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Check for complete and correct soil physical parameters

Source: R/check_soilphys.R
check_soilphys.Rd

This function analyses the soilphys dataframe before the flux calculation. It presents a warning, if there are variables missing and also looks for suspicious patterns that suggest an error in the interpolation made by discretize_depth. Mainly checks if certain columns are present and if they are missing, if they can be calculated from the data present. Looks for the following columns by default: "upper","lower","TPS","SWC","AFPS","t","p","DSD0","D0","DS"

Usage

check_soilphys(df, extra_vars = c(), id_cols)

Arguments

df

(dataframe) the soilphys dataframe

extra_vars

(character vector) column names of additional variables to be checked.

id_cols

(character vector) the columns that, together, identify a site uniquely (e.g. site, repetition)

Value

data frame of 'suspicious' parameter/depth combinations, where all values are NA.

See also

Other soilphys: complete_soilphys(), discretize_depth(), soilphys_layered()

Examples

{
data("soilphys")
check_soilphys(soilphys,id_cols = c("site"))
}
#> --------------------------------------------------------
#> your soilphys-dataframe is
#>  ready 
#> the following parameters are still missing: 
#> 
#> please note that for DSD0 calculation,
#>         there may be individual prerequesits of the
#>         fitting parameters you applied. (If so: provide extra_vars =
#>         c('my variable'))
#> 
#> the following parameters have depths with all NA
#> please check if they were discretized correctly
#> --------------------------------------------------------
#> $result
#> [1] TRUE
#> 
#> $suspects
#> # A tibble: 0 × 4
#> # Groups:   site [0]
#> # ℹ 4 variables: site <chr>, upper <dbl>, param <chr>, value <lgl>
#>