FOCUS PELMO crop acronyms used for naming sceneario files

Contents

diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html new file mode 100644 index 0000000..5777868 --- /dev/null +++ b/docs/reference/FOCUS_PELMO_crop_sze_names.html @@ -0,0 +1,121 @@ + + + + + + + + +FOCUS PELMO crop acronyms used for naming sceneario files — FOCUS_PELMO_crop_sze_names • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

A named character vector with the crop acronyms used in FOCUS PELMO 5.5.3 +for naming the .sze files located in the FOCUS directory. The crop acronyms +in the file names are sometimes capitalized, sometimes not. The scenario +files used for Beans (field) and Beans (vegetable) are the same.

+ + +

FOCUS_PELMO_crop_sze_names

+ +

Format

+ +

An object of class character of length 25.

+ + +

Examples

print(FOCUS_PELMO_crop_sze_names)
#>      app      gra      pot      sug      win      fbe      vbe      bus 
+#> "apples"  "grass" "potato" "sbeets" "wcerea"  "beans"  "beans"  "bushb" 
+#>      cab      car      cit      cot      lin      mai      soi      woi 
+#> "cabbag" "carrot" "citrus" "cotton"  "linse"  "maize" "rapesu" "rapewi" 
+#>      oni      ape      soy      spr      str      sun      tob      tom 
+#> "onions"   "peas"   "soyb" "scerea" "strawb" "sunflo" "tobacc" "tomato" 
+#>      vin 
+#>  "vines"

+ +

+ + +

+ + + diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html new file mode 100644 index 0000000..d9ad8d2 --- /dev/null +++ b/docs/reference/FOCUS_PELMO_crops.html @@ -0,0 +1,132 @@ + + + + + + + + +FOCUS PELMO crop names — FOCUS_PELMO_crops • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

A named character vector with the crop names used in the PELMO 5.5.3 GUI. +For the names, three letter codes were constructed by generally taking the +first three letters in lower case. Only when there is an expression in +parentheses, the first letter of this expression becomes the first letter +in the three letter code, i.e. 'Peas (animals)' has the code ape.

+ + +

FOCUS_PELMO_crops

+ +

Format

+ +

An object of class character of length 25.

+ + +

Examples

print(FOCUS_PELMO_crops)
#>                      app                      gra                      pot 
+#>                 "Apples"      "Grass and alfalfa"               "Potatoes" 
+#>                      sug                      win                      fbe 
+#>            "Sugar beets"         "Winter cereals"          "Beans (field)" 
+#>                      vbe                      bus                      cab 
+#>     "Beans (vegetables)"            "Bushberries"                "Cabbage" 
+#>                      car                      cit                      cot 
+#>                "Carrots"                 "Citrus"                 "Cotton" 
+#>                      lin                      mai                      soi 
+#>                "Linseed"                  "Maize" "Oil seed rape (summer)" 
+#>                      woi                      oni                      ape 
+#> "Oil seed rape (winter)"                 "Onions"         "Peas (animals)" 
+#>                      soy                      spr                      str 
+#>               "Soybeans"         "Spring cereals"           "Strawberries" 
+#>                      sun                      tob                      tom 
+#>              "Sunflower"                "Tobacco"               "Tomatoes" 
+#>                      vin 
+#>                  "Vines"

+ +

+ + +

+ + + diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html new file mode 100644 index 0000000..8051d42 --- /dev/null +++ b/docs/reference/FOCUS_PELMO_location_codes.html @@ -0,0 +1,113 @@ + + + + + + + + +Location codes in FOCUS PELMO — FOCUS_PELMO_location_codes • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

A named character vector of one letter location codes used in FOCUS PELMO, +indexed by three letter acronyms.

+ + +

FOCUS_PELMO_location_codes

+ +

Format

+ +

An object of class character of length 9.

+ + +

Examples

print(FOCUS_PELMO_location_codes)
#> Cha Ham Jok Kre Oke Pia Por Sev Thi 
+#> "C" "H" "J" "K" "N" "P" "O" "S" "T"

+ +

+ + +

+ + + diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html new file mode 100644 index 0000000..79aa89d --- /dev/null +++ b/docs/reference/PELMO_path.html @@ -0,0 +1,112 @@ + + + + + + + + +Create a path of run directories as the PELMO GUI does — PELMO_path • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Create a path of run directories as the PELMO GUI does

+ + +

PELMO_path(psm, crop, scenario)

+ +

Arguments

psm: The psm identifier
crop: The PELMO crop acronym
scenario: The scenario

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html new file mode 100644 index 0000000..e872196 --- /dev/null +++ b/docs/reference/PELMO_runs.html @@ -0,0 +1,144 @@ + + + + + + + + +Set up runs for FOCUS PELMO — PELMO_runs • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Per default, the runs are also executed with FOCUS PELMO, and the results are processed +and returned. Currently, only FOCUS PELMO as installed on Linux (or other Unix systems) +using the install_PELMO from the PELMO.installeR package +maintained on github is supported. In such installations, FOCUS PELMO is installed into +package installation directory of PELMO.installeR and run with wine.

+ + +

PELMO_runs(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
+  execute = TRUE, cores = getOption("mc.cores", 2L), evaluate = TRUE,
+  overwrite = FALSE)
+
+run_PELMO(runs, version = "5.5.3", PELMO_base = "auto",
+  cores = getOption("mc.cores", 2L))
+
+evaluate_PELMO(runs, version = "5.5.3", PELMO_base = "auto")

+ +

Arguments

runs: A list of lists. Each inner lists has an element named 'psm' +that holds the psm string, and elements named using three letter crop acronyms, +as used in FOCUS_PELMO_crops, +that hold character vectors of three letter scenario acronyms +as used in FOCUS_GW_scenarios_2012.
psm_dir: The directory where the psm files are located
version: The FOCUS PELMO version
PELMO_base: Where the FOCUS PELMO installation is located
execute: Should PELMO be executed directly?
cores: The number of cores to execute PELMO runs in parallel
evaluate: Should the results be returned?
overwrite: Should an existing run directories be overwritten

+ +

References

+ +

PELMO.installeR https://jranke.github.io/PELMO.installeR

Wine https://winehq.org

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html new file mode 100644 index 0000000..b2c9798 --- /dev/null +++ b/docs/reference/create_run_list.html @@ -0,0 +1,116 @@ + + + + + + + + +Create a list of runs that we can traverse — create_run_list • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Create a list of runs that we can traverse

+ + +

create_run_list(runs, psm_dir = ".", check_psm_files = FALSE)

+ +

Arguments

runs: A list of lists. Each inner lists has an element named 'psm' +that holds the psm string, and elements named using three letter crop acronyms, +as used in FOCUS_PELMO_crops, +that hold character vectors of three letter scenario acronyms +as used in FOCUS_GW_scenarios_2012.
psm_dir: The directory where the psm files are located
check_psm_files: Should we check if the psm file exists

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/evaluate_PELMO.html b/docs/reference/evaluate_PELMO.html new file mode 100644 index 0000000..58e7843 --- /dev/null +++ b/docs/reference/evaluate_PELMO.html @@ -0,0 +1,116 @@ + + + + + + + + +Evaluate PELMO runs — evaluate_PELMO • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Evaluate PELMO runs

+ + +

evaluate_PELMO(runs, version = "5.5.3", PELMO_base = "auto")

+ +

Arguments

runs: A list of lists. Each inner lists has an element named 'psm' +that holds the psm string, and elements named using three letter crop acronyms, +as used in FOCUS_PELMO_crops, +that hold character vectors of three letter scenario acronyms +as used in FOCUS_GW_scenarios_2012.
version: The FOCUS PELMO version
PELMO_base: Where the FOCUS PELMO installation is located

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html new file mode 100644 index 0000000..8160746 --- /dev/null +++ b/docs/reference/focus_80th.html @@ -0,0 +1,113 @@ + + + + + + + + +Calculate the 80th percentile according to FOCUS guidance — focus_80th • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

This is nowadays defined as the mean of the 16th and the 17th +highest value. Previously, the 17th highest values was used (FOCUS 2014, p. +18). NaN values need to be set to zero in order to reproduce the +values obtained by PELMO.

+ + +

focus_80th(c_period, old = FALSE)

+ +

Arguments

c_period: A numeric vector of values to calculate the percentile from
old: Should the old calculation method be used (the 17th highest value)?

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html new file mode 100644 index 0000000..64ea25e --- /dev/null +++ b/docs/reference/get_flux.html @@ -0,0 +1,101 @@ + + + + + + + + +Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file — get_flux • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file

+ + +

get_flux(chem_file)

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html new file mode 100644 index 0000000..13171c1 --- /dev/null +++ b/docs/reference/get_interval.html @@ -0,0 +1,101 @@ + + + + + + + + +Get the application interval in years from a psm file — get_interval • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Get the application interval in years from a psm file

+ + +

get_interval(psm_file, location_code)

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 8f57cd2..33713b6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@

@@ -116,6 +116,14 @@

Properties of the predefined scenarios from the EFSA guidance from 2015

soil_scenario_data_EFSA_2015

Predicted environmental concentrations in groundwater

+ + +

Set up runs for FOCUS PELMO

Predicted environmental concentrations in surface water

@@ -173,6 +181,7 @@

diff --git a/docs/reference/run_PELMO.html b/docs/reference/run_PELMO.html new file mode 100644 index 0000000..067d3c1 --- /dev/null +++ b/docs/reference/run_PELMO.html @@ -0,0 +1,119 @@ + + + + + + + + +Run PELMO — run_PELMO • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Run PELMO

+ + +

run_PELMO(runs, version = "5.5.3", PELMO_base = "auto",
+  cores = getOption("mc.cores", 2L))

+ +

Arguments

runs: A list of lists. Each inner lists has an element named 'psm' +that holds the psm string, and elements named using three letter crop acronyms, +as used in FOCUS_PELMO_crops, +that hold character vectors of three letter scenario acronyms +as used in FOCUS_GW_scenarios_2012.
version: The FOCUS PELMO version
PELMO_base: Where the FOCUS PELMO installation is located
cores: The number of cores to execute PELMO runs in parallel

+ + +

+ +

+ + +

+ + + diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html new file mode 100644 index 0000000..66466ac --- /dev/null +++ b/docs/reference/sum_periods.html @@ -0,0 +1,101 @@ + + + + + + + + +Sum up values according to FOCUS periods — sum_periods • pfm + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

Sum up values according to FOCUS periods

+ + +

sum_periods(annual, interval)

+ + +

+ +

+ + +

+ + + -- cgit v1.2.1

Format

References

Contents

Format

Examples

Contents

FOCUS PELMO crop names

Format

Examples

Contents

Location codes in FOCUS PELMO

Format

Examples

Contents

Create a path of run directories as the PELMO GUI does

Arguments

Contents

Set up runs for FOCUS PELMO

Arguments

References

Contents

Create a list of runs that we can traverse

Arguments

Contents

Evaluate PELMO runs

Arguments

Contents

Calculate the 80th percentile according to FOCUS guidance

Arguments

Contents

Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file

Contents

Get the application interval in years from a psm file

Contents

Function reference

version 0.4-1

version 0.4-2

Predicted environmental concentrations in groundwater

Predicted environmental concentrations in surface water

Run PELMO

Arguments

Contents

Sum up values according to FOCUS periods

Contents