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Changelog

Source: NEWS.md

erahumed (development version)

erahumed 0.5.1

Documentation

  • Emails and ORCID of additional package authors were added to the package metadata.

Bug fixes

  • Fix bug that was causing errors in the plots of Perellonet, Perelló and Pujol outflows in the Shiny interface (#90).

Other

erahumed 0.5.0

Breaking changes

  • Names of columns representing outflows in albufera_outflows have been prepended with outflow_.

  • Logic of albufera_hb_global() has been improved in such a way that the outflow columns are automatically recognized from the input data.frame, and do not need to be exactly "pujol", "perellonet" and `"perello", as before.

  • Former irrigation and draining columns from the output data.frame of albufera_hb_local() became ideal_irrigation and ideal_draining, to better reflect that these correspond to the originally scheduled irrigation and draining plans. In addition, new columns real_irrigation and real_draining were added to the data.frame, which provide the actual irrigation and draining plans followed, modified by the plan delay.

New features

  • Visualizations of the “extra outflow” variable have been added to the global hydrological balance module of the Shiny dashboard.

Bug fixes

  • Fixed broken functionality of ‘height_thresh_cm’ argument (#85).
  • Correct bug that was causing the wrong delay being applied to seed_day in the ca_choose_application_day_index() helper, building block of ca().

Under the hoods

  • Unit testing of CA model block (#77).

erahumed 0.4.1

New features

  • First draft of plot.erahumed_ca() (“cluster view”).

User visible changes

  • The default for the height_thresh_cm parameter of ca() has been changed from 2.5 to 2.

  • The albufera_management data-set has a new column seed_day, which counts the number of day elapsed from the sowing day. This is also returned in the output data.frame of albufera_hb_local().

  • erahumed_ca S3 class now inherits from hb_local.

Under the hoods

  • Improvement in data.frame validity checks. The assert_data.frame() helper is now able to check column types. Noteworthy, this allows for much stricter tests in the "hb_local" and "hb_global" functions.

  • Important performance improvements in the function ca(). These were mainly achieved by (i) removing validity checks in the low level function ca_to_cluster(), supplanted by less costly checks at the level of the hb_local() output; and (ii) bypassing computation using Date objects, thanks to the introduced seed_day column in the output of albufera_hb_local() (see above).

Documentation

erahumed 0.4.0

New features

This version introduces a first draft for the new Chemicals Applications (CA) model block, which is meant to simulate the application of chemicals (fertilizers and pesticides), according to the previously obtained simulation of local water levels and water flows, which is the output of the hydrological balance (HB) block.

The basic ca() function is provided, which takes as input an object of S3 class "hb_local" (plus a few other optional input parameters), and returns a similar data-frame, with additional columns that provide the time series of chemical applications.

The accompanying dataset albufera_ca_schedules provides the schedules for chemical applications in the Albufera lake, and is one of the customizable inputs to ca().

erahumed 0.3.2

Under the hoods

  • Shiny app continues to work if the Albufera Leaflet map cannot be loaded for any reason.

  • Added validation of date range to albufera_hb_local().

  • Tested exceptions raised by albufera_hb_local()s argument validity checks.

  • Documented plotting method for hb_local and hb_global S3 objects.

Miscellaneous

  • Added Pablo Amador and Andreu Rico to package .

erahumed 0.3.1

User visible changes

  • albufera_hb_local(), called with default arguments, now retrieves its value from disk, from data installed alongside with erahumed.

  • Due to the previous point, the package’s .tar.gz file size is much larger now, approximately 50MB. The file size will be tackled, as much as possible, in later releases.

  • Added light print() and summary() methods for the S3 objects returned by albufera_hb_local() and albufera_hb_global().

  • sf is no longer attached upon attaching erahumed.

Bug fixes

  • Package data is prefixed everywhere in the code by the erahumed:: NAMESPACE, so that executing this code without having the package attached does not lead to errors. In particular, calling erahumed::launch_app() without attaching erahumed does no longer lead to an error.

Under the hoods

  • Fixed R-CMD-check spurious NOTEs.

erahumed 0.3.0

User visible changes

  • New Shiny module to set parameters of the hydrological balance calculations.
  • New Shiny module to modify input data to the algorithms.

Under the hoods

  • Added shinytest2 testing infrastructure, for snapshot based tests to be developed later.
  • Basic tests for plotting utilities (succeed with default arguments).
  • Server testing of hb_shiny.R modules, #15.

erahumed 0.2.2

User visible changes

  • Documentation for the albufera_hb_global() and albufera_hb_local() wrappers.

  • Exported hbg_residence_time() doc page.

  • Former albufera_weather dataset becomes albufera_petp, and its structure is significantly simplified, now having only three columns: date, rain_mm and evapotranspiration_mm (previously named date, P and ETP respectively). All changes get propagated to downstream tables, such as e.g. albufera_hb_global().

Algorithm change

  • In previous versions of the algorithm, the plan delays upon failing to reach zero water levels on a given date were only being applied to the ideal_height_cm vector. In the present version, the draining and irrigation plan also get delayed. This has been observed to give rise to slightly more natural water profiles (in particular, the delay accumulated during summer is often less than 40 days, contrary to what used to happen with the previous version).

Under the hoods

  • Add "hb_local" S3 class internal constructor (#21).

erahumed 0.2.1

User visible changes

Under the hoods

  • Separated logical units of hb_global(), collected in hb_global_units.R.

  • Introduced argument checking for hb_global() and its wrapper albufera_hb_global().

  • Introduced S3 class constructor for "hb_global" class objects (see hb_global_units_s3_class.R).

  • Important improvements in the testing infrastructure of hb_global() and
    albufera_hb_global(), both at the algorithmic level (through testing of hb_global_units.R) and at the level of exceptions raised by these two functions.

erahumed 0.2.0

User visible changes

  • Reduced number of *_is_imputed entries in hb_global dataframes. Right now we are only providing level_is_imputed and outflow_is_imputed, which should suffice FAPP.

  • Big refactoring of the HB sector naming conventions. The wrappers become albufera_hb_global/local(), and the underlying functions are hb_global/local().

Under the hoods

  • We complete the work started with v0.1.2 to separate the algorithms for computing global and local hydrological balance, from the wrappers used to feed this algorithms with our prepared datasets. In this version, the wrappers got significantly simplified, their only function being extracting variables from the imported datasets and feeding them to the algorithms (as it should be).

erahumed 0.1.2

User visible changes

  • Improved appearance of cluster level plots in Shiny app UI.

Under the hoods

  • Important code refactors for the local balance algorithm, aiming to separate the abstract logic of the algorithm from our specific conventions used to pack together data for hydrological balance - the latter conventions being relegated to hb_wrappers.R functions. Fixes #3.

  • Extensive unit testing of the logical units for the local balance algorithm.

  • Performance optimizations in local balance algorithm.

  • Sanity check functional tests for plot.hb_local() and plot.hb_global().

erahumed 0.1.1

Algorithm

  • The main algorithm for local balance has been modified in such a way to ensure that the correct number of emptying events is always produced. This is achieved by delaying (by one day) the ideal water level plan whenever the ideal level is zero and the real level is above a certain threshold (2.5 mm by default). Moreover, outside of the sowing season, the water level plan is reset to the original one, in such a way that the Perellona does not get delayed.

Under the hoods

  • Re-enabled continuous integration, with some internal code improvements.
  • Sanitizing of warnings/notes from R-cmd-check.

erahumed 0.1.0

Algorithm

  • Switched to an improved version of the algorithm to compute the local balance at the cluster level. The exactness of total outflows is enforced, in such a way that the sum of outflows of cluster that belong to a given ditch equals the total inflow to the Albufera lake from said ditch. Also, the logic of the algorithm was changed in such a way to enforce that no evaporation can occur when the water level of a cluster is zero. Warning. While correctly enforcing mass conservation, the present algorithm does not guarantee that the clusters will always be emptied for periods as long as planned, for the application of pesticides - both aspects being at odds with the previous version. Correctly enforcing the emptying of clusters will is the object of ongoing work.

UI

  • The cluster to be plotted in the local balance tab of the shiny app can now be selected from an interactive leaflet map of the Albufera National Park.

Under the hoods

  • Added internal utility erahumed:::plot_albufera_clusters() to obtain a leaflet map of clusters.

  • Added internal utility erahumed:::plot_albufera_management() to obtain a plot of ideal water levels vs. day of year.

erahumed 0.0.6

Under the hoods

  • Fixed an important bug that was causing real outflows to be zero in most cases.

Testing

  • Added important functional tests for real outflows. In particular, we test that the sum of real outflows for clusters belonging to a given ditch is always equal to the minimum between the total ditch’s capacity and ideal required outflow.

erahumed 0.0.5

  • The outputs of albufera_hydro_balance_global() and albufera_hydro_balance_local() get class attributes "hb_global" and "hb_local", respectively.

  • Added cluster level plots to the shiny UI.

Under the hoods

  • New plot methods for "hb_global" and "hb_local" S3 classes. Currently not exported to NAMESPACE.

erahumed 0.0.4

Under the hoods

  • Ordering of clusters sampled by the local hydrological balance simulation algorithm does not depend anymore on the way these clusters are sorted in the input data.

  • Fixed issues in the logic of local hydrological balance.

  • Improved testing infrastructure

erahumed 0.0.3

User-visible changes

  • Big namespace refactor: all datasets get prepended with the prefix "albufera_".

  • The functions albufera_storage_curve() and petp_volume_change() were substituted by the function factories linear_storage_curve() and linear_petp_surface(), that create functions that perform affine transformations.

  • Function albufera_hydro_balance() was renamed albufera_hydro_balance_global(). Ditch inflows are not returned anymore. In correspondence, we add a new function albufera_hydro_balance_local(), which at the current moment is still WIP and for testing purposes.

  • Functions albufera_hydro_balance_*() now allow to specify storage curve and P-ETP surface by dedicated arguments. The defaults are defined throughout the new helpers mentioned in a previous point.

  • New function hydro_balance_global(), that is meant to capture the abstract part of the global hydrological balance calculations. The function albufera_hydro_balance() relies on this for its calculations of global balance.

  • Residence time is now computed in terms of the total outflow, rather than inflow as before. This reflects the way we handle cases of unaccounted outflow in hydro_balance_global() (set inflow to zero).

Documentation

  • Improved documentation of the hydro_balance_global() function, as well as other minor improvements on documentation of helpers.

Under the hoods

  • Started to work consistently on the testing infrastructure.

Notes

  • Function names and the general API of these early versions of the package are understood to be provisional.

erahumed 0.0.2

  • Added clusters and cluster_geometries datasets, containing information at the cluster (i.e. aggregate of rice paddies) level.

  • Separated computation of ditch inflow percents in a new function, compute_ditch_inflow_pct(), that leverages on the clusters dataset.

  • Corrected calculation of total outflow. In this calculation, the Perello daily outflow was being set to zero in the case of negative values. This does not make sense with the current computational approach.

  • Updated the paddy_management dataset: the irrigation and draining input binary vectors used previously were incomplete, with data until the middle of August. For this version, the inputs are defined until the 10th of September.

erahumed 0.0.1

First release. Contains a draft of the utilities for hydrological balance data analysis, and a skeleton of the visualization app (currently invoked with launch_app()).