Configuration: arguments and thresholds

2026-11-08

Authoritative index of every user-configurable component of the algorithm. For reference, hard-coded numeric threshold and reference-data-driven values are also provided. The algorithm vignettes (vignette("child-algorithm"), vignette("wrapper"), vignette("adult-algorithm")) cite this reference for defaults and thresholds rather than duplicating them.

If you are interested in the adult permissiveness presets, see Section 1D.

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How to Read This Reference

Three categories:

1. Arguments — arguments to cleangrowth() that change how growthcleanr cleans, runs, or what it returns. Organized by algorithm scope.
2. Hardcoded thresholds — numeric values baked into the code; a caller cannot change them without downloading and editing the package code. These are provided for reference and are organized by step.
3. Reference-data-driven values — loaded from external files in inst/extdata/ or defined in large lookup tables. Some can be replaced with your own values: sd.recenter takes a table of recentering medians (or "none" to turn recentering off), and ref.data.path points to a folder of reference files. Non-configurable, hard-coded reference-data-driven values are provided for reference.

Sections per category:

• Argument/threshold name (as written in code)
• Value (default for configurable; literal for hardcoded; “see file X” for ref-data)
• Scope (step, phase, or algorithm)
• Code location (file + function + sub-section)
• Brief role

Conventions:

• < / > = strict inequalities unless noted
• Param values: "WEIGHTKG", "HEIGHTCM", "HEADCM" (after input conversion)
• Sex: 0 = male, 1 = female
• All adult threshold comparisons include the 0.12 cm/kg adult rounding tolerance unless explicitly noted otherwise
• Exclusion-code strings shown in this reference are the algorithm’s internal literals (e.g. Exclude-C-PIV, Exclude-Missing, Exclude-Not-Cleaned, Exclude-A-Scale-Max) — the values the code assigns and tests internally. growthcleanr maps these to the user-facing Summary (exclude) and Detailed (exclude_detailed) output codes at output assembly; the internal literals are unchanged. For the output codes and the internal→Summary/Detailed crosswalk, see vignette("exclusion-codes").

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1. User arguments

1A. Wrapper-level (exposed in cleangrowth() signature)

Ready-to-run scripts for the most common of these (column names, sex_coding, param_coding, dates, input_format, parallel and checkpointing, adult settings) are in vignette("example-scripts").

Argument	Default	Used in	Role
id	NULL (optional)	cleangrowth preprocessing; output	Unique row identifier. Fully optional. When absent / NULL / contains NA / not unique, a warning is issued and sequential ids 1:N (in input row order) are auto-generated for internal use. The user’s original id (whatever was supplied — even if invalid) is preserved untouched in the output id column. To see the id growthcleanr actually used internally (= user’s id when valid, = regen otherwise), set display_gc_id = TRUE or full_detail = TRUE. Semi-wide/wide input: the id argument, or a column named id, identifies an input row (it need not be unique); growthcleanr mints its own per-measurement ids. In semi-wide input the id orders a subject’s visit rows when the minted ids are assigned (so it can decide which same-day value is kept when the id tiebreak applies); in wide input it does not affect cleaning. It is returned unchanged in semi-wide/wide output and, in long output, under its own column name on each measurement from that row, with growthcleanr’s number in gc_internal_id.
subjid	(required) — column name in data (data-frame style) or a vector (vector style)	cleangrowth preprocessing	Subject identifier vector
param	(required) — column name in data (data-frame style) or a vector (vector style)	cleangrowth preprocessing	Measurement-type vector. Canonical: WEIGHTKG, HEIGHTCM, LENGTHCM, HEADCM, WEIGHTLBS, HEIGHTIN, LENGTHIN, HEADIN. Matched case-insensitively. No built-in abbreviations — a bare WT/HT/HC is not assumed to be a gc parameter (may be a sample weight, etc.); map non-canonical labels with param_coding. See vignette("wrapper") → Flexible sex and parameter coding.
agedays	(required) — column name in data (data-frame style) or a vector (vector style)	cleangrowth preprocessing	Age in days at measurement
sex	(required) — column name in data (data-frame style) or a vector (vector style)	cleangrowth preprocessing	Sex indicator; default codes 0/"m"/"b"/"male"/"boy" = male, 1/"f"/"g"/"female"/"girl" = female (case-insensitive). Override with sex_coding. A 1=male/2=female column hard-stops unless declared. See vignette("wrapper") → Flexible sex and parameter coding.
sex_coding	list(male = c(0, "m", "b", "male", "boy"), female = c(1, "f", "g", "female", "girl"))	cleangrowth preprocessing (.gc_recode_sex, reshape_adapters.R)	Named list (male, female) of the codes denoting each sex; case-insensitive, whitespace-trimmed. Supplying a table replaces the defaults wholesale and suppresses the 1/2 guard. Errors if a code is under both sexes. Present-but-unrecognized codes → Exclude-Missing-Info + warning.
param_coding	NULL	cleangrowth preprocessing (.gc_recode_param, reshape_adapters.R)	Optional named list keyed by canonical parameter, values = your labels to remap (case-insensitive). The only way to have a non-canonical label recognized (there are no built-in abbreviations); also how you declare a remapped column is imperial (map to WEIGHTLBS/HEIGHTIN/LENGTHIN/HEADIN), else it defaults to its metric target. Errors if a name is not canonical or a label maps to two parameters.
measurement	(required) — column name in data (data-frame style) or a vector (vector style)	cleangrowth preprocessing	Recorded value in units specified by param
input_format	"long"	cleangrowth input dispatch (Hook A, reshape_adapters.R)	Shape of data: "long" (one row per measurement), "semi_wide" (one row per visit, one column per parameter), or "wide" (one row per subject, repeated observation blocks marked by a _N column suffix). Non-long input is reshaped to long before cleaning, so results match the equivalent long submission. Requires data-frame style. See vignette("wrapper") → Input format.
output_format	NULL	cleangrowth output (Hook B, reshape_adapters.R)	Shape of the returned results: "long", "semi_wide", or "wide". NULL mirrors input_format, so semi-wide input returns semi-wide output and wide input returns wide output. Re-widened output returns the submitted table with the growthcleanr columns named in widened_emit slotted in beside each value column (exclude_wt_cm for semi-wide, exclude_wt_1 for wide); it requires the matching input format (checkpointed runs are supported). See Output format: semi-wide / wide in vignette("wrapper").
widened_emit	"exclude"	.gc_semiwide_output / .gc_wide_output (reshape_adapters.R)	Which growthcleanr output columns to add to re-widened (semi-wide or wide) output. Any per-measurement column may be named ("bin_exclude", "exclude_detailed", "unit_error_range", "measurement", "agedays", …); naming one whose own switch is off is an error. gc output columns take the value-column suffix only (exclude_wt_kg; exclude_wt_1 for wide); gc’s internal version of a submitted value takes a gc_internal_ prefix (gc_internal_meas_wt_lbs). "measurement" also emits gc_internal_param_*. agedays is per visit in semi-wide, per block in wide (gc_internal_agedays_1, …). Used when output_format is "semi_wide" or "wide".
internal_detail	FALSE	Output assembly	Adds gc_internal_meas, gc_internal_param, gc_internal_sex, gc_internal_id, and gc_internal_agedays – growthcleanr’s working values for the key inputs the user supplied (imperial converted to metric, LENGTHCM relabeled, sex coerced to 0/1, age as whole days; the length.adjust offset is applied only to z-scores, so it is not reflected in gc_internal_meas) – plus gc_internal_dob / gc_internal_visit_date when a dob / visit_date column was supplied. The primary columns always return the verbatim submission. The imperial conversion and the LENGTHCM relabel are reflected for every row. Enabled by full_detail.
semiwide_cols	NULL	.gc_semiwide_to_long (reshape_adapters.R)	Named list/vector mapping gc parameters to their value columns for semi-wide input, e.g. list(WEIGHTKG = "wt_kg", HEIGHTCM = "ht_cm", HEADCM = "head_cm"). NULL uses columns literally named as recognized parameters. Only used when input_format = "semi_wide".
wide_cols	NULL	.gc_wide_to_long (reshape_adapters.R)	Named list/vector mapping gc parameters to their column-name prefixes for wide input, e.g. list(WEIGHTKG = "wt", HEIGHTCM = "ht", HEADCM = "hc") for wt_1, wt_2, ht_1, …. The user picks the prefix; growthcleanr requires the _N block suffix and discovers blocks from it. NULL uses prefixes literally named as recognized parameters (WEIGHTKG_1, …). A mapped prefix with no <prefix>_N columns is an error. subjid/sex are patient-level; the age source is per block (agedays_N, or dob + visit_date_N). Only used when input_format = "wide".
max_blocks	25	.gc_wide_to_long (reshape_adapters.R)	Highest number of wide observation blocks expected. Finding more warns (with guidance to raise it or reshape to long/semi-wide) but processes every block; an implausible count errors, since it usually means the _N suffixes parsed wrong. Only used when input_format = "wide".
dob	NULL	cleangrowth preprocessing (age)	Date-of-birth column name (data-frame style only). Column is class Date or a text date; a subject with more than one distinct dob value is set aside as Exclude-Missing-Info, with a warning. Supplied with visit_date to compute agedays as floor(visit_date - dob) in whole days. Text dates parse under order-free formats — year-first numeric (2013-03-04, 2013/03/04, 20130304) or English spelled-month (03mar2013, March 15, 2024) — or, for numeric day/month (3/4/2013), only with date_order. All dates in dob/visit_date share one format; four-digit years 1900–2099 only. Blank/NA and text with no digits (e.g. N/A) -> missing agedays; a few dates that are not real dates are set aside, more than a few stop the run; numeric date integers are rejected. See vignette("wrapper") → Date parsing.
visit_date	NULL	cleangrowth preprocessing (age)	Visit (measurement) date column name (data-frame style only). Class Date or a text date in the same accepted formats as dob. Supplied together with dob.
age_source	NULL	cleangrowth preprocessing (age)	Which age source to resolve agedays from: "agedays" (the agedays column) or "dates" (dob + visit_date). NULL auto-resolves (an agedays column wins when present; otherwise the dates). Set "dates" to force date-based ages even when an agedays column is present. With "dates" and an age column present, that column is returned as submitted and the computed ages as gc_internal_agedays.
date_order	NULL	cleangrowth preprocessing (age)	Day-vs-month order for ambiguous numeric dob/visit_date values (data-frame style only), e.g. "3/4/2013": "dmy" (day-month-year) or "mdy" (month-day-year), applied uniformly. NULL accepts only the order-free formats and errors on numeric day/month dates, so an ambiguous order is never guessed. growthcleanr never auto-detects order.
carry_through	TRUE	cleangrowth preprocessing; output	Data-frame style only. When TRUE (default), columns in data that are not resolved role columns (subjid/param/agedays/sex/measurement/id) are parked and returned appended after the gc output columns (original order/values; dob/visit_date are echoed back this way). A carried column whose name matches a column gc returns in this run (e.g. exclude) is returned as userinput_<name>, with a warning; names of gc columns not returned in the run are left alone. FALSE drops all non-role columns (prior behavior). Semi-wide/wide input: with semi-wide/wide output your table is the output base (TRUE keeps every column, FALSE keeps the role, id and value columns); with long output, your other columns (including dob/visit_date; in wide, not the per-block columns) are repeated on each measurement from their row.
adult_cutpoint	20	Preprocessing (pediatric/adult split)	Age (years) dividing pediatric/adult processing. Clamped to [18, 20], with a warning when a value is moved. growthcleanr never changes it based on the data (each subject is cleaned independently of the rest of the dataset); if it is left at the default and every known-age measurement is >= 18y with some in the 18-20y range, a warning suggests adult_cutpoint = 18 to clean those with the adult algorithm instead of the child path.
sd.recenter	NA	Recentering (Phase 11)	Recentering medians: NA (built-in rcfile-resmoothed.csv.gz), "none" (no recentering; tbc.sd = sd.orig), or your own table (a data.table or data.frame with columns param, sex, agedays, rcmedian.sd), which must cover every param, sex, and agedays of the child measurements to be cleaned, or cleangrowth() stops. See vignette("recentering").
ref.data.path	""	Preprocessing; Child Step 17	Override directory for reference files. "" uses package inst/extdata/.
batch_size	5000	Outer-wrapper batching	Subjects per processing batch (the in-memory unit); must be a single positive whole number. Independent of checkpoint_size.
checkpoint	TRUE	Checkpointed runs (cleangrowth_checkpoint.R)	Master on/off switch. TRUE (default) checkpoints to an ephemeral per-session temp dir, engaging only when subjects > checkpoint_size (small/typical data runs in memory, writing nothing); those files are auto-deleted (keep_checkpoints forced FALSE). FALSE disables checkpointing entirely (nothing written to disk) and overrides checkpoint_dir with a warning. Supplying checkpoint_dir makes checkpointing persistent + resumable. See vignette("large-datasets") for use; vignette("wrapper") -> Checkpointed runs for internals.
checkpoint_dir	NULL	Checkpointed runs (cleangrowth_checkpoint.R)	Persistent, resumable checkpoint location. When set, split subjects into checkpoints of checkpoint_size, clean each checkpoint, persist it to a checkpoint_NNNN.rds file here, and combine at the end. NULL (default) uses the ephemeral temp dir described under checkpoint (or no checkpointing when checkpoint = FALSE). Result is identical to a single-pass run (incl. wide/semi-wide input/output).
checkpoint_size	5000	Checkpointed runs	Subjects per checkpoint (the persist unit; one .rds per checkpoint), and the threshold above which the checkpoint = TRUE default engages. Independent of batch_size (batch_size < checkpoint_size allowed). Capped at 9999 checkpoints: a size that would exceed the cap is increased (with a warning if you set it).
checkpoint_resume	FALSE	Checkpointed runs	Only meaningful with a persistent checkpoint_dir (forced FALSE on the ephemeral default). FALSE starts fresh (deletes prior checkpoint files); TRUE reuses existing checkpoint files (skips completed checkpoints) to resume an interrupted run.
keep_checkpoints	TRUE	Checkpointed runs	TRUE leaves the per-checkpoint files after a successful run; FALSE deletes them once combined. Independent of checkpoint_resume. Forced FALSE on the ephemeral checkpoint = TRUE default (temp files are always cleaned up); the TRUE default applies when you set checkpoint_dir.
log_file	NULL	Checkpointed runs	Only used when checkpoint_dir is set. Path to also append progress messages to (console always gets them unless quietly), so a colleague can monitor a long run remotely.
parallel	FALSE	Inner batching	Run batches in parallel (foreach %dopar% dispatch)
cores	NULL	Inner batching	Number of parallel workers when parallel = TRUE; NULL auto-detects min(8, detectCores() - 1), capped at 8. An explicit value above detectCores() is reduced to it. Ignored when parallel = FALSE
log.path	NA	Parallel logging	Deprecated (warns when supplied); use log_file. Log directory for parallel mode
ref_tables	NULL	All reads	Pre-loaded reference closures from gc_preload_refs(); skips per-call disk reads (~0.93 sec/call)
tri_exclude	FALSE	Output assembly	Include tri_exclude column in output ("Include" / "Same-Day" / "Exclude")
corr_detail	FALSE	Output assembly	Add corr_val (per-value: "Corrected" / "Uncorrected" / "Adult") and corr_pt (per-subject) correction-status columns
recenter_detail	FALSE	Output assembly	Include the recentered CSD z-score columns tbc.sd, ctbc.sd, and rcmedian.sd (the per-row recentering median subtracted). Specialized output for a related tool in development. Child rows only (NA on adult).
qm_detail	FALSE	cleanchild per-step capture; output	For a related package in development — not used in cleaning (see vignette("output") §5c). Emit ten per-step eligibility flags for the child cleaning steps (qm_elig_c_cf, qm_elig_c_hardlimit, qm_elig_c_eviltwins, qm_elig_c_trajextreme, qm_elig_extraneous, qm_elig_c_traj, qm_elig_c_absdiff, qm_elig_c_pair, qm_elig_c_single, qm_elig_c_trajuneval): each logical column is TRUE where the row was eligible for (the denominator of) that step. Write-only — never affects any exclusion. Child rows only (NA on adult). For eligibility-normalized quality measures; usually paired with exclude_detail = TRUE. See vignette("output") §5c for the per-column definitions.
debug	FALSE	Output assembly	Retain intermediate CSD z-score columns (sd.orig, sd.corr, tbc.sd, ctbc.sd) plus ±5%-wt / ±1 cm plus/minus perturbation z-scores (tbc.p_plus, tbc.p_minus, ctbc.p_plus, ctbc.p_minus); z-scores are child rows only (NA on adult). Also adds gc_internal_sex — gc’s interpreted integer sex (0/1/NA, all rows); the primary sex column carries the user’s verbatim submission.
exclude_detail	FALSE	Output assembly	Add the step-level Detailed exclusion code in an exclude_detailed column (the default exclude column always carries the consolidated Summary code). See vignette("exclusion-codes") for the two levels and crosswalk.
mean_ht	returned when the data has adult rows	Output assembly	Include a mean_ht column (TRUE always returns it; FALSE omits it): the adult algorithm’s calculated mean height (cm) (Adult Step 11H). The mean_ht column can be used by researchers who want a consistent height for evaluation of body mass index. Computed only from the subject’s finally-included heights and populated on every adult height row (an excluded or missing height row takes the value of the included height nearest in age); NA for child rows, adult weight rows, and all height rows of a subject with no included height. The value is always computed; this switch controls only whether it is returned. Auto-set TRUE by full_detail = TRUE.
full_detail	FALSE	Output assembly	Convenience switch: enables exclude_detail + cf_detail + corr_detail + recenter_detail + debug + tri_exclude + display_gc_id + internal_detail + mean_ht together. Does not enable qm_detail (request it explicitly).
unit_error_range	TRUE (default ON)	Output assembly	Add informational unit_error_range logical column. TRUE when a value’s magnitude is consistent with a metric/imperial unit-conversion error AND it is outside the plausible z = −3 to +3 band. Never affects exclude; not in exclude.levels. Child zn3/zp3 from child_z3_reference.csv.gz; adult from the embedded NHANES CSD reference. Also drives a soft warning when > 20% of a parameter group’s cleaned values are flagged (whole column may be in the wrong unit). Set FALSE to omit the column (and the warning).
display_gc_id	FALSE	Output assembly	Add a gc_internal_id column to the output containing the id growthcleanr actually used internally: equals the user’s id when it was valid (no regen), or the auto-generated 1:N (in input row order) when id was absent / NA / non-unique and gc had to regenerate. Lets callers recover a reliable per-row key when their input id had problems (output id always preserves whatever the user supplied). Auto-set TRUE by full_detail = TRUE. Not needed for semi-wide/wide input returned as long output, where gc_internal_id is always returned.
quietly	FALSE	All steps	Progress level. Default FALSE prints the minimal view (a “cleaning in progress” header, an X/Y batch/checkpoint counter, and the end cleaning summary); TRUE turns off the progress lines and the summary (warnings, and the one-time note for vector-style calls, still appear). For the detailed per-step view use verbose. See vignette("wrapper") → Progress output.
verbose	FALSE	All steps	When TRUE, prints the detailed view: the milestone lines (preprocessing, per-batch cleaning-child / cleaning-adult) plus granular per-step diagnostics (CF/EWMA/SDE/Evil-twins pre-filter + iteration counts, adult step headers). Implies quietly = FALSE. Threaded into cleanchild() / cleanadult(). Development/debugging only.

1B. Child algorithm (passed through cleangrowth() into cleanchild())

Argument	Default	Used in	Role
piv.z.wt.high	22	Child Step 7	Upper unrecentered CSD z cutoff for WEIGHTKG (all ages). Weight has no standardized low cutoff — the low-WT z asymptotes near -10 with a positive weight, so the absolute floors v<0.2/v<1 kg do that job.
piv.z.ht.low.young	-25	Child Step 7	Lower unrecentered CSD z cutoff for HEIGHTCM at ageyears < 1
piv.z.ht.low.old	-15	Child Step 7	Lower unrecentered CSD z cutoff for HEIGHTCM at ageyears >= 1
piv.z.ht.high	8	Child Step 7	Upper unrecentered CSD z cutoff for HEIGHTCM (all ages)
piv.z.hc.low	-15	Child Step 7	Lower unrecentered CSD z cutoff for HEADCM (all ages)
piv.z.hc.high	15	Child Step 7	Upper unrecentered CSD z cutoff for HEADCM (all ages)
cf_rescue	"standard"	Child Step 6	CF rescue mode: "standard" (deltaz/nextz rule), "none" (all CFs excluded), "all" (all rescued). TRUE/FALSE stop with a pointer to the 2.x equivalent; other values are resolved by match.arg().
cf_detail	FALSE	Child Step 6; output	If TRUE, add diagnostic columns cf_status, cf_deltaz, cf_nextz, imperial, cf_dage_orig, and cf_dage_next to output. cf_status adds "CF-E" (same-day-extraneous CF) alongside Orig/CF-R/CF-NR/Not-CF/Adult; in cf_rescue = "all", same-day CFs are labelled CF-R instead, with cf_deltaz and cf_dage_orig NA. cf_nextz is the signed change in sd.orig from each CF row to the next non-CF Included value at the time of Step 6 (temp SDEs skipped). The last three are design aids for CF-logic development: imperial (whole/half imperial-unit flag), cf_dage_orig (originator→CF day gap), cf_dage_next (CF→next-Included day gap).
ewma_window	15	Child Steps 11, 13, 15/16, 17; Adult Steps 9Wb, 11Wb	Max observations on each side that contribute to EWMA weighting. Single parameter in cleangrowth() affecting both child and adult.
error.load.mincount	2	Child Step 21	Minimum “real” errors (not SDE / CF / Missing / Not-Cleaned) before error-load is evaluated
error.load.threshold	0.5	Child Step 21	Error ratio above which all remaining Include rows for the subject-param are excluded. Strict >.
length.adjust	FALSE	Preprocessing (before z-scores)	If TRUE, reconciles entered linear measurements with what the reference at that age expects, in both directions (±0.7 cm at the 2-year boundary, day 730; pediatric-only; long input only). Full behavior is the SSOT in vignette("wrapper"), section “Length vs. height handling”. Arithmetic in .gc_to_metric() (reshape_adapters.R); called from child_clean.R → cleangrowth() inside the outer batch loop.

1C. Adult algorithm (wrapper-exposed)

These adult arguments are exposed directly through cleangrowth(); the individual permissiveness settings (Section 1D) are set by the preset and, if needed, overridden through adult_overrides.

Argument	Default	Used in	Role
adult_permissiveness	"looser"	cleanadult preset resolver	Preset level: "loosest", "looser", "tighter", "tightest" (case and surrounding spaces are ignored). Sets defaults for all adult settings.
adult_scale_max_lbs	Inf	Adult Step 4W	Physical scale upper limit in pounds. Weights within ±0.1 kg of the cap are excluded if they are more than 50 kg different from their expected value, or if all of the subject’s weights (at least two) are the same value at the cap.
ewma_window	15	Adult Steps 9Wb, 11Wb	See Section 1B — shared parameter with child; single value in cleangrowth() affects both algorithms.
adult_overrides	NULL	cleanadult preset resolver	Optional named list overriding individual Section-1D settings, e.g. list(overall_ht_min = 120, allow_ht_gain = FALSE). Each named value replaces the preset value for that setting; unnamed or unrecognized names are an error. Adult rows only.

1D. Adult permissiveness presets (set by adult_permissiveness)

Cleaning is always imperfect, and there is always a tradeoff between over- and under-excluding measurements. Depending on the study population, research question, and analytic method, users may prioritize sensitivity or specificity. There are multiple settings in the adult algorithm that can be changed to adjust cleaning performance. The default values for these settings can be adjusted together using the adult_permissiveness argument or can be adjusted individually.

There are four permissiveness levels, set with the adult_permissiveness argument: loosest, looser, tighter, and tightest. The loosest setting will generally lead to the fewest exclusions, and tightest to the most exclusions. The looser setting is the default and is most similar to v2.2.3 (although not exactly the same). Descriptions and example use cases for the permissiveness options are below, followed by a table with the specific preset values and information regarding how to adjust settings individually. More detailed documentation of these settings is in vignette("adult-algorithm") (“Permissiveness Framework” and the step sections named in the Role column of the table below). Child-algorithm arguments are in Section 1B.

Permissiveness setting intended use and description

• loosest: Intended for studies of patients who may have extreme size changes, and for which the priority is to retain all plausible values. Allows extreme weight changes (bariatric surgery, rapid fluid status change), significant height measurement error, height gain in young adults, and height loss.

• looser (default): Intended for studies of a broad population of patients (who may include patients taking GLP-1 medication or having had bariatric surgery) but for which the user accepts exclusion of occasional plausible measurements for patients with extreme size or extreme size changes in order to exclude more values that likely represent error. Retains most plausible values. Slightly less extreme weights allowed. Height gain allowed; height loss beyond the 3-inch band is not.

• tighter: Intended for studies that may include patients with atypical size (e.g., class 3 obesity) or relatively significant change in size, but for which retention of true extreme values or very unusual patterns is a lower priority than excluding most implausible measurements. May result in exclusion of some plausible values likely reflecting illness with large effect on body size. Less permissive height limits. Height gain allowed; height loss beyond the 2-inch band is not. Repeated values treated as less informative (see “Repeated Value (RV) Handling” in vignette("adult-algorithm")).

• tightest: Intended for studies of relatively healthy populations and central tendencies. Excludes extreme measurements even if plausible given a patient’s other measurements. Tightest weight and height limits. No height gain or loss allowance. Repeated values treated as less informative (see “Repeated Value (RV) Handling” in vignette("adult-algorithm")). The allofus15 weight-allowance formula used at the tightest level was adapted from the algorithm developed by Guide et al. (2024) for the All of Us Research Program (full citation under “Permissiveness Framework” in vignette("adult-algorithm")).

Preset values

Setting	loosest	looser	tighter	tightest	Role
overall_ht_min (cm)	50	120	142	147	PIV lower HT limit (Adult Step 1)
overall_ht_max (cm)	244	230	213	208	PIV upper HT limit (Adult Step 1)
overall_wt_min (kg)	20	30	36	39	PIV lower WT limit (Adult Step 1)
overall_wt_max (kg)	500	270	159	136	PIV upper WT limit (Adult Step 1)
overall_bmi_min	5	12	16	18	PIV lower BMI limit (Adult Step 1); applied only when wider than the single-value BMI limits (at the presets, loosest only); at the other levels they equal the single-value limits, applied at Adult Step 13
overall_bmi_max	300	65	45	40	PIV upper BMI limit (Adult Step 1); applied only when wider than the single-value BMI limits (at the presets, loosest only); at the other levels they equal the single-value limits, applied at Adult Step 13
single_ht_min_bmi (cm)	60	120	142	147	1D HT lower limit when BMI available (Adult Step 13)
single_ht_max_bmi (cm)	245	230	213	208	1D HT upper limit when BMI available
single_wt_min_bmi (kg)	12	30	36	39	1D WT lower limit when BMI available
single_wt_max_bmi (kg)	350	270	159	136	1D WT upper limit when BMI available
single_ht_min_nobmi (cm)	120	120	142	147	1D HT lower limit when BMI not available
single_ht_max_nobmi (cm)	245	230	213	208	1D HT upper limit when BMI not available
single_wt_min_nobmi (kg)	30	30	36	39	1D WT lower limit when BMI not available
single_wt_max_nobmi (kg)	350	270	159	136	1D WT upper limit when BMI not available
single_bmi_min	10	12	16	18	1D BMI lower limit
single_bmi_max	250	65	45	40	1D BMI upper limit
wtallow_formula	PW-H ("piecewise")	PW-H ("piecewise")	PW-L ("piecewise-lower")	allofus15 ("allofus15")	Weight-allowance formula family (see vignette("adult-algorithm"); allofus15 is adapted from Guide et al. (2024), full citation there). Affects Adult Steps 9Wa, 9Wb, 11Wa, 11Wa2, 11Wb.
perclimit_low (wt ≤45 kg)	0.5	0.5	0.7	0.7	Percentage limit (Adult Steps 11Wa, 11Wb)
perclimit_mid (wt 45–80 kg)	0.4	0.4	0.4	0.4	Percentage limit
perclimit_high (wt >80 kg)	0 (disabled)	0 (disabled)	0.4	0.4	Percentage limit
mod_ewma_f	0.75	0.75	0.60	0.60	Moderate EWMA directional factor (Adult Step 11Wb)
error_load_threshold	0.41	0.41	0.29	0.29	Error ratio above which all remaining Includes excluded (Adult Step 14). Strict >.
ht_band (inches)	3	3	2	2	Height band tolerance (Adult Step 10H). Converted to cm via × 2.54 + 0.12.
allow_ht_loss	TRUE	FALSE	FALSE	FALSE	Whether height loss over time is allowed (Adult Step 10H)
allow_ht_gain	TRUE	TRUE	TRUE	FALSE	Whether height gain over time is allowed (Adult Step 10H)
repval_handling	independent	independent	linked	linked	Repeated-value handling mode (Adult Steps 2W, 9Wb, 11Wb)

To change one or a few without switching preset, pass them in the adult_overrides named list to cleangrowth() — e.g. cleangrowth(df, adult_permissiveness = "tighter", adult_overrides = list(overall_ht_min = 120)). The names must match the setting names in the table above; an unrecognized name is an error. (The value replaces the preset value for adult rows; it has no effect on child rows.)

1E. Removed arguments

include.carryforward and weight_cap are not valid cleangrowth() arguments. Use cf_rescue in place of include.carryforward, and adult_scale_max_lbs in place of weight_cap. For the full list of arguments removed since growthcleanr 2.2.3, see “Removed and renamed arguments” in vignette("experienced-start-here").

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2. Hardcoded thresholds (child)

2A. Preprocessing, Z-score calculation (wrapper phases, but scoped to child path)

See Section 4 for preprocessing-level values that apply before dispatch.

2B. Early Child Step 13 (SDE-Identicals)

Threshold	Value	Location	Role
Age-dependent tiebreaker (birth)	agedays == 0 → keep lowest internal_id	cleanchild, Early Child Step 13 inline block	Prefer earliest measurement at birth (before postnatal fluid shifts)
Age-dependent tiebreaker (other)	keep highest internal_id	cleanchild, Early Child Step 13	Prefer later measurement (likely more careful)

2C. Child Step 5 (Temporary SDE)

Threshold	Value	Location	Role
Fallback SP median is NA	use DOP median	identify_temp_sde() in child_clean.R	Use cross-parameter median when subject-parameter median unavailable
Fallback both medians NA	treat 0 as median (absdmedian.spz = |tbc.sd|)	identify_temp_sde()	Graceful degradation when no reference point
Fallback DOP median NA	absdmedian.dopz = Inf (sorts last)	identify_temp_sde()	Deprioritize rows with no DOP reference

2D. Child Step 6 (Carried Forwards)

Threshold	Value	Location	Role
CF detection	Exact equality on v.orig; prior unique ageday must have exactly one measurement	cleanchild Child Step 6 (detection)	Row is CF when !is.na(prior_single_val) & v.orig == prior_single_val
imperial WEIGHTKG	abs(x - round(x)) < 0.01 where x = v.orig * 2.20462262	cleanchild Child Step 6 (cf_detail)	Whole pounds detection, within 0.01 lb in either direction (design-aid column)
imperial HEIGHTCM / HEADCM	abs(x - round(x / 0.5) * 0.5) < 0.01 where x = v.orig / 2.54	cleanchild Child Step 6 (cf_detail)	Whole or half inches detection, within 0.01 in in either direction (design-aid column)
Standard rescue (with next value)	cf_deltaz + cf_nextz <= 1 AND cf_deltaz <= 1.5	cleanchild Child Step 6 (rescue decision)	Decided on each string’s last CF, applied to the whole string
Standard rescue (no next value)	cf_deltaz <= 0.5 if agedays < 13*365.25, else cf_deltaz <= 1	cleanchild Child Step 6 (rescue decision)	End-of-series age fallback

cf_deltaz = absdiff = |sd.orig - originator_z|; cf_nextz = signed z-change to the next Included value. See vignette("cf-rescue") for the full rule and rationale.

2E. Child Step 7 (PIV) — absolute thresholds

All strict < or >. Standardized z cutoffs (configurable) are in Section 1B.

Threshold	Value	Scope	Role
WEIGHTKG low, year 1	v < 0.2 kg	agedays <= 365	Published minimum viable birth weight
WEIGHTKG low, after year 1	v < 1 kg	agedays > 365	Minimum plausible outpatient weight
WEIGHTKG high at birth	v > 10.5 kg	agedays == 0	Maximum plausible birth weight
WEIGHTKG high, under 2y	v > 40 kg	ageyears < 2	Highest plausible weight under 2y
WEIGHTKG high, any age	v > 600 kg	All ages	Published maximum human weight
HEIGHTCM low	v < 18 cm	All ages	—
HEIGHTCM high	v > 244 cm	All ages	Published maximum
HEIGHTCM high at birth	v > 65 cm	agedays == 0	—
HEADCM low	v < 13 cm	All ages	—
HEADCM high	v > 75 cm	All ages	Published maximum
HEADCM high at birth	v > 50 cm	agedays == 0	Birth maximum
BMI low (same-day WT x HT)	BMI < 3	All ages	Impossible weight-height combination; runs after the individual limits
BMI high, under 2y	BMI > 50	ageyears < 2	Impossible weight-height combination
BMI high, 2y and over	BMI > 150	ageyears >= 2	Impossible weight-height combination
Standardized-PIV age boundary	ageyears < 1 vs ageyears >= 1	Child Step 7 standardized block	Splits the HT lower cutoff into “young” and “old” bands
Guard pattern	!grepl("^Exclude-C-PIV$", exclude)	Child Step 7 standardized block	Skip rows just assigned Exclude-C-PIV by absolute block

2F. Child Step 9 (Evil Twins)

Threshold	Value	Location	Role
OTL threshold	both |tbc.sd_next - tbc.sd_current| > 5 AND |ctbc.sd_next - ctbc.sd_current| > 5 (strict, dual); each outer neighbor anchors its adjacent inner value to within 3 on tbc.sd or ctbc.sd	calc_otl_evil_twins() in child_clean.R	Adjacent extreme pair
Pre-filter count	sp_count_9 >= 4L	cleanchild Child Step 9a	Requires 4+ eligible values per subject-param (an A,B,C,D group is the floor)
Minimum valid rows	< 4L breaks group loop	cleanchild Child Step 9b	Stop iteration when fewer than 4 eligible rows remain
Tiebreaker	lowest internal_id	cleanchild Child Step 9b	Deterministic (not age-dependent)

2G. Child Step 11 (EWMA1 — Extreme EWMA)

Threshold	Value	Location	Role
Count pre-filter	skip subject-params with <= 2 Include values	cleanchild Child Step 11a	EWMA needs 3+ points
Extreme pre-filter	skip if no Include has |tbc.sd| > 3.5	cleanchild Child Step 11a	Cheap bypass for subject-params that can’t meet criterion
EWMA exponent, gap ≤ 1y	-1.5	cleanchild Child Step 11b (age-gap-dependent exponent)	Less negative → nearby neighbors carry more weight
EWMA exponent, gap ≥ 3y	-3.5	cleanchild Child Step 11b	More negative → only closest values carry weight
EWMA exponent interpolation	-1.5 - (ageyears - 1) for gap between 1 and 3y	cleanchild Child Step 11b	Linear interpolation
Positive outlier dewma.all	> 3.5	cleanchild Child Step 11b pot_excl	Strict
Positive outlier dewma.before	> 3	Same	Strict
Positive outlier dewma.after	> 3	Same	Strict
Positive outlier tbc.sd	> 3.5	Same	Strict
Positive outlier corrected	c.dewma.all > 3.5 OR ctbc.sd is NA	Same	NA escape auto-satisfies for non-potcorr
Negative outlier mirrors	dewma.all < -3.5, dewma.before < -3, dewma.after < -3, tbc.sd < -3.5, c.dewma.all < -3.5	Same	Mirrors positive side
Plus/minus check	tbc.p_minus - ewma.all > 3.5 AND tbc.p_minus > 3.5 (mirrored with tbc.p_plus on the negative side; corrected versions also required)	cleanchild Child Step 11b	Protects a value when a ±5% weight or ±1 cm height/HC change would bring it within threshold
Preterm catch-up protection	Members of an early catch-up increase in GA-corrected subjects are protected	cleanchild Child Step 11b	See vignette("child-algorithm")
Endpoint rule	Last Include value never excluded; first/birth value NOT auto-protected (only via the preterm catch-up rule)	cleanchild Child Step 11b	EWMA one-sided at the last point; an extreme birth error should be catchable here
Per-iteration exclusion cap	At most 1 per subject-param	cleanchild Child Step 11b	Prevents cascade
Worst-value sort key	abs(tbc.sd + dewma.all) descending; tiebreaker lowest internal_id	cleanchild Child Step 11b	Combines z-score magnitude and EWMA deviation

2H. Child Step 13 (Final SDE Resolution)

Threshold	Value	Location	Role
One-day SDE-All-Extreme	min_absdiff_rel_to_median > 2 (strict)	cleanchild Child Step 13 Phase B1	If closest to median is > 2 SD away, all same-day values excluded
EWMA SDE-All-Extreme	min_absdewma > 1 (strict); on dates with GA-corrected values also c.min_absdewma > 1	cleanchild Child Step 13 Phase B2	If closest EWMA-wise is > 1 SD away (on both frames when the values are corrected), all same-day values excluded
Age-dependent tiebreaker	Same as Early Child Step 13	identify_temp_sde()	Birth: lowest; other ages: highest

2I. Child Steps 15/16 (EWMA2 — Moderate EWMA)

Perturbation magnitudes:

Parameter	Value	Scope
WEIGHTKG p_plus	1.05 × v	Child Step 15 pre-calc
WEIGHTKG p_minus	0.95 × v	Child Step 15 pre-calc
HEIGHTCM p_plus	v + 1 cm	Child Step 15 pre-calc
HEIGHTCM p_minus	v - 1 cm	Child Step 15 pre-calc
HEADCM p_plus	v + 1 cm	Child Step 15 pre-calc
HEADCM p_minus	v - 1 cm	Child Step 15 pre-calc

addcrit thresholds: all > 1 (high) or < -1 (low), strict.

Child Step 15 exclusion rules (all thresholds strict, hardcoded):

Rule	Position	Gap (days)	dewma.all	c.dewma.all	Extra condition
middle	Not first/last	—	> 1 / < -1	> 1 / < -1	addcrit
birth-WT	agedays == 0	next < 365.25	> 3 / < -3	> 3 / < -3	addcrit
birth-WT-ext	agedays == 0	next >= 365.25	> 4 / < -4	> 4 / < -4	addcrit
first	first_meas	next < 365.25	> 2 / < -2	> 2 / < -2	addcrit
first-ext	first_meas	next >= 365.25	> 3 / < -3	> 3 / < -3	addcrit
last	Last row	prev < 2*365.25	> 2 / < -2	> 2 / < -2	abs(tbc_prev) < 2
last-high	Last row	prev < 2*365.25	> abs(tbc_prev) / < -abs(tbc_prev)	> min(abs(tbc_prev), 3) / < -min(abs(tbc_prev), 3)	abs(tbc_prev) >= 2
last-ext	Last row	prev >= 2*365.25	> 3 / < -3	> 3 / < -3	abs(tbc_prev) < 2; DOP diff
last-ext-high	Last row	prev >= 2*365.25	> 1 + abs(tbc_prev) / < -1 - abs(tbc_prev)	> 3 / < -3	abs(tbc_prev) >= 2; DOP diff

DOP diff thresholds (last-ext, last-ext-high): tbc.sd - tbc_dop > 4 or < -4.

Child Step 16 (Birth HT/HC — separate step):

Rule	Gap to next	dewma.all	c.dewma.all
birth-HT-HC	< 365.25	> 2 / < -3	> 2 / < -3
birth-HT-HC-ext	>= 365.25	> 3 / < -4	> 3 / < -4

2J. Child Step 17 (Height/HC Velocity)

Velocity reference tables are reference-data (Section 4). Tolerance formulas below are hardcoded.

HEIGHTCM:

Item	Value	Role
Tanner age floor	midpoint age ≥ 18 months	Only apply Tanner at or above this; row = 6 + 12 × floor(midpoint years), with midpoints of 18–24 months using the 30-month row
max.ht.vel floor (always)	2.54 cm (1 inch)	Minimum allowable increase
max.ht.vel floor (gap > 2 months)	5.08 cm
max.ht.vel floor (gap > 6 months)	10.16 cm
max.ht.vel floor (gap > 1 year)	20.32 cm
mindiff (Tanner, gap < 1y)	0.5 × min.ht.vel × (gap_years)^2 - 3
mindiff (Tanner, gap > 1y)	0.5 × min.ht.vel - 3
maxdiff (Tanner, gap < 1y)	2 × max.ht.vel × (gap_years)^0.33 + 5.5
maxdiff (Tanner, gap > 1y)	2 × max.ht.vel × (gap_years)^1.5 + 5.5
WHO age cap	round(agedays / 30.4375) capped at 24
WHO gap→increment map	<20d, 20–45, 46–75, 76–106, 107–152, 153–198, ≥200 → 1/1/2/3/4/6/6 months
WHO mindiff (<9m)	who_mindiff × 0.5 - 3
WHO maxdiff (<9m)	who_maxdiff × 2 + 3
WHO fallback (≥9m, no Tanner)	Same transform
Default mindiff (no ref)	-3 cm

HEADCM:

Item	Value	Role
WHO gap→increment map	46–75→2, 76–106→3, 107–152→4, 153–199→6; gaps <46 or ≥200 → NA (no 1-month bin; distinct from HT)
mindiff transform	who_mindiff × 0.5 - 1.5	Tighter than HT
maxdiff transform	who_maxdiff × 2 + 1.5	Tighter than HT
Default mindiff (no ref, or gap outside 46–199)	-1.5 cm

Violation condition: diff_prev < mindiff_prior OR diff_next < mindiff OR diff_prev > maxdiff_prior OR diff_next > maxdiff. Strict inequalities.

Resolution with 3+ measurements: EWMA-based tiebreaker (bef.g.aftm1, aft.g.aftm1), internal_id tiebreaker. Resolution with 2 measurements: Higher abs(tbc.sd), internal_id tiebreaker.

2K. Child Step 19 (Pairs and Singles)

Threshold	Value	Role
Pair, gap ≥ 365.25	|diff_tbc| > 4 AND |diff_ctbc| > 4 (or NA)	Large-gap pair
Pair, gap < 365.25	|diff_tbc| > 2.5 AND |diff_ctbc| > 2.5 (or NA)	Small-gap pair
Single with DOP	|tbc.sd| > 3 AND comp_diff > 5	Single-measurement exclusion with cross-check
Single without DOP	|tbc.sd| > 5	Very extreme isolated measurement
Gap boundary	365.25 days (inclusive ≥ vs strict <)

2L. Child Step 21 (Error Load)

Configurable thresholds in Section 1B. Hardcoded component:

Item	Value
non_error_codes list	Exclude-C-Identical, Exclude-C-Extraneous, Exclude-C-CF, Exclude-Missing, Exclude-Not-Cleaned

Note: Exclude-C-Temp-Same-Day is NOT in non_error_codes. By the time Child Step 21 runs, Child Step 13 has resolved every temp SDE; any Exclude-C-Temp-Same-Day row at this point would be a bug and would correctly count as an error.

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3. Hardcoded thresholds (adult)

All adult threshold comparisons apply the 0.12 cm/kg rounding tolerance unless explicitly noted otherwise.

3A. Global

Threshold	Value	Location	Role
Adult rounding tolerance	0.12 cm/kg	All adult comparisons	Added to threshold comparisons (not BMI)
Adult EWMA exponent	-5	All adult EWMA steps	More negative than child’s -1.5
Adult EWMA anchor	0	All adult EWMA steps
BMI formula	weight_kg / (height_cm / 100)²	Multiple

3B. Adult Step 1 (PIV)

Configurable HT/WT/BMI limits in Section 1D. Guard:

Item	Value	Role
BMI PIV guard	Runs only when overall_bmi_min < single_bmi_min OR overall_bmi_max > single_bmi_max	Skip BMI-PIV when 1D limits are already tighter
BMI PIV rounding tolerance	Not applied	Unlike other comparisons, BMI PIV uses exact values

3C. Adult Step 4W (Scale Max)

Threshold	Value	Role
Scale cap conversion	round(adult_scale_max_lbs / 2.2046226, 1) ± 0.1 kg	Convert lbs to kg with detection tolerance
dewma50p threshold	dewma_all > 50 + 0.12	Large positive deviation
dewma50p before/after	> 45 + 0.12 (0.9 × 50)	Directional check
dewma50m mirror	< -(50 + 0.12); before/after < -(45 + 0.12)
d50p adjacency	d_prev > 50 + 0.12 AND d_next > 50 + 0.12
Missing adjacency neighbors	Treated as +Inf (positive) / -Inf (negative)	Confirms exclusion at edges
Minimum included	2+

3D. Adult Step 9Wa (Evil Twins)

Threshold	Value	Role
Interval boundary	≤6m vs >6m	Two ET-cap tiers
Minimum values	4+ eligible weights (A, B, C, D), re-checked every iteration	Count gate
Out-of-line inner pair	abs(B - C) > ET cap(B,C) + 0.12	Candidate pair
Anchors	abs(A - B) ≤ 0.60 × ET cap(A,B) + 0.12 and abs(C - D) ≤ 0.60 × ET cap(C,D) + 0.12; a missing A or D disqualifies the pair	Anchor rule
Median-band tiebreak	windowed median ±4 positions; band width 0.20 × ET cap	Worst-value selection
UER3 ratio	unit-error-group / plausible-group mean weight ratio in [1.7, 2.7]	Unit-error two-group split

3E. Adult Step 9H (Final SDE Height)

Threshold	Value	Role
Category 2	daystot >= 4 AND sderatio < 0.5
Category 3	daystot == 2 or 3 OR sderatio >= 0.5
Identical tiebreaker	lowest internal_id
Non-identical tiebreaker	highest internal_id	Differs from Category 2 identical

3F. Adult Step 9Wb (Extreme EWMA)

Threshold	Value	Role
Positive outlier (all)	dewma_all > threshold + 0.12	Main criterion
Positive outlier (before/after)	dewma_before > 0.9 × threshold + 0.12 AND dewma_after > 0.9 × threshold + 0.12	Directional
Negative outlier	Mirrors of positive with <
Directional factor	0.9	Before/after relaxation
Missing directional	Treated as Inf (confirms exclusion)
Minimum non-extraneous	3+
Threshold source	compute_et_limit(min_gap_months, formula, uw) where uw = max(wt, ewma_all)
Round limit	None (R implementation)

3G. Adult Step 10H (Height Distinct)

Threshold	Value	Role
Effective band	ht_band × 2.54 + 0.12 cm	Converts inches to cm
Gain rescue age boundary	ageyears1 < 25	Below this age, allow height gain
htallow formula	velocity × (ln(age2 - 16.9) - ln(age1 - 16.9))
htallow coefficient (gap <2yr)	15.5	2D gain
htallow coefficient (gap 2–3yr inclusive)	13	2D gain
htallow coefficient (gap >3yr)	12	2D gain
Age cap for htallow	25
Gain rescue tolerance	(htallow + 2) × 2.54 + 0.12 cm	2-inch buffer
Loss rescue tolerance (age <50)	5 × 2.54 + 0.12 cm	5 inches
Loss rescue tolerance (age ≥50)	7 × 2.54 + 0.12 cm	7 inches
Frequency rescue ratio	count ≥ count × 4/3
w2 window step	ht_band × 2.54 + 0.12 cm
w2/o2 ratio minimum	≥ 3/2
w2 selection score	tot_w2 + 0.5 × numdistinct_w2
Loss group band	2 inches = 5.08 + 0.12 cm
Loss group max count	3
Gain group max count	6
Loss group cumulative limit	6/8/9 inches depending on age pattern
Gain group htallow (<1yr)	20
Gain group htallow (1–3yr)	15
Gain group htallow (>3yr)	12
Loss magnitude 3D (age <50)	≤ 5 inches
Loss magnitude 3D (age ≥50)	≤ 7 inches

3H. Adult Step 11Wa (2D Ordered Weight)

Threshold	Value	Role
Rounding tolerance	0.12 kg
wtallow source	compute_wtallow(months, formula, uw) (see vignette("adult-algorithm"))

3I. Adult Step 11Wa2 (2D Non-Ordered Weight)

Threshold	Value	Role
Rounding tolerance	0.12 kg
Dominance threshold	dominant_pct > 0.65 (strict)
Interval conversion	abs(age_days[i+1] - age_days[i]) / 30.4375	Days to months
Prior non-SDE exclusion set	Include, temp extraneous, Exclude-A-Identical, Exclude-A-Extraneous, empty, NA

3J. Adult Step 11Wb (Moderate EWMA)

Threshold	Value	Role
Minimum distinct values	3+
Minimum included	3+
Standard pathway main	|dewma_all| > wtallow + 0.12
Standard pathway directional	Both directional > mod_ewma_f × wtallow + 0.12 (same direction)
Trajectory rescue error margin	±5 kg
Trajectory rescue rounding	Nearest 0.2 kg
Extrapolation distance	≤ 2× source interval
Run-length thresholds	4+ consecutive → error load; 1 → isolated; 2–3 → pair/trio
Unreliable neighbor threshold	≤ 14 days AND > wtallow apart
Alternate pathway criterion	|dewma_all| > wtallow + 0.12 AND |dewma_aft| > 0.75 × wtallow + 0.12 (or |dewma_bef|)
Alternate pathway factor	0.75	Relaxed directional factor
Percentage criterion	wt/ewma_all < perclimit AND wt/ewma_bef < perclimit AND wt/ewma_aft < perclimit	All three must pass
Graduated scoring multiplier	min(1.0, 0.6 + 0.4 × min_excess)
Edge scoring formula	pmax(0, |dewma_all| - wta) / wta_base
wta_base	wtallow at UW = 120 (no adjustment)
max_rounds	100	Maximum iterations of the moderate EWMA loop; the same at every permissiveness level and not changeable

3K. Adult Step 13 (Single Distinct 1D)

All limits configurable (Section 1D). No additional hardcoded thresholds besides BMI formula.

3L. Adult Step 14 (Error Load)

Threshold	Value	Role
Minimum denominator	≥ 3
SDE excluded from counts	Exclude-A-Identical, Exclude-A-Extraneous
RV-propagated codes	Excluded from error count

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4. Reference-data-driven values

4A. Growth reference tables (inst/extdata/)

File	Loaded by	Consumed by	User-overridable?
growthfile_who.csv.gz	read_anthro(), gc_preload_refs()	Z-score calculation (wrapper preprocessing)	Via ref.data.path
growthfile_cdc_ext_infants.csv.gz	read_anthro(), gc_preload_refs()	Z-score calculation	Via ref.data.path
fent_foraga.csv.gz	cleangrowth() Phase 10 (GA correction)	Approximated Fenton median weights by gestational age (weight → GA) for potcorr	No (always read from the installed package)
fenton2025_ms_lookup_smoothed.csv	cleangrowth() Phase 10	Approximated Fenton CSD values (M, S_upper, S_lower) for corrected z-scores	No (always read from the installed package)
rcfile-resmoothed.csv.gz	Recentering (Phase 11)	rcmedian.sd lookup for recentering	Via the sd.recenter argument; the file location can also be changed with ref.data.path
Tanner height velocity table (Tanner and Davies, 1985)	cleanchild Child Step 17	HT velocity tolerance	Via ref.data.path
WHO HT velocity table (WHO growth velocity standards, 2009)	cleanchild Child Step 17	HT velocity (<9m)	Via ref.data.path
WHO HC velocity table (WHO growth velocity standards, 2009)	cleanchild Child Step 17	HC velocity	Via ref.data.path

4B. Lookup tables defined in code

Lookup	Location	Consumed by	Overridable?
DOP mapping	WT↔︎HT, HC→HT	get_dop() in child_clean.R	Not overridable
Adult permissiveness presets	Section 1D values	resolve_permissiveness() in adult_support.R	Override individual params via cleangrowth(adult_overrides = list(...))
Adult wtallow formulas (PW-H, PW-L, allofus15)	compute_wtallow() / compute_et_limit() in adult_support.R; full spec in vignette("adult-algorithm")	Adult Steps 9Wa, 9Wb, 11Wa, 11Wa2, 11Wb	Custom CSV also supported

The current CF-rescue rule (deltaz/nextz) is documented in vignette("cf-rescue"). The full wtallow formula spec is in vignette("adult-algorithm").

4C. Z-score / age-blending constants

Item	Value	Location
WHO-only range (HT/WT)	< 2 years	Z-score infrastructure
WHO/CDC blend range (HT/WT)	2–5 years; formula (cdc × (age-2) + who × (5-age)) / 3	Z-score infrastructure
CDC-only range (HT/WT)	> 5 years	Z-score infrastructure
HEADCM age policy	WHO only at all ages (z-source available through 5y); cleaned only through 5y	Z-score infrastructure
HEADCM age cutoff	agedays > 5 × 365.25 → Exclude-Not-Cleaned (WHO HC z-score reference ends at 5y; the recentering file provides HC rcmedian.sd through 5y); re-asserted post-recentering at agedays > 5 × 365.25	Preprocessing + Phase 11
Imperial → metric (HEIGHTIN)	× 2.54	Preprocessing Phase 7
Imperial → metric (WEIGHTLBS)	÷ 2.2046226	Preprocessing Phase 7
Sex encoding	Default sex_coding (case-insensitive): 0/"m"/"b"/"male"/"boy" → 0L; 1/"f"/"g"/"female"/"girl" → 1L; see sex_coding in Section 1A	Preprocessing Phase 3
measurement == 0 → NaN	Hardcoded conversion	Preprocessing Phase 3

4D. Gestational Age Correction (Child Step 2b / Phase 10)

Item	Value	Role
potcorr_wt condition	First weight for subject AND sd.orig < -2 AND age < 10 months	Flag potentially preterm subject
intwt formula	trunc(v × 100) × 10 (grams)	Integer weight for GA-reference merge
intwt floor	Values in [100, 500) → 500	Clamp low values to GA-reference table minimum
pmagedays	agedays + fengadays	Postmenstrual age in days
cagedays	pmagedays - 280	Corrected age (days)
GA-correction term cutoff	fengadays < 259	Below this → considered preterm for correction
GA-reference weight scaling	v_fenton = v × 1000 for WT; v otherwise	GA-reference table is in grams
GA-reference CSD z-score	(v_fenton − M) / (S_upper × M) if v_fenton >= M, else / (S_lower × M)	Split-normal CSD
Recumbent/standing offset (WHO and CDC)	+0.7 cm (.gc_len_offset, shared with length.adjust); boundary day 730 (.gc_ht_start_day)	Chronological age at or past day 730 but corrected age before day 730; under the default the same 0.7 cm is first subtracted from the value used for the uncorrected z (see vignette("wrapper"), Phase 8, fact 6)
GA-reference precedence ≤ 2y	sd.c := unmod_zscore when ageyears_2b ≤ 2
Smoothing range	2–4 years; formula (sd.orig × (4 - age) + sd.c × (age - 2)) / 2
Above-4y policy	sd.corr = sd.orig
uncorr revert rule	Revert correction if sd.corr_abssumdiff > sd.orig_abssumdiff	Correction worsens trajectory
uncorr window	First 4 weights AND ageyears_2b < 2	Where revert check runs

The confirm-correction rule (a same-day HT or HC may corroborate a corrected first weight, capped at 3.5 z) is described in vignette("wrapper") (Phase 4) and vignette("child-algorithm") (Child Step 2b).