Get variable from aeme

Usage

get_var(
  aeme,
  model,
  var_sim,
  depth = NULL,
  depth_ref = c("surface", "bottom"),
  return_df = TRUE,
  ens_n = 1,
  use_obs = FALSE,
  remove_spin_up = TRUE,
  cumulative = FALSE,
  zone = NULL,
  sed_layer = NULL
)

Arguments

aeme: Aeme object.
model: character vector; models to use. One or more of "dy_cd", "glm_aed", "gotm_wet", "simstrat_aed2". Defaults to all models if not found in aeme.
var_sim: character; variable in the AEME format (e.g. "HYD_temp").
depth: numeric; depth of the variable to extract, referenced to depth_ref. Default is NULL. If NULL, the variable profiles are extracted.
depth_ref: character; what depth is measured from when a single depth is extracted. "surface" (default): metres below the water surface. "bottom": metres above the lake bed, so depth = 1 is the water 1 m above the bottom. That is level - depth metres below the surface, with level the modelled water level (LKE_lvlwtr) on each date, so it follows the surface as the level rises and falls. On a date when the level is below depth (the point would be above the surface) the value is NA. Ignored when depth is NULL. (Before AEME 0.4.0 "bottom" was measured from the basin's full depth, which only matches when the level equals that depth.)
return_df: logical; if TRUE, return a dataframe; if FALSE, return a list. Default is TRUE.
ens_n: integer; ensemble number to plot. Default is 1.
use_obs: logical; if TRUE, use observations to extract the variable at time and depth of observations. Default is FALSE. Use this option if you want to compare model output to observations. Observations recorded as a height above the lake bed (see add_obs()) are compared with the model profile at (the model's water level - that height) on each date, so they follow the model's own level rather than the depth they were placed at when added.
remove_spin_up: logical; remove spin-up period from plot. Default is TRUE.
cumulative: logical; if TRUE, return cumulative sum of variable
zone: integer; for GLM-AED sediment-zone variables (those with an nzones column, e.g. "SED_Fsed_oxy", "SED_temp"), keep only these sediment zones (GLM zone order, 1 = deepest). NULL (default) keeps all.
sed_layer: integer; for variables with a sediment-layer dimension ("SED_temp"), keep only these layers (1 = shallowest). NULL (default) keeps all. Sediment variables are returned in long format with one column per dimension (nzones, sed_layers); depth_ref/depth do not apply.

Value

dataframe or list