53 stage 7 data qa by csjones8 · Pull Request #82 · egouldo/VEFMAP_VEG_Stage6

csjones8 · 2024-04-16T11:34:36Z

Changes to species labels for Poa and Juncus at the Spencer site so that the Spencer figures of the 4 example species will be accurate. Updates made to the two separate Campaspe point data files.

copilot hallucinated functions!

…ore checking ground layer total hits

… output

… be ignored

…adata

- call fun on hit reductions in QA template

- and ensure eval is conditional on presence of sugested replacements

- script only, not yet executed

- add map helper functions for creating species fixes named vector - add ma[ helper fucntion for recoding veg data - restructure funs/obj setup - apply recoding in map/dplyr approach - delete dev code - Note: not yet executed, draft script only

- fix error where fn used dev object, not named arg - update .ignore_species after checking Glenelg suggested spelling fixes

- now outputs suggested fixes files - Add README to relevant suggested fixes dir

- calling input arg df instead of transformed object out - ifelse vectorised out instead of retaining df, now fixed

- and rerun QA reporting after updated

- resulted in .ignore_suggestions not being applied!! - re-executed map_fix_spelling_fixes with new updates for Moorabool and Glenelg S7

- and expand for application on spp to recode - ignore spp to recode where there are multiple suggestions per spp. in veg_data - add write flag arg

- fix tidyeval group_by call in fn - ensure score filter doesn't eval if xol doesn't exist (only exists for spp fixes)

- fix tidyeval execution

- delete write code outside of fun - write application for species_to_recode

- with species present in species master, but incorrectly recorded in points data

- move execution into example for apply_veg_data_fixes_from_files() - add ungroup to apply...() fn

- execution script in generate_manual_spp_recode_files - updated recode_species_points_data to apply fixes outlined in manual_spp_recode_files

egouldo added 30 commits April 3, 2024 11:02

#53 draft initial QA tests on single dataframe

9fb384d

#53 draft script to report species checks outcomes

6730bdf

#53 add checks for species ID spelling

ff5d169

#53 add tests for hits col and ground layer tally range

db4ab9f

#53 add checks for ground layer hits range

825e017

#53 add checks for ground layer sum hits, reduce species with max hits

e1a8af1

#53 replace ground_spp with species_master schema

dafc338

#53 rewrite hits column tests

e8cb8f4

copilot hallucinated functions!

#53 move ground_layer_hits checking into pointblank preconditions arg

bca97b8

#53 ensure duplicate native/exotic entries rm from master species bef…

0205e2e

…ore checking ground layer total hits

#53 add parameterised template .qmd for QA

c3e9638

#53 add poinblank QA for data structure checking

137bd9b

#53 use code-folding in rendered report

bb0f973

#53 set show_col_types to FALSE on read_csv to stop rendering console…

37491ab

… output

#53 Describe test in main text

e2f7800

#53 use caps for colnames on read_csv(), mismatch caused col_types to…

291d1ed

… be ignored

#53 output agent_data_structure to raw html

f5e8add

#53 Check species entries

d2e7ca2

#53 check ground layer hits with pointblank and extract report

3ca7d13

#53 report on ground layer hits issues

05c0224

#53 correctly summarise ground layer hits in preconditions

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#53 report data structure issues

0be870f

#53 add gluedown reporting when values not in expected set - site met…

4f9d9fd

…adata

#53 report cols with > 1 system/waterway values.

68bc398

#53 for col vals checks, switch to f_pass < 1 filter

24b2379

#53 update task checklist

a5de4df

#53 add context to reporting if there are fails.

3c33437

#53 check if missing (NA) vals in cols

1d19ba1

#53 fix indentation in code

80ea4e6

#53 rm TODO text and ensure results: asis for md output.

b7a83fc

egouldo added 12 commits April 17, 2024 23:33

#53 regen QA reports after S7 file changes

3b236db

add imports to quarto_render_move doc

4baf3cc

#53 add fun for writing QA outputs

3ae11c5

- call fun on hit reductions in QA template

#53 add alt options to write_QA_outputs type

ac90deb

#53 write_QA_outputs() for suggested replacements

4103250

- and ensure eval is conditional on presence of sugested replacements

#53 update spelling for multiple S7 files

ec8917b

- script only, not yet executed

#53 complete map fix spelling errors

d58970b

- add map helper functions for creating species fixes named vector - add ma[ helper fucntion for recoding veg data - restructure funs/obj setup - apply recoding in map/dplyr approach - delete dev code - Note: not yet executed, draft script only

#53 update spelling fixes map script

e4a92cd

- fix error where fn used dev object, not named arg - update .ignore_species after checking Glenelg suggested spelling fixes

#53 reexecute QA after QA wflow updates

2e2307c

- now outputs suggested fixes files - Add README to relevant suggested fixes dir

#53 fix error in get_spp_fixes()

57cf778

- calling input arg df instead of transformed object out - ifelse vectorised out instead of retaining df, now fixed

#53 uncomment write_csv and fix walk execution

80a5c1f

#53 Fix spelling in S7 Moorabool, Glenelg

e3fb8b7

- and rerun QA reporting after updated

egouldo force-pushed the 53-stage-7-data-QA branch from d55f208 to e3fb8b7 Compare April 18, 2024 06:48

egouldo added 2 commits April 18, 2024 17:54

#53 fix error in get_spp_fixes

e1c351a

- resulted in .ignore_suggestions not being applied!! - re-executed map_fix_spelling_fixes with new updates for Moorabool and Glenelg S7

#53 Functionalise map_fix_spelling_fixes

879fb85

- and expand for application on spp to recode - ignore spp to recode where there are multiple suggestions per spp. in veg_data - add write flag arg

egouldo force-pushed the 53-stage-7-data-QA branch from aa51235 to 879fb85 Compare April 18, 2024 08:21

egouldo and others added 14 commits April 18, 2024 18:44

#53 fix get_spp_fixes() for species_to_recode

35b5c01

- fix tidyeval group_by call in fn - ensure score filter doesn't eval if xol doesn't exist (only exists for spp fixes)

#53 fix apply_veg_data_fixes_from_files() for species_to_recode

9e226b0

- fix tidyeval execution

#53 fix apply_veg_data_fixes_from_files() for species_to_recode

5a99b28

- delete write code outside of fun - write application for species_to_recode

#53 recode Moorabool and Glenelg S7

cee69bd

- with species present in species master, but incorrectly recorded in points data

#53 reorganize and document fns

c829600

- move execution into example for apply_veg_data_fixes_from_files() - add ungroup to apply...() fn

Add %nin% fn to utils.R

55071b2

#53 rerun QA after recoding species for Moorabool and Glenelg

8acd048

#53 rename script with recode fns

29b3c37

#53 recode Moorabool spp from comments

508de03

- execution script in generate_manual_spp_recode_files - updated recode_species_points_data to apply fixes outlined in manual_spp_recode_files

#53 regenerate QA after update files

8a08dfb

#53 render S6 QA reports programmatically

d7dcdde

separate failed model out for investigation

df0d853

Updates related to Stage 7 data and analysis

9ad9e51

Stage 7 veg corrections

47b5590

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53 stage 7 data qa#82

53 stage 7 data qa#82
csjones8 wants to merge 91 commits intomasterfrom
53-stage-7-data-QA

csjones8 commented Apr 16, 2024 •

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csjones8 commented Apr 16, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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csjones8 commented Apr 16, 2024 •

edited

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