Error in R

[Biophysicist24]

Hello! When running your example with CO in R, an error occurs in (1b):
"""
params_file <- system.file("validation", "CO_compensated_charParams.csv",
package = "CharAnalysis")
library(CharAnalysis)
out <- CharAnalysis(params_file)
(1) Reading input file...
...done.
(1b) Validating input parameters...
Error in if (pretreatment$yrInterp < 0) { :
missing value, need TRUE/FALSE
"""
The same happens with my data. Help me understand what is the problem.

[phiguera]

Thanks for the report. The cause is in how the parameter file is read: values are mapped by row position, so a difference in the number of zoneDiv rows shifts everything below it and leaves yrInterp as NA, which triggers missing value, need TRUE/FALSE at the first validation check.

What you can do now (current released version)

The quickest fix is to rebuild your parameter file from a clean template rather than hand-editing the misaligned one. The template already has the exact row layout the reader expects, so the key is to change values only, never the number of rows:

1. Open an unedited template_charParams.csv from DataTemplates_and_Examples/ and save it under your site name, e.g. MYSITE_charParams.csv.
2. Enter your values into the "Parameters" column only, matching each label in the "Variable" column. Do not insert or delete any rows.
3. For zoneDiv, enter your zone boundaries from the top down in the rows provided, and set every unused zoneDiv row to -9999. Leave yrInterpolate and everything below it in the rows the template already provides.
4. Keep the companion data file named to match, e.g. MYSITE_charData.csv, in the same folder.

As long as the row structure matches the template, the reader stays aligned and the error goes away, with no reinstall.

Fix

I have reworked the reader so it locates each parameter by its label in the "Variable" column rather than by row position, which removes this whole class of problem, and it now stops with a clear, named message if a required row is missing or non-numeric. The change is on the dev branch and will be included in the next release. Once that ships, the row-count constraint above no longer applies.

If you would like to verify the fix early (optional):

remotes::install_github("phiguera/CharAnalysis", subdir = "CharAnalysis_2_0_R", ref = "dev")

I will leave this issue open until the next release is out. Confirmation that the workaround unblocks you in the meantime would be helpful.

Note: the diagnosis and fix were prepared with the assistance of Claude (Claude Opus 4.8, Anthropic) and reviewed by me before posting.