From 03bda75d343402dad99df2aad55611e11279b833 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Jan 2017 18:04:53 +0100 Subject: Correct psm file in the example with metabolites --- docs/index.html | 1 + docs/reference/PELMO_path.html | 2 +- docs/reference/PELMO_runs.html | 75 +++++++++++++++++++++++++++++++++++++++++- 3 files changed, 76 insertions(+), 2 deletions(-) (limited to 'docs') diff --git a/docs/index.html b/docs/index.html index db22eb0..0c53fe9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -75,6 +75,7 @@ this program. If not, see <http://www.gnu.org/license

Examples

One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown here.

+

Another, even more recent example shows how FOCUS PELMO can be run in parallel under Linux as shown here.

diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html index 79aa89d..ab24341 100644 --- a/docs/reference/PELMO_path.html +++ b/docs/reference/PELMO_path.html @@ -73,7 +73,7 @@

Create a path of run directories as the PELMO GUI does

- 
PELMO_path(psm, crop, scenario)
+ 
PELMO_path(psm, crop, scenario = NA)

Arguments

diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 03b7b7b..e299b7c 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -112,20 +112,93 @@ as used in FOCUS_GW_scenarios_2012<
Should an existing run directories be overwritten
+

Value

+ +

If evaluate is TRUE, a list of lists of matrices holding the + PEC data.

+ +

Details

+ +

As a side effect, an R data file (period_pfm.rda) is generated in each +run directory, holding the results for all FOCUS periods, equivalent to +the period.plm file generated by the FOCUS PELMO GUI.

+

References

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

Wine https://winehq.org

+

PELMO test results http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc

+

Examples

+ 
# Reproduce the official test results for annual application of Pesticide D
+# to winter cereals at the day before emergence
+runs_1 <- list(
+  list(psm = 'Pesticide_D',
+       win = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")),
+  list(psm = 'Pesticide_D_1_day_pre_em_every_third_year',
+       pot = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")))
+time_1 <- system.time(
+  PECgw_1 <- PELMO_runs(runs_1, psm_dir = system.file("testdata", package = "pfm"),
+    cores = 6, overwrite = TRUE)
+)
+print(PECgw_1)
#> $Pesticide_D
+#> $Pesticide_D$win
+#>     FOCUS DUMMY D
+#> Cha         0.025
+#> Ham         1.621
+#> Jok         0.388
+#> Kre         0.467
+#> Oke         1.608
+#> Pia         0.848
+#> Por         2.386
+#> Sev         0.009
+#> Thi         0.030
+#> 
+#> 
+#> $Pesticide_D_1_day_pre_em_every_third_year
+#> $Pesticide_D_1_day_pre_em_every_third_year$pot
+#>     FOCUS DUMMY D
+#> Cha         0.010
+#> Ham         0.014
+#> Jok         0.009
+#> Kre         0.027
+#> Oke         0.085
+#> Pia         0.051
+#> Por         0.021
+#> Sev         0.000
+#> Thi         0.001
+#> 
+#> 
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
+print(time_1)
#>        User      System verstrichen 
+#>     231.892       0.496      57.056 

+# Demonstrate some results with metabolites.
+runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets',
+                    win = c("Cha", "Ham", "Kre")))
+PECgw_2 <- PELMO_runs(runs_2, psm_dir = system.file("testdata", package = "pfm"),
+  cores = 3, overwrite = TRUE)
+print(PECgw_2)
#> $Pesticide_D_1_May_every_other_year_mets
+#> $Pesticide_D_1_May_every_other_year_mets$win
+#>     FOCUS DUMMY D      M1    M2
+#> Cha         0.001 126.195 0.000
+#> Ham         0.054  82.196 0.001
+#> Kre         0.103  75.494 0.001
+#> 
+#>
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