CroPlotR

CroPlotR standardizes the analysis and visualization of crop model outputs, including models such as STICS, APSIM, and others.

The package works seamlessly with models wrapped using the CroptimizR package through the cropr_simulation data format (see section Data structure).

Stay updated: To receive notifications about new releases, click “Watch” → “Custom” → “Releases” at the top of this repository.

1. Installation

Install the latest release from GitHub using either devtools or remotes:

Using remotes (recommended):

# install.packages("remotes")
remotes::install_github("SticsRPacks/CroPlotR@*release")

Using devtools:

devtools::install_github("SticsRPacks/CroPlotR@*release")

2. Introduction

Core Functions

CroPlotR provides two main functions:

plot() (alias: autoplot()) for creating visualizations
summary() for computing statistical metrics

These functions cover most visualization and analysis needs. Additional helper functions are available for data manipulation (see section Data manipulation).

Using CroPlotR with Model Wrappers

If you’re using a model wrapper from the CroptimizR package, you can simply extract the simulations with: sim <- result$sim_list, where result is the object returned by the model wrapper. For detailed examples with STICS and APSIM, visit CroptimizR’s documentation (Articles tab).

Example Data

The following examples use simulation and observation data from the STICS crop model:

Sole crops (objects sim and obs):

Pea in sole crop (situation: SC_Pea_2005-2006_N0)
Wheat in sole crop (situation: SC_Wheat_2005-2006_N0)

Intercrop (sim_intercrop and obs_intercrop):

Wheat and Pea intercrop (situation: IC_Wheat_Pea_2005-2006_N0)

Click to view code for loading example data

library(CroPlotR)
#> Registered S3 method overwritten by 'CroPlotR':
#>   method             from       
#>   [.cropr_simulation SticsRFiles
#> Learn CroPlotR at: https://SticsRPacks.github.io/CroPlotR
#> 
#> Please cite CroPlotR in your work:
#> Vezy R, Buis S, Midingoyi C, Lecharpentier P, Giner M (2025).
#> CroPlotR: A Package to Analyze Crop Model Simulations Outputs with
#> Plots and Statistics. R package version 0.11.0,
#> https://doi.org/10.5281/zenodo.4442330,
#> <https://github.com/SticsRPacks/CroPlotR>.
rdata_path <- system.file(file.path("extdata", "readme_sim_obs_example.RData"), package = "CroPlotR")
load(rdata_path)

3. Dynamic Plots

Dynamic plots show variable values over time, making them ideal for visualizing temporal patterns in crop model outputs.

3.1. Simple Dynamic Plot

Create basic time-series plots for all variables and situations simulated (in this example, three variables, lai_n, masec_n and mafruit, and two situations, SC_Pea_2005-2006_N0 and SC_Wheat_2005-2006_N0):

plot(sim)
#> $`SC_Pea_2005-2006_N0`

#> 
#> $`SC_Wheat_2005-2006_N0`

3.2. Adding Observations

Overlay observed data on simulated outputs using the obs argument:

plots <- plot(sim, obs = obs)
# Only displaying the first situation for this one:
plots[[1]]

Note: The obs argument must be explicitly named.

3.3. Filtering Variables

By default, all variables are plotted. Use var to select specific variables:

plots <- plot(sim, obs = obs, var = c("lai_n"))
# Only displaying the first situation for this one:
plots[[1]]

3.4. Successive Situations

Combine multiple sequential situations (e.g., crop rotations) into a single continuous timeline using the successive parameter:

plot(
  sim_rot,
  var = c("resmes", "masec_n"),
  successive = list(list("demo_Wheat1", "demo_BareSoil2", "demo_maize3"))
)
#> $`demo_Wheat1 | demo_BareSoil2 | demo_maize3 | `

3.5. Overlaying Variables

Plot multiple variables on the same graph using the overlap parameter:

plots <- plot(sim, obs = obs, overlap = list(list("lai_n", "masec_n")))
# Only displaying the first situation for this one:
plots[[1]]

Note: Automatic variable scaling is not yet available (see issue). To scale variables, transform your data before plotting and add a secondary axis using sec_axis().

4. Scatter Plots

Scatter plots compare simulated versus observed values, providing visual assessment of model performance.

4.1. Simple Scatter Plot

Create observed vs. simulated scatter plots by setting type = "scatter":

plots <- plot(sim, obs = obs, type = "scatter", all_situations = FALSE)
# Only displaying the first situation for this one:
plots[[1]]

4.2. Plotting Residuals

Visualize model residuals (observed - simulated values) using select_scat = "res":

plots <- plot(
  sim,
  obs = obs,
  type = "scatter",
  select_scat = "res",
  all_situations = FALSE
)
# Only displaying the first situation again, but this time using its name:
plots$`SC_Pea_2005-2006_N0`

4.3. Grouping Situations

Combine data from all situations in a single plot using all_situations = TRUE:

plot(sim, obs = obs, type = "scatter", all_situations = TRUE)
#> $all_situations

4.4. Reference Variable on the X-axis

Use reference_var to specify which variable appears on the x-axis. Suffix the variable name with _obs, _sim or _res to choose observed, simulated or residual values:

plot(
  sim,
  obs = obs,
  type = "scatter",
  select_scat = "res",
  all_situations = TRUE,
  reference_var = "lai_n_sim"
)
#> $all_situations

4.5. Distinguishing Situations with Shapes

When plotting multiple situations together (all_situations = TRUE), differentiate them using the shape_sit parameter.

Display situation names as text labels:

plot(
  sim,
  obs = obs,
  type = "scatter",
  all_situations = TRUE,
  shape_sit = "txt"
)
#> $all_situations

Text labels can become cluttered with many data points. Use distinct symbols instead:

plot(
  sim,
  obs = obs,
  type = "scatter",
  all_situations = TRUE,
  shape_sit = "symbol"
)
#> $all_situations

Group multiple situations under a single symbol (e.g., for identified clusters):

plot(
  sim,
  obs = obs,
  type = "scatter",
  all_situations = TRUE,
  shape_sit = "group",
  situation_group = list(list("SC_Pea_2005-2006_N0", "SC_Wheat_2005-2006_N0"))
)
#> $all_situations

Customize legend labels by naming your situation_group list:

plot(
  sim,
  obs = obs,
  type = "scatter",
  all_situations = TRUE,
  shape_sit = "group",
  situation_group = list(
    "Two Single Crops" = list("SC_Pea_2005-2006_N0", "SC_Wheat_2005-2006_N0")
  )
)
#> $all_situations

5. Comparing Model Versions

Compare different model versions or parameter sets by passing multiple simulation objects to plot(). This is why the obs argument must be explicitly named.

Dynamic Plot Comparison

plots <- plot(sim, sim2, obs = obs, all_situations = FALSE)
# Only displaying the first situation for this one:
plots[[1]]

Naming Model Versions

Provide descriptive names for each simulation group:

plots <- plot(
  original = sim,
  "New version" = sim2,
  obs = obs
)
# Only displaying the first situation for this one:
plots[[1]]

Scatter Plot Comparison

Model versions can also be compared using scatter plots:

plots <- plot(
  original = sim,
  "New version" = sim2,
  obs = obs,
  type = "scatter",
  all_situations = FALSE
)
# Only displaying the first situation for this one:
plots[[1]]

6. Error Bars

Add uncertainty estimates to observations using the obs_sd parameter, which must have the same structure as obs. Error bars are then displayed as ±2 standard deviations, corresponding to an approximate 95% confidence interval under the assumption of Gaussian observation errors.

plot(sim, obs = obs, obs_sd = obs_sd, type = "scatter", all_situations = TRUE)
#> $all_situations

7. Intercrops

CroPlotR automatically handles simulations of intercrop situations where multiple plant species are grown together.

Dynamic Plots for Intercrops

plot(sim_intercrop, obs = obs_intercrop)
#> $`IC_Wheat_Pea_2005-2006_N0`

Scatter Plots for Intercrops

plot(sim_intercrop, obs = obs_intercrop, type = "scatter", all_situations = TRUE)
#> $all_situations

8. Saving Plots

Save as PNG

Export individual plots as PNG files using save_plot_png():

plots <- plot("New version" = sim, original = sim2, obs = obs, type = "scatter")

save_plot_png(plot = plots, out_dir = "path/to/directory", suffix = "_scatter")

# or by piping:
plots <- plot(
  "New version" = sim,
  original = sim2,
  obs = obs,
  type = "scatter"
) %>%
  save_plot_png(., out_dir = "path/to/directory", suffix = "_scatter")

Save as PDF

Export plots to PDF using save_plot_pdf(). Set file_per_var = TRUE to create separate PDFs for each variable:

plots <- plot(sim, obs = obs)

save_plot_pdf(plot = plots, out_dir = "path/to/directory", file_per_var = FALSE)

9. Extracting Individual Plots

The plot() function returns a named list of ggplot objects, where names correspond to situations:

p <- plot(sim)

names(p)
#> [1] "SC_Pea_2005-2006_N0"   "SC_Wheat_2005-2006_N0"

Access by Name

Access individual plots using their situation name (use backticks if the name contains special characters):

p$`SC_Wheat_2005-2006_N0`

Access by Index

Alternatively, use numeric indexing:

p[[1]]

Filtering Plots

Use extract_plot() to filter plots by situation and/or variable. This is useful when working with many situations and variables.

Example: Extract only the wheat situation and the masec_n variable:

plots <- plot(sim, obs = obs, type = "scatter", all_situations = FALSE)

extract_plot(
  plots,
  situation = c("SC_Wheat_2005-2006_N0"), var = c("masec_n")
)
#> $`SC_Wheat_2005-2006_N0`

10. Statistics

Compute performance metrics to quantitatively compare simulated and observed values.

10.1. Basic Usage

Calculate statistics for each situation individually:

summary(sim, obs = obs, all_situations = FALSE)

group	situation	variable	n_obs	mean_obs	mean_sim	r_means	sd_obs	sd_sim	CV_obs	CV_sim	R2	SS_res	Inter	Slope	RMSE	RMSEs	RMSEu	nRMSE	rRMSE	rRMSEs	rRMSEu	pMSEs	pMSEu	Bias2	SDSD	LCS	rbias2	rSDSD	rLCS	MAE	FVU	MSE	EF	Bias	ABS	MAPE	RME	tSTUD	tLimit	Decision
Version_1	SC_Pea_2005-2006_N0	lai_n	3	2.622222	1.738637	66.30394	1.5135732	1.3463799	57.72101	77.43883	0.6945994	3.7558828	-0.2053841	0.7413638	1.1189106	0.9396204	0.6075149	42.670319	0.4267032	0.3583298	0.2316794	0.7052029	0.2947971	0.7807234	0.0279536	0.6789027	0.1135424	0.0040654	0.0987344	0.8835856	0.3085491	1.2519609	0.1802618	-0.8835856	0.8835856	0.3901011	-0.3901011	-1.8203030	4.302653	OK
Version_1	SC_Pea_2005-2006_N0	mafruit	1	4.355000	4.742713	108.90270	NA	NA	NA	NA	0.0000000	0.1503211	4.7427127	NA	0.3877127	0.3877127	0.0000000	8.902703	0.0890270	0.0890270	0.0000000	1.0000000	0.0000000	0.1503211	NA	NA	0.0079258	NA	NA	0.3877127	NA	0.1503211	-Inf	0.3877127	0.3877127	0.0890270	0.0890270	NA	NaN	Insufficient size
Version_1	SC_Pea_2005-2006_N0	masec_n	4	5.451667	4.382542	80.38904	3.7848396	3.7494028	69.42537	85.55314	0.8907017	9.3636018	-0.7144037	0.9349336	1.5300001	1.0901888	1.0734937	28.064815	0.2806481	0.1999735	0.1969111	0.5077156	0.4922844	1.1430265	0.0012558	1.5959095	0.0384590	0.0000423	0.0536970	1.1660625	0.1114949	2.3409005	0.7821153	-1.0691242	1.1660625	0.3308096	-0.3198354	-1.6919332	3.182446	OK
Version_1	SC_Wheat_2005-2006_N0	lai_n	3	1.273333	1.402287	110.12723	0.4396684	0.6236645	34.52893	44.47482	0.0098002	1.1058377	1.2234797	0.1404243	0.6071347	0.3344381	0.5067186	47.680736	0.4768074	0.2626477	0.3979465	0.3034319	0.6965681	0.0166290	0.0338546	0.4941208	0.0102561	0.0208801	0.3047537	0.5115933	2.7312604	0.3686126	-1.8602948	0.1289533	0.5115933	0.4881989	0.1825306	0.3073876	4.302653	OK
Version_1	SC_Wheat_2005-2006_N0	mafruit	1	3.825000	5.675395	148.37634	NA	NA	NA	NA	0.0000000	3.4239617	5.6753950	NA	1.8503950	1.8503950	0.0000000	48.376340	0.4837634	0.4837634	0.0000000	1.0000000	0.0000000	3.4239617	NA	NA	0.2340270	NA	NA	1.8503950	NA	3.4239617	-Inf	1.8503950	1.8503950	0.4837634	0.4837634	NA	NaN	Insufficient size
Version_1	SC_Wheat_2005-2006_N0	masec_n	4	5.393750	6.015903	111.53469	3.1594630	3.9552603	58.57637	65.74675	0.9637756	4.8187352	-0.6129841	1.2289940	1.0975809	0.8829841	0.6519378	20.349124	0.2034912	0.1637050	0.1208691	0.6471914	0.3528086	0.3870737	0.6332935	0.4568533	0.0133049	0.0217682	0.0157035	0.6221525	0.1092090	1.2046838	0.8390892	0.6221525	0.6221525	0.0866369	0.0866369	1.1917478	3.182446	OK

Note: The obs argument must be explicitly named (same reason as for plot()).

Aggregated Statistics

Compute statistics across all situations simultaneously:

summary(sim, obs = obs, all_situations = TRUE)

group	situation	variable	n_obs	mean_obs	mean_sim	r_means	sd_obs	sd_sim	CV_obs	CV_sim	R2	SS_res	Inter	Slope	RMSE	RMSEs	RMSEu	nRMSE	rRMSE	rRMSEs	rRMSEu	pMSEs	pMSEu	Bias2	SDSD	LCS	rbias2	rSDSD	rLCS	MAE	FVU	MSE	EF	Bias	ABS	MAPE	RME	tSTUD	tLimit	Decision
Version_1	all_situations	lai_n	6	1.947778	1.570462	80.62838	1.2407801	0.9563566	63.702343	60.89653	0.4849226	4.861720	0.5250179	0.5367367	0.9001593	0.6463004	0.6265641	46.21468	0.4621468	0.3318142	0.3216815	0.5155017	0.4844983	0.1423674	0.0808967	0.7206064	0.0375260	0.0213232	0.1899413	0.6975894	0.5206137	0.8102867	0.3684171	-0.3773161	0.6975894	0.4391500	-0.1037853	-1.0323533	2.570582	OK
Version_1	all_situations	mafruit	2	4.090000	5.209054	127.36073	0.3747666	0.6595060	9.162997	12.66076	1.0000000	3.574283	12.4065456	-1.7597779	1.3368401	1.3368401	0.0000000	32.68558	0.3268558	0.3268558	0.0000000	1.0000000	0.0000000	1.2522815	0.0810765	0.9886432	0.0748610	0.0048467	0.0591007	1.1190538	7.6163742	1.7871414	-24.4487917	1.1190538	1.1190538	0.2863952	0.2863952	1.5301393	12.706205	OK
Version_1	all_situations	masec_n	8	5.422708	5.199223	95.87870	3.2277449	3.6731078	59.522746	70.64725	0.8562305	14.182337	-0.5109084	1.0530035	1.3314624	0.2748750	1.3027800	24.55346	0.2455346	0.0506896	0.2402453	0.0426199	0.9573801	0.0499459	0.1983481	1.7706190	0.0016985	0.0067452	0.0602133	0.8941075	0.1889905	1.7727921	0.8055306	-0.2234858	0.8941075	0.2087232	-0.1165992	-0.4504803	2.364624	OK

10.2. Comparing Multiple Groups

Compute statistics for multiple simulation groups (e.g., different model versions or parameter sets):

summary(sim, sim2, obs = obs)

group	situation	variable	n_obs	mean_obs	mean_sim	r_means	sd_obs	sd_sim	CV_obs	CV_sim	R2	SS_res	Inter	Slope	RMSE	RMSEs	RMSEu	nRMSE	rRMSE	rRMSEs	rRMSEu	pMSEs	pMSEu	Bias2	SDSD	LCS	rbias2	rSDSD	rLCS	MAE	FVU	MSE	EF	Bias	ABS	MAPE	RME	tSTUD	tLimit	Decision
Version_1	all_situations	lai_n	6	1.947778	1.570462	80.62838	1.2407801	0.9563566	63.702343	60.89653	0.4849226	4.861720	0.5250179	0.5367367	0.9001593	0.6463004	0.6265641	46.21468	0.4621468	0.3318142	0.3216815	0.5155017	0.4844983	0.1423674	0.0808967	0.7206064	0.0375260	0.0213232	0.1899413	0.6975894	0.5206137	0.8102867	0.3684171	-0.3773161	0.6975894	0.4391500	-0.1037853	-1.0323533	2.570582	OK
Version_1	all_situations	mafruit	2	4.090000	5.209054	127.36073	0.3747666	0.6595060	9.162997	12.66076	1.0000000	3.574283	12.4065456	-1.7597779	1.3368401	1.3368401	0.0000000	32.68558	0.3268558	0.3268558	0.0000000	1.0000000	0.0000000	1.2522815	0.0810765	0.9886432	0.0748610	0.0048467	0.0591007	1.1190538	7.6163742	1.7871414	-24.4487917	1.1190538	1.1190538	0.2863952	0.2863952	1.5301393	12.706205	OK
Version_1	all_situations	masec_n	8	5.422708	5.199223	95.87870	3.2277449	3.6731078	59.522746	70.64725	0.8562305	14.182337	-0.5109084	1.0530035	1.3314624	0.2748750	1.3027800	24.55346	0.2455346	0.0506896	0.2402453	0.0426199	0.9573801	0.0499459	0.1983481	1.7706190	0.0016985	0.0067452	0.0602133	0.8941075	0.1889905	1.7727921	0.8055306	-0.2234858	0.8941075	0.2087232	-0.1165992	-0.4504803	2.364624	OK
Version_2	all_situations	lai_n	6	1.947778	1.727508	88.69122	1.2407801	1.0519922	63.702343	60.89653	0.4849226	4.432653	0.5775197	0.5904103	0.8595205	0.5135666	0.6892205	44.12826	0.4412826	0.2636679	0.3538496	0.3570105	0.6429895	0.0485188	0.0356408	0.7926671	0.0127889	0.0093944	0.2089354	0.6060845	0.5380247	0.7387754	0.4241570	-0.2202699	0.6060845	0.4168965	-0.0141638	-0.5928365	2.570582	OK
Version_2	all_situations	mafruit	2	4.090000	5.729959	140.09680	0.3747666	0.7254566	9.162997	12.66076	1.0000000	6.589424	13.6472001	-1.9357557	1.8151341	1.8151341	0.0000000	44.37981	0.4437981	0.4437981	0.0000000	1.0000000	0.0000000	2.6894663	0.1229835	1.0875076	0.1607754	0.0073519	0.0650108	1.6399592	8.6186616	3.2947118	-45.9165084	1.6399592	1.6399592	0.4150347	0.4150347	2.1079838	12.706205	OK
Version_2	all_situations	masec_n	8	5.422708	5.719145	105.46658	3.2277449	4.0404186	59.522746	70.64725	0.8562305	18.959832	-0.5619992	1.1583039	1.5394736	0.5624266	1.4330581	28.38939	0.2838939	0.1037169	0.2642698	0.1334711	0.8665289	0.0878745	0.6604385	1.9476809	0.0029883	0.0224595	0.0662347	1.2014558	0.2503393	2.3699790	0.7400211	0.2964364	1.2014558	0.2545956	-0.0282592	0.5191739	2.364624	OK

Provide descriptive names for clarity:

summary("New version" = sim, original = sim2, obs = obs)

group	situation	variable	n_obs	mean_obs	mean_sim	r_means	sd_obs	sd_sim	CV_obs	CV_sim	R2	SS_res	Inter	Slope	RMSE	RMSEs	RMSEu	nRMSE	rRMSE	rRMSEs	rRMSEu	pMSEs	pMSEu	Bias2	SDSD	LCS	rbias2	rSDSD	rLCS	MAE	FVU	MSE	EF	Bias	ABS	MAPE	RME	tSTUD	tLimit	Decision
New version	all_situations	lai_n	6	1.947778	1.570462	80.62838	1.2407801	0.9563566	63.702343	60.89653	0.4849226	4.861720	0.5250179	0.5367367	0.9001593	0.6463004	0.6265641	46.21468	0.4621468	0.3318142	0.3216815	0.5155017	0.4844983	0.1423674	0.0808967	0.7206064	0.0375260	0.0213232	0.1899413	0.6975894	0.5206137	0.8102867	0.3684171	-0.3773161	0.6975894	0.4391500	-0.1037853	-1.0323533	2.570582	OK
New version	all_situations	mafruit	2	4.090000	5.209054	127.36073	0.3747666	0.6595060	9.162997	12.66076	1.0000000	3.574283	12.4065456	-1.7597779	1.3368401	1.3368401	0.0000000	32.68558	0.3268558	0.3268558	0.0000000	1.0000000	0.0000000	1.2522815	0.0810765	0.9886432	0.0748610	0.0048467	0.0591007	1.1190538	7.6163742	1.7871414	-24.4487917	1.1190538	1.1190538	0.2863952	0.2863952	1.5301393	12.706205	OK
New version	all_situations	masec_n	8	5.422708	5.199223	95.87870	3.2277449	3.6731078	59.522746	70.64725	0.8562305	14.182337	-0.5109084	1.0530035	1.3314624	0.2748750	1.3027800	24.55346	0.2455346	0.0506896	0.2402453	0.0426199	0.9573801	0.0499459	0.1983481	1.7706190	0.0016985	0.0067452	0.0602133	0.8941075	0.1889905	1.7727921	0.8055306	-0.2234858	0.8941075	0.2087232	-0.1165992	-0.4504803	2.364624	OK
original	all_situations	lai_n	6	1.947778	1.727508	88.69122	1.2407801	1.0519922	63.702343	60.89653	0.4849226	4.432653	0.5775197	0.5904103	0.8595205	0.5135666	0.6892205	44.12826	0.4412826	0.2636679	0.3538496	0.3570105	0.6429895	0.0485188	0.0356408	0.7926671	0.0127889	0.0093944	0.2089354	0.6060845	0.5380247	0.7387754	0.4241570	-0.2202699	0.6060845	0.4168965	-0.0141638	-0.5928365	2.570582	OK
original	all_situations	mafruit	2	4.090000	5.729959	140.09680	0.3747666	0.7254566	9.162997	12.66076	1.0000000	6.589424	13.6472001	-1.9357557	1.8151341	1.8151341	0.0000000	44.37981	0.4437981	0.4437981	0.0000000	1.0000000	0.0000000	2.6894663	0.1229835	1.0875076	0.1607754	0.0073519	0.0650108	1.6399592	8.6186616	3.2947118	-45.9165084	1.6399592	1.6399592	0.4150347	0.4150347	2.1079838	12.706205	OK
original	all_situations	masec_n	8	5.422708	5.719145	105.46658	3.2277449	4.0404186	59.522746	70.64725	0.8562305	18.959832	-0.5619992	1.1583039	1.5394736	0.5624266	1.4330581	28.38939	0.2838939	0.1037169	0.2642698	0.1334711	0.8665289	0.0878745	0.6604385	1.9476809	0.0029883	0.0224595	0.0662347	1.2014558	0.2503393	2.3699790	0.7400211	0.2964364	1.2014558	0.2545956	-0.0282592	0.5191739	2.364624	OK

Selecting Specific Statistics

By default, all available statistics are computed. Use the stats argument to select specific metrics:

summary(
  "New version" = sim, original = sim2, obs = obs,
  stats = c("R2", "nRMSE")
)

group	situation	variable	R2	nRMSE
New version	all_situations	lai_n	0.4849226	46.21468
New version	all_situations	mafruit	1.0000000	32.68558
New version	all_situations	masec_n	0.8562305	24.55346
original	all_situations	lai_n	0.4849226	44.12826
original	all_situations	mafruit	1.0000000	44.37981
original	all_situations	masec_n	0.8562305	28.38939

For more details about the list of available statistical criterion and their definition, please read the help from predictor_assessment().

10.3. Visualizing Statistics

Plot statistical metrics for visual comparison using plot() on the summary output.

Separate plots per situation (all_situations = FALSE):

stats <- summary(
  "New version" = sim,
  original = sim2,
  obs = obs,
  stats = c("R2", "nRMSE"),
  all_situations = FALSE
)
plot(stats)

Combined plot for all situations (all_situations = TRUE):

stats <- summary(
  "New version" = sim,
  original = sim2,
  obs = obs,
  stats = c("R2", "nRMSE"),
  all_situations = TRUE
)

plot(stats)

Customizing Plot Layout

Control which variable appears on the x-axis using the xvar parameter. The other variable is used for grouping and color coding:

stats <- summary(
  "New version" = sim,
  original = sim2,
  obs = obs,
  stats = c("R2", "nRMSE"),
  all_situations = FALSE
)

plot(stats, xvar = "situation", title = "Situation in X")

Bar Chart Layouts

Stacked bars (group_bar = "stack"):

stats <- summary(
  "New version" = sim,
  original = sim2,
  obs = obs,
  stats = c("pMSEs", "pMSEu"),
  all_situations = FALSE
)

plot(stats, xvar = "situation", title = "Stacked columns", group_bar = "stack")

Side-by-side bars (group_bar = "dodge"):

stats <- summary(
  "New version" = sim,
  original = sim2,
  obs = obs,
  stats = c("pMSEs", "pMSEu"),
  all_situations = FALSE
)

plot(
  stats,
  xvar = "situation",
  title = "Side-by-side columns",
  group_bar = "dodge"
)

Radar Charts

Compare model versions across multiple variables using a radar chart (type = "radar") for a single metric:

stats <- summary(
  "New version" = sim,
  original = sim2,
  obs = obs,
  stats = c("nRMSE"),
  all_situations = TRUE
)

plot(
  stats,
  type = "radar",
  crit_radar = "nRMSE",
  title = "Radar chart : nRMSE"
)

11. Data Manipulation

Working with Standard R Packages

Observation data can be easily manipulated using packages like dplyr, tidyr, or tibble.

However, the cropr_simulation attribute on simulated data can interfere with some operations. CroPlotR provides two helper functions to facilitate data manipulation:

Converting to Data Frame

Use bind_rows() to combine all situations into a single data frame:

df <- bind_rows(sim)
head(df)
#>             situation       Date lai_n masec_n mafruit Plant
#> 1 SC_Pea_2005-2006_N0 2005-09-26     0       0       0   poi
#> 2 SC_Pea_2005-2006_N0 2005-09-27     0       0       0   poi
#> 3 SC_Pea_2005-2006_N0 2005-09-28     0       0       0   poi
#> 4 SC_Pea_2005-2006_N0 2005-09-29     0       0       0   poi
#> 5 SC_Pea_2005-2006_N0 2005-09-30     0       0       0   poi
#> 6 SC_Pea_2005-2006_N0 2005-10-01     0       0       0   poi

The situation column identifies the source situation for each row. This format is compatible with standard data manipulation packages.

Converting Back to CroPlotR Format

After manipulation, use split_df2sim() to restore the original cropr_simulation structure:

sim_new <- split_df2sim(df)
lapply(sim_new, head)
#> $`SC_Pea_2005-2006_N0`
#>         Date lai_n masec_n mafruit Plant
#> 1 2005-09-26     0       0       0   poi
#> 2 2005-09-27     0       0       0   poi
#> 3 2005-09-28     0       0       0   poi
#> 4 2005-09-29     0       0       0   poi
#> 5 2005-09-30     0       0       0   poi
#> 6 2005-10-01     0       0       0   poi
#> 
#> $`SC_Wheat_2005-2006_N0`
#>         Date lai_n masec_n mafruit Plant
#> 1 2005-09-26     0       0       0   ble
#> 2 2005-09-27     0       0       0   ble
#> 3 2005-09-28     0       0       0   ble
#> 4 2005-09-29     0       0       0   ble
#> 5 2005-09-30     0       0       0   ble
#> 6 2005-10-01     0       0       0   ble

12. Integration with Other Packages

CroPlotR works seamlessly with popular R visualization packages to enhance your plots.

12.1. Interactive Plots with plotly

Convert any ggplot to an interactive visualization using plotly::ggplotly():

library(plotly)

ggplotly(plot(sim, obs = obs, type = "dynamic")[[1]])

12.2. Combining Plots with patchwork

Create complex multi-panel layouts using the patchwork package:

library(patchwork)
#> Warning: le package 'patchwork' a été compilé avec la version R 4.4.3

plot1 <- plot(sim, obs = obs, type = "scatter", var = "lai_n")[[1]]
plot2 <- plot(sim, obs = obs, var = "lai_n")[[1]]
plot3 <- plot(sim, obs = obs, type = "scatter", var = "masec_n")[[1]]
plot4 <- plot(sim, obs = obs, var = "masec_n")[[1]]

plot1 + plot2 + plot3 + plot4 + plot_layout(ncol = 2)

13. Data Structure

Understanding the `cropr_simulation` Format

Both sim and obs objects are named lists of data frames:

List names: Correspond to situation identifiers (e.g., crop-year-management combinations)
Data frames: Store variable values for each situation, with one row per time step and one column per simulated or observed variable. They include a Date column as a time reference (at Date or POSIXct format), and may optionally contain Plant and Dominance columns to indicate crop names and their status (“Principal” or “Associated”) in intercrop datasets.

Simulation Data Structure

lapply(sim, head)
#> $`SC_Pea_2005-2006_N0`
#>         Date lai_n masec_n mafruit Plant
#> 1 2005-09-26     0       0       0   poi
#> 2 2005-09-27     0       0       0   poi
#> 3 2005-09-28     0       0       0   poi
#> 4 2005-09-29     0       0       0   poi
#> 5 2005-09-30     0       0       0   poi
#> 6 2005-10-01     0       0       0   poi
#> 
#> $`SC_Wheat_2005-2006_N0`
#>         Date lai_n masec_n mafruit Plant
#> 1 2005-09-26     0       0       0   ble
#> 2 2005-09-27     0       0       0   ble
#> 3 2005-09-28     0       0       0   ble
#> 4 2005-09-29     0       0       0   ble
#> 5 2005-09-30     0       0       0   ble
#> 6 2005-10-01     0       0       0   ble

Observation Data Structure

Observations follow the same structure:

lapply(obs, head)
#> $`SC_Pea_2005-2006_N0`
#>         Date mafruit   masec_n    lai_n Plant
#> 1 2006-03-29      NA 0.7833333 0.880000   poi
#> 2 2006-04-26      NA 3.9833333 3.613333   poi
#> 3 2006-05-15      NA 8.2066667 3.373333   poi
#> 4 2006-06-13   4.355        NA       NA   poi
#> 5 2006-06-14      NA 8.8333333       NA   poi
#> 
#> $`SC_Wheat_2005-2006_N0`
#>         Date mafruit masec_n lai_n Plant
#> 1 2006-03-29      NA   1.430 1.090   ble
#> 2 2006-04-26      NA   4.405 1.775   ble
#> 3 2006-05-15      NA   7.165 0.955   ble
#> 4 2006-06-14      NA   8.575    NA   ble
#> 5 2006-07-04   3.825      NA    NA   ble

Creating Custom `cropr_simulation` Objects

You can create compatible simulation objects from your own data by adding the cropr_simulation class attribute to a named list of data frames:

sim_test <- list(
  situation_1 = data.frame(
    Date = as.Date("2000-01-01") + 0:9,
    var1 = rnorm(10),
    var2 = rnorm(10)
  ),
  situation_2 = data.frame(
    Date = as.Date("2001-01-01") + 0:9,
    var1 = rnorm(10),
    var2 = rnorm(10)
  )
)

class(sim_test) <- append(class(sim_test), "cropr_simulation")
head(sim_test)
#> $situation_1
#>          Date        var1        var2
#> 1  2000-01-01  0.17851245  0.99830079
#> 2  2000-01-02 -0.18501293 -1.40498186
#> 3  2000-01-03  0.99458587 -2.51209777
#> 4  2000-01-04  1.42358872  1.49718481
#> 5  2000-01-05  0.99588785 -1.15765880
#> 6  2000-01-06  1.80768707 -0.38440228
#> 7  2000-01-07 -1.57172087 -0.06107318
#> 8  2000-01-08  1.03827066 -1.73751647
#> 9  2000-01-09 -0.02226482 -0.31848179
#> 10 2000-01-10  1.44859084  0.63979278
#> 
#> $situation_2
#>          Date       var1        var2
#> 1  2001-01-01  0.7242881 -2.32230396
#> 2  2001-01-02 -1.7797979  0.57906373
#> 3  2001-01-03 -1.1308429  0.84785651
#> 4  2001-01-04  0.5645866 -0.33415060
#> 5  2001-01-05  0.5719987  1.00692496
#> 6  2001-01-06  2.0015839 -0.08801978
#> 7  2001-01-07 -1.1901460 -0.17226188
#> 8  2001-01-08 -1.5696923  0.26070868
#> 9  2001-01-09 -0.2458506  0.25828618
#> 10 2001-01-10  1.5008699 -0.14129121
#> 
#> attr(,"class")
#> [1] "list"             "cropr_simulation"

14. Getting Help

Documentation

Access help for specific functions by specifying the class:

For plotting functions:

?plot.cropr_simulation

?plot.statistics

For statistical functions:

?summary.cropr_simulation

Reporting Issues

If you encounter problems or have suggestions, please open an issue on GitHub.

15. Citation

If CroPlotR contributed to a publication or report, please cite it using the reference corresponding to the version you used. To obtain the correct citation, run citation(“CroPlotR”) in R.

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inst		inst
man		man
tests		tests
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CITATION.cff		CITATION.cff
CroPlotR.Rproj		CroPlotR.Rproj
DESCRIPTION		DESCRIPTION
LICENSE		LICENSE
NAMESPACE		NAMESPACE
NEWS.md		NEWS.md
README.Rmd		README.Rmd
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CroPlotR

Table of Contents

1. Installation

2. Introduction

Core Functions

Using CroPlotR with Model Wrappers

Example Data

3. Dynamic Plots

3.1. Simple Dynamic Plot

3.2. Adding Observations

3.3. Filtering Variables

3.4. Successive Situations

3.5. Overlaying Variables

4. Scatter Plots

4.1. Simple Scatter Plot

4.2. Plotting Residuals

4.3. Grouping Situations

4.4. Reference Variable on the X-axis

4.5. Distinguishing Situations with Shapes

5. Comparing Model Versions

Dynamic Plot Comparison

Naming Model Versions

Scatter Plot Comparison

6. Error Bars

7. Intercrops

Dynamic Plots for Intercrops

Scatter Plots for Intercrops

8. Saving Plots

Save as PNG

Save as PDF

9. Extracting Individual Plots

Access by Name

Access by Index

Filtering Plots

10. Statistics

10.1. Basic Usage

Aggregated Statistics

10.2. Comparing Multiple Groups

Selecting Specific Statistics

10.3. Visualizing Statistics

Customizing Plot Layout

Bar Chart Layouts

Radar Charts

11. Data Manipulation

Working with Standard R Packages

Converting to Data Frame

Converting Back to CroPlotR Format

12. Integration with Other Packages

12.1. Interactive Plots with plotly

12.2. Combining Plots with patchwork

13. Data Structure

Understanding the cropr_simulation Format

Simulation Data Structure

Observation Data Structure

Creating Custom cropr_simulation Objects

14. Getting Help

Documentation

Reporting Issues

15. Citation

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Understanding the `cropr_simulation` Format

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