Fix deprecated arma::is_finite calls to resolve CRAN warnings

[Copilot]

This PR fixes CRAN package check warnings caused by deprecated arma::is_finite() function calls in the C++ code. The warnings were appearing across multiple R platforms and preventing successful CRAN submission.

Issue

CRAN checks were failing with deprecation warnings:

infection.cpp:58:25: warning: 'bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double]' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]

Changes

• Added #include <cmath> header to src/infection.cpp to support std::isfinite()
• Replaced arma::is_finite(times(i)) with std::isfinite(times(i)) at two locations:
  • Line 59 in infection_cpp() function
  • Line 163 in susceptibility_cpp() function

Testing

• Verified C++ code compiles successfully with sourceCpp()
• Confirmed std::isfinite() has identical behavior to arma::is_finite() for finite/NaN/infinite values
• No breaking changes - both functions serve the same purpose of checking if a value is finite

This minimal change addresses the exact deprecation warnings specified by CRAN and should allow the package to pass all checks for resubmission.

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Original prompt

---

This section details on the original issue you should resolve

<issue_title>Fix issues associated with Rcpp</issue_title>
<issue_description>I recently got this email from CRAN about the R package. We need to fix the issues associated with the changes in the Rcpp package to resubmit the package to CRAN.

Dear maintainer,

Please see the problems shown on
https://cran.r-project.org/web/checks/check_results_netdiffuseR.html.

Specifically, please see the compilation warnings about deprecated
declarations.

These are from a recent upgrade of RcppArmadillo which now uses
Armadillo 15 by default. See
RcppCore/RcppArmadillo#485 for more
information.

Please correct before 2025-10-23 to safely retain your package on CRAN.

Best wishes,
The CRAN Team

• Results file: https://cran.r-project.org/web/checks/check_results_netdiffuseR.html

More details

<h2 style="background: white; color: rgb(102, 102, 102); font-family: monospace; font-size: large; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; white-space: normal; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;">CRAN Package Check Results for Package<span> </span><a href="https://cran.r-project.org/web/packages/netdiffuseR/index.html" style="background: white; color: blue;"><span class="CRAN" style="color: rgb(39, 109, 195); text-decoration: underline;">netdiffuseR</span></a></h2><p style="color: rgb(0, 0, 0); font-family: Times; font-size: medium; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; white-space: normal; background-color: rgb(255, 255, 255); text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;">Last updated on 2025-09-29 16:49:55 CEST.</p>
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags
-- | -- | -- | -- | -- | -- | --
r-devel-linux-x86_64-debian-clang | 1.23.0 | 102.60 | 335.19 | 437.79 | WARN |  
r-devel-linux-x86_64-debian-gcc | 1.23.0 | 71.35 | 211.72 | 283.07 | WARN |  
r-devel-linux-x86_64-fedora-clang | 1.23.0 |   |   | 726.03 | WARN |  
r-devel-linux-x86_64-fedora-gcc | 1.23.0 |   |   | 703.81 | WARN |  
r-devel-windows-x86_64 | 1.23.0 | 128.00 | 261.00 | 389.00 | WARN | --no-vignettes
r-patched-linux-x86_64 | 1.23.0 | 110.31 | 310.09 | 420.40 | WARN |  
r-release-linux-x86_64 | 1.23.0 | 110.21 | 309.67 | 419.88 | WARN |  
r-release-macos-arm64 | 1.23.0 |   |   | 145.00 | OK |  
r-release-macos-x86_64 | 1.23.0 |   |   | 260.00 | OK |  
r-release-windows-x86_64 | 1.23.0 | 126.00 | 216.00 | 342.00 | WARN | --no-vignettes
r-oldrel-macos-arm64 | 1.23.0 |   |   | 162.00 | NOTE |  
r-oldrel-macos-x86_64 | 1.23.0 |   |   | 265.00 | NOTE |  
r-oldrel-windows-x86_64 | 1.23.0 | 154.00 | 262.00 | 416.00 | WARN | --no-vignettes

<h3 style="background: white; color: rgb(102, 102, 102); font-family: monospace; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; white-space: normal; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;">Check Details</h3><p style="color: rgb(0, 0, 0); font-family: Times; font-size: medium; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; white-space: normal; background-color: rgb(255, 255, 255); text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;">Version: 1.23.0<br>Check: whether package can be installed<br>Result: WARN<span> </span><span style="font-family: monospace; white-space: pre;">
  Found the following significant warnings:
    infection.cpp:58:16: warning: 'is_finite&lt;double&gt;' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
    infection.cpp:162:16: warning: 'is_finite&lt;double&gt;' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/netdiffuseR.Rcheck/00install.out’ for details.
  * used C++ compiler: ‘Debian clang version 19.1.7 (3+b2)’
</span>Flavor:<span> </span><a href="https://www.r-project.org/nosvn/R.check/r-...

</details>
Fixes USCCANA/netdiffuseR#59

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