config_to_data: Convert config specifications into a data input table

In USGS-R/mda.streams: Data Preparation, Access, and Analysis Functions for the Powell Center Continental Stream Metabolism Project

Convert config specifications into a data input table

Description

Turns a single config row into a data.frame of input data for the specified metabolism modeling function

Usage

config_to_data(config_row, row_num, metab_fun, on_error = c("stop", "warn",
  "quiet"))

Arguments

config_row	a 1-row config data.frame
row_num	the row number/name that this config_row held in the original config
metab_fun	a metabolism modeling function
on_error	character. What to do if data cannot be acquired or merged? If 'stop' or 'warn', the appropriate condition is thrown. If 'warn' or 'quiet', the function [also] returns a character of errors and/or a character of warnings, attached as attributes of the output object

Value

NA or a unitted data.frame, possibly with attributes "errors" and/or "warnings" attached (see on_error)

Examples

## Not run: 
depth_file <- download_ts("depth_calcDischHarvey", "nwis_04087142", 
  on_local_exists="replace")
config <- stage_metab_config(tag="0.0.1", strategy="try stage_metab_config", 
  site="nwis_04087142", dosat=choose_data_source("dosat", "nwis_04087142", 
    logic="simple dosat", type="const", src="12,mg L^-1"), 
    disch=choose_data_source("disch", "nwis_04087142"),
  depth=choose_data_source("depth", "nwis_04087142", logic="local file", 
    type="ts_file", src=depth_file), filename=NULL)
cdat <- config_to_data(config[1,], row_num=1, metab_fun=streamMetabolizer::metab_bayes)
names(cdat)
head(cdat[['data']][which(complete.cases(cdat[['data']])),])
 
login_sb()
site="nwis_01646000"
config <- stage_metab_config(tag="0.0.1", strategy="try stage_metab_config", 
  model="metab_Kmodel", site=site, filename=NULL,
  sitetime=choose_data_source("sitetime", site, logic="unused var"),
  doobs=choose_data_source("doobs", site, logic="unused var"),
  dosat=choose_data_source("dosat", site, logic="unused var"),
  depth=choose_data_source("depth", site, logic="unused var"),
  wtr=choose_data_source("wtr", site, logic="unused var"),
  par=choose_data_source("par", site, logic="unused var"),
  sitedate=choose_data_source("sitedate", site, logic="priority local"),
  K600=choose_data_source("K600", site, logic="nighttime", src="0.0.6", type="pred"),
  dischdaily=choose_data_source("dischdaily", site, logic="priority local"),
  velocdaily=choose_data_source("velocdaily", site, logic="priority local"),
  omit_incomplete=FALSE)
cdat <- config_to_data(config[1,], row_num=1, 
  metab_fun=streamMetabolizer::metab_Kmodel)

## End(Not run)

USGS-R/mda.streams documentation built on June 3, 2023, 8:43 a.m.