Merge pull request #12 from biocro/improve-write-model

Improve write_model

Author: eloch216

NEWS.md

@@ -47,6 +47,10 @@ be directly added to this file to describe the related changes.
   (`minimal`) only prints info to the terminal when an issue with a simulation
   occurs
 
+- Improved formatting of output from `write_module`, so that initial value and
+  parameter lists are alphabetized, equals signs are aligned, and module names
+  are preserved
+
 # Changes in BioCroValidation Version 0.2.0 (2025-05-23)
 
 - Added 2002 and 2005 SoyFACE biomass and standard deviation data.

R/write_model.R

@@ -7,19 +7,39 @@ write_model <- function(
     ode_solver
 )
 {
+    # Get the longest name among the initial values and parameters
+    all_names <- c(
+        names(initial_values),
+        names(parameters)
+    )
+
+    name_width <- max(sapply(all_names, nchar))
+
+    # Alphabetize the initial values and parameters
+    initial_values <- initial_values[order(tolower(names(initial_values)))]
+    parameters     <- parameters[order(tolower(names(parameters)))]
+
+    # Prepare the module list strings
+    dir_module_string <- paste(paste0('        ', names(direct_modules), ' = "', direct_modules, '"'), collapse = ',\n')
+    diff_module_string <- paste(paste0('        ', names(differential_modules), ' = "', differential_modules, '"'), collapse = ',\n')
+
+    # Remove any lines without names
+    dir_module_string <- gsub('         = ', '        ', dir_module_string)
+    diff_module_string <- gsub('         = ', '        ', diff_module_string)
+
     # Fill in the module definition template (defined below)
     model_text <- sprintf(
         model_definition_template,
         name,
-        paste(paste0('        "', direct_modules, '"'), collapse = ',\n'),
-        paste(paste0('        "', differential_modules, '"'), collapse = ',\n'),
+        dir_module_string,
+        diff_module_string,
         ode_solver[['type']],
         ode_solver[['output_step_size']],
         ode_solver[['adaptive_rel_error_tol']],
         ode_solver[['adaptive_abs_error_tol']],
         ode_solver[['adaptive_max_steps']],
-        paste(paste0('        "', names(initial_values), '" = ', initial_values), collapse = ',\n'),
-        paste(paste0('        "', names(parameters), '" = ', parameters), collapse = ',\n')
+        paste(paste0('        ', format(names(initial_values), width = name_width), ' = ', initial_values), collapse = ',\n'),
+        paste(paste0('        ', format(names(parameters), width = name_width), ' = ', parameters), collapse = ',\n')
     )
 }
 
@@ -31,11 +51,11 @@ model_definition_template <- '%s <- list(
 %s
     ),
     ode_solver = list(
-        type = "%s",
-        output_step_size = %f,
+        type                   = "%s",
+        output_step_size       = %f,
         adaptive_rel_error_tol = %e,
         adaptive_abs_error_tol = %e,
-        adaptive_max_steps = %i
+        adaptive_max_steps     = %i
     ),
     initial_values = list(
 %s

man/write_model.Rd

@@ -62,6 +62,11 @@
   output. See examples below. Note that it is customary to name the R script
   file as \code{name.R}, where \code{name} is the value provided to the function
   itself.
+
+  The \code{initial_values} and \code{parameters} will be alphabetized
+  (case-insensitive). The \code{ode_solver} elements will be printed in the
+  customary BioCro order. The \code{direct_modules} and
+  \code{differential_modules} will not be reordered.
 }
 
 \value{
@@ -85,7 +90,7 @@ if (require(BioCro)) {
 
   if (interactive()) {
     # Use writeLines to save as a `.R` file
-    writeLines(out, "./test_soybean_model.h")
+    writeLines(out, "./test_soybean_model.R")
   }
 }
 }

tests/test_data/test_model.R

@@ -6,19 +6,19 @@ test_model <- list(
         "BioCro:harmonic_oscillator"
     ),
     ode_solver = list(
-        type = "boost_rkck54",
-        output_step_size = 1.000000,
+        type                   = "boost_rkck54",
+        output_step_size       = 1.000000,
         adaptive_rel_error_tol = 1.000000e-04,
         adaptive_abs_error_tol = 1.000000e-04,
-        adaptive_max_steps = 200
+        adaptive_max_steps     = 200
     ),
     initial_values = list(
-        "position" = 1,
-        "velocity" = 0
+        position        = 1,
+        velocity        = 0
     ),
     parameters = list(
-        "timestep" = 1,
-        "mass" = 1,
-        "spring_constant" = 0.5
+        mass            = 1,
+        spring_constant = 0.5,
+        timestep        = 1
     )
 )