Using ‘apsimx’
Running a built-in example with ‘apsimx_example’
To get started you can run one of the examples distributed with APSIM-X. This function does the following: it detects where the APSIM examples are located, it runs the example indicated and it returns the ‘report’ as a data.frame. After that you can do the usual manipulations, including visualization.
After we run this example we can treat it as a standard data frame in R.
## CheckpointID SimulationID Zone Clock.Today
## Min. :1 Min. :1 Length:10 Length:10
## 1st Qu.:1 1st Qu.:1 Class :character Class :character
## Median :1 Median :1 Mode :character Mode :character
## Mean :1 Mean :1
## 3rd Qu.:1 3rd Qu.:1
## Max. :1 Max. :1
## Maize.Phenology.CurrentStageName Maize.AboveGround.Wt Maize.AboveGround.N
## Length:10 Min. : 198.5 Min. : 2.103
## Class :character 1st Qu.: 887.8 1st Qu.: 9.149
## Mode :character Median :1347.2 Median :13.543
## Mean :1261.5 Mean :12.749
## 3rd Qu.:1620.2 3rd Qu.:17.056
## Max. :1995.9 Max. :18.327
## Maize.Grain.Wt Maize.Grain.Size Maize.Grain.NumberFunction Maize.Grain.N
## Min. : 70.35 Min. :0.2205 Min. : 232.3 Min. : 0.9447
## 1st Qu.:381.36 1st Qu.:0.2820 1st Qu.:1440.0 1st Qu.: 5.2682
## Median :636.27 Median :0.2926 Median :2220.7 Median : 8.4116
## Mean :585.84 Mean :0.2850 Mean :2058.2 Mean : 7.7509
## 3rd Qu.:836.26 3rd Qu.:0.2988 3rd Qu.:2880.1 3rd Qu.:11.0796
## Max. :885.18 Max. :0.3028 Max. :3058.4 Max. :11.3600
## Maize.Total.Wt Date
## Min. : 221.6 Min. :1991-05-28
## 1st Qu.: 984.6 1st Qu.:1993-06-15
## Median :1493.8 Median :1995-09-24
## Mean :1379.6 Mean :1995-10-01
## 3rd Qu.:1757.4 3rd Qu.:1997-12-12
## Max. :2152.1 Max. :2000-04-04## Simple data plotting
ggplot(data = maize , aes(x = Date, y = Maize.AboveGround.Wt)) +
geom_point()
Inspecting a file with ‘inspect_apsimx’: Why?
Being able to inspect a file from within R is a functionality which was not considered in previous R packages. My first motivation for doing this was to be able to verify from within R that if I edited an APSIM(X) file, the editing worked as expected. The second use of ‘inspect’ is to be able to understand the structure of ‘apsim’ files better. A third useful aspect of ‘inspect’ is that it can be used to supply the path for a parameter that will be later edited. Another benefit of the inpspect functions is that if you are running APSIM in a cluster, you do not have access to the GUI, so these functions allow you to inspect your files in that environment. In addition, having this functionality within R allows to make these tasks repeatable. For complex inspections and manipulations of an .apsim(x) file the GUI is recommended. However, this package is designed to work with relatively simple .apsim(x) files.
Inspecting and Editing the ‘Maize’ example
Here I’m using the ‘Maize’ example distributed with APSIM-X but stored in the package and the specific task is: we want to make sure that the intended component was edited as expected. Let’s look at the weather file used.
extd.dir <- system.file("extdata", package = "apsimx")
inspect_apsimx("Maize.apsimx", src.dir = extd.dir, node = "Weather")## Met file: %root%\Examples\WeatherFiles\Dalby.metEditing a file has the side effect of creating a new file with ‘-edited’ added to the name to avoid conflict or unintended consequences, but it is also possible to overwrite it. This follows the same style as in the ‘apsimr’ package. One difference is that it is possible to supply a different ‘edit.tag’. This code does not run an APSIM simulation, it only edits the file.
Let’s say we want to modify the values of ‘Organic Carbon’ in the soil in the ‘Maize.apsimx’ example. First we should inspect the current values.
## Soil Type: Clay
## Latitude: -27.58184
## Longitude: 151.3202
## Soil children: Physical SoilWater Organic Chemical InitialWater InitialN CERESSoilTemperature Nutrient
##
##
## |parm |value |
## |:----------|:-----|
## |FOMCNRatio |40 |
##
##
## |Depth |Thickness |Carbon |SoilCNRatio |FBiom |FInert |FOM |
## |:-------|:---------|:------|:-----------|:-----|:------|:----------------|
## |0-15 |150 |1.2 |12 |0.04 |0.4 |347.129032312756 |
## |15-30 |150 |0.96 |12 |0.02 |0.6 |270.344362191994 |
## |30-60 |300 |0.6 |12 |0.02 |0.8 |163.972144349901 |
## |60-90 |300 |0.3 |12 |0.02 |1 |99.4541328870406 |
## |90-120 |300 |0.18 |12 |0.01 |1 |60.3219808311247 |
## |120-150 |300 |0.12 |12 |0.01 |1 |36.5871308286749 |
## |150-180 |300 |0.12 |12 |0.01 |1 |22.1912165985086 |The function ‘inspect_apsimx’, in this example, displays various information about the organic matter in the soil. (See the help page - ?inspect_apsimx - for more options). In the next step, we ‘edit’ the values.
ocs <- c(1.5, 1.4, 1.3, 1.2, 1.1, 1.0, 0.9)
edit_apsimx("Maize.apsimx",
src.dir = extd.dir,
wrt.dir = ".",
node = "Soil",
soil.child = "Organic",
parm = "Carbon", value = ocs)## Edited (node): Soil
## Edited (child): Organic
## Edited parameters: Carbon
## New values: 1.5 1.4 1.3 1.2 1.1 1 0.9
## Created: ./Maize-edited.apsimxLet’s make sure that we have changed the values successfully.
## Soil Type: Clay
## Latitude: -27.58184
## Longitude: 151.3202
## Soil children: Physical SoilWater Organic Chemical InitialWater InitialN CERESSoilTemperature Nutrient
##
##
## |parm |value |
## |:----------|:-----|
## |FOMCNRatio |40 |
##
##
## |Depth |Thickness |Carbon |SoilCNRatio |FBiom |FInert |FOM |
## |:-------|:---------|:------|:-----------|:-----|:------|:----------------|
## |0-15 |150 |1.5 |12 |0.04 |0.4 |347.129032312756 |
## |15-30 |150 |1.4 |12 |0.02 |0.6 |270.344362191994 |
## |30-60 |300 |1.3 |12 |0.02 |0.8 |163.972144349901 |
## |60-90 |300 |1.2 |12 |0.02 |1 |99.4541328870406 |
## |90-120 |300 |1.1 |12 |0.01 |1 |60.3219808311247 |
## |120-150 |300 |1 |12 |0.01 |1 |36.5871308286749 |
## |150-180 |300 |0.9 |12 |0.01 |1 |22.1912165985086 |There is another function that might be useful inspect_apsimx_json which can be more flexible and a variation of grep grep_json_list.
