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

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.