NEWS.md
First stable release on GitHub.
Fixes function title formatting.
Replaces outdated {tidyverse} functions found in vignettes with modern versions.
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.
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.
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.
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.
SEIR() where Rc value was calculated incorrectly that was introduced with commit https://github.com/r-forge/cropsim/commit/ba093b252deb222f1ffe54b3a7f0d14b6192f18c#diff-17fd120d02f173b87db7e09b563e2057b95391bef823eee29cbff30cb3d80287. See Lines 124:126 that were changed to Lines 118:120 where
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.
RcA values for predict_bacterial_blight() and predict_sheath_blight().
predict_bacterial_blight() the eighth entry was improperly encoded as 0.42, it has been corrected to 0.41, commit 8b2c36b61d4f949385dcac4c03ff435b8400e335.predict_sheath_blight() the seventh entry was improperly encoded as 0.83, it has been corrected to 0.84, Commit: 69b89ce24dd41c16d4627225c028355f76a64b80.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}.
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.
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.
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, $\frac{diseased\ sites}{total\ sites}\times100$.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, $\frac{(diseased\ sites-removed\ sites)}{(total\ sites-removed\ sites)}\times100$.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.
Optimise SEIR() internal functionality.
Minor improvements to documentation.
Polish NEWS.md.
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.Edit documentation for better clarity
Better commenting in code for self and others’ reference
SEIR() is simplified and further optimised
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.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.