Data quality control considerations in multivariate environmental monitoring: experience of the French coastal network SOMLIT

Introduction

In the context of global change, the number of studies that include meta-analytical combinations of environmental data increased at a fast pace in the past decades (e.g., Duarte et al., 2009; Harvey et al., 2013; Talarmin et al., 2016; McCrackin et al., 2017; Carstensen and Duarte, 2019; Lheureux et al., 2021; Lheureux et al., 2023). In these studies, it is assumed that the data were of similar quality and reliability, which is not necessarily true: measurement processes are all subject to systematic (i.e., bias) and random (i.e., variations) errors of various types, such as the choice of the method, ambient conditions, or the working practices of analysts (Taverniers et al., 2004; de Boer, 2016). At a time when high-quality scientific journals require a comprehensive documentation of data quality control (QC) procedures for publication (de Boer, 2016), and because erroneous conclusions may arise from studies using inappropriate methods, it is important to increase the confidence levels of data QC, which is often poorly documented in environmental monitoring datasets.

By using the 20 years of experience of the French coastal monitoring SOMLIT network (https://www.SOMLIT.fr/), the goal of our paper is to share a pragmatic approach to QC that focuses on annual inter-laboratory comparison (ILC) exercises as an indication of measurement uncertainty. The SOMLIT network currently includes 12 laboratories and 22 permanent sampling stations distributed along the French littoral (Figure 1) and covers a wide range of environmental and trophic conditions (Goberville et al., 2010; Liénart et al., 2017; Liénart et al., 2018; Lheureux et al., 2021). Implemented by CNRS (Centre National de la Recherche Scientifique) in 1997 to increase our scientific knowledge of the responses of marine coastal ecosystems to natural and human-induced influences, the SOMLIT network is part of the national research infrastructure ILICO (Infrastructure de recherche LIttorale et CÔtière; Cocquempot et al., 2019). Common standard operating protocols are used and all data are continuously routinely quality-controlled since 2006 by means of robust quality assurance procedures guided by the ISO-17025 standard (ISO-17025, 2005, then ISO-17025, 2017).

FIGURE 1

Figure 1 Location of the sites and stations belonging to the French coastal monitoring network SOMLIT (the logotype is in the center of the map).

After an overview of the different QC actions implemented by the SOMLIT to fulfill requirements for quality and competence, we report equipment, accommodation, design of the ILC exercises and statistical methodology to assess individual performance specifically adapted to small (<20 laboratories) environmental networks and multivariate datasets, based on the ISO-13528 standard (ISO-13528, 2005), Héberger and Kollár-Hunek (2011), and procedures for measurement uncertainty assessment. Finally, we provide an expanded uncertainty of measurement for 20 environmental variables routinely measured by SOMLIT from discrete sampling (Table 1), including Essential Ocean Variables (Miloslavich et al., 2018).

TABLE 1

Table 1 Range, reproducibility, and expanded uncertainty of the environmental variables measured during inter-laboratory comparison exercises of the SOMLIT network over the last 6 years.

Data quality control overview

Data QC within the SOMLIT network is composed of five actions (Figure 2). Within-laboratory control is continuously performed by each laboratory on the basis of control charts (Figure 3; Table S1) and the Nordtest TR 569 principles (Nordtest TR 569, 2007): control charts ensure the quality of produced data according to statistical or reference criteria—when available—and represent an essential step for the calculation of uncertainty. Control charts may also be performed (1) to objectively compare different analytical methods, (2) for new method validation, (3) to qualify an inexperienced analyst, or (4) to ensure stable ambient conditions (e.g., temperature and hygrometry) for measurements. There are two kinds of control charts: X-charts and R-charts for controlling systematic errors and random variations, respectively (Nordtest TR 569, 2007). The setting control limits used to build the control charts used by the SOMLIT network are given in Table S1.

FIGURE 2

Figure 2 Scheme of the different actions for data quality control implemented in the SOMLIT network and their frequency based on ISO 17025 (2017).

FIGURE 3

Figure 3 Within-laboratory control: example of control chart based on Nordtest TR 569 (2007) for ensuring that the data are of good quality and the measurement process is statistically stable. Black line: the central line; thin red line: the warming limits; and thick red line: the action limits. The data value is considered in control if it is within the warming limits or if the value is between the warming and action limits but the two previous ones are within the warming limits. In this case, data are considered of good quality. The data value is considered outside control if the data value is outside action limits or between the warming and action limits and at least one of the two previous values are between warming and action limits too. In this case, measurement analysis must be made again once the problems are resolved if possible. The data value is considered in control but must be scrupulously monitored if the last 7 previous values exhibit a trend or 10 of the last 11 control values are on the same side and far from the central line.

SOMLIT data are qualified on a trimonthly basis using QC flags (see Table 2), which are derived from the World Ocean Circulation Experiment (WOCE; https://exchange-format.readthedocs.io/en/latest/quality.html#woce-bottle-quality-codes). QC flags include two levels. Level 1 ensures interoperability, but the codification is simplified to provide QC flags easily understandable by end-users. Level 2 is detailed in order to answer to the needs of data producers; it corresponds to internal QC according to the ISO 17025 standard (ISO-17025, 2017). Internal and external audits guided by the ISO 17025 standard (ISO-17025, 2017) are made on an annual and triennial basis, respectively, for ensuring laboratory quality management and technical requirements. We provide an example of the report in Figure 4.

TABLE 2

Table 2 Primary and secondary level quality control flags (QCF) used by the SOMLIT network for the data qualification step.

FIGURE 4

Figure 4 Internal/external audits of the SOMLIT network guided by the ISO 17025 standard (ISO-13528, 2005) to ensure the integrity of data and minimize errors: example of reports provided by one SOMLIT laboratory. (A, B) Management and technical requirements, respectively. (C) Temporal variations of the percentage (%) of satisfaction to meet the requirements.

ILCs are undertaken annually at the end of summer in one of the SOMLIT laboratories (Figure 1). To strengthen the robustness of comparisons, we alternate among different hosting laboratories, with sampling stations in the oligo- to ultra-oligotrophic Mediterranean Sea, oligo- to mesotrophic Atlantic waters, and the meso-eutrophic English Channel (Table S2). ILC allows best practices to be shared among participants from different laboratories, to evaluate data reliability (uncertainty calculation), and to assess the performance of individual operators from each laboratory. If issues are identified, ILC provides a forum to help participants to improve their practices and to correct their errors. In the following sections, we describe the methodology used during ILC and show how efforts to fulfill quality requirements have helped to improve the trueness and reproducibility of SOMLIT data over time.

Design of ILC exercises and sample testing preparation

Although the SOMLIT program routinely measures 25 environmental variables, only the 22 variables subjected to discrete sampling (Table 1) were considered each year. Figure 5 describes the different steps involved in the ILC exercises. Given that stable reference material is lacking for most of the environmental variables measured by the SOMLIT network, performance in total measurement was evaluated by robust analysis, using measurement data from real natural seawater (see below).

FIGURE 5

Figure 5 Scheme of the different steps of the annual ILC exercises implemented by the SOMLIT network since 2001.

Sampling at sea

Sampling at sea was carried out onboard the research vessel of the hosting laboratory, using Niskin bottles or a pump. Approximately 2–3 m³ of seawater was collected with ten 50-L tanks. The sampling was performed a few hours (less than 1 day) before the start of the ILC exercise.

Sub-sampling and conditioning

Back to the host laboratory, seawater was transferred to a large-volume stainless-steel tank equipped with 15 petcock assemblies (Figure S1) and gently and continuously mixed with a rotating blade system inside (80 min at approximately 10 rpm). Mixing was stopped during sub-sampling. For the dissolved matter analysis, samples were first successively sub-sampled in 5 replicates in the following order: dissolved oxygen (hereafter O₂), pH, ammonium (${\text{NH}}_4^{+}$), nitrate (${\text{NO}}_3^{-}$), nitrite (${\text{NO}}_2^{-}$), phosphate (${\text{PO}}_4^{3-}$), and silicate [Si(OH)₄]. Conditioning and storage were the same as conducted routinely (Table S3). To reduce as far as possible any sampling inhomogeneity between participants, samples for each variable were sub-sampled at the same time by the different participants. Before filling, vials were rinsed three times with sampling seawater. Samples were also successively sub-sampled for particulate matter analysis: pico- and nanoplankton, chlorophyll a (Chla) and phaeopigments, particulate organic carbon (POC), particulate organic nitrogen (PON), suspended particulate matter (SPM), and δ¹³C and δ¹⁵N.

Processing and storage during transport and back to home laboratory (Figure 5) were carried out following the methodology given in Table S3. Each year, the Quality Manager allows laboratory participants to perform analyses within 1 to 3 months, depending on the variables. The list of analytical techniques for each environmental variable is given in Table S3. Finally, the Quality Manager collects replicate measurement results for each environmental variable and from each participating laboratory, as well as information on the date of analysis and potential problems that may have occurred during sub-sampling, processing, storage, and/or analysis.

Once the performance scores in repeatability and trueness are obtained for the different participating laboratories, and after calculation of the annual reproducibility of the SOMLIT network (see below), a quality report is written by the Quality Manager and sent to each participating laboratory. In the case of “questionable” performance during two consecutive ILC exercises or “unsatisfactory” performance in the current ILC exercise, the laboratory in question must take corrective actions, such as to redo a calibration, to improve dim light conditions for chlorophyll a analysis, in order to achieve satisfactory performance and/or reproducibility in accordance with other participating laboratories.

Calculation of systematic and random errors and performance

The different steps of the statistical methodology used to assess the total measurement accuracy (trueness and precision) for the 22 environmental variables during ILC exercises, as well as the overall performance of the participating laboratory, are described in Figure 6. The methodology has been adapted for small (<20 participating laboratories) networks, using the algorithm A mentioned in the ISO-13528 standard (see the freeware using Microsoft Excel^© in Table 1 of the Supplementary Materials) for non-parametric data, and the user-friendly macro created by Héberger and Kollár-Hunek (2011) for both non-parametric and multivariate datasets. The application of the latter approach allows a better appraisal of proficiency testing (PT) in the case of multivariate monitoring in comparison with the ISO-13528 standard (ISO-13528, 2005, see Medina-Pastor et al., 2010; Stoyke et al., 2012): it ranks the performance of the different laboratories on the basis of data of different units and explores overall improvement of performance over time.

FIGURE 6

Figure 6 Annual ILC exercises implemented by the SOMLIT network: the different steps in the statistical methodology used to assess the total measurement accuracy of the 22 environmental variables and the participating laboratory performance. Step 1: Calculation of the mean (x) and the standard deviation (s) of replicates as well as that of the robust mean (X), standard deviation (s*), and uncertainty (u_x) of total measurement of the measurand, by applying the algorithm A. Steps 2 and 3: Calculation of the individual deviations (z′-score) to the SOMLIT robust for assessing the trueness (systematic bias) and precision (random variations). Steps 4 and 5: Calculation of the final rank of each participating laboratory for the overall performance for trueness and precision (Héberger and Kollár-Hunek, 2011).

Robust statistics are used without outlier exclusion before calculation (Analytical Methods Committee, 1989). For each environmental variable, performance in trueness of total measurement (i.e., from sampling to data reporting) was assessed by calculating a z′-score according to Equation 1 (ISO-13528, 2005):

$\begin{array}{ll}z\text{'}=(x_i-x*)/\sqrt{(\sigma {*}^2+u_x^2)}& (1)\end{array}$

where x_i is the mean value of five replicates obtained by the participating laboratories i, x* and $\sigma *$ are the robust average and the robust standard deviation of the different x_i, respectively, and u_x is the uncertainty of total measurement of the measurand, as mentioned in Equation 2:

$\begin{array}{ll}{u}_x=1.25\frac{\sigma *}{\sqrt{p}}& (2)\end{array}$

where p is the number of participating laboratories at the ILC exercise. The robust average and robust standard deviation were calculated using the algorithm A (see the freeware using Microsoft Excel^© in Table 1 of the Supplementary Materials) of ISO-13528 (2005). z′-score was chosen against z-score because of the small size of the SOMLIT network and because the uncertainty of the assigned value was considered to be not negligible given that most environmental variables never met the following inequality (Equation 3):

$\begin{array}{ll}ux\le 0.3\sigma *& (3)\end{array}$

According to ISO-13528:

● |z′| ≤ 2 was considered as “satisfactory”

● 2< |z′|< 3 was considered as “questionable”

● |z′| ≥ 3 was considered as “unsatisfactory”

For each laboratory, performance in repeatability was assessed by comparing the standard deviation of five replicate measurements with the limit of acceptable precision given in the literature, when available (see Table S4). Reproducibility (between-laboratory precision) was evaluated by calculating the robust standard deviation x* of the different reported mean values of the measurand using the algorithm A. To classify the different participating laboratories according to their respective overall performance in trueness and repeatability, we performed a Sum of Ranking Difference (SRD, see the Supplementary Materials for file format) test, a non-parametric multivariate technique recommended when the number of participating laboratories is less than 13 (Héberger and Kollár-Hunek, 2011). While SRD has multiple applications (e.g., Andrić and Héberger, 2015; Kalivas et al., 2015; Sziklai and Héberger, 2020), it allows us to analyze similarities between laboratories by ranking (columns of the input matrix relative to trueness and replicability targets, across the measurement of several environmental variables, and rows of the input matrix). The closer to zero the SRD value, the better the overall performance of the laboratory. The SRD test was validated by a random test called Comparison of Ranks with Random Numbers (CRRN) by ensuring that no participating laboratory is randomly ranked (the black curve is the cumulative distribution function of the random SRD values; Figure 6). The method is described in detail in Héberger and Kollár-Hunek (2011). A freeware for the calculation of SRD-CRNN with Microsoft Excel^© is available at http://aki.ttk.mta.hu/srd. We chose the zero value for trueness targets and the reproducibility targets given in Table 3.

TABLE 3

Table 3 Reproducibility targets and reference used to calculate the overall performance of the participating laboratories to the inter-laboratory comparison exercises of the SOMLIT network.

Figure 7 shows the inter-annual (2001–2021) variations of the within-laboratory and between-laboratory reproducibility (Figures 7A, B)—the opposite of the robust coefficient of variation s*—as well as the trueness—the bias is measured as the absolute difference between the inter-laboratory median value and the robust mean—obtained during the ILC exercises. We here demonstrate how efforts made to fulfill quality requirements for trueness and reproducibility have contributed to improve the quality of SOMLIT data over time, confirming the essential role of ILC exercises as a tool for continuous improvement of long-term monitoring networks.

FIGURE 7

Figure 7 Long-term variations in (A) within-laboratory reproducibility (SRD-CRNN-CV, %), (B) between-laboratory reproducibility (the opposite of the robust coefficient of variation; SRD-CRNN-CV, %), and (C) trueness (bias measured as absolute difference between the inter-laboratory median value and the robust mean; SRD-CRNN-Abs. difference, nu) obtained during the inter-laboratory comparison exercises of the SOMLIT network over the period 2001–2021. The solid blue line and ribbon represent Locally Estimated Scatterplot Smoothing (LOESS) smoothing and the 95% confidence interval. SRD-CRNN, sum of ranking differences and comparison of ranks by random numbers; CV, coefficient of variation; nu, no unit.

Estimation of total measurement uncertainty (U) of the SOMLIT network

Two approaches exist for the evaluation of measurement uncertainty. The first is based on a physical model relating the measuring process at all steps, using the propagation law of uncertainty (GUM, 1993). The second relies on a statistical model that uses data from within-laboratory control and/or ILC exercises or PT exercises (ISO-13528, 2005; Ferretti, 2011; Magnusson et al., 2012; de Boer, 2016). The statistical model is often favored, however, and was chosen by the SOMLIT network both for its less apparent mathematical complexity and for the lack of knowledge about the processes that need to be measured for the physical model (e.g., firm statistical background). For that purpose, we used the data from ILC exercises from the last 6 years. Note that the values we obtained are an approximation of the total measurement uncertainty, given that sampling uncertainty was never investigated.

Total measurement uncertainty of the SOMLIT network (U, in ± Unit and/or in %) was calculated following Equation 4 (Magnusson et al., 2012):

$\begin{array}{ll}U=2\sqrt{b^2+u_{Rw}^2}& (4)\end{array}$

where u_RW is the precision uncertainty and b is the bias uncertainty obtained from Equations 5 and 6, respectively:

$\begin{array}{ll}{u}_{RW}=\sqrt{\frac{{\displaystyle {\sum }_{i=1}^{i=n}{({\sigma }_i)}^2}}{n}}& (5)\end{array}$

$\begin{array}{ll}b=\sqrt{{\Delta }_{RMSbias}^2+{\text{ux}}_{ }^2+\frac{s_{bias}^2}{\sqrt{n}}}& (6)\end{array}$

$\begin{array}{ll}\text{with }{\Delta }_{RMSbias}=\sqrt{{\frac{{\displaystyle {\sum }_{i=1}^{i=n}(xi-x*)}}{n}}^2}& (7)\end{array}$

with σ_ι and x_i being the median and mean, respectively, of the repeatability values obtained by the different laboratories during one ILC exercise for one measure, s_bias being the standard deviation of the different median values of b for at least six different ILC exercises, n being the number of ILC exercises used for uncertainty calculation, and u_x being the median value of the uncertainty of the assigned values calculated for at least six ILC exercises. U is the expanded uncertainty at a confidence interval of 95% (k = 2).

The resulting expanded uncertainty values of the total measurement of the 22 environmental variables monitored by the SOMLIT network given in Table 1 (see also Table S3) are either below or very close to those found in the literature, when available.

Conclusion

In this paper, we presented the “road map” and the statistical methodology for the ILC exercises performed by the SOMLIT network, a framework especially adapted to small (<20 participating laboratories) and multivariate environmental datasets. By applying this framework to data acquired during 21 years, we showed that the SOMLIT program provided reliable data, and that the data quality increased over time thanks to the implementation of ILCs. Given the paucity of uncertainty values of the measurement of environmental variables—such as measured by the SOMLIT network—in the literature, our study stresses the importance of implementing ILC exercises in order to improve the quality of data representative of long-term environmental monitoring. We also highlight general acceptance limits in the measurement of these environmental variables.

Data availability statement

The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

Author contributions

Conceptualization and methodology: EBr, NS, PR-M, BS, TC, SF, ACai, VD, YA, GGr, EGr, AG, OJ, VL, EMac, DM, FM, SM, DP, PP, FR-J, IS, P-GS, and NG. Data collection and curation: EBr, NS, PR-M, TC, SF, SAl, FA, SAu, EBe, HB, LB, SB, ACau, J-BC, LCh, RC’h, M-AC, LCo, OC, MC, HL, GD, JD, AD, MD, CE, SG, EGr, AG, JG, KG, GGu, VG, MH, OJ, PL, NLab, ML, VL, CLa, JL, NLac, BL, EL, DL, CLe, CLi, EMac, EMar, BMa, SM, LMor, LMou, AN, SN, RP, DP, FP, PP, FR-J, PRIM, CS, ES, RVa, FVi, FVo, LZ, and NG. Formal analysis: EBR and ALh. Project administration, funding acquisition, and resources: EBr, NS, PR-M, BS, TC, HA, CB, YB, SB, PCl, PCo, OC, ACai, YA, GGr, EGr, AG, MC, JF, MG, OJ, JL, LL, ALe, SL’H, YL, SM, FM, BMo, LMou, SN, PP, PRIM, ES, IS, LS, VV, RVu, P-GS, and NG. Writing—original draft preparation and writing—review and editing: EBr, NS, PR-M, EGo, ALh, VD, BL, BMo, PRIM, P-GS, FV, and NG. All authors contributed to the article and approved the submitted version.

Funding

This research received no specific grant from any funding agency.

Acknowledgments

The authors thank all the past participants involved in the inter-laboratory comparison exercises, especially Louise Oriol and Nicole Degros who greatly contributed to the implementation of the first exercises and the continuous improvement of SOMLIT data quality up to their retirement, as well as our enthusiastic and retired colleague Jean-Paul Lehodey and the numerous persons who contributed to the smooth running of the SOMLIT network: C. Arnaud, L. Beaugeard, G. Beaugrand, M. Breret, Y. Brizard, A. Brouquier, H. Derriennic, C. Desnos, V. Ferrer, M. Ferreri, L. Giannecchini, F. Guyon, G. Izabel, J-L Jung, V. Kempf, C. Larvor, S. Marro, M-L Pedrotti, Mireille Pujo-Pay, C. Rouzier, S. Soriano, E. Thiébaut, and H. Violette. The authors would also like to thank the different laboratories we visited over the last two decades for providing space and facilities, as well as the different captains and crew members of the research vessels of the marine stations and of the French National Fleet (Flotte Océanographique Française, FOF).

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Publisher’s note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

Supplementary material

The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmars.2023.1135446/full#supplementary-material

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