Tutorial: Use Cases • LHTpicker

# installed_packages <- rownames(installed.packages())
# if (!'LHTPicker' %in% installed_packages) {
#   devtools::install_github("https://github.com/d2gex/LHTPicker", dep=TRUE)
# }
# Ensure knitr does run the vignette from the same folder as interactively
knitr::opts_knit$set(root.dir = dirname(getwd()))
library(LHTpicker)

1. Fetch wanted LHTs from FishLife

1.1 Inputted taxa details

A csv file with the taxon names you are after and the wanted LHTs is required as shown below

taxon_lhts_to_fetch <- readRDS("vignettes/data/wanted_taxon_details.rds")
head(taxon_lhts_to_fetch)
#>                   taxon Linf Winf  K L50  M Amat Amax Temperature
#> 1    Trisopterus luscus   NA   NA NA  NA NA   NA   NA          NA
#> 2 Pollachius pollachius   NA   NA NA  NA NA   NA   NA          NA

1.2 Fetching predicted LHTs

p_lht_picker <- PredictedLHTPicker$new(FishLife::FishBase_and_Morphometrics,
                                       fishlife_context$lht_names,
                                       fishlife_context$backtransform_function_list,
                                       taxon_lhts_to_fetch)
predicted_lht_df <- p_lht_picker$pick_and_backtransform()
head(predicted_lht_df)
#>                   taxon     Linf      Winf         K      L50         M
#> 1    Trisopterus luscus 43.86770  833.9878 0.3737931 19.52203 0.5981946
#> 2 Pollachius pollachius 87.30785 5819.9735 0.1867131 34.71789 0.3085845
#>       Amat      Amax Temperature
#> 1 1.400562  6.458926    17.36961
#> 2 3.456610 12.138258    12.11773

2 Fetch updated LHTs given new data

2.1 Inputted predicting taxa details

A csv file with the taxon names you are after and the wanted-to-update LHTs is required as shown below

taxon_lhts_to_update <- readRDS("vignettes/data/wanted_update_taxon_details.rds")
head(taxon_lhts_to_update)
#>                   taxon   Linf  Winf     K   L50     M Amat Amax Temperature
#> 1    Trisopterus luscus  42.41   921 0.210 19.45 0.254   NA    9        14.3
#> 2 Pollachius pollachius 102.14 12045 0.193 41.60 0.284   NA    8        14.3

2.2 Fetching updated LHTs


u_lht_picker <- UpdatedLHTPicker$new(
  FishLife::FishBase_and_Morphometrics,
  taxon_lhts_to_update,
  fishlife_context$updated_prefix,
  fishlife_context$transform_function_list,
  fishlife_context$backtransform_function_list,
  fishlife_context$lht_names
)
updated_lht_df <- u_lht_picker$pick_and_backtransform()
head(updated_lht_df)
#>                   taxon   Linf  Winf     K   L50     M Amat Amax Temperature
#> 1    Trisopterus luscus  42.41   921 0.210 19.45 0.254   NA    9        14.3
#> 2 Pollachius pollachius 102.14 12045 0.193 41.60 0.284   NA    8        14.3
#>   updated_Linf updated_Winf updated_K updated_M updated_L50 updated_Amax
#> 1     44.24669     846.1382 0.3422767 0.5655704    19.91196     7.024725
#> 2     95.11434    8399.8020 0.1878959 0.2989860    36.52335    11.118416
#>   updated_Amat updated_Temperature
#> 1     1.445218            16.72769
#> 2     3.418150            13.05402