The derappp data object

Code

library(dplyr, warn.conflicts = FALSE)
library(dm, warn.conflicts = FALSE)
library(derappp)
library(units)

The data contained in this package is mainly provided in the form of the data object derappp::derappp. This data object is a so-called dm object that can be seen as a collection of tables. The relations between the tables are shown in Figure 1.

Code

dm_draw(derappp)

Figure 1: Diagram showing the relation between the different tables in the data object. Unique keys are underlined, foreign key relationships are displayed as curved arrows between the tables.

The tables containing the endpoints (dark blue), like p0 for the vapour pressure, or soil_sorption for data on sorption to soils, contain references to the table of substances (substances) and to the table of information sources (sources). Tables containing endpoints from toxicity tests additionally contain references to the table of test species (species). The table substance_keys contains mappings of the substance names to identifiers used in other relevant data sources. The compositions of the substances are defined in substance_compositions, which contains references to the table of chemical entities (chents).

The tables in the data object are described in the following sections.

Substances and their compositions

There are three types of substances in this table. Pure, well-defined chemical substances are considered to be chemical entities and have type chent. For all chemical entities, the structure is available in the form of a SMILES code. Substances can also be of the type mixture or undefined.

Code

derappp$substances

# A tibble: 390 × 3
   substance                       n_chents type     
   <chr>                              <int> <fct>    
 1 1-Decanol                              1 chent    
 2 1-Methylcyclopropene                   1 chent    
 3 1-Naphthylacetic acid                  1 chent    
 4 2,4-D                                  1 chent    
 5 2,4-DB                                 1 chent    
 6 2,6-Dichlorobenzamide                  1 chent    
 7 2-(1-Naphthyl) acetamide               1 chent    
 8 2-Amino-4,6-dimethoxypyrimidine        1 chent    
 9 3AEY                                   0 undefined
10 6-Benzyladenine                        1 chent    
# ℹ 380 more rows

Pure substances with defined chemical structure (chemical entities)

The chemical composition of the substances is stored in substance_compositions as follows. Chemical entities are substances with only one component. The name of the substance is equal to the name of the chemical entity, and the minimum as well as the maximum content is equal to one.

Code

derappp$substance_compositions |> filter(min == 1)

# A tibble: 358 × 6
   substance                       chent                   min   max doi    page
   <chr>                           <chr>                 <dbl> <dbl> <chr> <int>
 1 1-Decanol                       1-Decanol                 1     1 <NA>     NA
 2 1-Methylcyclopropene            1-Methylcyclopropene      1     1 <NA>     NA
 3 1-Naphthylacetic acid           1-Naphthylacetic acid     1     1 <NA>     NA
 4 2,4-D                           2,4-D                     1     1 <NA>     NA
 5 2,4-DB                          2,4-DB                    1     1 <NA>     NA
 6 2,6-Dichlorobenzamide           2,6-Dichlorobenzamide     1     1 <NA>     NA
 7 2-(1-Naphthyl) acetamide        2-(1-Naphthyl) aceta…     1     1 <NA>     NA
 8 2-Amino-4,6-dimethoxypyrimidine 2-Amino-4,6-dimethox…     1     1 <NA>     NA
 9 6-Benzyladenine                 6-Benzyladenine           1     1 <NA>     NA
10 Acequinocyl                     Acequinocyl               1     1 <NA>     NA
# ℹ 348 more rows

Mixtures of chemical entities

For mixtures, the minimum content of at least one component is less than one. The source of the compositional information is given via a DOI and a page number.

Code

derappp$substance_compositions |> filter(min < 1)

# A tibble: 34 × 6
   substance        chent                       min   max doi               page
   <chr>            <chr>                     <dbl> <dbl> <chr>            <int>
 1 Abamectin        Avermectin B1a              0.8 1     10.2903/j.efsa.…     2
 2 Abamectin        Avermectin B1b              0   0.2   10.2903/j.efsa.…     2
 3 Beta-cyfluthrin  Cyfluthrin-(1S,3S,alphaR)   0   0.334 10.2903/j.efsa.…     7
 4 Beta-cyfluthrin  Cyfluthrin-(1R,3R,alphaS)   0   0.334 10.2903/j.efsa.…     7
 5 Beta-cyfluthrin  Cyfluthrin-(1S,3R,alphaR)   0   0.667 10.2903/j.efsa.…     7
 6 Beta-cyfluthrin  Cyfluthrin-(1R,3S,alphaS)   0   0.667 10.2903/j.efsa.…     7
 7 Bifenthrin       Bifenthrin-(1R,3R)          0   1     10.2903/j.efsa.…    11
 8 Bifenthrin       Bifenthrin-(1S,3S)          0   1     10.2903/j.efsa.…    11
 9 Bordeaux mixture Copper(II) sulfate          0   1     10.2903/j.efsa.…     7
10 Bordeaux mixture Calcium hydroxide           0   1     10.2903/j.efsa.…     7
# ℹ 24 more rows

Substances without specified composition

Substances for which no minimum content is recorded for any chemical entity are considered undefined and listed as such in the substances table.

Code

derappp$substance_compositions |> filter(is.na(min))

# A tibble: 19 × 6
   substance                                       chent   min   max doi    page
   <chr>                                           <chr> <dbl> <dbl> <chr> <int>
 1 3AEY                                            <NA>     NA    NA <NA>     NA
 2 Aqueous Extract of sweet Lupinus albus          <NA>     NA    NA <NA>     NA
 3 Aureobasidium pullulans                         <NA>     NA    NA <NA>     NA
 4 Cydia pomonella granulovirus                    <NA>     NA    NA <NA>     NA
 5 Ethoxylated triglyceride 10 OE                  <NA>     NA    NA <NA>     NA
 6 Fatty acids                                     <NA>     NA    NA <NA>     NA
 7 Fatty acids, C7-18 and C18-unsatd., potassium … <NA>     NA    NA <NA>     NA
 8 Horsetail extract                               <NA>     NA    NA <NA>     NA
 9 Maltodextrin                                    <NA>     NA    NA <NA>     NA
10 Mancozeb                                        <NA>     NA    NA <NA>     NA
11 Meptyldinocap                                   <NA>     NA    NA <NA>     NA
12 Metiram                                         <NA>     NA    NA <NA>     NA
13 Mineral oil                                     <NA>     NA    NA <NA>     NA
14 Orange oil                                      <NA>     NA    NA <NA>     NA
15 Paraffin oil                                    <NA>     NA    NA <NA>     NA
16 Soy lecithin                                    <NA>     NA    NA <NA>     NA
17 Tea tree oil                                    <NA>     NA    NA <NA>     NA
18 Terpenoid Blend QRD 460                         <NA>     NA    NA <NA>     NA
19 Zineb                                           <NA>     NA    NA <NA>     NA

Chemical entities

The table of chemical entities in the package is shown below.

Code

derappp$chents

# A tibble: 358 × 8
   chent                 ai    iso      mw smiles pubchem inchikey bcpc_activity
   <chr>                 <lgl> <chr> <dbl> <chr>    <int> <chr>    <chr>        
 1 1-Decanol             TRUE  <NA>  158.  CCCCC…    8174 MWKFXSU… <NA>         
 2 1-Methylcyclopropene  TRUE  <NA>   54.1 CC1=C…  151080 SHDPRTQ… plant growth…
 3 1-Naphthylacetic acid TRUE  <NA>  186.  C1=CC…    6862 PRPINYU… <NA>         
 4 2,4-D                 TRUE  2,4-D 221.  C1=CC…    1486 OVSKIKF… herbicides   
 5 2,4-DB                TRUE  2,4-… 249.  C1=CC…    1489 YIVXMZJ… herbicides   
 6 2,6-Dichlorobenzamide FALSE <NA>  190.  C1=CC…   16183 JHSPCUH… <NA>         
 7 2-(1-Naphthyl) aceta… TRUE  <NA>  185.  C1=CC…    6861 XFNJVKM… <NA>         
 8 2-Amino-4,6-dimethox… FALSE <NA>  155.  COC1=…  118946 LVFRCHI… <NA>         
 9 6-Benzyladenine       TRUE  <NA>  225.  C1=CC…   62389 NWBJYWH… <NA>         
10 Acequinocyl           TRUE  Aceq… 384.  CCCCC…   93315 QDRXWCA… acaricides   
# ℹ 348 more rows

In the package, there is also a list of chent objects that can be used to plot any of the structures, if the chents package is installed, as illustrated in Figure 2 below.

Code

if (requireNamespace("chents")) {
    plot(derappp_chents[["Tebufenozide"]])
}

Chemical structure diagram of tebufenozide — Figure 2: Chemical structure of tebufenozide, plotted using the chents package

Sources

The table of sources that can be referenced is given below.

Code

derappp$sources

# A tibble: 564 × 5
   sk                        reference                         year  url   file 
   <chr>                     <chr>                             <chr> <chr> <chr>
 1 derappp                   "E. Lutz, M. Mathis, and J. Rank… 2026  http… <NA> 
 2 szocs2020webchem          "E. Szöcs, T. Stirling, E. R. Sc… 2020  <NA>  <NA> 
 3 ranke2026chents           "J. Ranke. _chents: Chemical Ent… 2026  http… <NA> 
 4 BCPC_Compendium           "British Crop Protection Council… 2024  http… <NA> 
 5 PubChem                   "National Center for Biotechnolo… 2024  http… <NA> 
 6 CAS_Common_Chemistry      "CAS Division of the American Ch… 2024  http… <NA> 
 7 envipath                  "enviPath UG & Co KG. _envipath:… 2024  http… <NA> 
 8 PPDB_Agroscope_2024-07-01 "University of Hertfordshire, ed… 2024  <NA>  <NA> 
 9 PIERIS_2024-06-05         "Agroscope, ed. _Pesticides and … 2024  <NA>  <NA> 
10 ranke2026openfoodtox      "J. Ranke. _OpenFoodTox: EFSA Op… 2026  http… <NA> 
# ℹ 554 more rows

Any of the sources can be referenced in any vignette in this package. For example, we can refer to the derapp package (Lutz et al. 2026), to the website of the British Crop Protection Council for the ISO names (British Crop Protection Council 2024), or to any of the EFSA conclusions, e.g. the one for cyprodinil (EFSA 2006), or the Listing of Endpoints for acetamiprid (EFSA 2016).

Species

The table of species observed in the toxicity tests is given below.

Code

derappp$species

# A tibble: 199 × 7
   species      group derappp_species ott_id is_synonym flags salt_water_species
   <chr>        <chr> <chr>            <int> <lgl>      <chr> <lgl>             
 1 Acipenser t… Fish  Acipenser tran… 3.79e5 FALSE      ""    FALSE             
 2 Americamysi… Aqua… Americamysis b… 3.34e5 FALSE      ""    TRUE              
 3 American fl… Fish  Jordanella flo… 8.23e4 FALSE      ""    FALSE             
 4 American wa… Aqua… Elodea canaden… 1.07e6 FALSE      ""    FALSE             
 5 Amphiascus … Aqua… Amphiascus ten… 5.95e5 FALSE      ""    FALSE             
 6 Anabaena fl… Aqua… Dolichospermum… 3.69e5 FALSE      "sib… FALSE             
 7 Anabaena fl… Aqua… Dolichospermum… 3.69e5 FALSE      "sib… FALSE             
 8 Anabaena va… Aqua… Trichormus var… 5.24e5 TRUE       "inc… FALSE             
 9 Ankistrodes… Aqua… Ankistrodesmus… 7.28e5 FALSE      ""    FALSE             
10 Aphanizomen… Aqua… Aphanizomenon … 8.94e5 FALSE      "sib… FALSE             
# ℹ 189 more rows

Endpoint tables

The endpoint tables make use of the units package, where applicable. As the tibble package supports printing these units, they are shown in the output listings below.

Vapour pressure `p0`

Code

derappp$p0

# A tibble: 5 × 8
  substance          sign           p0    T purity sk               page comment
  <chr>              <lgl>        [Pa] [°C] <chr>  <chr>           <int> <chr>  
1 Acetamiprid        NA    0.000000173   50 ≥99.9% j.efsa.2016.46…     2 <NA>   
2 Captan             NA    0.0000042     20 99.8%  j.efsa.2020.62…     3 <NA>   
3 Captan             NA    0.000201      50 98.95% j.efsa.2020.62…     3 <NA>   
4 Copper oxychloride NA    0             20 <NA>   j.efsa.2013.32…     6 Expect…
5 Cyprodinil         NA    0.00049       25 <NA>   j.efsa.2006.51r    39 Midpoi…

Water solubility `cwsat`

Code

derappp$cwsat

# A tibble: 12 × 9
   substance          sign       cwsat    T    pH purity sk         page comment
   <chr>              <lgl>     [mg/L] [°C] <dbl> <chr>  <chr>     <int> <chr>  
 1 Acetamiprid        NA      4250       25  5    ≥99%   j.efsa.2…     2 <NA>   
 2 Acetamiprid        NA      2950       25  7    ≥99%   j.efsa.2…     2 <NA>   
 3 Acetamiprid        NA      3960       25  9    ≥99%   j.efsa.2…     2 <NA>   
 4 Captan             NA         4.8     20  5    99.8%  j.efsa.2…     3 <NA>   
 5 Captan             NA         5.2     20  7    99.8%  j.efsa.2…     3 <NA>   
 6 Captan             NA        NA       20  9    99.8%  j.efsa.2…     3 Rapid …
 7 Copper oxychloride NA         1.19    20  6.55 <NA>   j.efsa.2…     6 pH val…
 8 Copper oxychloride NA    101000       20  3.1  <NA>   j.efsa.2…     6 <NA>   
 9 Copper oxychloride NA         0.525   20 10.1  <NA>   j.efsa.2…     6 <NA>   
10 Cyprodinil         NA        20       25  5    <NA>   j.efsa.2…    39 HPLC m…
11 Cyprodinil         NA        13       25  7    <NA>   j.efsa.2…    39 HPLC m…
12 Cyprodinil         NA        15       25  9    <NA>   j.efsa.2…    39 HPLC m…

Soil sorption

Code

print(derappp$soil_sorption[c("substance", "soil_type", "soil_pH",
  "Kd", "Koc", "Kf", "Kfoc", "n", "sk")])

# A tibble: 12 × 9
   substance          soil_type  soil_pH    Kd     Koc    Kf   Kfoc      n sk   
   <chr>              <chr>        <dbl> [L/k…  [L/kg] [L/k… [L/kg]  <dbl> <chr>
 1 Acetamiprid        Sand           5.7    NA    NA    0.6   138.   0.842 j.ef…
 2 Acetamiprid        Loamy sand     7.6    NA    NA    1.35  130.   0.825 j.ef…
 3 Acetamiprid        Sandy loam     7.1    NA    NA    1.12   71.1  0.893 j.ef…
 4 Acetamiprid        Silt loam      7.7    NA    NA    1.69  122.   0.835 j.ef…
 5 Acetamiprid        Silt loam      7.1    NA    NA    3.13   71.4  0.907 j.ef…
 6 Captan             <NA>          NA      NA    76.8 NA      NA   NA     j.ef…
 7 Copper oxychloride <NA>           4.5    NA 19510.  NA      NA   NA     j.ef…
 8 Copper oxychloride <NA>           6      NA 33918.  NA      NA   NA     j.ef…
 9 Cyprodinil         <NA>           5.6    NA    NA   16.9  2098.   0.816 j.ef…
10 Cyprodinil         <NA>           6.7    NA    NA   14.4  1794.   0.787 j.ef…
11 Cyprodinil         <NA>           7.3    NA    NA   32    1593    0.833 j.ef…
12 Cyprodinil         <NA>           7      NA    NA   25    1678.   0.874 j.ef…

Soil degradation

A table of worst‑case soil degradation values, most of them as used for PECsoil calculations in EFSA Conclusions. Actual half‑life values are reported in the column DT50 when the Simple First‑Order (SFO) kinetic model provided the best fit to the degradation data. When other kinetic models were used (FOMC, DFOP, HS), the corresponding model parameters are recorded, and a pseudo‑DT50 value is calculated for comparison purposes (DT90/3.32 for FOMC, and ln(2)/k₂ for DFOP and HS).

Code

print(derappp$soil_degradation[c("substance", "DT50", "kinetics",
  "alpha", "beta", "k1", "k2", "g", "tb", "sk")])

# A tibble: 71 × 10
   substance       DT50 kinetics alpha  beta      k1       k2   g  tb sk        
   <chr>            [d] <chr>      [1] [1/d]   [1/d]    [1/d] [1] [d] <chr>     
 1 Amisulbrom      12.6 SFO      NA     NA   NA      NA        NA  NA j.efsa.20…
 2 Azoxystrobin   262   SFO      NA     NA   NA      NA        NA  NA j.efsa.20…
 3 Benalaxyl      128.  SFO      NA     NA   NA      NA        NA  NA j.efsa.20…
 4 Bixafen       3014.  HS       NA     NA    0.0081  0.00023  NA  53 j.efsa.20…
 5 Boscalid       227.  SFO      NA     NA   NA      NA        NA  NA Boscalid_…
 6 Bupirimate     119.  FOMC      1.12  58.4 NA      NA        NA  NA j.efsa.20…
 7 Buprofezin     166.  SFO      NA     NA   NA      NA        NA  NA j.efsa.20…
 8 Carbendazim     78   SFO      NA     NA   NA      NA        NA  NA j.efsa.20…
 9 Chloridazon     78.5 SFO      NA     NA   NA      NA        NA  NA j.efsa.20…
10 Chlorotoluron  107.  SFO      NA     NA   NA      NA        NA  NA Chlorotol…
# ℹ 61 more rows

Aquatic toxicity

Code

derappp$aquatic_toxicity[c("substance", "derappp_species", "duration", "effect",
  "sign", "value", "sk")]

# A tibble: 977 × 7
   substance derappp_species                 duration effect sign    value sk   
   <chr>     <chr>                                [d] <chr>  <chr>  [mg/L] <chr>
 1 Abamectin Pimephales promelas                    4 <NA>   =     1.47e+1 j.ef…
 2 Abamectin Oncorhynchus mykiss (species i…        4 <NA>   =     7   e+0 j.ef…
 3 Abamectin Oncorhynchus mykiss (species i…        4 <NA>   =     2.5 e+0 j.ef…
 4 Abamectin Danio rerio                            4 <NA>   =     4.9 e+1 j.ef…
 5 Abamectin Oncorhynchus mykiss (species i…       72 <NA>   =     5.2 e-1 j.ef…
 6 Abamectin Daphnia magna                          2 <NA>   =     5.6 e-1 j.ef…
 7 Abamectin Daphnia longispina                     2 <NA>   =     3.5 e-1 j.ef…
 8 Abamectin Daphnia pulex                          2 <NA>   =     9.6 e-2 j.ef…
 9 Abamectin Simocephalus (genus in Protost…        2 <NA>   =     3   e-1 j.ef…
10 Abamectin Brachionus calyciflorus                1 <NA>   =     3.78e+3 j.ef…
# ℹ 967 more rows

Soil toxicity

As soil toxicity values can have incompatible unit types, as some values are expressed as rates (e.g. in g/ha) and some are expressed as concentrations (e.g. mg/kg dry soil), there is a dedicated unit column in the soil_toxicity table.

Code

derappp$soil_toxicity[c("substance", "derappp_species", "duration", "effect",
  "sign", "value", "unit", "sk")]

# A tibble: 461 × 8
   substance             derappp_species duration effect sign  value unit  sk   
   <chr>                 <chr>                [d] <chr>  <chr> <dbl> <chr> <chr>
 1 2,6-Dichlorobenzamide Eisenia fetida        56 repro… =     250   mg/kg Dich…
 2 2,6-Dichlorobenzamide Folsomia candi…       28 repro… =      25   mg/kg j.ef…
 3 2-Amino-4,6-dimethox… Eisenia fetida        56 repro… =      10   mg/kg j.ef…
 4 2-Amino-4,6-dimethox… Eisenia fetida        56 repro… =      15.5 mg/kg j.ef…
 5 2-Amino-4,6-dimethox… Gaeolaelaps ac…       14 repro… ≥     100   mg/kg Fora…
 6 2-Amino-4,6-dimethox… Folsomia candi…       28 repro… ≥     100   mg/kg Fora…
 7 2-Amino-4,6-dimethox… Eisenia fetida        56 repro… ≥     100   mg/kg Flaz…
 8 2-Amino-4,6-dimethox… Folsomia candi…       28 repro… ≥     100   mg/kg Flaz…
 9 2-Amino-4,6-dimethox… Gaeolaelaps ac…       14 repro… ≥     100   mg/kg Flaz…
10 Amisulbrom            Eisenia fetida        56 repro… ≥      93.7 mg/kg amis…
# ℹ 451 more rows

References

British Crop Protection Council. 2024. “Compendium of Pesticide Common Names.” http://www.bcpcpesticidecompendium.org/.

EFSA. 2006. Conclusion Regarding the Peer Review of the Pesticide Risk Assessment of the Active Substance Cyprodinil. EFSA conclusion. European Food Safety Authority. https://doi.org/doi:10.2903/j.efsa.2006.51r.

EFSA. 2016. Appendix to: Peer Review of the Pesticide Risk Assessment of the Active Substance Acetamiprid. EFSA conclusion. European Food Safety Authority. https://doi.org/doi:10.2903/j.efsa.2016.4610.

Lutz, Elisabeth, Marcel Mathis, and Johannes Ranke. 2026. Derappp: Data for Environmental Risk Assessment of Plant Protection Products. https://agroscope-ch.github.io/derappp/.

The derappp data object

Substances and their compositions

Pure substances with defined chemical structure (chemical entities)

Mixtures of chemical entities

Substances without specified composition

Chemical entities

Sources

Species

Endpoint tables

Vapour pressure p0

Water solubility cwsat

Soil sorption

Soil degradation

Aquatic toxicity

Soil toxicity

References

Vapour pressure `p0`

Water solubility `cwsat`