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Supplement to "Discriminating non-stationary flood hazard effects via probabilistic estimation of sparse residuals from rescued and rated stage–discharge data"
<p><span>This supplement contains the data and script associated with “Sparse hydrometric data rescue for exploratory analyses of conveyance-driven flood hazard trends and controls,” which has been submitted to a journal for consideration. This supplement is deposited on Zenodo.</span></p> <p><span> </span></p> <p><strong><span>Code, Data, and Attribute Descriptions</span></strong></p> <p><span> </span></p> <p><span>Uploaded are five directories (indicated in <strong>bold </strong>font, with their contents detailed below) containing input data and various outputs of the analyses performed for our case study on the Pulangi River at Lumayong (Philippines). Please consider this description equivalent to an omnibus README file for the deposited files. Note that we collected and rescued the hydrometric data herein from the archives of the Water Projects Division (WPD) of the Philippine Department of Public Works and Highways (DPWH).</span></p> <p><span> </span></p> <p><span><span>●<span> </span></span></span><strong><span>Pln_R_code </span></strong><span>contains (1) <em>Pln_RC.R, </em>the <em>R</em> script file, and (2) <em>240601_Pln_RC.RData</em>, which stores objects generated from the script based on the last execution (on 1 June 2024). The script consists of admittedly too many lines of code (e.g., for data wrangling, formal analyses, and producing figures used in the manuscript) that should have been split into multiple .R files. Apologies. Please be guided by the outline and the comments and kindly reach out lest issues with the code arise.</span></p> <p><strong><span> </span></strong></p> <p><span><span>●<span> </span></span></span><strong><span>Pln_GH_PDFs </span></strong><span>contains the scanned gaugekeeper’s reports of gauge heights (“stages”).<span> </span></span></p> <p><span><span>○<span> </span></span></span><span>The name of each file varies. For example, <em>Pln-GH-1100.pdf </em>contains daily stage readings for all months in the year 2011. But, if the last two digits are not zeroes, as in <em>Pln-GH-1204.pdf</em>, they refer to the month of that year; in this case, for example, the PDF file contains stage data for the month of April in the year 2012.</span></p> <p><span><span>○<span> </span></span></span><span>Each scanned sheet contains sub-daily (with readings at “AM,” “NOON,” and “PM”) and mean daily stages for a given month. </span></p> <p><span><span>○<span> </span></span></span><span>Also indicated are the gaugekeeper’s remarks on the daily weather (e.g., “fair,” “cloudy”). Under inclement weather, the gaugekeeper would note the duration of rainfall and its intensity and might, at times, record extra stage readings. </span></p> <p><span> </span></p> <p><span><span>●<span> </span></span></span><strong><span>Pln_DM_PDFs </span></strong><span>contains the following PDF files and a sub-directory:</span></p> <p><span><span>○<span> </span></span></span><em><span>Pln-DM-<XXXXXX>.pdf </span></em><span>contains the scanned log for each direct stage—discharge measurement, otherwise known as “gaugings.” Each file is named according to the date of gauging (YYMMDD). For example, the log for the gauging performed on 24 February 2011 can be found in the file <em>Pln-DM-110224.pdf. </em>Data from these gaugings are summarized in <em>Pln-DM-filtered.csv</em> in the <strong>Pln_In_CSVs</strong> directory.</span></p> <p><span><span>■<span> </span></span></span><span>The readability of each file varies based on the original quality of the original paper-format data. </span></p> <p><span><span>■<span> </span></span></span><span>The first page in each file contains, on the left side, a summary of the gauging data and metadata (e.g., date of measurement, number of gauging verticals or “sections” used, method of crossing or measuring the cross-section), and on the right side, the velocity—area readings at each gauging vertical. </span></p> <p><span><span>■<span> </span></span></span><span>The second page in each file contains the plotted cross-section of the channel at the time of measurement. </span></p> <p><span><span>○<span> </span></span></span><em><span>Pln-RC.pdf </span></em><span>contains various other paper-format data and some annotations relevant to the historical rating at the station. </span></p> <p><span><span>■<span> </span></span></span><span>P. 1: The hydrographic engineer’s comment (dated 19 January 2012) on the evaluation of the discharge data, specifically detailing the periods of validity of the rating curves developed for different sub-periods of monitoring.</span></p> <p><span><span>■<span> </span></span></span><span>PP. 2—3: A summary table of all the gaugings performed from 1983 to 2010 whose logs were no longer retrievable (and hence not included as a DM-PDF file in this directory). </span></p> <p><span><span>■<span> </span></span></span><span>PP. 4—5: Plots of the official stage—discharge rating curves developed by DPWH hydrographers.</span></p> <p><span><span>■<span> </span></span></span><span>PP. 6—8: Rating tables used to convert daily mean stages to deterministic discharge estimates. Two of these rating tables were digitized and can be found in the <strong><em>Pln_RatingTables</em></strong> sub-directory in <strong>Pln_In_CSVs.</strong></span></p> <p><span><span>■<span> </span></span></span><span>PP. 9—22: Daily stage (m) and its corresponding daily discharge (L/s) for the 2004—2010 sub-period. The stages were digitized and included in <em>Pln-H_arch.csv </em>in the <strong>Pln_In_CSVs </strong>directory.</span></p> <p><span><span>○<span> </span></span></span><strong><em><span>Pln_DM_unused </span></em></strong><span>contains the PDF files of logs (including data and metadata) corresponding to the gaugings that were excluded from our analysis following our filtering step for gauging location consistency.</span></p> <p><strong><span> </span></strong></p> <p><span><span>●<span> </span></span></span><strong><span>Pln_In_CSVs </span></strong><span>contains the following CSV files and two sub-directories; these files were used as inputs to the <em>R </em>script for formal analyses:</span></p> <p><span><span>○<span> </span></span></span><em><span>Pln-H_arch.csv </span></em><span>contains the mean daily stage values [“H_bar_arch”] (m) for every day in the 2004—2020 sub-period [“Date”] (YYYY-MM-DD). The stages in this file are already corrected for gross errors.</span></p> <p><span><span>○<span> </span></span></span><em><span>Pln-DM-filtered.csv </span></em><span>contains the following information on the gaugings performed on the Pulangi at Lumayong (1983—2020): (i) date [“Date”] (YYYY-MM-DD); (ii) stage [“H”] (m); (iii) discharge in L/s [“Q_lps”] and m<sup>3</sup>/s [“Q_cms”]; (iv) wetted area [“A_sqm”] (m<sup>2</sup>); (v) mean flow velocity [“Vel_mps”] (m/s); (vi) channel width [“W_m”] (m); (vii) mean flow depth [“D_ave_m”] (m); (viii) location of the measurement cross-section with respect to the staff gauge, with negative values meaning downstream of the gauge and positive values meaning upstream of the gauge [“XS_loc_wrt_gage”]; (ix) maximum flow depth [“Max_Depth_m”] (m); and (x) minimum streambed elevation [“MINSBE”] (m). Note that this file includes only gaugings that passed our filtering step for measurement location consistency. </span></p> <p><span><span>○<span> </span></span></span><em><span>Pln-DM_oview.csv </span></em><span>contains information on the temporal coverage (bounded by “Start_date” and “End_date”) of the available hydrometric data from the station archives.</span></p> <p><span><span>○<span> </span></span></span><em><span>Pln-H_sample_GrossE_corr.csv </span></em><span>contains a sample sub-period (2017-06-15 through 2017-11-30) and the corresponding values of stages (m), uncorrected [“H_uncorrected”] and corrected for gross errors [“H_corrected”]. This CSV file was used as an input to the <em>R </em>script to produce one of the figures in the manuscript.<span> </span></span></p> <p><span><span>○<span> </span></span></span><em><span>Pln-XS-csv.csv</span></em><span> contains data on the gauging transects: gauging ID [“GaugingID”]; date [“Date”] (YYYY-MM-DD); lateral distance from a fixed initial point [“Lat_distance”] (m); width of the gauging vertical [“Width_vert..m.”] (m); depth relative to the water surface [“Depth..m.”] (m); stage at the gauging vertical [“H_m_vert..m.”] (m); and elevation with respect to a fixed arbitrary datum at the station [“Elev..m.”] (m).</span></p> <p><span><span>○<span> </span></span></span><strong><em><span>Pln_Rating_Tables</span></em> </strong><span>contains two rating tables, <em>Pln-DM - RatingTable_A.csv </em>and <em>Pln-DM - RatingTable_B.csv</em>, prepared and used by DPWH hydrographers for converting stage values to deterministic discharge estimates for the Pulangi River at Lumayong for the 1980s—early 2000s sub-period. Each rating table contains columns for stage [“H”], discharge in L/s [“Q_lps”], and discharge in m<sup>3</sup>/s [“Q_cms”].</span></p> <p><span><span>○<span> </span></span></span><strong><em><span>Pln_Q_rated </span></em></strong><span>contains two CSV files: <em>Pulangi.csv </em>has the columns “YEAR”, “DAY”, and every month of the year [“JAN” through “DEC”] for the 1983—2003 sub-period, with the values under each month column indicating the deterministic discharge estimates in L/s; <em>Pulangi_trunc.csv </em>contains similarly formatted data, but for the 2009—2010 sub-period.</span></p> <p><span><span> </span></span></p> <p><span><span>●<span> </span></span></span><strong><span>Pln_Out_CSVs </span></strong><span>contains two CSV files, the primary outputs of the hydrometric data rescue effort. </span></p> <p><span><span>○<span> </span></span></span><em><span>Pln_Q_recon.csv </span></em><span>contains the reconstructed discharge time series (1983—2020) and its associated uncertainties at the 95% credibility interval. It has the following columns: date [“Date”] (YYYY-MM-DD); daily stage [“H”] (m); lower bound of the discharge estimate [“Q_lwr”] (m<sup>3</sup>/s); median discharge estimate [“Q_med”] (m<sup>3</sup>/s); and the upper bound of the discharge estimate [“Q_upr”] (m<sup>3</sup>/s).</span></p> <p><em><span>Pln_H_recon.csv </span></em><span>contains the reconstructed and quality-controlled stage time series (1983—2020). It has the following columns: date [“Date”] (YYYY-MM-DD); mean daily stage that has been corrected for gross errors, but not yet filtered through other quality checks [“H_bar_arch”] (m); quality check for low outliers [“Low_Outlier”] (TRUE/FALSE); quality check for flatliners [“Flatliner”] (TRUE/FALSE); difference between the stage values on day <em>i </em>and day <em>i-1</em> [“Daily_Step”] (m); quality check for large steps [“Large_Step”] (TRUE/FALSE); and the corrected and quality-controlled mean daily stage values [“H”] (m).</span></p>
Data from: The effects of hybridization and parasite infection on predation survival and behaviour of endangered landlocked salmon – implications for genetic rescue
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Codes and data from: The effect of habitat choice on evolutionary rescue in subdivided populations
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Data from: Rescue or murder? The effect of prey adaptation to the predator subjected to fisheries
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The rescue effect and inference from isolation-extinction relationships
<p>The rescue effect in metapopulations hypothesizes that less isolated patches are unlikely to go extinct because recolonization may occur between breeding seasons ("recolonization rescue"), or immigrants may sufficiently bolster population size to prevent extinction altogether ("demographic rescue"). These mechanisms have rarely been demonstrated directly, and most evidence of the rescue effect is from relationships between isolation and extinction. We determined the frequency of recolonization rescue for metapopulations of black rails (<i>Laterallus jamaicensis</i>) and Virginia rails (<i>Rallus limicola</i>) from occupancy surveys conducted during and between breeding seasons, and assessed the reliability of inferences about the occurrence of rescue drawn from isolation-extinction relationships, including autologistic isolation measures that corrected for unsurveyed patches and imperfect detection. Recolonization rescue occurred at expected rates, but was elevated during periods of disturbance that resulted in nonequilibrium metapopulation dynamics. Inferences from extinction-isolation relationships were unreliable, particularly for autologistic measures and for the more vagile Virginia rail.</p>
Exposure to exogenous egg cortisol does not rescue juvenile Chinook salmon body size, condition, or survival from the effects of elevated water temperatures
<p class="NormalThesis">Climate change is leading to altered temperature regimes which are impacting aquatic life, particularly for ectothermic fish. The impacts of environmental stress can be translated across generations through maternally-derived glucocorticoids, leading to altered offspring phenotypes. Although these maternal stress effects are often considered negative, recent studies suggest this maternal stress signal may prepare offspring for a similarly stressful environment (environmental match). We applied the environmental match hypothesis to examine whether a prenatal stress signal can dampen the effects of elevated water temperatures on body size, condition, and survival during early development in Chinook salmon <i>Oncorhynchus tshawytscha</i> from Lake Ontario, Canada. We exposed fertilized eggs to prenatal exogenous egg cortisol (1000ng*mL<sup>-1</sup> cortisol or 0ng*mL<sup>-1</sup> control) and then reared these dosed groups at temperatures indicative of current (+0°C) and future (+3°C) temperature conditions. Offspring reared in elevated temperatures were smaller and had a lower survival at the hatchling developmental stage. Overall, we found that our exogenous cortisol dose did not dampen effects of elevated rearing temperatures (environmental match) on body size or early survival. Instead, our eyed stage survival indicates that our prenatal cortisol dose may be detrimental, as cortisol-dosed offspring raised in elevated temperatures had lower survival than cortisol-dosed and control reared in current temperatures. Our results suggest that a maternal stress signal may not be able to ameliorate the effects of thermal stress during early development. However, we highlight the importance of interpreting the fitness impacts of maternal stress within an environmentally relevant context.</p>
Exposure to exogenous egg cortisol does not rescue juvenile Chinook salmon body size, condition, or survival from the effects of elevated water temperatures
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The rescue effect and inference from isolation-extinction relationships
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Data from: Rapid evolution rescues hosts from competition and disease but—despite a dilution effect—increases the density of infected hosts
Virulent parasites can depress the densities of their hosts. Taxa that reduce disease via dilution effects might alleviate this burden. However, 'diluter' taxa can also depress host densities through competition for shared resources. The combination of disease and interspecific competition could even drive hosts extinct. Then again, genetically variable host populations can evolve in response to both competitors and parasites. Can rapid evolution rescue host density from the harm caused by these ecological enemies? How might such evolution influence dilution effects or the size of epidemics? In a mesocosm experiment with planktonic hosts, we illustrate the joint harm of competition and disease: hosts with constrained evolutionary ability (limited phenotypic variation) suffered greatly from both. However, populations starting with broader phenotypic variation evolved stronger competitive ability during epidemics. In turn, enhanced competitive ability—driven especially by parasites—rescued host densities from the negative impacts of competition, disease, and especially their combination. Interspecific competitors reduced disease (supporting dilution effects) even when hosts rapidly evolved. However, this evolutionary response also elicited a potential problem. Populations that evolved enhanced competitive ability and maintained robust total densities also supported higher densities of infections. Thus, rapid evolution rescued host densities but also unleashed larger epidemics.
The Importance of Embryo Transfer Day Progesterone Value in Natural Cycle Frozen Embryo Transfers and the Evaluation of the Effect of Rescue Therapy on Pregnancy Outcomes in Patients With Low Progeste
ClinicalTrials.gov study NCT05481684. IPD Sharing: NO. Countries: 1. Publications: 3.
Comparison of Effectiveness of Nasal CPAP and Nasal IMV in Early Rescue Surfactant Treatment in Preterm Infants
ClinicalTrials.gov study NCT01741129. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Rescuing the Microbiome Effectively With Different Doses of B. Infantis in Infants
ClinicalTrials.gov study NCT03476447. IPD Sharing: NO. Countries: 1. Publications: 1.
The Effect of Age on the Median Effective Dose (ED50) of Intranasal Dexmedetomidine for Rescue Sedation Following Failed Sedation With Oral Chloral Hydrate During Magnetic Resonance Imaging
ClinicalTrials.gov study NCT02253199. IPD Sharing: Not stated. Countries: 1. Publications: 1.
The Effect of Time Intervals for Rescue Treatment on Eradication Effect of Helicobacter Pylori Infection
ClinicalTrials.gov study NCT05620589. IPD Sharing: Not stated. Countries: 1. Publications: 15.
Exercise Intervention to Rescue the Adverse Effect of Preterm Birth on Cardiovascular and Pulmonary Health.
ClinicalTrials.gov study NCT03504215. IPD Sharing: Not stated. Countries: 1. Publications: 1.
The Effects of High-dose Dual Therapy With Probiotics on Gut Microbiota for Helicobacter Pylori Rescue Treatment
ClinicalTrials.gov study NCT06292546. IPD Sharing: NO. Countries: 1. Publications: 1.
Effects of Induced Moderate HYPOthermia on Mortality in Cardiogenic Shock Patients Rescued by Veno-arterial ExtraCorporeal Membrane Oxygenation (ECMO)
ClinicalTrials.gov study NCT02754193. IPD Sharing: NO. Countries: 1. Publications: 5.
The Effect of Time Intervals for Rescue Treatment on Eradication Effect of Helicobacter Pylori Infection
ClinicalTrials.gov study NCT05620602. IPD Sharing: Not stated. Countries: 1. Publications: 15.
Data from: Habitat enhancements rescue bee body size from the negative effects of landscape simplification
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Code for: Environmental fluctuations dampen the effects of clonal reproduction on evolutionary rescue
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