cran-comments.md

In jmzobitz/MAT369Code: Simulating Differential Equations with Data

Resubmission 15-09-22

In README.md fixed the link to the package on CRAN to a canonical URL

There were no ERRORs or WARNINGs or NOTEs

Patch update 11-09-22

This is a patch update, fixing a data frame (global_temperature) with the correct and desired variables.

There were no ERRORs or WARNINGs or NOTEs

Resubmission 21-06-22

This is a re-resubmission. There were no ERRORs or WARNINGs or NOTEs

My apologies - I didn't realize that my comments file was entirely completed. Please ignore my previous submission.

I have revised the Description in the DESCRIPTION file to remove any extraneous spaces, to the best of my ability. The reference to the online text is now written in the form ".. "Exploring modeling with data and differential equations using R" by John Zobitz (2021) https://jmzobitz.github.io/ModelingWithR/index.html"

Resubmission 17-06-22

This is a resubmission. There were no ERRORs or WARNINGs or NOTEs

Thank you for providing more information on how to structure my DESCRIPTION file. Based on the previous review I have created a more extensive Description as written below:

Designed to support the visualization, numerical computation, qualitative analysis, model-data fusion, and stochastic simulation for autonomous systems of differential equations. Euler and Runge-Kutta methods are implemented, along with tools to visualize the two-dimensional phaseplane. Likelihood surfaces and a simple Markov Chain Monte Carlo parameter estimator can be used for model-data fusion of differential equations and empirical models. The Euler-Maruyama method is provided for simulation of stochastic differential equations. The package was originally written for internal use to support teaching by Zobitz, and refined to support the text "Exploring modeling with data and differential equations using R" by John Zobitz. See online text: https://jmzobitz.github.io/ModelingWithR/index.html.

Resubmission 15-06-2022

This is a resubmission. There were no ERRORs or WARNINGs or NOTEs

Thank you for reviewing my previous submission. Based on the previous review I have changed the following:

• The DESCRIPTION file contains a reference to a forthcoming textbook that describes the methods in this package as shown below:

Description: Functions to support "Exploring modeling with data and differential equations using R"" by John Zobitz. See online text: https://jmzobitz.github.io/ModelingWithR/index.html.

• mcmc_analyze.Rd now has \value tag describing the exported method:

Two plots: (1) fitted model results compared to data, and (2) pairwise parameter histograms and scatterplots to test model equifinality.

• Examples in (1) phaseplane.Rd, (2) mcmc_analyze.Rd, and (3) mcmc_estimate.Rd now are wrapped in \donttest rather than commented out code lines.

• The files phaseplane.R and mcmc_analyze.R both had information messages provided to the console. These messages are first captured with utils::capture.output and a message is subsequently written to the console. The information messages can be supressed with the parameter eq_soln in phaseplane.R and verbose in mcmc_analyze.R

Resubmission 08-06-2022

This is a resubmission. There were no ERRORs or WARNINGs or NOTEs

In this version I have changed the following:

• Changed the DESCRIPTION file to remove the Maintainer and used an Authors field that has similar information as given in the following NOTE: Check: CRAN incoming feasibility, Result: NOTE Maintainer: 'John Zobitz [e-mail]'

• Changed the R code for phaseplane to remove the following NOTE: Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64 Check: R code for possible problems, Result: NOTE phaseplane: no visible binding for global variable '.' Undefined global functions or variables:

• Modified the examples for mcmc_analyze and mcmc_estimate so that the CPU time does not exceed 5 seconds as given in the following NOTE: Check: examples, Result: NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed mcmc_analyze 138.19 3.12 141.32 mcmc_estimate 136.17 3.52 139.69

R CMD check results

There were no ERRORs or WARNINGs.

There was 1 NOTE:

• checking R code for possible problems ... NOTE phaseplane: no visible binding for global variable ‘.’ Undefined global functions or variables:

I am aware of this note - this was the easiest way to redefine a user-defined variable name in the code to produce a plot (lines 148-149 in phaseplane).

jmzobitz/MAT369Code documentation built on March 4, 2024, 12:27 a.m.