From 2f618da8cfbeb0379f4d38af6f608a69c6d54bd5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 30 Jul 2016 11:29:09 +0200 Subject: Update static documentation --- pkg/inst/web/FOCUS_GW_scenarios_2012.html | 6 +++--- pkg/inst/web/GUS.html | 4 ++-- pkg/inst/web/PEC_soil.html | 4 ++-- pkg/inst/web/PEC_sw_drainage_UK.html | 4 ++-- pkg/inst/web/PEC_sw_drift.html | 9 ++++++--- pkg/inst/web/PEC_sw_sed.html | 4 ++-- pkg/inst/web/SFO_actual_twa.html | 4 ++-- pkg/inst/web/SSLRC_mobility_classification.html | 4 ++-- pkg/inst/web/TOXSWA_cwa.html | 4 ++-- pkg/inst/web/drift_data_JKI.html | 4 ++-- pkg/inst/web/endpoint.html | 6 +++--- pkg/inst/web/geomean.html | 4 ++-- pkg/inst/web/index.html | 6 +++--- pkg/inst/web/pfm_degradation.html | 4 ++-- pkg/inst/web/plot.TOXSWA_cwa.html | 4 ++-- pkg/inst/web/read.TOXSWA_cwa.html | 21 ++++++++++++++++----- pkg/inst/web/soil_scenario_data_EFSA_2015.html | 4 ++-- 17 files changed, 55 insertions(+), 41 deletions(-) diff --git a/pkg/inst/web/FOCUS_GW_scenarios_2012.html b/pkg/inst/web/FOCUS_GW_scenarios_2012.html index 43fc3a3..43ac090 100644 --- a/pkg/inst/web/FOCUS_GW_scenarios_2012.html +++ b/pkg/inst/web/FOCUS_GW_scenarios_2012.html @@ -2,7 +2,7 @@ -FOCUS_GW_scenarios_2012. pfm 0.3-1 +FOCUS_GW_scenarios_2012. pfm 0.3-7 @@ -32,7 +32,7 @@
- pfm 0.3-1 + pfm 0.3-7
$names Cha Ham Jok Kre Oke - "Châteadun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" + "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" Pia Por Sev Thi "Piacenza" "Porto" "Sevilla" "Thiva" diff --git a/pkg/inst/web/GUS.html b/pkg/inst/web/GUS.html index dae2e5f..a330be2 100644 --- a/pkg/inst/web/GUS.html +++ b/pkg/inst/web/GUS.html @@ -2,7 +2,7 @@ -GUS. pfm 0.3-1 +GUS. pfm 0.3-7
- pfm 0.3-1 + pfm 0.3-7
  • Index
    • diff --git a/pkg/inst/web/PEC_soil.html b/pkg/inst/web/PEC_soil.html index d74a49f..1304d19 100644 --- a/pkg/inst/web/PEC_soil.html +++ b/pkg/inst/web/PEC_soil.html @@ -2,7 +2,7 @@ -PEC_soil. pfm 0.3-1 +PEC_soil. pfm 0.3-7
    - pfm 0.3-1 + pfm 0.3-7
    • Index
      • diff --git a/pkg/inst/web/PEC_sw_drainage_UK.html b/pkg/inst/web/PEC_sw_drainage_UK.html index 1cbac88..bf97fea 100644 --- a/pkg/inst/web/PEC_sw_drainage_UK.html +++ b/pkg/inst/web/PEC_sw_drainage_UK.html @@ -2,7 +2,7 @@ -PEC_sw_drainage_UK. pfm 0.3-1 +PEC_sw_drainage_UK. pfm 0.3-7
      - pfm 0.3-1 + pfm 0.3-7
      • Index
        • diff --git a/pkg/inst/web/PEC_sw_drift.html b/pkg/inst/web/PEC_sw_drift.html index 4a097fc..5d4bb47 100644 --- a/pkg/inst/web/PEC_sw_drift.html +++ b/pkg/inst/web/PEC_sw_drift.html @@ -2,7 +2,7 @@ -PEC_sw_drift. pfm 0.3-1 +PEC_sw_drift. pfm 0.3-7
        - pfm 0.3-1 + pfm 0.3-7
        • Index
          • @@ -54,7 +54,7 @@ Johannes Ranke

          Usage

          - 
          PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
          + 
          PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")

          Arguments

          @@ -64,6 +64,9 @@ Johannes Ranke
          Number of applications for selection of drift percentile
          water_depth
          Depth of the water body in cm
          +
          drift_percentages
          +
          Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.
          drift_data
          Source of drift percentage data
          crop
          diff --git a/pkg/inst/web/PEC_sw_sed.html b/pkg/inst/web/PEC_sw_sed.html index 231c48f..4eda1d7 100644 --- a/pkg/inst/web/PEC_sw_sed.html +++ b/pkg/inst/web/PEC_sw_sed.html @@ -2,7 +2,7 @@ -PEC_sw_sed. pfm 0.3-1 +PEC_sw_sed. pfm 0.3-7
          - pfm 0.3-1 + pfm 0.3-7
          • Index
            • diff --git a/pkg/inst/web/SFO_actual_twa.html b/pkg/inst/web/SFO_actual_twa.html index e132828..3ce9220 100644 --- a/pkg/inst/web/SFO_actual_twa.html +++ b/pkg/inst/web/SFO_actual_twa.html @@ -2,7 +2,7 @@ -SFO_actual_twa. pfm 0.3-1 +SFO_actual_twa. pfm 0.3-7
            - pfm 0.3-1 + pfm 0.3-7
            • Index
              • diff --git a/pkg/inst/web/SSLRC_mobility_classification.html b/pkg/inst/web/SSLRC_mobility_classification.html index 06c6119..43d701e 100644 --- a/pkg/inst/web/SSLRC_mobility_classification.html +++ b/pkg/inst/web/SSLRC_mobility_classification.html @@ -2,7 +2,7 @@ -SSLRC_mobility_classification. pfm 0.3-1 +SSLRC_mobility_classification. pfm 0.3-7
              - pfm 0.3-1 + pfm 0.3-7
              • Index
                • diff --git a/pkg/inst/web/TOXSWA_cwa.html b/pkg/inst/web/TOXSWA_cwa.html index 8edb15a..0d8ae17 100644 --- a/pkg/inst/web/TOXSWA_cwa.html +++ b/pkg/inst/web/TOXSWA_cwa.html @@ -2,7 +2,7 @@ -TOXSWA_cwa. pfm 0.3-1 +TOXSWA_cwa. pfm 0.3-7 @@ -32,7 +32,7 @@
                - pfm 0.3-1 + pfm 0.3-7
                • Index
                  • diff --git a/pkg/inst/web/drift_data_JKI.html b/pkg/inst/web/drift_data_JKI.html index 865e7fa..c3471c9 100644 --- a/pkg/inst/web/drift_data_JKI.html +++ b/pkg/inst/web/drift_data_JKI.html @@ -2,7 +2,7 @@ -drift_data_JKI. pfm 0.3-1 +drift_data_JKI. pfm 0.3-7 @@ -32,7 +32,7 @@
                  - pfm 0.3-1 + pfm 0.3-7
                  • Index
                    • diff --git a/pkg/inst/web/endpoint.html b/pkg/inst/web/endpoint.html index 0789d95..521f7f4 100644 --- a/pkg/inst/web/endpoint.html +++ b/pkg/inst/web/endpoint.html @@ -2,7 +2,7 @@ -endpoint. pfm 0.3-1 +endpoint. pfm 0.3-7 @@ -32,7 +32,7 @@
                    - pfm 0.3-1 + pfm 0.3-7
                    • Index
                      • @@ -56,7 +56,7 @@
                      soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)
                      soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)
                      soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)
                      -
                      soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = rep(3, length(values)), raw = FALSE)
                      +
                      soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE)

                      Arguments

                      diff --git a/pkg/inst/web/geomean.html b/pkg/inst/web/geomean.html index fb859fa..672e9b5 100644 --- a/pkg/inst/web/geomean.html +++ b/pkg/inst/web/geomean.html @@ -2,7 +2,7 @@ -geomean. pfm 0.3-1 +geomean. pfm 0.3-7
                      - pfm 0.3-1 + pfm 0.3-7
                      • Index
                        • diff --git a/pkg/inst/web/index.html b/pkg/inst/web/index.html index 3eb1ad1..54f0f35 100644 --- a/pkg/inst/web/index.html +++ b/pkg/inst/web/index.html @@ -2,7 +2,7 @@ -Index. pfm 0.3-1 +Index. pfm 0.3-7 @@ -32,7 +32,7 @@
                        - pfm 0.3-1 + pfm 0.3-7
                        • Index
                          • @@ -161,7 +161,7 @@ fate modelling software packages.

                          Dependencies

                          • Depends: R6, mkin
                            • -
                          • Imports: graphics, chents
                            • +
                          • Imports: graphics, chents, readr, methods
                          • Suggests: testthat
                          diff --git a/pkg/inst/web/pfm_degradation.html b/pkg/inst/web/pfm_degradation.html index 68e8859..fad64be 100644 --- a/pkg/inst/web/pfm_degradation.html +++ b/pkg/inst/web/pfm_degradation.html @@ -2,7 +2,7 @@ -pfm_degradation. pfm 0.3-1 +pfm_degradation. pfm 0.3-7
                          - pfm 0.3-1 + pfm 0.3-7
                          • Index
                            • diff --git a/pkg/inst/web/plot.TOXSWA_cwa.html b/pkg/inst/web/plot.TOXSWA_cwa.html index 184c4f6..a6118df 100644 --- a/pkg/inst/web/plot.TOXSWA_cwa.html +++ b/pkg/inst/web/plot.TOXSWA_cwa.html @@ -2,7 +2,7 @@ -plot.TOXSWA_cwa. pfm 0.3-1 +plot.TOXSWA_cwa. pfm 0.3-7
                            - pfm 0.3-1 + pfm 0.3-7
                            • Index
                              • diff --git a/pkg/inst/web/read.TOXSWA_cwa.html b/pkg/inst/web/read.TOXSWA_cwa.html index 5542fca..3f2d997 100644 --- a/pkg/inst/web/read.TOXSWA_cwa.html +++ b/pkg/inst/web/read.TOXSWA_cwa.html @@ -2,7 +2,7 @@ -read.TOXSWA_cwa. pfm 0.3-1 +read.TOXSWA_cwa. pfm 0.3-7
                              - pfm 0.3-1 + pfm 0.3-7
                              • Index
                                • @@ -54,12 +54,13 @@ Johannes Ranke

                                Usage

                                - 
                                read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", windows = NULL, thresholds = NULL)
                                + 
                                read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", substance = "parent", total = FALSE, windows = NULL, thresholds = NULL)

                                Arguments

                                filename
                                -
                                The filename of the cwa file.
                                +
                                The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
                                basedir
                                The path to the directory where the cwa file resides.
                                zipfile
                                @@ -67,6 +68,14 @@ Johannes Ranke
                                segment
                                The segment for which the data should be read. Either "last", or the segment number.
                                +
                                substance
                                +
                                For TOXSWA 4 .out files, the default value "parent" leads +to reading concentrations of the parent compound. Alternatively, the substance +of interested can be selected by its code name.
                                +
                                total
                                +
                                Set this to TRUE in order to read total concentrations as well. This is +only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa +files. For .cwa files, the total concentration is always read as well.
                                windows
                                Numeric vector of width of moving windows in days, for calculating maximum time weighted average concentrations and areas under the curve.
                                @@ -90,7 +99,9 @@ An instance of an R6 object of class

                                Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last -segment are imported.

                                +segment are imported. As TOXSWA 4 reports the values at the end of the hour +(ConLiqWatLayCur) in its summary file, we use this value as well instead +of the hourly averages (ConLiqWatLay).

                                diff --git a/pkg/inst/web/soil_scenario_data_EFSA_2015.html b/pkg/inst/web/soil_scenario_data_EFSA_2015.html index 1d4328f..0230afb 100644 --- a/pkg/inst/web/soil_scenario_data_EFSA_2015.html +++ b/pkg/inst/web/soil_scenario_data_EFSA_2015.html @@ -2,7 +2,7 @@ -soil_scenario_data_EFSA_2015. pfm 0.3-1 +soil_scenario_data_EFSA_2015. pfm 0.3-7 @@ -32,7 +32,7 @@
                                - pfm 0.3-1 + pfm 0.3-7