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Changelog

epicrop 1.0.9000

Major Changes

  • Version now 1.0.0.9000, almost ready for first major release

  • SEIR() is now seir()

  • All helper functions drop the predict_ prefix for simplicity, e.g., predict_bacterial_blight() becomes just bacterial_blight()

  • Addition of functions to predict rice blast and sheath blight based on Kim et al. 2015.

  • Adds the RcRH parameter to seir() to calculate the relative humidity correction factor for the disease progress curve as published in Savary et al. 2012.

  • Adds the RcRH parameter to all helper functions.

New Functionality

  • Adds functions from Kim et al. 2015 for:

    • Leaf blast in South Korean varieties
    • Sheath blight in South Korean varieties

  • Adds functionality missing in original {cropsim} to handle complex leaf wetness calculations using daily RH to calculate hourly RH and then modify the value of RcW using .fn_Rc() as already existing with RcT and RcA by setting the argument, simple_wetness == FALSE in seir()

  • Adds functionality to use a matrix in RRG and modify it with .fn_Rc over time as with RcA and RcT as found in Kim et al. 2015 (though not implemented in Kim et al. 2015)

  • Allow pass through of more arguments from helper functions to seir() via ... argument

  • Strict checking of user-inputs with informative messages now provided if inputs are invalid

Minor Changes

  • Improvements to the documentation

  • Spelling corrections

  • Code linting

epicrop 0.0.3

Minor changes

  • Extend the RcA curve for bacterial blight, the original version of EPIRICE had ...0.43, 0.41, 0.42, 0.41, previous versions of {epicrop} had ...0.43, 0.41, 0.41, 0.41, now we have ...0.43, 0.42, 0.42, 0.41....

Bug fixes

  • Corrected documentation for get_wth(), {nasapower} is only client used.

epicrop 0.0.2

Minor changes

  • Simplify inputs in helper functions, don’t create a vector, just use in function call.

  • Use {vcr} for tests involving weather data fetching.

Bug fixes

  • Correct issue where {dplyr} library was not loaded in vignette, causing example to error when run.

epicrop 0.0.1

  • First stable release on GitHub.

  • Fixes function title formatting.

  • Replaces outdated {tidyverse} functions found in vignettes with modern versions.

epicrop 0.0.0.9018

  • Remove {chirps} functionality to simplify package structure.

epicrop 0.0.0.9017

  • Update README R output.

  • Polish map output in the mapping vignette.

  • Polish names for figure in multiple locations figure.

  • Remove references and functionality called from {epifitter}; AUDPC is calculated internally now.

epicrop 0.0.0.9016

Minor changes

  • Change audpc to AUDPC for easier graphing.

  • Add new vignette to demonstrate mapping AUDPC values using lat/lon from model output.

epicrop 0.0.0.9015

Minor changes

  • Add area under the disease progress curve (AUDPC) values to model output.

  • Adds shorthand versions of functions for:

    • predict_bacterial_blight() > predict_bb()
    • predict_brown_spot() > predict_bs()
    • predict_leaf_blast() > predict_lb()
    • predict_sheath_blight() > predict_sb()

Bug fixes

  • Fixes bug when that caused a failure fetching CHIRPS weather data.

epicrop 0.0.0.9014

Minor changes

  • Check user inputs for H0 and I0 to ensure that they are >= 0.

  • 100% complete test coverage.

  • The final data.frame created from vectors of state values in SEIR() is simplified into one step, creating a named data.table rather than create a data.table and then naming cols.

epicrop 0.0.0.9013

Bug fixes

  • Fixes a bug introduced into SEIR() with the last round of bug fixes. The calculations for latent and infectious sites were still calculating for the next, not current, day in the for() loop.

  • Corrects values in the example for SEIR() to run the model for brown spot.

Minor changes

  • Updates input values for Rc curves in each of the EPIRICE models such that the values used to compute the curve are all supplied, none are computed before the interpolation is performed. This leads to longer, but clearer lines of code.

  • All of the help files now reference NASA POWER and CHIRPS both as sources of possible weather data for use in the model.

epicrop 0.0.0.9012

Bug fixes

Rc[day+1] <- baseRc * AFGen(ageRc, day) * AFGen(tmpRc, wthsub$tavg[day+1]) * RHCoef[day+1]

should have been

Rc[day+1] <- baseRc * AFGen(ageRc, day+1) * AFGen(tmpRc, wthsub$tavg[day+1]) * RHCoef[day+1]

to calculate the basic infection rate, Rc, for day + 1. Commit: 248df5512b5897e950dd58a0a8b3fd57922add47.

  • Fixes typos in RcA values for predict_bacterial_blight() and predict_sheath_blight().

Major changes

  • Implements a new function to calculate the correction values for crop age, RcA, and temperature, RcT, using approx() in a custom function that is faster than the select_mod_value() function.

  • Implements new functionality for get_wth() to optionally get data from the CHIRPS/CHIRTS APIs in addition to the default NASA POWER API.

  • Uses one-indexed for() loop, in place of the zero-indexed for() loop found in {cropsim}.

epicrop 0.0.0.9011

Minor changes

  • Fix title in vignette entry.

  • Remove lazyData field from DESCRIPTION.

  • Remove redundant maintainer field from DESCRIPTION.

  • Remove dates (date when knit) from vignettes.

  • Fix/clean up note on parallel processing in “Multiples” vignette.

  • Better, more consistent documentation.

  • Update get_wth() to work with the new (unreleased) version of {nasapower} that works with the new version of the POWER API.

epicrop 0.0.0.9010-1

Minor changes

  • Fixes issue in vignettes with duplicate titles and plot theming.

epicrop 0.0.0.9010

Major changes

  • BREAKING CHANGE intensity column, in SEIR() is now a proportion, i.e. values range between 0 - 1. If you wish to have the same values as previously reported, df$intensity*100 will give you these values.

  • BREAKING CHANGE Removes column, severity, in SEIR() output.

  • Adds a new vignette illustrating how to run multiple simulations and use parallel processing to reduce run time for these simulations.

epicrop 0.0.0.9009

Major changes

  • BREAKING CHANGE Add a new column to SEIR() output, severity, not to be confused with the previous column called severity (now called intensity), which represents the cumulative proportion of diseased sites on day “x” expressed as, diseasedsitestotalsites×100\frac{diseased\ sites}{total\ sites}\times100.

Minor changes

  • More improvements to function documentation, include #' @family predict functions in each of the predict functions rather than only using '# @seealso.

epicrop 0.0.0.9008

Major changes

    • BREAKING CHANGE The severity output column from SEIR() has been renamed as intensity to follow the nomenclature of Savary et al. 2012. This column represents the proportion of actively diseased sites on day “x” expressed as, (diseasedsites−removedsites)(totalsites−removedsites)×100\frac{(diseased\ sites-removed\ sites)}{(total\ sites-removed\ sites)}\times100.

epicrop 0.0.0.9007

Minor changes

  • Only include Lat/Lon values if the wth object provides them.

  • Better documentation about the Lat/Lon values in the output of SEIR()

  • Parameters for predict_bacterial_blight() are used as basis for all of the other predict_*() family of functions.

  • Add DOI to CITATION and DESCRIPTION files.

  • Add Lifecycle and DOI badges to README files.

epicrop 0.0.0.9006

Minor changes

  • Optimise SEIR() internal functionality.

  • Minor improvements to documentation.

  • Polish NEWS.md.

epicrop 0.0.0.9005

Minor changes

  • Only import {data.table} functions as necessary, don’t import whole package.

Bug fixes

  • Convert wth (weather input object) to a data.table type object internally if it is not already one. Prior, if the object was not a data.table, SEIR() would fail with a message that the dates did not align. This should fix that issue and any data.frame type object including a tibble can be provided now. Thanks to Jean Fabrice Adanve for helping me find this bug.

epicrop 0.0.0.9004

Bug fixes

  • Fixes bug where the relative humidity checks in SEIR() only checked if the daily RH value was equal to (==) not equal to or greater than (>=) the set parameter for rhlim (default is 90%).

  • Example for SEIR() in {roxygen} section now works properly when executed by the user.

Major changes

  • Any default parameter values are moved from SEIR() to the predict_() functions themselves, so any calls directly to SEIR() must specify all parameters.

  • Deleted inst/alt_versions/tungrov2.R file.

  • Deleted inst/workflows/spatsim.R file.

Minor changes

  • Edit documentation for better clarity

  • Better commenting in code for self and others’ reference

  • SEIR() is simplified and further optimised

    • In some cases in the for() loop, the value of day + 1 was repeatedly calculated and assigned to a new object. This has been corrected with a single object, d1 being created at the beginning of each loop instance.
    • In some cases where RH, TEMP or RAIN are repeatedly checked against, vectors of these three values are created outside the loop to save time when checking or extracting values.
    • Redundant code and other unused objects are cleaned up and removed.

  • Standardise library loading calls to use standard evaluation in documentation.

  • Standardise italics to use “_” rather than “*”.

  • Use ggplot2::theme_classic() for example figures in README and {epicrop} vignette.

epicrop 0.0.0.9003

  • Added a NEWS.md file to track changes to the package.