Data Validation

Heliconia Demographic Survey Data

We use the R package pointblank to review and validate the plot-level descriptors (HDP_plots.csv) and clean demographic data set (heliconia_survey_clean.csv) in preparation for archiving in Dryad and publication in Bruna et al. (2023). The report below includes:

the different validation tests that were conducted,
the date of the most recent test,
each test’s criteria for ‘pass’, ‘warn’ and ‘stop’,
the number of ‘units’ (i.e., rows or columns) assessed in each test,
how many of these units passed or failed, and
a button for downloading a .csv file of the records flagged by a particular validation test. Note that these are not necessarily errors. For instance, the validation procedure for ‘plant size - height’ returns as ‘stop’ all plants >2 m tall. Heliconia plants can exceed this threshold; this test is simply designed to flag any such individuals. In contrast, the data set should not have any duplicated rows. A notification of ‘fail’ for this test indicates an error that can be corrected by downloading the csv file, reviewing the duplicated rows, and uploading the necessary corrections.

Last run: 2024-07-29

Dataset Structure: Data types

Tests to determine if columns are correctly coded as integer, character, etc.
Test criteria: Strict (‘stop’ if any rows fail).

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N	EXT
Pointblank Validation
Data Validation tibbleWARN 1 STOP 0.02 NOTIFY —
	1	Height is measured to nearest cm `col_vals_expr()`	—	`ht%%1 == 0`	✓	`57K`	`57K` `1.00`	`0` `0.00`	—	○	—	—
	2	Shoots is interger `col_vals_expr()`	—	`shts%%1 == 0`	✓	`57K`	`57K` `1.00`	`0` `0.00`	—	○	—	—
	3	Number of inflorescences is integer `col_vals_expr()`	—	`infl%%1 == 0`	✓	`2K`	`2K` `1.00`	`0` `0.00`	—	○	—	—
2024-07-29 15:26:55 UTC < 1 s 2024-07-29 15:26:55 UTC

Dataset Structure: Plot & Subplot IDs

Test for any nonexistent values of plot_id (e.g., ‘FF-10’, ‘CF-23’) or subplot (e.g., ‘H23’, ‘A11’).
Test criteria: Strict (‘stop’ if any rows fail).

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N	EXT
Pointblank Validation
Data Validation tibbleWARN 1 STOP 0.02 NOTIFY —
	1	`col_vals_in_set()`	`▮plot_id`	`CF-1, CF-2, CF-3, CF-4, CF-5, CF-6, FF-1, FF-2, FF-3, FF-4, FF-5, FF-6, FF-7`	✓	`66K`	`66K` `1.00`	`0` `0.00`	—	○	—	—
	2	`col_vals_in_set()`	`▮subplot`	`A1, A2, A3, A4, A5, A6, A7, A8, A9, A10, B1, B2, B3, B4, B5, B6, B7, B8, B9, B10, C1, C2, C3, C4, C5, C6, C7, C8, C9, C10, D1, D2, D3, D4, D5, D6, D7, D8, D9, D10, E1, E2, E3, E4, E5, E6, E7, E8, E9, E10, F1, F2, F3, F4, F5, F6, F7, F8, F9, F10, G1, G2, G3, G4, G5, G6, G7, G8, G9, G10, H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, I1, I2, I3, I4, I5, I6, I7, I8, I9, I10, J1, J2, J3, J4, J5, J6, J7, J8, J9, J10`	✓	`66K`	`66K` `1.00`	`0` `0.00`	—	○	—	—
2024-07-29 15:26:56 UTC < 1 s 2024-07-29 15:26:56 UTC

Dataset Structure: Duplicated or Missing Values

Tests for duplicated rows, missing plant_ID numbers, or duplicate plant_id numbers (test is done for every survey year).
Test criteria: Strict (‘stop’ if any rows fail).

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N	EXT
Pointblank Validation
Data Validation tibbleWARN 1 STOP 0.02 NOTIFY —
	1	duplicated rows `rows_distinct()`	`▮plant_id, ▮plot, ▮habitat, ▮ranch, ▮bdffp_reserve_no, ▮tag_number, ▮row, ▮column, ▮x_09, ▮y_09, ▮plot_id, ▮year, ▮shts, ▮ht, ▮infl, ▮code, ▮notes, ▮duplicate_tag, ▮adult_no_tag, ▮recorded_sdlg, ▮treefall_status, ▮condition, ▮census_status, ▮subplot`	—	✓	`66K`	`66K` `1.00`	`0` `0.00`	—	○	—	—
	2	`col_vals_not_null()`	`▮plant_id`	—	✓	`66K`	`66K` `1.00`	`0` `0.00`	—	○	—	—
	3	Check for duplicate plant ID numbers `rows_distinct()`	`▮plant_id`	—	✓	`9K`	`9K` `1.00`	`0` `0.00`	—	○	—	—
	4	Check for duplicate tag numbers in a plot `rows_distinct()`	`▮tag_number`	—	✓	`64`	`0` `0.00`	`64` `1.00`	—	●	—
2024-07-29 15:26:56 UTC 1.5 s 2024-07-29 15:26:58 UTC

Plant Characteristics: Size & Flowering

Tests to determine how many values of plant size (shts, ht) or infloresence number (infl) are outside the range of most values.
Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if \(\geq\) 2% of rows fail conditions.

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N
Pointblank Validation
Data Validation tibbleWARN 1 STOP 0.02 NOTIFY —
	1	shoots between 0 and 20 `col_vals_between()`	`▮shts`	`[0, 20]`	✓	`66K`	`66K` `0.99`	`8` `0.01`	●	○	—
	2	height between 0 and 200cm `col_vals_between()`	`▮ht`	`[0, 200]`	✓	`66K`	`66K` `0.99`	`2` `0.01`	●	○	—
	3	infloresences between 0 and 3 `col_vals_between()`	`▮infl`	`[0, 3]`	✓	`66K`	`66K` `0.99`	`15` `0.01`	●	○	—
2024-07-29 15:26:58 UTC < 1 s 2024-07-29 15:26:58 UTC

Plant Characteristics: Growth

Tests for unusual changes in plant size (both height and shoot number) from \(Year_{t}\) to \(Year_{t+1}\).
Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if \(\geq\) 2% of rows fail conditions.

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N
Pointblank Validation
Check growth & regression tibbleWARN 1 STOP 0.02 NOTIFY —
	1	\|% change in height\| < 200% `col_vals_lt()`	`▮ht_pc`	`2`	✓	`66K`	`66K` `0.99`	`420` `0.01`	●	○	—
	2	\|∆ height\| < 100cm `col_vals_between()`	`▮ht_diff`	`[−100, 100]`	✓	`66K`	`66K` `0.99`	`11` `0.01`	—	●	—
	3	\|∆ shoot number\| < 5 `col_vals_between()`	`▮shts_diff`	`[−5, 5]`	✓	`66K`	`66K` `0.99`	`201` `0.01`	—	●	—
2024-07-29 15:26:59 UTC < 1 s 2024-07-29 15:26:59 UTC

Seedlings: Initial size

Tests for seedlings whose size at initial marking was unusually large. Conducted for both height and shoot number.
Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if \(\geq\) 2% of rows fail conditions.

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N
Pointblank Validation
Check seedlings tibbleWARN 1 STOP 0.02 NOTIFY —
	1	shoots < 3 `col_vals_lt()`	`▮shts`	`3`	✓	`3K`	`3K` `0.99`	`12` `0.01`	●	○	—
	2	height < 30cm `col_vals_lt()`	`▮ht`	`30`	✓	`3K`	`3K` `0.99`	`3` `0.01`	●	○	—
2024-07-29 15:26:59 UTC < 1 s 2024-07-29 15:26:59 UTC

Seedlings: Data Entry Errors

Check if during data entry the size of seedlings (1) wasn’t accidentally transposed to the “inflorescences” column, which would code a new seedling as being reproductive.

Test criteria: Strict (‘stop’ if any rows fail).

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N	EXT
Pointblank Validation
Check for ‘reproductive’ seedlings tibbleWARN — STOP 1 NOTIFY —
	1	infl < 1 `col_vals_lt()`	`▮infl`	`1`	✓	`3K`	`3K` `1.00`	`0` `0.00`	—	○	—	—
2024-07-29 15:27:00 UTC < 1 s 2024-07-29 15:27:00 UTC

Zombie plants

Zombie plants are those that were recorded as ‘Dead’ in a survey but for which there is a measurement in a subsequent year (indicative of the plant losing all below-ground parts and then new shoots emerging prior to the next survey). This validation generates a .csv of any plants meeting this condition (labeled as ’zombie` for review and correction.

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N	EXT
Pointblank Validation
Check for zombies tibbleWARN 1 STOP 0.02 NOTIFY —
	1	Check for Zombies `col_vals_equal()`	`▮zombie`	`zombie`	✓	`0`	`0` `NA`	`0` `NA`	—	○	—	—
2024-07-29 15:27:01 UTC < 1 s 2024-07-29 15:27:01 UTC

Plant Mortality: Plant size

Tests for plants 6 or more shoots dying from one year to the next. Note: These are not errors, these are plants whose size the year prior to being recorded as ‘dead’ in a survey was in the top 2% of dying plants.

Test criteria: ‘warn’ if \(\geq\) 1 rows fail conditions, ‘stop’ if \(\geq\) 2% of rows fail conditions.

		STEP	COLUMNS	VALUES	EVAL	UNITS	PASS	FAIL	W	S	N
Pointblank Validation
Check large plants dying tibbleWARN 1 STOP 0.02 NOTIFY —
	1	6 or more shoots `col_vals_lt()`	`▮shts`	`6`	✓	`2K`	`2K` `0.98`	`32` `0.02`	●	○	—
2024-07-29 15:27:02 UTC < 1 s 2024-07-29 15:27:02 UTC

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