Make species report — make_new_report • BirdFlowPipeline

Note: I ran this on unity after using devtools::load_all() it seemed to be writing temporary files to the inst/rmd directory. This suggests that it might not work with an installed version of BirdFlowPipeline. If that's the case we'd have to copy the Rmd from the package to a temorary location before knitting.

Usage

make_new_report(
  model,
  bmtr,
  anim,
  html,
  routes,
  prevlink = NA,
  nextlink = NA,
  test_metrics = NA,
  train_metrics = NA,
  title = NA,
  cor_threshold = NA,
  cor_metric = NA,
  mean_rating = NA
)

Arguments

model: path to HDF5 model file
bmtr: path to BMTR RDS file containing output from BirdFlowR::calc_bmtr()
anim: path to abundance and flux animation GIF
html: path to output html file
routes: path to routes plot
prevlink: relative path to the previous species report or NULL if there is none.
nextlink: relative path to the next species report or NULL if none.
test_metrics, train_metrics: Optional data frame containing performance metrics from the grid search for the training and test datasets respectively. If NA than the tuning section isn't included in the report. @param title Title for report, default of NA results in " BMTR" @param cor_threshold,cor_metric Threshold and metric used to exclude models that are not sufficient close to the training S&T distributions
mean_rating: Mean rating from 1 (worst) to 5 (best), assigned to the BirdFlow model by a minimum of two reviewers on the BirdFlow team.

Value

Nothing is returned, a report is created at html

Examples

if (FALSE) { # \dontrun{

p <- list()
p$model <-  system.file("rmd/example_data/sstspa_model.hdf5", package = "BirdFlowPipeline") 
p$bmtr <-  system.file("rmd/example_data/sstspa_bmtr.Rds", package = "BirdFlowPipeline") 
p$anim <-  system.file("rmd/example_data/sstspa_anim.gif", package = "BirdFlowPipeline") 
p$html <-  tempfile(fileext = ".html", pattern = "report")
p$routes <-  system.file("rmd/example_data/sstspa_routes.hdf5", package = "BirdFlowPipeline") 
p$prevlink <-  NA
p$nextlink <-  NA
p$test_metrics <-  system.file("rmd/example_data/sstspa_test_metrics.rds", package = "BirdFlowPipeline") |> readRDS()                             
p$train_metrics <-  system.file("rmd/example_data/sstspa_train_metrics.rds", package = "BirdFlowPipeline")   |> readRDS()
p$title <- "Example Species Report"
p$cor_threshold <- 0.9
p$cor_metric <- "min_dist_cor"  
p$mean_rating <- 4

do.call(make_new_report, args = p)

} # }