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R script to produce final plots for the interpretation of the time series of daily metabolic estimates within a river reach

Authors: Sandra Villamizar
Owners: Sandra Villamizar
Resource type:Generic
Created:June 10, 2016, 10:01 p.m.
Last updated: Aug. 15, 2016, 11:46 p.m. by Sandra Villamizar


We describe the procedure for the consolidation of the daily metabolic rate estimates along with summary weather, reach and water derived data that may be used for the interpretation of the processes happening along the reach of interest.
Sections 1 and 2 of the R script define the working directory and read the file containing the time series of daily metabolic rate estimates for the study period (related variable: ´table1´). Section 3 converts to NAs the daily metabolic rates that are of bad quality. The considerations to do this are first, daily metabolic rate estimates for days in which the available number of DO or temperature data points were less than 65% of the maximum daily total (this criterion may be modified by the user) and second, daily outputs that reflect failure on model performance due to either reaeration rates much higher than metabolic processes or DO concentrations increasing during night time (these resulted in positive values of the estimated CR24 and/or negative values of GPP).
Section 4 reads the daily solar radiation and reference PAR estimates and together with the filtered metabolic rates conform the final results table (related variable: ´main1´). Next, in section 5, the script reads the daily averages of ancillary water data (turbidity and chlorophyll for our case) and appends them to the final results table (related variable: ´main 4´). In section 6 the script creates figures 2, 3, and 4 of the publication. Figure 2 presents stacked panels of time series of mean daily discharge, water temperature, and DO (daily maximum, minimum and range); figure 3 presents stacked panels of the daily metabolic estimates (GPP, CR24 and NDM) in the context of the flow dynamics of the reach; figure 4 presents the ancillary data that is expected to support the analysis of the daily metabolic rates within the reach (turbidity, chlorophyll and reference PAR). Finally, section 7 prints the final results table that contains all the daily variables for the period of analysis.
DOI: 10.6084/m9.figshare.3427892


Time Series,Whole-stream metabolism,Interpretation of reach-estimates,River ecohydrology

How to cite

Villamizar, S. (2016). R script to produce final plots for the interpretation of the time series of daily metabolic estimates within a river reach, HydroShare, http://www.hydroshare.org/resource/885906ef97e542a8a33048ea486ddfdf

This resource is shared under the Creative Commons Attribution CC BY.


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  • Sharable Resource  Shareable


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The people or organizations that created the intellectual content of the resource.

Name Organization Address Phone
Sandra Villamizar Universidad Pontificia Bolivariana, Bucaramanga Km 7 vía Piedecuesta
Name Value
Takes data from source 3 https://www.hydroshare.org/resource/29c5ce6c1f3146538d252bc15ad5a976/
Takes data from source 2 https://www.hydroshare.org/resource/5c2c3dbf13174147a5109b84c62a142b/
Takes data from source 1 https://www.hydroshare.org/resource/aadd7dd60f31498590de32c9b14446c3/


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