Guidelines for implementing a crop model R wrapper for CroptimizR

Samuel Buis

INRAE - EMMAH

Patrice Lecharpentier

INRAE - Agroclim

2023-12-22

Introduction

R wrappers are necessary to couple crop models with CroptimizR. Indeed, the estim_param function will need to run the model (for which parameters have to be estimated), on a set of observed situations and for values of estimated parameters proposed by the selected algorithm. It will then compute the selected (least-square or likelihood) criterion using the resulting simulated values and corresponding observations. An R wrapper is thus basically an R function able to run model simulations for prescribed values of some of its input parameters and to return the values of its simulated outputs. It must have specific arguments, returned values and behavior, as detailed in the following.

The first section presents the concepts for building a basic version of a model wrapper. The second section section presents optional issues. The third one shows examples on a simple toy model.

How to write a basic version of a model wrapper for CroptimizR

We will detail here what is mandatory in terms of interface of the wrapper and expected behavior. Optional issues for more advanced users are detailed in the next section.

Please note that this basic version does not allow to perform simultaneous estimation of specific and varietal parameters on a dataset including several cultivars (i.e. as in the example detailed in https://sticsrpacks.github.io/CroptimizR/articles/Parameter_estimation_Specific_and_Varietal.html). Additional functionnalities are needed for that, as detailed in section “Optional issues”.

Model wrapper interface

Here’s a header for a basic version of a model wrapper:

#' @title My model wrapper for CroptimizR
#'
#' @description This function runs my crop model on a set of situations
#' (i.e. environments) using the values of the parameters defined in the
#' param_values argument. It returns the values of the simulated outputs.
#'
#' @param param_values (optional) a named vector that contains the value(s) and
#' name(s) of the parameters to force for each situation to simulate.
#' If not provided (or if is NULL), the simulations will be performed using
#' default values of the parameters (e.g. as read in the model input files).
#'
#' @param situation Vector of situations names for which results must be
#' returned.
#'
#' @param model_options List containing any information needed to run the model
#' (e.g. path to model input files and executable, ...)
#'
#' @return A list containing:
#'     o `sim_list`: a `named list` (names = situations names) of data.frames
#'     (or tibbles) of simulated output values (one element of the list per
#`      simulated situation)
#'     o `error`: an error code indicating if at least one simulation ended
#'     with an error.

model_wrapper <- function(param_values = NULL, situation, model_options, ...) {

}

Each argument detailed here must be defined for any CroptimizR model wrapper. You can use this header to develop yours. Be careful, “…” is mandatory at the end of the argument list since CroptimizR may give additional arguments for more advanced wrappers.

The shape of the param_values and situation arguments are imposed by CroptimizR. This is not the case of the model_options argument (except the fact that is must be a list): its content must be defined by the developper of the model wrapper. It is typically used to provide to the model wrapper what it needs to run the model (e.g. path to the model executable, path to the directory containing model input files for the situations to simulate, …). The user provides model_options to estim_param which gives it as is to the model wrapper.

It is advisable to define param_values as an optional argument, so that the model wrapper can be used directly by the user (i.e. outside of estim_param) to run the model using default values for all of its parameters.

Minimum required functionalities

• Run the model on a specified set of situations

A situation corresponds to a simulation (for example a specific treatment on a given soil for a given period).

To run your model from R, several technical solutions are possible depending on the language it is implemented with. A simple solution (although not the most computationally efficient) is to run its executable using the R function system2. Otherwise, different languages can be directly interfaced in R: for example Python, using the R package reticulate, C and C++ (see e.g. https://www.r-bloggers.com/2014/02/three-ways-to-call-cc-from-r/), fortran (see e.g. https://www.r-bloggers.com/2014/04/fortran-and-r-speed-things-up/)…

• Force the model with specified values of its parameters

The values of the parameters are specified in the param_values vector. The names of the parameters can be retrieved using names(param_values).

• Return the simulated results for all simulated variables

The value returned by the model wrapper must be a list, noted results in the following. This list must contain an element named sim_list. sim_list must be a named list (names = situations names) of size the number of situations to simulate and having the attribute “cropr_simulation” (to use the CroPlotR package). You can initialize it like this:

results$sim_list <- setNames(vector("list",length(situation)), nm = situation)

attr(results$sim_list, "class") <- "cropr_simulation"

Each element of the list should be a data.frame (or a tibble) with the results obtained for all simulated variables and dates for the given situation.

The data.frames must have one column called Date containing the simulations dates, in Date or POSIXct format (see R function base::as.Date or base::as.POSIXct). The other columns contain the values of the simulated variables, and the names of the columns must be the simulated variables names.

For example, if situation is `c(“situation1”,“situation2”,“situation3”), sim_list should look like:

sim_list$situation1

#> A tibble: *** x ***
#>   Date         var1    var2    var3    var4 ...
#>   <dttm>     <dbl>   <dbl>   <dbl>   <dbl>
#> 1 1994-10-17   0      2.53    4.80   150 
#> 2 1994-10-18   0      2.31    4.66   150
#> 3 1994-10-19   0      4.55    4.44   150
#>
#>

sim_list$situation2

#> A tibble: *** x ***
#>   Date         var1    var2    var3    var4...
#>   <dttm>     <dbl>   <dbl>   <dbl>   <dbl>
#> 1 1995-10-17   0      2.60    4.80   138
#> 2 1995-10-18   0      3.42    4.70   138
#> 3 1995-10-19   0      5.25    4.45   138


sim_list$situation3

#> A tibble: *** x ***
#>   Date         var1    var2    var3    var4  ...
#>   <dttm>     <dbl>   <dbl>   <dbl>   <dbl>
#> 1 1996-10-17   0      2.41    4.81   142
#> 2 1996-10-18   0      3.03    4.71   142
#> 3 1996-10-19   0      5.10    4.47   142

** Note that there is not for the moment any dedicated data structure handled in CroptimizR and CroPlotR for storing simulated variables that do no depend on time (e.g. such as the julian day of a given phenological stage). You must thus include them in the data.frames described here-before. For this variables, it is strongly advised to replicate their (unique) values for all rows of the data.frames (see e.g. var4 in the data.frames described here-before). This makes it possible to compare these simulated values to the corresponding observed values regardless of the dates with which they are associated in the data.frames including the observations.**

• Return an error code if any simulation failed

If any simulation failed for any reason, use the R function warning to print any useful information about the error and set the variable results$error to TRUE (and to FALSE otherwise).

In CroptimizR, parameter estimation is based on the comparison between the values of the observed and simulated variables at corresponding dates. Only the situations, variables and dates common to both observations provided to the estim_param function, and simulations returned by the wrapper used, will be taken into account in the parameter estimation process. In case where the value of an observed variable is NA for a given situation and date, it will not be taken into account. In case where the value of a simulated variable is NA (or Inf) for a given situation and date for which there is an observation, the optimized criterion will take the NA value, which may stop the process, and the user will be warned.

Implementation

A typical pseudo-code implementation of a basic wrapper function is thus:

model_wrapper <- function(param_values = NULL, situation, model_options, ...) {
  # Initializations
  # param_names <- names(param_values)
  results <- list(sim_list = setNames(vector("list", length(situation)),
                                      nm = situation),
                  error = FALSE)
  attr(results$sim_list, "class") <- "cropr_simulation"

  for (situation in situation) {
    # overwrite model input parameters of names contained in param_names with
    # values retrieved in param_values
    # run the model for the given situation
    # read the results and store the data.frame in result$sim_list[[situation]]

    if (any_error_returned_by_the_model_or_detected_in_its_results) {
      warning("any_useful_information_to_describe_the_error")
      results$error <- TRUE
    }
  }
  return(results)
}

Test your wrapper

• Check the results returned by the wrapper are identical to what is given by your model when used in a standard way (i.e. not through the wrapper)

• Run the test_wrapper function

test_wrapper(model_function, model_options, param_values, situation, var=NULL)

This function has been created to perfom several checks on user model wrappers.

It takes in input:

• model_function: the crop Model wrapper function to use.
• model_options: the list of options of the Crop Model wrapper.
• param_values: a named vector that contains values and names for AT LEAST TWO model parameters THAT ARE EXPECTED TO PLAY ON ITS RESULTS (e.g. param_values <- c(P1=10, P2=50))
• situation: a vector of situations names for which results must be tested.
• var (optional): a vector of variables names for which results must be tested (if taken into account by the wrapper)

It runs the given model wrapper consecutively with different subsets of param_values.

It then checks:

• the format of the returned results
• the results are different when different subsets of param_values are used,
• the results are identical when same subsets of param_values are used.

If all tests succeed, it returns:

## Test the wrapper returns outputs in expected format ...
## 

## ... OK
## 

## Test the wrapper gives identical results when running with same inputs ...
## 

## ... OK
## 

## Test the wrapper gives different results when running with different inputs ...
## 

## ... OK
## 

If some test fails, information written in red should help you understanding the problem.

Examples of use of this function are given in section Examples

• Try to play with the estim_param function on your wrapper for a simple case (see e.g. examples in section Examples or https://sticsrpacks.github.io/CroptimizR/articles/Parameter_estimation_simple_case.html).

Optional issues

• Take into account different parameters values depending on the situation to simulate

If you want your model wrapper to be used for simultaneous estimation of specific and varietal parameters on a dataset including several cultivars (e.g. as in the example detailed in https://sticsrpacks.github.io/CroptimizR/articles/Parameter_estimation_Specific_and_Varietal.html), the param_values argument must be able to receive a data.frame (or tibble) including a specific column named situation. In this case, the different lines of the data.frame will specify the values of the parameters to use in the model for the situation given in the column situation, as in the example below:

# A tibble: 4 x 4
#>    situation  p1     p2     p3
#>    <chr>     <dbl>  <dbl>  <dbl>
#>  1 sit1      50.14  1.14   340.43
#>  2 sit2      55.37  1.23   126.47
#>  3 sit3      43.22  2.12   234.56
#>  4 sit4      38.49  2.02   236.45

Depending on the application (simple case or simultaneous specific and varietal parameters estimation), the estim_param function will thus pass to the model wrapper either a named vector or a data.frame, including or not the situation column. Both shapes have thus to be handled in the model wrapper in this case. This may be done as in the following piece of code:

# convert param_values in a tibble
param_values <- tibble::tibble(!!!param_values)

# loop on the situations to simulate
for (sit in situation_list) {

  # extract the parameters values to apply for the given situation
  params <- NULL
  if (!is.null(param_values)) {
    if (! "situation" %in% names(param_values)) {
      params <- param_values
    } else {
      params <- dplyr::filter(param_values, situation == sit) %>%
        dplyr::select(-situation)
    }
  }

  # run the model with parameters values defined by params

}

• Check wrapper arguments:

If possible implement any check you can concerning what is given to the wrapper. Print a message using the warning function and return TRUE in results$error if a problem is detected. It may be an unknown parameter name given in param_values, an unknown situation name given in sit_name, an incorrect model option (field of model_option) such as an incorrect model path for example …

• Perform parallel calculations:

If possible with your model (pay attention to concurrency access to model input and output files), managing parallel simulations of the different situations to simulate may drastically reduce the execution time.

The doParallel package can be used for that. There are specificities when coding a parallel loop: in particular, a list pre allocated outside of the loop is not shared between cores so return statements must be used inside. Here is an example for illustrating this issue:

# Code of an example of foreach loop algo
library("doParallel")

## Loading required package: foreach

## Loading required package: iterators

## Loading required package: parallel

test_parallel <- function(cores_nb = 1,
                          pa = FALSE,
                          max_it = 5) {
  # pa: flag to switch from case with pre-allocated list to case with
  #returned statement

  # Launching the cluster
  cl <- parallel::makeCluster(cores_nb)
  doParallel::registerDoParallel(cl)

  # List preallocation
  out_pa <- vector(mode = "list", max_it)

  # Parallel loop
  out <- foreach(i = 1:max_it) %dopar% {
    if (pa) {
      out_pa[[i]] <- i  # store results in a pre-allocted list
    } else {
      return(i)         # return the results
    }
  }

  # Stopping the cluster
  parallel::stopCluster(cl)

  if (pa) {
    return(out_pa)
  } else {
    return(out)
  }
}

cores_nb <- 2

# Case with returned statement
out <- test_parallel(cores_nb)

# Case with pre-allocated list
out_pa <- test_parallel(cores_nb, TRUE)

out

## [[1]]
## [1] 1
## 
## [[2]]
## [1] 2
## 
## [[3]]
## [1] 3
## 
## [[4]]
## [1] 4
## 
## [[5]]
## [1] 5

out_pa

## [[1]]
## NULL
## 
## [[2]]
## NULL
## 
## [[3]]
## NULL
## 
## [[4]]
## NULL
## 
## [[5]]
## NULL

• Outputs selection

Two additional arguments (var and sit_var_dates_mask) can be defined in the wrapper and are provided by the estim_param function when it calls the wrapper. They can be used to select the results to return and are particularly useful if this selection allows saving computation time or memory (for example if model results are read in a databasis with specific request per variable and/or date, or if model results are read in different files depending on the variables …).

var is a vector of variables names for which results must be returned.

sit_var_dates_mask is a list of data.frame similar to results$sim_list. It indicates the list of variables and dates for each situation for which results must be returned: if sit_var_dates_mask$situation1[j,"var1"] does not contain NA, then the simulated value of variable “var1” at date sit_var_dates_mask$situation1[j,"Date"] must be returned in results$sim_list[["situation1"]].

It is advised to define them as optionnal arguments with default value equal to NULL. If not given or if they are NULL, the wrapper should return results for all simulated variables. If both arguments are handled in the model wrapper code (which is not mandatory: none of them or only one of them can be handled) and non-null values are given for both, only sit_var_dates_mask should be taken into account since it is more detailed.

Examples

Example of a basic wrapper for an LAI toy model

lai_toymodel <- function(year, max_lai = 8, julday_incslope = 100,
                         inc_slope = 5, julday_decslope = 200, dec_slope = 2) {
  # Simulate lai for a single crop over 2 years
  # (from 01/01/year to 31/12/(year+1) with a simple double-logistic function
  #
  # Arguments
  #   - year: first year of simulation
  #   - max_lai: max value for lai
  #   - inc_slope and dec_slope: increasing and decreasing slope
  #   - julday_incslope and julday_decslope: julian days of maximal increasing
  #     and decreasing slopes
  #
  # Value
  #   - lai: vector of simulated lai
  #   - dates: vector of dates (POSIXct) for which lai is computed

  end_day <- format(as.Date(paste0(year + 1, "-12-31"), format = "%Y-%m-%d",
                            origin = paste0(year, "-01-01")), "%j")
  jul_days <- 1:as.numeric(end_day)

  lai <- max_lai * (1 / (1 + exp((julday_incslope - jul_days) / inc_slope)) -
                       1 / (1 + exp((julday_decslope - jul_days) / dec_slope)))
  lai[lai < 0] <- 0

  dates <-
    as.POSIXct(
      as.character(
        as.Date(
          jul_days,
          origin = paste0(year, "-01-01"))
      ),
      format = "%Y-%m-%d", tz = "UTC"
    )

  return(list(dates = dates, lai = lai))
}


laitm_simple_wrapper <- function(param_values = NULL, situation,
                                 model_options, ...) {

  # A basic wrapper for lai_toymodel
  #
  # Arguments
  #   - param_values: (optional) named vector containing the values of the
  #     lay_toymodel parameters to force among max_lai, inc_slope, dec_slope,
  #     julday_incslope and julday_decslope
  #   - situation: Vector of situations names for which results must be returned
  #     In this case, the names of the situations are coded as "year_suffix"
  #   - model_options: not used in this case
  #   - ...: mandatory since CroptimizR will give additional arguments not used
  #   here
  #
  # Value:
  #   A named list of tibble per situation.
  #   Each tibble contains columns:
  #      - Date (POSIXct dates of simulated results),
  #      - One column per simulated variable (lai in this case)
  #
  # Details:
  #  - Runs the lai_toymodel for a set of situations defined in situation
  #  - Forces the parameters of lai_toymodel with the values given in
  #    param_values argument
  #  - Returns the required simulated values
  #

  results <-
    list(
      sim_list =
        setNames(
          vector("list", length(situation)),
          nm = situation
        ),
      error = FALSE
    )
  attr(results$sim_list, "class") <- "cropr_simulation"

  for (sit in situation) {

    # Retrieve year, emergence and crop_duration from situation name
    tmp <- stringr::str_split(sit, "_")
    year <- as.numeric(tmp[[1]][[1]])

    # Check inputs
    if (year < 1) {
      warning(
        paste(
          "sit_name",
          sit,
          "not well defined, first part is supposed to be a = year!"
        )
      )
      results$error <- TRUE
      return(results)
    }
    if (!all(names(param_values) %in% c(
      "max_lai",
      "inc_slope",
      "dec_slope",
      "julday_incslope",
      "julday_decslope"
    )
    )) {
      warning(
        paste(
          "Unknown parameters in param_values:",
          paste(names(param_values), collapse = ",")
        )
      )
      results$error <- TRUE
      return(results)
    }

    # Call the lai_toymodel with varying arguments depending on what is given in
    # param_values
    res_laitm <-
      do.call(
        "lai_toymodel",
        c(as.list(param_values), list(year = year))
      )
    # Fill the result variable
    results$sim_list[[sit]] <-
      dplyr::tibble(
        Date = res_laitm$dates,
        lai = res_laitm$lai
      )
  }
  return(results)
}

Testing this wrapper using the test_wrapper function:

library(CroptimizR)

test_wrapper(
  model_function = laitm_simple_wrapper,
  model_options = NULL,
  param_values = c(inc_slope = 25, dec_slope = 10),
  situation = c("2005_a")
)

## Test the wrapper returns outputs in expected format ...
## ... OK
## 
## Test the wrapper gives identical results when running with same inputs ...
## ... OK
## 
## Test the wrapper gives different results when running with different inputs ...
## ... OK
## 

The little piece of code below shows an example of parameter estimation using this wrapper:

library(CroptimizR)
library(dplyr)


tmp <- laitm_simple_wrapper(
  situation = "2005_a",
  param_values = c(inc_slope = 25, dec_slope = 10)
)

# Create synthetic observations by selecting simulated results
ind <- sort(sample(nrow(tmp$sim_list$`2005_a`), 50))
obs_synth <- list(`2005_a` = tmp$sim_list$`2005_a`[ind, ])

# Try to retrieve inc_slope and dec_slope values
param_info <- list(
  lb = c(inc_slope = 1, dec_slope = 1),
  ub = c(inc_slope = 100, dec_slope = 100)
)

optim_options <- list(nb_rep = 5, maxeval = 100, xtol_rel = 1e-2)
res <- estim_param(
  obs_synth,
  crit_function = crit_ols,
  model_function = laitm_simple_wrapper,
  optim_options = optim_options,
  param_info = param_info
)

## 
## ---------------------
## Estimated parameters: inc_slope dec_slope 
## ---------------------
## Working: 20.00%. Estimated remaining time: 1.63 secs
## Working: 40.00%. Estimated remaining time: 1.08 secs
## Working: 60.00%. Estimated remaining time: 0.74 secs
## Working: 80.00%. Estimated remaining time: 0.39 secs
## Working: 100.00%. Estimated remaining time: 0.00 secs
## $inc_slope

## 
## $dec_slope

## 
## $inc_slope

## 
## $dec_slope

## 
## $criterion

## 
## [[1]]

## 
## 
## List of observed variables used: lai 
## 
## Estimated value for inc_slope :  25 
## 
## Estimated value for dec_slope :  10 
## Minimum value of the criterion: 0.00032 
## Complementary graphs and results can be found in  /Users/runner/work/CroptimizR/CroptimizR/vignettes 
## 
## Average time for the model to simulate all required situations: 0.0031 sec elapsed
## Total number of criterion evaluation: 197 
## Total time of model simulations: 0.6 sec elapsed
## Total time of parameter estimation process: 4 sec elapsed
## ----------------------

res$final_values

## inc_slope dec_slope 
## 24.981130  9.958293

# Plot the simulations obtained with the optimized values of the parameters VS
# the observed ones using the CroPlotR package.
if (!require("CroPlotR")) {
  devtools::install_github("SticsRPacks/CroPlotR@*release")
  library("CroPlotR")
}
tmp <- laitm_simple_wrapper(situation = c("2005_a", "2006_b"),
                            param_values = res$final_values)
plot(tmp$sim_list, obs = obs_synth, type = "scatter")

## $all_situations

Another version taking into account the different shapes param_values can take

This one can be used to perform simultaneous estimation of specific and varietal parameters on a dataset including several cultivars.

laitm_simple_wrapper_v2 <- function(param_values = NULL, situation,
                                    model_options, ...) {

  # A basic wrapper for lai_toymodel
  #
  # Arguments
  #   - param_values: (optional) a named vector or a tibble containing the
  #     values of the lay_toymodel parameters to force among max_lai, inc_slope,
  #     dec_slope,julday_incslope and julday_decslope. An optional column named
  #     Situation containing the name of the situations allows to define
  #     different values of the parameters for different situations.
  #   - situation: Vector of situations names for which results must be
  #     returned.
  #     In this case, the names of the situations are coded as "year_suffix"
  #   - model_options: not used in this case
  #   - ...: mandatory since CroptimizR will give additional arguments not used
  #     here
  #
  # Value:
  #   A named list of tibble per situation.
  #   Each tibble contains columns:
  #      - Date (POSIXct dates of simulated results),
  #      - One column per simulated variable (lai in this case)
  #
  # Details:
  #  - Runs the lai_toymodel for a set of situations defined in situation
  #  - Forces the parameters of lai_toymodel with the values given in
  #   param_values argument
  #  - Returns the required simulated values
  #

  results <- list(
    sim_list = setNames(
      vector("list", length(situation)),
      nm = situation
    ),
    error = FALSE
  )
  attr(results$sim_list, "class") <- "cropr_simulation"

  param_values <- tibble::tibble(!!!param_values)  # convert param_values
  # in a tibble

  for (sit in situation) {
    # Retrieve year, emergence and crop_duration from situation name
    tmp <- stringr::str_split(sit, "_")
    year <- as.numeric(tmp[[1]][[1]])

    # Check inputs
    if (year < 1) {
      warning(
        paste(
          "sit_name",
          sit,
          "not well defined, first part is supposed to be a year!"
        )
      )
      results$error <- TRUE
      return(results)
    }
    # extract the parameters values to apply for the given situation
    params <- NULL
    if (!is.null(param_values)) {
      if (! "situation" %in% names(param_values)) {
        params <- param_values
      } else {
        params <-
          dplyr::filter(param_values, situation == sit) %>%
          dplyr::select(-situation)
      }
    }
    if (!all(names(params) %in% c(
      "max_lai",
      "inc_slope",
      "dec_slope",
      "julday_incslope",
      "julday_decslope"
    )
    )) {
      warning(
        paste(
          "Unknown parameters in param_values:",
          paste(names(param_values), collapse = ",")
        )
      )
      results$error <- TRUE
      return(results)
    }

    # Call the lai_toymodel with varying arguments depending on what is given in
    # param_values
    res_laitm <- do.call(
      "lai_toymodel",
      c(as.list(params), list(year = year))
    )

    # Fill the result variable
    results$sim_list[[sit]] <-
      dplyr::tibble(
        Date = res_laitm$dates,
        lai = res_laitm$lai
      )
  }
  return(results)
}

Testing this wrapper using the test_wrapper function:

library(CroptimizR)

test_wrapper(
  model_function = laitm_simple_wrapper_v2,
  model_options = NULL,
  param_values = c(inc_slope = 25, dec_slope = 10),
  situation = c("2005_a")
)

## Test the wrapper returns outputs in expected format ...
## ... OK
## 
## Test the wrapper gives identical results when running with same inputs ...
## ... OK
## 
## Test the wrapper gives different results when running with different inputs ...
## ... OK
## 

The code below shows an example of a simultaneous estimation of specific (dec_slope here) and varietal (inc_slope) parameters using this wrapper:

library(CroptimizR)
library(dplyr)

tmp <- laitm_simple_wrapper_v2(
  situation = c("2005_a", "2006_b"),
  param_values = dplyr::tibble(
    situation = c("2005_a", "2006_b"),
    inc_slope = c(25, 50),
    dec_slope = c(10, 10)
  )
)

# Create synthetic observations by selecting simulated results
length_2005_a <- nrow(tmp$sim_list$`2005_a`)
length_2006_b <- nrow(tmp$sim_list$`2006_b`)
obs_synth <- list(
  `2005_a` =
    tmp$sim_list$`2005_a`[
      seq(from = 1, to = length_2005_a, by = 3),
    ],
  `2006_b` =
    tmp$sim_list$`2006_b`[
      seq(from = 1, to = length_2006_b, by = 3),
    ]
)

# Try to retrieve inc_slope and dec_slope values on both situations
param_info <- list(
  inc_slope = list(
    sit_list = list("2005_a", "2006_b"),
    lb = c(1, 1),
    ub = c(100, 100)
  ),
  dec_slope = list(
    sit_list = list(c("2005_a", "2006_b")),
    lb = 1, ub = 100
  )
)

optim_options <- list(nb_rep = 5, maxeval = 100, xtol_rel = 1e-2)
res <- estim_param(obs_synth, crit_function = crit_ols,
                   model_function = laitm_simple_wrapper_v2,
                   optim_options = optim_options,
                   param_info = param_info)

## 
## ---------------------
## Estimated parameters: inc_slope dec_slope 
## ---------------------
## Working: 20.00%. Estimated remaining time: 5.59 secs
## Working: 40.00%. Estimated remaining time: 6.79 secs
## Working: 60.00%. Estimated remaining time: 4.82 secs
## Working: 80.00%. Estimated remaining time: 2.41 secs
## Working: 100.00%. Estimated remaining time: 0.00 secs
## $inc_slope1

## 
## $inc_slope2

## 
## $dec_slope

## 
## $inc_slope1

## 
## $inc_slope2

## 
## $dec_slope

## 
## $criterion

## 
## [[1]]

## 
## [[2]]

## 
## [[3]]

## 
## 
## List of observed variables used: lai 
## 
## Estimated value for inc_slope1 :  25 
## 
## Estimated value for inc_slope2 :  50 
## 
## Estimated value for dec_slope :  9.9 
## Minimum value of the criterion: 0.0079 
## Complementary graphs and results can be found in  /Users/runner/work/CroptimizR/CroptimizR/vignettes 
## 
## Average time for the model to simulate all required situations: 0.014 sec elapsed
## Total number of criterion evaluation: 425 
## Total time of model simulations: 6 sec elapsed
## Total time of parameter estimation process: 15 sec elapsed
## ----------------------

res$final_values

## inc_slope1 inc_slope2  dec_slope 
##  25.065216  49.949588   9.907467

# Plot the simulations obtained with the optimized values of the parameters VS
# the observed ones using the CroPlotR package.
if (!require("CroPlotR")) {
  devtools::install_github("SticsRPacks/CroPlotR@*release")
  library("CroPlotR")
}
tmp <- laitm_simple_wrapper_v2(
  situation = c("2005_a", "2006_b"),
  param_values = dplyr::tibble(
    situation = c("2005_a", "2006_b"),
    inc_slope = c(
      res$final_values[["inc_slope1"]],
      res$final_values[["inc_slope2"]]
    ),
    dec_slope = res$final_values[["dec_slope"]]
  )
)
plot(tmp$sim_list, obs = obs_synth, type = "scatter")

## $all_situations

Other examples

More complex examples of crop model wrappers for CroptimizR can be found in the SticsOnR and ApsimOnR packages for the Stics and Apsim models.