vignettes/Generating_Stics_text_files.Rmd
Generating_Stics_text_files.Rmd
In this part information are focusing on functionalities related to generation of text input files for the STICS model.
Generated files will be directly usable for running the model with SticsOnR package functions. See the documentation here.
For using the model directly neither using the JavaSTICS graphical
interface nor the run_javastics
function interface, we
provide a function, gen_usms_xml2txt
, for converting
JavaSTICS XML files to STICS text files from a JavaStics workspace.
Then, the model can be run using the run_stics()
function from SticsOnR
Observation files may also be copied if they have a standard name
corresponding to a usm name and a .obs
extension. If not,
they must be renamed to do so.
# Specifying the JavaSTICS folder
javastics_path <- "/path/to/JavaSTICS-1.5.2-STICS-10.1.0"
# Specifying a workspace as a subfolder of JavaSTICS
workspace_path <- "example"
# or an absolute path to an external folder
# workspace_path <- "/path/to/javastics/workspace"
# Specifying an output folder path
output_path <- "/path/to/output/folder"
## Generating files for all the usms contained in the workspace
# Into the workspace directory
gen_usms_xml2txt(javastics_path,
workspace_path)
#> ℹ USM 'SugarCane' successfully created
#> ℹ USM 'potato' successfully created
#> ℹ USM 'banana' successfully created
#> ℹ USM 'sorghum' successfully created
#> ℹ USM 'barley' successfully created
#> ℹ USM 'sugarbeet' successfully created
#> ℹ USM 'wheat' successfully created
#> ℹ USM 'maize' successfully created
#> ℹ USM 'soybean' successfully created
#> ℹ USM 'lettuce' successfully created
#> ℹ USM 'tomato' successfully created
#> ℹ USM 'DurumWheat' successfully created
#> ℹ USM 'rapeseed' successfully created
#> ℹ USM 'sunflower' successfully created
#> ℹ USM 'grass' successfully created
#> ℹ USM 'BareSoil' successfully created
#> ! Obs file not found for USM
#> "demo_Wheat1": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/demo_Wheat1.obs'
#> ℹ USM 'demo_Wheat1' successfully created
#> ! Obs file not found for USM
#> "demo_BareSoil2": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/demo_BareSoil2.obs'
#> ℹ USM 'demo_BareSoil2' successfully created
#> ! Obs file not found for USM
#> "demo_maize3": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/demo_maize3.obs'
#> ℹ USM 'demo_maize3' successfully created
#> ! Obs file not found for USM
#> "DurumWheat_4years": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/DurumWheat_4years.obs'
#> ℹ USM 'DurumWheat_4years' successfully created
#> ! Obs file not found for USM
#> "maize_4years": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/maize_4years.obs'
#> ℹ USM 'maize_4years' successfully created
#> ℹ USM 'strawberry' successfully created
#> ℹ USM 'pea' successfully created
#> ℹ USM 'vine' successfully created
#> ℹ USM 'fescue' successfully created
#> ℹ USM 'flax' successfully created
#> ! Obs file not found for USM
#> "intercrop_pea_barley": '/tmp/JavaSTICS-1.5.2-STICS-10.1.0/example/intercrop_pea_barley.obs'
#> ℹ USM 'intercrop_pea_barley' successfully created
#> ℹ USM 'timothy' successfully created
#> ℹ USM 'DurumWheat_snow' successfully created
#> ℹ USM 'Turmeric' successfully created
#> ℹ USM 'cc_BristleOat' successfully created
#> ℹ USM 'cc_mustard' successfully created
#> ℹ USM 'cc_ItalianRyegrass' successfully created
#> ℹ USM 'cc_vetch' successfully created
#> ℹ USM 'cc_CrimsonClover' successfully created
#> ℹ USM 'proto_rice' successfully created
# Into a specific output folder, with verbose mode turned off
gen_usms_xml2txt(javastics_path,
workspace_path,
out_dir = output_path,
verbose = FALSE)
## Generating files for a subset of usms
# Into the workspace directory
gen_usms_xml2txt(javastics_path,
workspace_path,
usm = c("banana", "wheat"))
#> ℹ USM 'banana' successfully created
#> ℹ USM 'wheat' successfully created
# Into a specific folder
gen_usms_xml2txt(javastics_path,
workspace_path,
usm = c("banana", "wheat"),
out_dir = output_path)
#> ℹ USM 'banana' successfully created
#> ℹ USM 'wheat' successfully created
## Getting returned information about files generation
gen_info <- gen_usms_xml2txt(javastics_path,
workspace_path,
usm = c("banana", "wheat"),
out_dir = output_path)
#> ℹ USM 'banana' successfully created
#> ℹ USM 'wheat' successfully created
gen_info
#> $usms_path
#> [1] "/path/to/output/folder/banana"
#> [2] "/path/to/output/folder/wheat"
#>
#> $files
#> [1] "climat.txt" "param.sol" "ficini.txt" "ficplt1.txt"
#> [5] "fictec1.txt" "station.txt" "new_travail.usm" "tempopar.sti"
#> [9] "tempoparv6.sti" "ficplt2.txt" "fictec2.txt"
#>
#> $copy_status
#> [1] TRUE TRUE
#>
#> $obs_copy_status
#> [1] TRUE TRUE
#>
#> $lai_copy_status
#> [1] FALSE FALSE
# Generating files directly in the workspace or a specific folder
# (no usm sub-folder)
# In this case the model files are overwritten at each gen_usms_xml2txt call !
# In the workspace
gen_usms_xml2txt(javastics_path,
workspace_path,
usm = "banana",
dir_per_usm_flag = FALSE,
verbose = FALSE)
# In a specific folder
gen_usms_xml2txt(javastics_path,
workspace_path,
usm = "banana",
out_dir = output_path,
dir_per_usm_flag = FALSE,
verbose = FALSE)