Author: Matthias Templ
Date: 2026-04-23

# Data Quality Assessment

#### Matthias Templ1

#### Barbara Templ2

#### 2026-04-23

Vignette 2 of 4 for the pep725 R package. The most current version is available on GitHub and CRAN.

## Introduction

Data quality assessment is a critical but often overlooked step in phenological analysis. Before calculating trends, normals, or climate sensitivities, you need to understand what’s in your data and make informed decisions about unusual observations.

### The Data Quality Challenge

Long-term phenological datasets such as PEP725 are compiled from many observers over decades. This richness enables large-scale analyses, but it also introduces data quality challenges that need to be assessed:

Issue Type | Examples | Consequence if Ignored
--- | --- | ---
Recording errors | Typographical errors (DOY 150 instead of 105), incorrect year | Outliers bias statistics
Identification errors | Confusion between morphologically similar species | Inconsistent or mixed time series
Protocol changes | Changes in the definition of phenological phases over time | Artificial shifts or trends
Biological anomalies | Irregular phenological events as a result of climate extremes | May represent real biological signals

The following sections introduce practical tools in pep725 package for diagnosing and handling these issues in a transparent and reproducible way.

### What You’ll Learn

Section | Topic | Key Functions
--- | --- | ---
Part 1 | Detecting statistical outliers | `pep_flag_outliers()`, `pep_plot_outliers()`
Part 2 | Temporal coverage and completeness | `pep_completeness()`
Part 3 | Phase presence validation | `pep_check_phases()`
Part 4 | Integrated workflow | Combining all approaches

### Prerequisites

This vignette assumes you are familiar with:

- Basic phenological concepts (from “Getting Started” vignette)
- Day of Year (DOY) as a timing metric
- BBCH phenological phase codes

## Setup

    library(pep725)
    library(data.table)

    # Download the synthetic dataset
    pep <- pep_download()

    # For this vignette, we'll focus on flowering phases
    flowering <- pep[phase_id %in% c(60, 65)]
    cat("Flowering observations:", nrow(flowering), "\n")
    #> Flowering observations: 1310094
    cat("Species:", length(unique(flowering$species)), "\n")
    #> Species: 36
    cat("Year range:", min(flowering$year), "-", max(flowering$year), "\n")
    #> Year range: 1868 - 2025

# Part 1: Outlier Detection

## Why Detect Outliers?

An outlier is an observation that differs substantially from the expected pattern. In phenological data, outliers may indicate:

1. Recording errors that should be excluded from analysis
   - A typo: DOY 250 instead of DOY 150 (roughly 3 months difference)
   - Wrong year entered: observation assigned to incorrect season
2. Unusual weather events worth investigating
   - Very warm winter causing early flowering
   - Late frost delaying spring phenology
3. Second flowering or other abnormal phenological events
   - Plants flowering again in autumn/winter after spring flowering
   - Increasingly observed with climate change

The challenge: You can’t simply delete all outliers. Some are errors, but others are scientifically valuable observations of unusual events.

## Statistical Methods for Outlier Detection

The `pep_flag_outliers()` function provides four statistical methods for identifying potential outliers. Each method has different assumptions and strengths:

### Method 1: 30-Day Rule (Simple Threshold)

The simplest approach: flag any observation more than 30 days from the median for that species/phase combination.

    # Flag outliers using the default 30-day rule
    outliers <- pep_flag_outliers(
      pep = flowering,
      method = "30day",
      by = c("species", "phase_id")
    )

    print(outliers)
    #> Phenological Outlier Detection Results
    #> =============================================
    #> Method: 30day
    #> Threshold: 30 days
    #> Grouping: species, phase_id
    #>
    #> Total observations: 1,310,094
    #> Outliers flagged: 26573 (2.03%)
    #>   - Early outliers: 15011
    #>   - Late outliers: 11562
    #>
    #> Deviation summary for outliers:
    #>   Min: -167.0 days
    #>   Max: 223.0 days
    #>   Mean |deviation|: 38.4 days

How it works:

                         Distribution of flowering dates

            ← Early                                    Late →

       ----|----[=======|=======]----|-----
            ^           ^           ^
         -30 days    median      +30 days

       Anything outside the brackets is flagged as an outlier

### Understanding the Output

The function adds new columns to your original data:

Column | What It Contains | How to Use It
--- | --- | ---
`is_outlier` | TRUE/FALSE flag | Filter data: `data[is_outlier == FALSE]`
`deviation` | Days from expected | Prioritize investigation: larger = more extreme
`expected_doy` | Reference DOY (median) | Understand what “normal” looks like

### Method 2: MAD (Median Absolute Deviation) - Recommended

The MAD method is robust to the presence of multiple outliers. This is important because if your data contains many outliers, they can distort mean-based methods.

    # MAD method: flag if > 3 MAD from median (robust)
    outliers_mad <- pep_flag_outliers(flowering, method = "mad", threshold = 3)

Why MAD is recommended:

Scenario | Mean-based method | MAD method
--- | --- | ---
1-2 outliers | Works reasonably | Works well
Many outliers | Outliers inflate SD, may miss more | Stays robust
Asymmetric data | Assumes symmetry | Handles asymmetry

### Method 3: IQR (Interquartile Range) - Also Robust

The IQR method uses quartiles and is familiar from boxplot “whiskers”:

    # IQR method: flag if outside 1.5 * IQR (standard boxplot rule)
    outliers_iqr <- pep_flag_outliers(flowering, method = "iqr", threshold = 1.5)

How it works: - Q1 = 25th percentile, Q3 = 75th percentile - IQR = Q3 - Q1 - Outlier if: value < Q1 - 1.5×IQR OR value > Q3 + 1.5×IQR

### Method 4: Z-Score - Sensitive but Less Robust

The z-score method assumes normally distributed data:

    # Z-score method: flag if |z| > 3 (assumes normal distribution)
    outliers_zscore <- pep_flag_outliers(flowering, method = "zscore", threshold = 3)

Caution: The z-score method is sensitive to existing outliers. If your data has many outliers, they will inflate the standard deviation, making the z-score threshold less effective at detecting them.

### Method 5: GAM Residual - Model-based, Covariate-aware

The four methods above are all univariate within a group — they compare each observation to the central tendency of its own station-species-phase combination. That misses three realistic outlier patterns:

1. Year-effect outliers. In a year where most of central Europe bloomed 8 days earlier, a station that flowered on its 30-year median looks “late” only because the reference ignores the shared weather signal.
2. Covariate-inconsistent reports. A lowland station that reports a DOY typical of a mountain station is invisible to a within-station detector because the station’s own history may be short.
3. Trend-inconsistent reports. A station whose DOY is constant while every other station in the network has a trend is anomalous only in relation to the trend.

`method = "gam_residual"` tackles all three. For each group (typically species × phase), it fits a GAM of DOY on year, altitude, latitude, and a station random intercept (customisable via `formula =`) and flags observations whose residual — standardised by a robust MAD scale — exceeds the threshold:

    # Model-based detection across the whole species x phase group.
    outliers_gam <- pep_flag_outliers(
      apple_flowering,
      by = c("genus", "species", "phase_id"),
      method = "gam_residual",
      threshold = 3.5
    )

The `deviation` column now holds GAM residuals in days (not deviations from a within-station median), and `expected_doy` holds the fitted values — so the station-year whose residual is 20 days above the fit is flagged whether or not its station’s history made that value look “normal”.

Groups with fewer observations than `min_n_per_group` (default 50) or where the GAM fails to converge silently fall back to the 30-day rule.

### Method 6: Mahalanobis - Multivariate, Robust (MCD)

All methods above flag observations one at a time. A station-year could have an entirely reasonable BBCH 60 date and an entirely reasonable BBCH 65 date, but only one day apart — biologically impossible, because first flowering precedes full flowering by ~10 days.

`method = "mahalanobis"` catches this by treating each station-year as a vector across phases and computing the robust Mahalanobis distance of that vector from the centre of the rest of the network. “Robust” matters: the classical Mahalanobis distance uses the sample mean and covariance, which are themselves pulled by outliers (masking). We use the Minimum Covariance Determinant estimator (Rousseeuw 1984, `robustbase::covMcd()`) which gives a high-breakdown robust centre and scatter, so the outliers stay outside the robust ellipsoid instead of contaminating it:

    # Multivariate detection on the phase profile per station-year.
    # by = c("genus", "species") pools across phases so the covariance
    # is estimated from the joint (BBCH 60, BBCH 65, BBCH 89) distribution.
    outliers_mahal <- pep_flag_outliers(
      apple,
      by = c("genus", "species"),
      method = "mahalanobis"
    )

The default threshold is `sqrt(qchisq(0.975, df = p))` where p is the number of phases — the standard chi-square containment cut-off under multivariate normality. Flagged station-years get all their phase rows marked; `deviation` stores the robust MD (not a day-count, so it is unitless).

### Choosing a Method

Method | Best For | Threshold Meaning
--- | --- | ---
`30day` | Simple, interpretable threshold | Absolute days from median
`mad` | Most situations (recommended for single-phase) | Number of MADs from median
`iqr` | Familiar boxplot-style detection | IQR multiplier
`zscore` | Clean data, normal distribution | Standard deviations
`gam_residual` | Year / elevation / station covariates available | Robust z on GAM residuals
`mahalanobis` | Multiple phases per station-year | `sqrt(chi^2_{0.975, p})` default

### Summary Statistics

    summary(outliers)
    #> Phenological Outlier Summary
    #> =============================================
    #>
    #> Total observations: 1,310,094
    #> Total outliers: 26573 (2.03%)
    #>
    #> Groups with most outliers:
    #>               species phase_id  n_obs n_outliers pct_outliers mean_dev
    #>                <fctr>    <int>  <int>      <int>        <num>    <num>
    #>  1: Solanum tuberosum       60 114245       6420         5.62     12.0
    #>  2:  Prunus domestica       60 114641       2958         2.58     10.5
    #>  3:  Prunus domestica       65  77393       2146         2.77     10.8
    #>  4:   Malus domestica       60 205403       1957         0.95      9.1
    #>  5:   Malus domestica       65 175706       1770         1.01      9.1
    #>  6:    Prunus persica       60  48074       1515         3.15     11.0
    #>  7:    Prunus cerasus       60 136588       1227         0.90      9.0
    #>  8:    Prunus cerasus       65 112597       1042         0.93      9.0
    #>  9:  Prunus armeniaca       60  22692        943         4.16     12.1
    #> 10:    Pyrus communis       60  50335        940         1.87      9.5
    #>
    #> Deviation distribution (all data):
    #>  1%  5% 25% 50% 75% 95% 99%
    #> -31 -21  -8   0   8  20  30

### Comparing Outlier Rates Across Species

Different species may have different outlier rates due to observation difficulty or data quality:

    # Check outliers for grapevine
    vine_flowering <- pep[species == "Vitis vinifera" & phase_id %in% c(60, 65)]

    if (nrow(vine_flowering) > 0) {
      outliers_vine <- pep_flag_outliers(
        pep = vine_flowering,
        method = "30day",
        by = c("species", "phase_id")
      )

      cat("Outlier comparison:\n")
      cat("All flowering species: ", round(100 * mean(outliers$is_outlier), 2), "%\n")
      cat("Grapevine only:        ", round(100 * mean(outliers_vine$is_outlier), 2), "%\n")
    } else {
      cat("No grapevine flowering data available for comparison.\n")
    }
    #> Outlier comparison:
    #> All flowering species:  2.03 %
    #> Grapevine only:         3.68 %

## Visualizing Outliers

Visual inspection is essential for understanding outlier patterns. The `pep_plot_outliers()` function provides several visualization types — four for the univariate methods plus two targeted at the model-based and multivariate methods:

### 1. Overview Plot

Shows the big picture: how many outliers, which species/phases are affected:

    # Overview of outlier patterns
    pep_plot_outliers(outliers, type = "overview")
    #> Warning: Removed 16 rows containing non-finite outside the scale range
    #> (`stat_bin()`).

What to look for: - Which species have the most outliers? (Might indicate data quality issues) - Are outliers concentrated in certain phases? (Might indicate definition problems) - What’s the overall outlier rate? (Typical: 1-5% for well-curated data)

### 2. Seasonal Distribution

When in the year do outliers occur?

    # When do outliers occur in the year?
    pep_plot_outliers(outliers, type = "seasonal")

Interpretation guide:

Outlier Timing | Likely Explanation
--- | ---
Very early (DOY < 50) | Possible data errors (flowering in January/February unlikely for most species)
Somewhat early | Warm winters or Mediterranean locations
Somewhat late | Cool springs or high-altitude stations
Very late (DOY > 250) | Possible second flowering events - investigate!

### 3. Detailed Context

See outliers alongside normal observations:

    # See outliers in context of all observations
    pep_plot_outliers(outliers, type = "detail", n_top = 15)

This plot shows: - Full distribution of observations (gray) - Flagged outliers (highlighted) - The `n_top` parameter controls how many species/phases to show

### 4. Geographic Distribution

Where are outliers located?

    # Where are outliers located?
    pep_plot_outliers(outliers, type = "map")

What to look for: - Clustered outliers in one region? Might indicate local data quality issues - Outliers at network edges? Might be at environmental limits - Random scatter? Suggests individual observation errors

### 5. Model Diagnostic (for `gam_residual` / `mahalanobis`)

`type = "diagnostic"` produces a paper-ready 4-panel figure tailored to the detection method. For `gam_residual` the panels are classical GAM diagnostics — residuals vs fitted, Q-Q against Normal, |residual| vs altitude, and a per-station worst-case-residual map. For `mahalanobis` the panels switch automatically to MD-specific diagnostics: sorted MD with the chi-square threshold line, Q-Q of MD² against χ²_p, mean/max MD over time (exposes network-wide anomalous epochs), and the per-station worst-case MD map.

    # For gam_residual: classical model diagnostics
    outliers_gam <- pep_flag_outliers(
      apple_flowering,
      by = c("genus", "species", "phase_id"),
      method = "gam_residual"
    )
    pep_plot_outliers(outliers_gam, type = "diagnostic")

GAM-residual diagnostic on a synthetic fixture with one injected contamination at station 1, year 2000. Panel A: residuals vs fitted; the injected point appears at residual ≈ +50 days. Panel B: Q-Q against N(0,1); the right-tail departure corresponds to the outlier. Panel C: |residual| vs altitude, showing the model has no altitude bias away from the outlier. Panel D: per-station worst-case residual map.

    # For mahalanobis: MD-specific diagnostics
    outliers_mahal <- pep_flag_outliers(
      apple,
      by = c("genus", "species"),
      method = "mahalanobis"
    )
    pep_plot_outliers(outliers_mahal, type = "diagnostic")

Mahalanobis-specific diagnostic on the same synthetic fixture. Panel A: sorted robust Mahalanobis distances across all station-years, with the \(\sqrt{\chi^2_{0.975,\,3}} \approx 3.06\) threshold as a red dashed line; flagged points are red. Panel B: Q-Q of observed \(\mathrm{MD}^2\) against \(\chi^2_3\) — upper-tail departure identifies the outlier mass. Panel C: mean (blue) and max (red dotted) MD per year — the spike at year 2000 coincides with the injected anomaly. Panel D: per-station worst-case MD map.

What to look for:

- Residuals vs fitted (GAM): a level trend with no structure is ideal; a funnel or curve signals model misspecification, not outliers.
- Q-Q (GAM): heavy-tailed deviations in the corners are the real outlier signal — light tails mean the threshold is picking up noise.
- Sorted MD with threshold (Mahalanobis): the steep rise at the right-hand end is where flagged station-years sit; a long flat “knee” across the threshold means the threshold is arguably too loose or too strict.
- Mean / max MD over time (Mahalanobis): spikes in the max line identify years in which many stations reported biologically inconsistent phase sequences — useful for correlating with known data-collection or instrumental events.

### 6. Phase-profile Plot (primary Mahalanobis figure)

The MD detector flags station-years whose shape across phases is atypical, even when each marginal DOY looks fine. `type = "profile"` plots the phase profile as parallel coordinates — one line per station-year, flagged ones in red, with the robust median profile overlaid in black as a reference:

    # Phase-profile parallel coordinates (primary Mahalanobis figure).
    pep_plot_outliers(outliers_mahal, type = "profile")

Phase-profile parallel-coordinates plot. Each line is one station-year; the grey envelope shows the natural variability of the network, the red lines are station-years flagged by the robust Mahalanobis detector, and the thick black line is the MCD robust per-phase median profile. Red lines that cross the phases at atypical angles — not just at unusual absolute DOYs — are the classic Mahalanobis flags.

How to read it:

- Every grey line is a “normal-looking” station-year; together they form the envelope of the robust ellipsoid.
- Red lines are flagged. Look where they bend oddly: a station-year whose BBCH 60 → 65 slope is much flatter or steeper than the reference is the classic MD flag.
- The black reference profile is the robust (MCD) per-phase median — the centre of the ellipsoid. Anything strongly parallel to this is safe; anything that crosses multiple phases at unusual angles is suspect.

# Part 2: Data Completeness

## Why Check Completeness?

Data completeness refers to how many years of observations exist for each station/phase combination. This matters because:

1. Trend analysis requires continuous data: Gaps can bias trend estimates
2. Normals require representative coverage: WMO recommends 24+ years in a 30-year period
3. Missing data isn’t random: Stations often drop out or are added systematically

### Visualizing Completeness Issues

    Station A: ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●  <- 100% complete
               1990                      2020

    Station B: ●●●●●●●●●●○○○○○○○○○○●●●●●●●●●●  <- Gap in middle
               1990                      2020

    Station C: ○○○○○○○○○○○○○○○○○○○○●●●●●●●●●●  <- Only recent data
               1990                      2020

    Station D: ●●●●●●●●●●●●●●●●●●●●○○○○○○○○○○  <- Discontinued
               1990                      2020

Different completeness patterns have different implications:

Pattern | Implications for Analysis
--- | ---
Full coverage | Ideal - reliable trends and normals
Gap in middle | Careful - may miss important changes
Only recent | Cannot compare to historical period
Discontinued | Cannot assess recent changes

## Assessing Completeness

    # Check completeness by station and phase
    # Use year_range to focus on a specific period
    completeness <- pep_completeness(
      pep = flowering,
      by = c("s_id", "phase_id"),
      year_range = c(1990, 2020)
    )

    print(completeness)
    #> Phenological Data Completeness Assessment
    #> --------------------------------------------------
    #> Grouping by: s_id, phase_id
    #> Year range: 1990-2020
    #> Total groups: 8390
    #> Mean completeness: 95.1%
    #> Groups with >80% completeness: 7686 (91.6%)
    #> --------------------------------------------------
    #>
    #>       s_id phase_id n_obs n_stations n_years year_min year_max year_span
    #>     <fctr>    <int> <int>      <int>   <int>    <int>    <int>     <int>
    #>  1:      1       60    33          1      10     1990     1999        10
    #>  2:      1       65    25          1       8     1990     1998         9
    #>  3:      3       60    30          1      17     1990     2006        17
    #>  4:      3       65    27          1      16     1991     2006        16
    #>  5:      4       60    62          1      26     1990     2015        26
    #>  6:      4       65    55          1      26     1990     2015        26
    #>  7:      5       60    10          1       6     1990     1995         6
    #>  8:      5       65     7          1       4     1991     1994         4
    #>  9:      9       60     6          1       3     1990     1992         3
    #> 10:      9       65     4          1       3     1990     1992         3
    #> 11:     11       60    16          1       7     1990     1996         7
    #> 12:     11       65    15          1       7     1990     1996         7
    #> 13:     13       60     3          1       3     1990     1995         6
    #> 14:     13       65     4          1       4     1993     1998         6
    #> 15:     15       60    27          1      10     1994     2012        19
    #>     completeness_pct median_doy iqr_doy
    #>                <num>      <num>   <num>
    #>  1:            100.0      129.0    13.0
    #>  2:             88.9      137.0    12.0
    #>  3:            100.0      116.0    13.8
    #>  4:            100.0      125.0     8.0
    #>  5:            100.0      119.0    17.0
    #>  6:            100.0      123.0    12.5
    #>  7:            100.0      116.0    13.5
    #>  8:            100.0      129.0     6.5
    #>  9:            100.0      121.5    21.0
    #> 10:            100.0      126.0    22.5
    #> 11:            100.0      121.5    10.0
    #> 12:            100.0      134.0     7.0
    #> 13:             50.0      134.0    11.0
    #> 14:             66.7      133.0     2.8
    #> 15:             52.6      123.0    11.0
    #>
    #> ... and 8375 more rows

### Understanding Completeness Metrics

The function calculates several metrics:

Metric | What It Measures | Interpretation
--- | --- | ---
`n_years` | Total years with data | More = better
`completeness_pct` | % of year span covered | 70%+ for trends, 80%+ for normals
`year_span` | Total span (year_max - year_min + 1) | Context for completeness
`year_min` | Earliest observation | Needed for historical comparison
`year_max` | Most recent observation | Needed for current status

### Summary Statistics

    summary(completeness)
    #> Phenological Data Completeness Summary
    #> ==================================================
    #>
    #> Total groups: 8390
    #> Total observations: 441,295
    #> Total unique stations: 8,390
    #>
    #> Completeness Distribution:
    #>   0-20%:   33 (  0.4%)
    #>   20-40%:   99 (  1.2%)
    #>   40-60%:  224 (  2.7%) *
    #>   60-80%:  413 (  4.9%) *
    #>   80-100%: 7621 ( 90.8%) ******************
    #>
    #> Year Coverage Statistics:
    #>   Mean year span: 14.1 years
    #>   Mean years with data: 13.2
    #>   Earliest data: 1990
    #>   Latest data: 2020
    #>
    #> Observation Statistics:
    #>   Mean observations per group: 52.6
    #>   Median observations per group: 38
    #>   Max observations: 346
    #>
    #> Phenology Statistics:
    #>   DOY range: 6 - 304

## Filtering by Completeness

Use completeness information to select stations appropriate for your analysis:

    # Get stations with good coverage (>= 70%)
    good_coverage <- completeness[completeness_pct >= 70]
    cat("Stations with >= 70% coverage:", nrow(good_coverage), "\n")
    #> Stations with >= 70% coverage: 7893

    # Use these for trend analysis
    good_stations <- unique(good_coverage$s_id)
    flowering_complete <- flowering[s_id %in% good_stations]
    cat("Observations from complete stations:", nrow(flowering_complete), "\n")
    #> Observations from complete stations: 935551

### Completeness Thresholds for Different Analyses

Analysis Type | Minimum Completeness | Reasoning
--- | --- | ---
Trend detection | 50% (15+ years) | Need enough points for trend fitting
Climate sensitivity | 60% | Need variability across climate conditions
30-year normals | 80% (24+ years) | WMO standard requirement
Station comparison | Same time period | Avoid bias from different eras

## Visualizing Completeness

    plot(completeness)

# Part 3: Phase Presence Validation

## Why Check Phase Presence?

Before starting an analysis, it’s important to verify that your data contains the phenological phases you need. The `pep_check_phases()` function validates that expected BBCH phase codes are present in your data.

Common questions this helps answer:

- Does my dataset have flowering observations (phase 60)?
- Are flowering and fruit maturity phases both available for apple?
- Which phases are missing for my species of interest?

## Checking Phase Presence

    # Check if expected phases are present for apple
    apple <- pep[species == "Malus domestica"]

    phase_check <- pep_check_phases(
      pep = apple,
      expected = c(60, 65, 87)  # flowering, full flowering, fruit maturity
    )

    print(phase_check)
    #> Phenological Phase Availability Check
    #> ---------------------------------------------
    #>
    #> Expected phases: 60, 65, 87
    #> Status: COMPLETE - all expected phases present
    #>
    #> Phases found:
    #>   Phase   0: 1 observations [extra]
    #>   Phase   7: 33 observations [extra]
    #>   Phase  10: 1,394 observations [extra]
    #>   Phase  11: 700 observations [extra]
    #>   Phase  15: 159 observations [extra]
    #>   Phase  57: 26 observations [extra]
    #>   Phase  59: 25 observations [extra]
    #>   Phase  60: 205,403 observations
    #>   Phase  61: 1,055 observations [extra]
    #>   Phase  63: 80 observations [extra]
    #>   Phase  65: 175,706 observations
    #>   Phase  67: 29 observations [extra]
    #>   Phase  69: 170,323 observations [extra]
    #>   Phase  81: 151 observations [extra]
    #>   Phase  85: 93 observations [extra]
    #>   Phase  87: 253,169 observations
    #>   Phase  89: 17 observations [extra]
    #>   Phase  91: 80 observations [extra]
    #>   Phase  93: 617 observations [extra]
    #>   Phase  95: 76,453 observations [extra]
    #>   Phase  97: 2,470 observations [extra]
    #>   Phase 100: 225 observations [extra]
    #>   Phase 200: 3 observations [extra]
    #>   Phase 201: 517 observations [extra]
    #>   Phase 203: 1 observations [extra]
    #>   Phase 205: 7,912 observations [extra]
    #>   Phase 209: 2,358 observations [extra]
    #>   Phase 213: 1 observations [extra]
    #>   Phase 380: 208 observations [extra]
    #>   Phase 381: 7 observations [extra]
    #>   Phase 385: 95 observations [extra]
    #>
    #> Detailed coverage:
    #>     phase_id  n_obs n_stations n_years year_min year_max
    #>        <int>  <int>      <int>   <int>    <int>    <int>
    #>  1:        0      1          1       1     2022     2022
    #>  2:        7     33          5      11     2014     2025
    #>  3:       10   1394        258      26     2000     2025
    #>  4:       11    700        157      65     1961     2025
    #>  5:       15    159         53      14     2009     2025
    #>  6:       57     26          1       7     1942     1949
    #>  7:       59     25          4      14     1949     2025
    #>  8:       60 205403       7947     100     1926     2025
    #>  9:       61   1055        192      69     1936     2025
    #> 10:       63     80          5      39     1986     2025
    #> 11:       65 175706       7272     125     1896     2025
    #> 12:       67     29          5      10     2016     2025
    #> 13:       69 170323       7192      86     1937     2025
    #> 14:       81    151          5      54     1952     2021
    #> 15:       85     93         19       8     2013     2020
    #> 16:       87 253169       7504      86     1928     2024
    #> 17:       89     17          5      10     2000     2024
    #> 18:       91     80         26      13     2013     2025
    #> 19:       93    617         76      55     1970     2024
    #> 20:       95  76453       4120      78     1944     2024
    #> 21:       97   2470        368      32     1966     2024
    #> 22:      100    225         18      64     1951     2024
    #> 23:      200      3          2       2     2016     2017
    #> 24:      201    517         64      55     1970     2024
    #> 25:      203      1          1       1     2016     2016
    #> 26:      205   7912        779      79     1943     2025
    #> 27:      209   2358        357      25     1966     2014
    #> 28:      213      1          1       1     2012     2012
    #> 29:      380    208         10      63     1961     2024
    #> 30:      381      7          4       2     2023     2024
    #> 31:      385     95         37      13     2013     2025
    #>     phase_id  n_obs n_stations n_years year_min year_max
    #>        <int>  <int>      <int>   <int>    <int>    <int>

### Understanding the Output

The function returns information about phase coverage:

Output | What It Shows
--- | ---
`expected` | The phases you asked for
`present` | Which expected phases were found
`missing` | Which expected phases are absent
`complete` | TRUE if all expected phases are present
`n_obs` | Number of observations per phase

## Checking Multiple Species

To check phase presence across multiple species at once:

    # Check phases for multiple species
    multi_check <- pep_check_phases_multi(
      pep = pep,
      species_list = c("Malus domestica", "Vitis vinifera"),
      expected = c(60, 65, 87)
    )

    print(multi_check)
    #> Multi-Species Phase Availability Check
    #> ==================================================
    #> Expected phases: 60, 65, 87
    #>
    #> Species with all phases: 2 / 2 (100%)
    #> --------------------------------------------------
    #>
    #>            species complete n_expected n_present n_missing missing_phases
    #>             <char>   <lgcl>      <int>     <int>     <int>         <char>
    #> 1: Malus domestica     TRUE          3         3         0           <NA>
    #> 2:  Vitis vinifera     TRUE          3         3         0           <NA>
    #>    total_obs
    #>        <int>
    #> 1:    899311
    #> 2:    146667

### Common Phases to Check

Plant Type | Common Phases | BBCH Codes
--- | --- | ---
Cereals | Heading, Flowering, Harvest | 60, 65, 100
Fruit trees | Flowering, Full flowering, Fruit maturity | 60, 65, 87
Deciduous trees | Leaf unfolding, Flowering, Leaf fall | 11, 60, 95

# Part 4: Integrated Quality Workflow

## Putting It All Together

Here’s a recommended workflow for data quality assessment that combines all the tools covered in this vignette:

    # ══════════════════════════════════════════════════════════════════════════════
    # STEP 1: Assess temporal completeness
    # ══════════════════════════════════════════════════════════════════════════════
    # Why: Incomplete stations can bias trend estimates and normals

    completeness <- pep_completeness(flowering, by = c("s_id", "phase_id"))
    good_stations <- completeness[completeness_pct >= 50, s_id]
    fl_filtered <- flowering[s_id %in% good_stations]

    cat("Kept", length(good_stations), "stations with >= 50% completeness\n")
    #> Kept 15213 stations with >= 50% completeness

    # ══════════════════════════════════════════════════════════════════════════════
    # STEP 2: Flag statistical outliers
    # ══════════════════════════════════════════════════════════════════════════════
    # Why: Identify observations that deviate from expected patterns

    outliers_wf <- pep_flag_outliers(fl_filtered, method = "mad", threshold = 3)

    cat("Flagged", sum(outliers_wf$is_outlier), "outliers",
        "(", round(100 * mean(outliers_wf$is_outlier), 1), "% )\n")
    #> Flagged 20449 outliers ( 1.6 % )

    # ══════════════════════════════════════════════════════════════════════════════
    # STEP 3: Make informed decisions about exclusion
    # ══════════════════════════════════════════════════════════════════════════════
    # Key principle: Document your decisions!

    # Option A: Strict cleaning (for normals calculation)
    fl_strict <- outliers_wf[is_outlier == FALSE]

    # Option B: Moderate cleaning (keep moderate outliers)
    fl_moderate <- outliers_wf[is_outlier == FALSE | abs(deviation) < 60]

    cat("Strict cleaning keeps:", nrow(fl_strict), "obs\n")
    #> Strict cleaning keeps: 1252610 obs
    cat("Moderate cleaning keeps:", nrow(fl_moderate), "obs\n")
    #> Moderate cleaning keeps: 1272698 obs

    # ══════════════════════════════════════════════════════════════════════════════
    # STEP 4: Proceed with analysis on cleaned data
    # ══════════════════════════════════════════════════════════════════════════════

    normals <- pheno_normals(fl_moderate, period = 1991:2020, min_years = 5)
    #> Note: 44 group(s) have fewer than 5 years of data and return NA values.
    cat("Normals calculated for", sum(!is.na(normals$mean_doy)), "groups\n")
    #> Normals calculated for 202 groups

## Documentation Template

When publishing research, document your quality control decisions:

    Data Quality Control:
    1. Completeness filtering: Excluded stations with < 50% temporal coverage
       (reduced dataset from N to M stations)

    2. Outlier detection: Used MAD method with threshold = 3
       (flagged X observations as outliers, Y% of total)

    3. Outlier disposition:
       - Excluded: Z observations with deviations > 60 days (likely errors)
       - Retained: W observations identified as abnormal events (e.g., second flowering)

    4. Phase validation: Checked for sequence violations in [species list]
       (identified V cases for manual review)

# Best Practices Summary

## For Outlier Detection

1. Use robust methods: MAD or IQR methods handle multiple outliers better than z-scores. The MAD method is generally recommended.

2. Check seasonally: Late-season outliers (DOY > 250) may be biologically meaningful events (e.g. second flowering) rather than errors.

3. Verify extremes: For observations with very large deviations (> 60 days), try to check original data sources or contact data providers.

4. Document decisions: Record which outliers you exclude and why. This is essential for reproducibility and peer review.

5. Don’t delete automatically: Human judgment is needed to distinguish errors from genuine unusual events.

## For Abnormal Event Detection

1. Consider species biology: Some species (e.g., certain Rosaceae) are more prone to second flowering than others.

2. Check geographic patterns: If multiple nearby stations report late events in the same year, this suggests a real regional phenomenon.

3. Look at weather context: Link abnormal events to weather extremes - drought is a common trigger.

4. Distinguish from errors: Very isolated observations (single station, single year) need verification before treating them as e.g. second flowering.

5. Keep for separate analysis: Abnormal phenological events are scientifically interesting (proof of climate change) - don’t just delete them!

## For Completeness Assessment

1. Set appropriate thresholds: Use 80%+ coverage for calculating normals, 50%+ for trend analysis.

2. Consider gap patterns: Many small gaps are usually better than one long gap that might coincide with important climate changes.

3. Check temporal bias: Ensure you’re not comparing stations with data only from early periods to stations with only recent data.

4. Document station selection: Report how many stations met your completeness criteria and how this affected your sample.

## For Phase Presence Checking

1. Check early: Run `pep_check_phases()` at the start of your analysis to verify required phases are available in your data.

2. Know required phases: Different analyses need different phases - know which BBCH codes you need before starting.

3. Check across species: Use `pep_check_phases_multi()` to verify data availability for all species you plan to analyze.

## Summary

This vignette covered data quality tools for phenological analysis:

Function | Purpose | Key Output
--- | --- | ---
`pep_flag_outliers()` | Identify unusual observations | `is_outlier` flag, `deviation` in days
`pep_plot_outliers()` | Visualize outlier patterns | Four plot types: overview, seasonal, detail, map
`pep_completeness()` | Assess temporal coverage | Completeness %, gaps, year range
`pep_check_phases()` | Check phase presence | Missing phases, observation counts

### Key Take-Home Messages

1. Data quality assessment is not optional - it’s a critical step that affects the validity of all downstream analyses.

2. Not all outliers are errors - some represent genuine biological phenomena like second flowering that deserve further study.

3. Document your decisions - quality control choices should be transparent and reproducible.

4. Use robust methods - the MAD method is recommended for phenological data because it handles multiple outliers well.

5. Visual inspection matters - plots often reveal patterns that summary statistics miss.

## Next Steps

Explore the other vignettes for complementary analyses:

- Getting Started: Data access, the `pep` class, and basic exploration

    vignette("getting-started", package = "pep725")

- Phenological Analysis: Normals, anomalies, quality grading, and trends

    vignette("phenological-analysis", package = "pep725")

- Spatial Phenological Patterns: Gradients, synchrony, and mapping

    vignette("spatial-patterns", package = "pep725")

## Session Info

    sessionInfo()
    #> R version 4.5.2 (2025-10-31)
    #> Platform: aarch64-apple-darwin20
    #> Running under: macOS Tahoe 26.0.1
    #>
    #> Matrix products: default
    #> BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    #> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
    #>
    #> locale:
    #> [1] C/UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8
    #>
    #> time zone: Europe/Zurich
    #> tzcode source: internal
    #>
    #> attached base packages:
    #> [1] stats     graphics  grDevices utils     datasets  methods   base
    #>
    #> other attached packages:
    #> [1] pep725_1.1.0        ggplot2_4.0.2       data.table_1.18.2.1
    #>
    #> loaded via a namespace (and not attached):
    #>  [1] gtable_0.3.6        jsonlite_2.0.0      dplyr_1.2.0
    #>  [4] compiler_4.5.2      Rcpp_1.1.1          tidyselect_1.2.1
    #>  [7] tidyr_1.3.2         jquerylib_0.1.4     scales_1.4.0
    #> [10] yaml_2.3.12         fastmap_1.2.0       R6_2.6.1
    #> [13] labeling_0.4.3      generics_0.1.4      patchwork_1.3.2
    #> [16] classInt_0.4-11     robustbase_0.99-7   sf_1.0-24
    #> [19] knitr_1.51          tibble_3.3.1        units_1.0-0
    #> [22] DBI_1.2.3           bslib_0.10.0        pillar_1.11.1
    #> [25] RColorBrewer_1.1-3  rlang_1.1.7         cachem_1.1.0
    #> [28] xfun_0.56           sass_0.4.10         S7_0.2.1
    #> [31] otel_0.2.0          rnaturalearth_1.2.0 viridisLite_0.4.3
    #> [34] cli_3.6.5           withr_3.0.2         magrittr_2.0.4
    #> [37] class_7.3-23        digest_0.6.39       grid_4.5.2
    #> [40] lifecycle_1.0.5     DEoptimR_1.1-4      vctrs_0.7.1
    #> [43] KernSmooth_2.23-26  proxy_0.4-29        evaluate_1.0.5
    #> [46] glue_1.8.0          farver_2.1.2        e1071_1.7-17
    #> [49] rmarkdown_2.30      purrr_1.2.1         tools_4.5.2
    #> [52] pkgconfig_2.0.3     htmltools_0.5.9

1. University of Applied Sciences Northwestern Switzerland (FHNW)↩︎

2. Swiss Federal Institute for Forest, Snow and Landscape Research (WSL)↩︎