compare_apsim: Compare two or more apsim output objects

In femiguez/apsimx: Inspect, Read, Edit and Run 'APSIM' "Next Generation" and 'APSIM' Classic

Compare two or more apsim output objects

Description

Function which allows for a simple comparison between APSIM output objects

print method for ‘out_mrg’

plotting function for compare_apsim, it requires ggplot2

Usage

compare_apsim(
  ...,
  variable,
  index = "Date",
  by,
  labels,
  cRSS = FALSE,
  weights,
  verbose = FALSE
)

## S3 method for class 'out_mrg'
print(x, ..., digits = 2)

## S3 method for class 'out_mrg'
plot(
  x,
  ...,
  plot.type = c("vs", "diff", "resid", "ts", "density"),
  pairs = c(1, 2),
  cumulative = FALSE,
  variable,
  id,
  id.label,
  by,
  facet = FALSE,
  span = 0.75,
  dodge.width = NULL
)

Arguments

...	data frames with APSIM output or observed data.
variable	variable to plot
index	index for merging objects. Default is ‘Date’
by	variable in ‘index’ used for plotting
labels	labels for plotting and identification of objects.
cRSS	compute (weighted) combined residual sum of squares using some or all variables
weights	optional weights for computing the (weighted) combined sum of squares
verbose	whether to print indexes to console (default is FALSE).
x	object of class ‘out_mrg’
digits	digits to print (default is 2)
plot.type	either ‘vs’, ‘diff’, ‘ts’ - for time series or ‘density’
pairs	pair of objects to compare, defaults to 1 and 2 but others are possible
cumulative	whether to plot cumulative values (default FALSE)
id	identification. Useful for finding extreme values. If this values is equal to 1 and no id.label is provided all observations are labeled by the row number. If it is less than one points are labeled if their probability is equal or less than the id value. For example, a value of 0.05 will label values that have a probability of 0.05 (or less) under a normal distribution.
id.label	optional label for the id
facet	whether to facet or use color for the by variable (default is FALSE, meaning ‘color’)
span	argument passed to ‘geom_smooth’
dodge.width	optional argument to control the ‘dodge’ for the ‘id.label’

Details

There are different metrics with different interpretations produced by this function. Many of them take one object (assuming that is the observed data) and another object (assuming that is the simulated or predicted) object. Some of these metrics are a result from the regression.

- metrics that do not rely on regression (obs vs. pred): bias, mean bias, rss, rmse, corr, concorr, mod.eff

- metrics that do depend on a regression model (Reg): intercept, slope, rsigma, R2. In this case, a simple linear regression is first adjusted to the two variables and the parameters and statistics are derived from that model.

‘rsigma’ is the regression residual standard deviation obtained by using the function sigma to the regression object.

Plotting function for observed and simulated data

Value

object of class ‘out_mrg’, which can be used for further plotting

it prints the index.table data.frame

it produces a plot

Note

‘Con Corr’ is the concordance correlation coefficient (https://en.wikipedia.org/wiki/Concordance_correlation_coefficient); ‘ME’ is the model efficiency (https://en.wikipedia.org/wiki/Nash-Sutcliffe_model_efficiency_coefficient)

Examples

## Directory with files
extd.dir <- system.file("extdata", package = "apsimx")
## Comparing observed and simulated for Wheat
data(obsWheat)
sim.opt <- read.csv(file.path(extd.dir, "wheat-sim-opt.csv"))
sim.opt$Date <- as.Date(sim.opt$Date)

cap <- compare_apsim(obsWheat, sim.opt, labels = c("obs", "sim"))

plot(cap)
plot(cap, plot.type = "diff")
plot(cap, plot.type = "resid")
plot(cap, plot.type = "ts")

plot(cap, variable = "AboveGround")
plot(cap, variable = "AboveGround", plot.type = "diff")
plot(cap, variable = "AboveGround", plot.type = "ts")

## Selecting a variable
cap <- compare_apsim(obsWheat, sim.opt, variable = "AboveGround", 
                     labels = c("obs", "sim"))
                     
## Using id
plot(cap, variable = "AboveGround", id = 0.05)
                     

femiguez/apsimx documentation built on June 11, 2025, 5:36 a.m.