Kmodel_allply: Fit a K model

In USGS-R/streamMetabolizer: Models for Estimating Aquatic Photosynthesis and Respiration

Fit a K model

Description

The model will predict daily K estimates from preliminary daily K estimates. Called from metab_Kmodel().

Usage

Kmodel_allply(
  data_daily_all,
  engine,
  weights,
  predictors,
  transforms,
  other_args
)

Arguments

data_daily_all	data to use as input, with columns including K600.daily.obs, weight, and any predictors
engine	The software or function to use in fitting the model. Should be specified via mm_name rather than here. For type='bayes', always 'stan' indicating the software package to use for the MCMC process (see http://mc-stan.org/). For types in c('mle','night','sim') there's again only one option per model (R functions; these need not be named here but will be noted in the suffix of the model name, e.g., "m_np_oi_tr_plrckm.nlm" uses nlm() for model fitting). For type='Kmodel', the name of an interpolation or regression method relating K to the predictor[s] of choice. One of c("mean", "lm", "loess").
weights	For Kmodel, character vector indicating the type of weighting to use. Set to c() for no weights. One of c("1/CI", "K600/CI", c()).
predictors	For Kmodel, character vector of variables (column names in data or data_daily) to use in predicting K. Leave blank or set to c() for no predictors. Otherwise, one or more of these may be included: c("date", "velocity.daily", "discharge.daily").
transforms	For Kmodel, a named character vector of names of functions (probably 'log' or NA) to apply to K600.daily and/or the predictors. K600.daily should probably be logged. The vector names must match the values of predictors, although not all elements of predictors must be included in transforms. Recommended transforms include c(K600.daily='log', date=NA, velocity.daily="log", discharge.daily="log")
other_args	Other arguments passed to the fitting function given by specs$engine. na.rm=TRUE is already passed to mean (which is actually implemented as sum, anyway).

USGS-R/streamMetabolizer documentation built on Aug. 15, 2023, 7:50 a.m.