Inspecting a ‘Replacement’ component
Many additional options in an APSIM-X simulation can be realized
through the use of ‘Replacements’. For this, there is a function that
allows inspection. In this case, it is important to know the structure
of the ‘replacement’ and explore the available components. For example,
if we want to display the xy pair for the thermal time in the phenology
component of the ‘Maize’ replacement we might go through the following
steps:
State the node (“Maize”) and display available components:
inspect_apsimx_replacement("MaizeSoybean.apsimx", src.dir = extd.dir,
node = "Maize", display.available = TRUE)
## Replacements: Maize Soybean
## node: Maize
## Level: node
## list Name: Maize
## list length: 11
## list names: $type PlantType IsAlive IsEnding DaysAfterEnding ResourceName Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 21
## Children Names: Arbitrator Phenology Structure Grain Root Leaf Husk Rachis Stem AboveGround BelowGround Total TotalLive TotalDead EarLive AboveGroundLive AboveGroundDead Future Development Needs CultivarFolder Spike MortalityRate
## missing node.child
apsimx.R
Choose ‘Phenology’ as a ‘child’ of ‘Maize’:
inspect_apsimx_replacement("MaizeSoybean.apsimx", src.dir = extd.dir,
node = "Maize", node.child = "Phenology",
display.available = TRUE)
## Replacements: Maize Soybean
## node: Maize
## Level: node
## list Name: Maize
## list length: 11
## list names: $type PlantType IsAlive IsEnding DaysAfterEnding ResourceName Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 21
## Children Names: Arbitrator Phenology Structure Grain Root Leaf Husk Rachis Stem AboveGround BelowGround Total TotalLive TotalDead EarLive AboveGroundLive AboveGroundDead Future Development Needs CultivarFolder Spike MortalityRate
## node child: Phenology
## list Name: Phenology
## list length: 6
## list names: $type Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 16
## Children Names: ThermalTime Germinating Emerging Juvenile Photosensitive LeafAppearance FlagLeafToFlowering FloweringToGrainFilling GrainFilling Maturing MaturityToHarvestRipe ReadyForHarvesting Photoperiod FloweringDAS MaturityDAS BBCH
## node subchild:
## missing node.subchild
apsimx.R
Choose ‘ThermalTime’ as a ‘sub.child’ of ‘Phenology’:
inspect_apsimx_replacement("MaizeSoybean.apsimx", src.dir = extd.dir,
node = "Maize", node.child = "Phenology",
node.subchild = "ThermalTime",
display.available = TRUE)
## Replacements: Maize Soybean
## node: Maize
## Level: node
## list Name: Maize
## list length: 11
## list names: $type PlantType IsAlive IsEnding DaysAfterEnding ResourceName Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 21
## Children Names: Arbitrator Phenology Structure Grain Root Leaf Husk Rachis Stem AboveGround BelowGround Total TotalLive TotalDead EarLive AboveGroundLive AboveGroundDead Future Development Needs CultivarFolder Spike MortalityRate
## node child: Phenology
## list Name: Phenology
## list length: 6
## list names: $type Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 16
## Children Names: ThermalTime Germinating Emerging Juvenile Photosensitive LeafAppearance FlagLeafToFlowering FloweringToGrainFilling GrainFilling Maturing MaturityToHarvestRipe ReadyForHarvesting Photoperiod FloweringDAS MaturityDAS BBCH
## node subchild: ThermalTime
## Subchild Name: ThermalTime
## list Name: ThermalTime
## list length: 6
## list names: $type Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 1
## Children Names: BaseThermalTime
## missing node.subsubchild
apsimx.R
Now we need to pick from within ‘ThermalTime’. There is a component
named “BaseThermalTime”.
inspect_apsimx_replacement("MaizeSoybean.apsimx", src.dir = extd.dir,
node = "Maize", node.child = "Phenology",
node.subchild = "ThermalTime",
node.subsubchild = "BaseThermalTime",
display.available = TRUE)
## Replacements: Maize Soybean
## node: Maize
## Level: node
## list Name: Maize
## list length: 11
## list names: $type PlantType IsAlive IsEnding DaysAfterEnding ResourceName Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 21
## Children Names: Arbitrator Phenology Structure Grain Root Leaf Husk Rachis Stem AboveGround BelowGround Total TotalLive TotalDead EarLive AboveGroundLive AboveGroundDead Future Development Needs CultivarFolder Spike MortalityRate
## node child: Phenology
## list Name: Phenology
## list length: 6
## list names: $type Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 16
## Children Names: ThermalTime Germinating Emerging Juvenile Photosensitive LeafAppearance FlagLeafToFlowering FloweringToGrainFilling GrainFilling Maturing MaturityToHarvestRipe ReadyForHarvesting Photoperiod FloweringDAS MaturityDAS BBCH
## node subchild: ThermalTime
## Subchild Name: ThermalTime
## list Name: ThermalTime
## list length: 6
## list names: $type Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 1
## Children Names: BaseThermalTime
## Name sub-sub-child: BaseThermalTime
## Available node children (unpack_node):
## $type : Models.Functions.XYPairs, Models
## X : 0 18 26 34 44
## Y : 0 10 18 26 0
## Name : Response
## Children :
## IncludeInDocumentation : TRUE
## Enabled : TRUE
## ReadOnly : FALSE
##
## $type : Models.Functions.ThreeHourSin, Models
## TempRangeFactors :
## Name : InterpolationMethod
## Children :
## IncludeInDocumentation : TRUE
## Enabled : TRUE
## ReadOnly : FALSE
##
## missing node.sub3child
apsimx.R
‘BaseThermalTime’ is the only child inside ‘ThermalTime’, but within
‘BaseThermalTime’ there are two Children: ‘Response’ and
‘InterpolationMethod’. There is not much to edit for
‘InterpolationMethod’, so we choose ‘Response’.
inspect_apsimx_replacement("MaizeSoybean.apsimx", src.dir = extd.dir,
node = "Maize", node.child = "Phenology",
node.subchild = "ThermalTime",
node.subsubchild = "BaseThermalTime",
node.sub3child = "Response")
## Replacements: Maize Soybean
## node: Maize
## node child: Phenology
## node subchild: ThermalTime
## Subchild Name: ThermalTime
## Name sub-sub-child: BaseThermalTime
## Name sub-sub-sub-child: Response
## $type : Models.Functions.XYPairs, Models
## X : 0 18 26 34 44
## Y : 0 10 18 26 0
## Name : Response
## Children :
## IncludeInDocumentation : TRUE
## Enabled : TRUE
## ReadOnly : FALSE
apsimx.R
Choose the ‘Y’ parameter within ‘Response’.
inspect_apsimx_replacement("MaizeSoybean.apsimx", src.dir = extd.dir,
node = "Maize", node.child = "Phenology",
node.subchild = "ThermalTime",
node.subsubchild = "BaseThermalTime",
node.sub3child = "Response",
parm = "Y")
## Replacements: Maize Soybean
## node: Maize
## node child: Phenology
## node subchild: ThermalTime
## Subchild Name: ThermalTime
## Name sub-sub-child: BaseThermalTime
## Name sub-sub-sub-child: Response
## Y : 0 10 18 26 0
apsimx.R
The function shows the available replacements (“Maize” and
“Soybean”), the ‘CropType’ if available, the subchild name and the ‘Y’
vector in this example. If parm is not specified all elements will be
displayed.
Let’s say we want to inspect details of soybean cultivars in the same
file:
inspect_apsimx_replacement("MaizeSoybean.apsimx", src.dir = extd.dir,
node = "Soybean", display.available = TRUE)
## Replacements: Maize Soybean
## node: Soybean
## Level: node
## list Name: Soybean
## list length: 11
## list names: $type PlantType IsAlive IsEnding DaysAfterEnding ResourceName Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 17
## Children Names: Arbitrator Phenology Leaf Grain Root Nodule Shell Stem AboveGround BelowGround AboveGroundLive Total TotalLive TotalDead Pod MortalityRate Cultivars
## missing node.child
apsimx.R
The cultivars are at the node.child level.
inspect_apsimx_replacement("MaizeSoybean.apsimx",
src.dir = extd.dir,
node = "Soybean",
node.child = "Cultivars",
node.subchild = "USA",
node.subsubchild = "PioneerP22T61_MG22",
display.available = FALSE)
## Replacements: Maize Soybean
## node: Soybean
## node child: Cultivars
## node subchild: USA
## Subchild Name: USA
## Name sub-sub-child: PioneerP22T61_MG22
## $type : Models.PMF.Cultivar, Models
## : [Phenology].Vegetative.Target.FixedValue = 328
## : [Phenology].EarlyFlowering.Target.FixedValue = 106
## : [Phenology].EarlyGrainFilling.Target.FractionofGrainfilling.FixedValue = 0.3
## : [Phenology].LateGrainFilling.Target.EntireGrainfillPeriod.FixedValue = 499
## : [Phenology].VegetativePhotoperiodModifier.XYPairs.X = 13.59, 17.6
## : [Phenology].ReproductivePhotoperiodModifier.XYPairs.X = 13.59, 17.6
## Command
## Name : PioneerP22T61_MG22
## IncludeInDocumentation : TRUE
## Enabled : TRUE
## ReadOnly : FALSE
## no node sub-sub-sub-children available or parm is not null
apsimx.R
The function inspect_apsimx_replacement can also be
used to inspect more complex file structures such as the ‘Factorial’
example distributed with APSIM-X. See ‘?inspect_apsimx_replacement’.
Editing a ‘Replacement’
After using the ‘inspect’ version of the file, editing should be much
more straight forward.
edit_apsimx_replacement("MaizeSoybean.apsimx",
src.dir = extd.dir, wrt.dir = tmp.dir,
node = "Maize", node.child = "Phenology",
node.subchild = "ThermalTime",
node.subsubchild = "BaseThermalTime",
node.sub3child = "Response",
parm = "Y", value = c(0, 12, 20, 28, 0))
## Replacements: Maize Soybean
## Available node children: Arbitrator Phenology Structure Grain Root Leaf Husk Rachis Stem AboveGround BelowGround Total TotalLive TotalDead EarLive AboveGroundLive AboveGroundDead Future Development Needs CultivarFolder Spike MortalityRate
## Subchild Name: ThermalTime
## Subsubchild Name: BaseThermalTime
## Sub-sub-subchild Name: Response
## Edited (node): Maize
## Edited (node.child): Phenology
## Edited (node.subchild): ThermalTime
## Edited (node.subsubchild): BaseThermalTime
## Edited (node.sub3child): Response
## Edit (level): 6
## Edited parameter: Y
## New values: 0 12 20 28 0
## Created: /var/folders/6j/xksd1tld70q91h73d5s0ln7c0000gn/T//Rtmp7cAnAb/MaizeSoybean-edited.apsimx
apsimx.R
Let’s inspect the edited file
inspect_apsimx_replacement("MaizeSoybean-edited.apsimx",
src.dir = tmp.dir,
node = "Maize",
node.child = "Phenology",
node.subchild = "ThermalTime",
node.subsubchild = "BaseThermalTime",
node.sub3child = "Response",
parm = "Y")
## Replacements: Maize Soybean
## node: Maize
## node child: Phenology
## node subchild: ThermalTime
## Subchild Name: ThermalTime
## Name sub-sub-child: BaseThermalTime
## Name sub-sub-sub-child: Response
## Y : 0 12 20 28 0
apsimx.R
Inspecting and editing a Factorial
The complexity of APSIM-X files can be mind-boggling and it makes it
difficult to write robust functions across all tasks that APSIM is able
to accomplish. I wrote the ‘inspect_apsimx_replacement’ and
‘edit_apsimx_replacement’ specifically to edit replacements but these
functions have much more flexibility than ‘inspect_apsimx’ and
‘edit_apsimx’. The function ‘apsimx_example’ is limited in the number of
examples that it is allowed to run, but this does not mean that you
cannot run the other examples which are distributed with APSIM-X. Let’s
take the ‘Factorial’ example:
If we want to inspect and edit this file, we need the
‘inspect_apsimx_replacement’ function.
## There are multiple 'Experiments' so we need to pick one
inspect_apsimx_replacement("Factorial", src.dir = extd.dir,
root = list("Experiment", NA))
##These positions matched Experiment 1 2 3 4 5
##Error in inspect_apsimx_replacement("Factorial", src.dir = ex.dir, root = ##list("Experiment", : Multiple root nodes found. Please provide a position
apsimx.R
## There are multiple 'Experiments' so we need to pick one
inspect_apsimx_replacement("Factorial", src.dir = extd.dir,
root = list("Experiment", 1))
## Warning in inspect_apsimx_replacement("Factorial", src.dir = extd.dir, root =
## list("Experiment", : Node does not appear to be a 'Replacements' node
## Replacements: Factors Base
## Please provide a node
## We need to provide a node
inspect_apsimx_replacement("Factorial", src.dir = extd.dir,
root = list("Experiment", 1),
node = "Base", display.available = TRUE)
## Warning in inspect_apsimx_replacement("Factorial", src.dir = extd.dir, root =
## list("Experiment", : Node does not appear to be a 'Replacements' node
## Replacements: Factors Base
## node: Base
## Level: node
## list Name: Base
## list length: 7
## list names: $type Descriptors Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 4
## Children Names: Weather Clock Summary Field
## missing node.child
## We need to provide a node child
inspect_apsimx_replacement("Factorial", src.dir = extd.dir,
root = list("Experiment", 1),
node = "Base", node.child = "Clock",
display.available = TRUE)
## Warning in inspect_apsimx_replacement("Factorial", src.dir = extd.dir, root =
## list("Experiment", : Node does not appear to be a 'Replacements' node
## Replacements: Factors Base
## node: Base
## Level: node
## list Name: Base
## list length: 7
## list names: $type Descriptors Name Children IncludeInDocumentation Enabled ReadOnly
## Children: Yes
## Children length: 4
## Children Names: Weather Clock Summary Field
## node child: Clock
## Available node children (unpack_node): $type StartDate EndDate Name Children IncludeInDocumentation Enabled ReadOnly
## $type : Models.Clock, Models
## StartDate : 2003-10-20T00:00:00
## EndDate : 2004-05-23T00:00:00
## Name : Clock
## IncludeInDocumentation : TRUE
## Enabled : TRUE
## ReadOnly : FALSE
## no node sub-children available or parm not equal to null
apsimx.R
Here we stop at this level but it is possible to dig deeper using
‘node.subchild’ and ‘node.subsubchild’. It is not possible at this point
to dig deeper than ‘node.sub5child’ in the hierarchy level.
The inspect_apsimx function can also handle
factorials.
inspect_apsimx("Factorial.apsimx", src.dir = extd.dir)
## Simulation structure:
## list Name: Simulations
# list length: 8
# list names: $type ExplorerWidth Version Name Children IncludeInDocumentation Enabled ReadOnly
# Children: Yes
# Children length: 6
# Children Names: Experiment RangeExperiment OperationsExpt Compound ManagerExpt DataStore
# Error in inspect_apsimx("Factorial", src.dir = ex.dir) :
# more than one simulation found and no root node label has been specified
# select one of the children names above
apsimx.R
We need to pick one out of the possible factorials. If you check this
file with the APSIM GUI, you’ll see that within ‘RangeExperiment’ there
is ‘Factors’ and ‘Base2’, but the core simulation is within ‘Base2’. The
‘root’ argument provides the specific factorial and the node ‘Base2’
within that factorial.
inspect_apsimx("Factorial.apsimx", src.dir = extd.dir,
root = c("RangeExperiment", "Base2"),
node = "Weather")
## Met file: WeatherFiles\lincoln.met
apsimx.R
Following this structure, if we want to edit the path to the weather
file we can use the following example.
edit_apsimx("Factorial.apsimx",
src.dir = extd.dir, wrt.dir = tmp.dir,
root = c("RangeExperiment", "Base2"),
node = "Weather",
value = "Ames.met")
## Edited (node): Weather
## Edited (child): none
## Edited parameters:
## New values: Ames.met
## Created: /var/folders/6j/xksd1tld70q91h73d5s0ln7c0000gn/T//Rtmp7cAnAb/Factorial-edited.apsimx
apsimx.R
I won’t be running the ‘Factorial’ example here, but if you are
interested this is done in the folder ‘tests’ in the pacakge source.
apsimx.R