three
Conversion done.
Starting false detections test
False detection test done.
position set
Error in .local(x, y, ...) : extents do not overlap
file: A69-9002-13809_77523181_77523186, 4 of 5    StartingQC
Configuring temporal outcome vector
Temporal outcome vector configured
shapefile not null, starting lat/lon conversion to SpatialPoints
Step one
Step two
Step three
Conversion done.
Starting false detections test
False detection test done.
position set
Error in .local(x, y, ...) : extents do not overlap
file: A69-9002-13824_93016177_93016182, 5 of 5    StartingQC
Configuring temporal outcome vector
Temporal outcome vector configured
shapefile not null, starting lat/lon conversion to SpatialPoints
Step one
Step two
Step three
Conversion done.
Starting false detections test
False detection test done.
position set
Error in .local(x, y, ...) : extents do not overlap


 Please see QC_logfile.txt for potential data and/or metadata issues

Error in shortest_dist(position, x$installation_name, rast = world_raster_sub,  : 
  detection locations outside extent of land raster

Error in `bind_rows()`:
! Argument 1 must have names.
Run `rlang::last_error()` to see where the error occurred.
Warning message:
5 tag detection file(s) could not be QC'd