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1. Introduction


The metrica package was developed to assess the prediction performance of, among other, crop simulation models such as APSIM.

This vignette introduces the functionality of the metrica package applied to facilitate opening APSIM output files in R.

Import data from APSIM


1. APSIM Classic (.out)

# Use import_apsim_out for APSIM Classic output
soybean.out <- metrica::import_apsim_out(filepath = "../tests/testthat/examples/soybean.out")

head(soybean.out)
#>   Date (dd/mm/yyyy) yield (kg/ha) biomass (kg/ha) grain_protein (%)
#> 1        16/05/2001        1449.8          2915.9            37.115
#> 2        10/05/2002        1092.5          2965.1            37.115
#> 3        23/04/2003        1368.9          3529.6            37.115
#> 4        26/04/2004        2121.6          4710.3            37.115
#> 5        09/05/2005        1950.3          4303.9            37.115
#> 6        20/04/2006        1670.6          3806.6            37.115
#>   GrainN (g/m^2) lai (m^2/m^2) oilGrainN (g/m^2) grain_oil_conc (%)
#> 1           0.00             0                 0                0.4
#> 2           7.10             0                 0                0.4
#> 3           8.90             0                 0                0.4
#> 4          13.79             0                 0                0.4
#> 5          12.68             0                 0                0.4
#> 6          10.86             0                 0                0.4

1. APSIM NextGeneration (.db)

# Use import_apsim_db for APSIM NextGeneration output
soybean.db <- metrica::import_apsim_db(filename = "soybean.example.db", folder = "../tests/testthat/examples/")

head(soybean.db)
#>   CheckpointID SimulationID    Zone         Clock.Today Soybean.Phenology.Stage
#> 1            1            1 paddock 2018-01-01 12:00:00                       1
#> 2            1            1 paddock 2018-01-02 12:00:00                       1
#> 3            1            1 paddock 2018-01-03 12:00:00                       1
#> 4            1            1 paddock 2018-01-04 12:00:00                       1
#> 5            1            1 paddock 2018-01-05 12:00:00                       1
#> 6            1            1 paddock 2018-01-06 12:00:00                       1
#>   Soybean.Phenology.CurrentStageName Soybean.AboveGround.Wt Yield
#> 1                                                         0     0
#> 2                                                         0     0
#> 3                                                         0     0
#> 4                                                         0     0
#> 5                                                         0     0
#> 6                                                         0     0
#>   Soybean.Grain.Size Soybean.Grain.Number Soybean.Total.Wt Soybean.Leaf.FRGR
#> 1                  0                    0                0                 0
#> 2                  0                    0                0                 0
#> 3                  0                    0                0                 0
#> 4                  0                    0                0                 0
#> 5                  0                    0                0                 0
#> 6                  0                    0                0                 0
#>   Soybean.Leaf.Fw Soybean.Leaf.Photosynthesis.FT Soybean.Leaf.Photosynthesis.FW
#> 1               1                              0                              1
#> 2               1                              0                              1
#> 3               1                              0                              1
#> 4               1                              0                              1
#> 5               1                              0                              1
#> 6               1                              0                              1
#>   Soybean.WaterUptake(1) Soybean.WaterUptake(2) Soybean.WaterUptake(3)
#> 1                     NA                     NA                     NA
#> 2                     NA                     NA                     NA
#> 3                     NA                     NA                     NA
#> 4                     NA                     NA                     NA
#> 5                     NA                     NA                     NA
#> 6                     NA                     NA                     NA
#>   Soybean.WaterUptake(4) Soybean.WaterUptake(5) Soybean.WaterUptake(6)
#> 1                     NA                     NA                     NA
#> 2                     NA                     NA                     NA
#> 3                     NA                     NA                     NA
#> 4                     NA                     NA                     NA
#> 5                     NA                     NA                     NA
#> 6                     NA                     NA                     NA
#>   Soybean.WaterUptake(7) Soybean.WaterUptake(8) Soybean.WaterUptake(9)
#> 1                     NA                     NA                     NA
#> 2                     NA                     NA                     NA
#> 3                     NA                     NA                     NA
#> 4                     NA                     NA                     NA
#> 5                     NA                     NA                     NA
#> 6                     NA                     NA                     NA
#>   Soybean.WaterUptake(10)       Date
#> 1                      NA 2018-01-01
#> 2                      NA 2018-01-02
#> 3                      NA 2018-01-03
#> 4                      NA 2018-01-04
#> 5                      NA 2018-01-05
#> 6                      NA 2018-01-06

# If observed.data is already as a dataframe, the user may do the match using a simple code like this:
# PO.dataframe <- simulated.data %>% left_join(., observed.data) *by = "col" arg. could be required*