Nothing
R/prm.R
In fluxtools: A 'shiny' App for Reproducible QA/QC of Eddy Covariance Data
Defines functions
apply_prm
get_prm_rules
.prm_desc
.prm_units
.prm_rules
Documented in
apply_prm
get_prm_rules
if (getRversion() >= "2.15.1") {
utils::globalVariables(c("n_non_na_before", "n_replaced"))
}
# --- INTERNAL: PRM rules (single source of truth) -----------------------------
.prm_rules <- function() {
list(
"^COND_WATER($|_)" = c(0, 10000), # uS cm^-1
"^DO($|_)" = c(0, NA_real_), # umol L^-1
"^PCH4($|_)" = c(0, NA_real_), # nmolCH4 mol^-1
"^PCO2($|_)" = c(0, 10000), # umolCO2 mol^-1
"^PN2O($|_)" = c(0, NA_real_), # nmolN2O mol^-1
"^PPFD_UW_IN($|_)" = c(0, 2400), # umolPhotons m^-2 s^-1
"^TW($|_)" = c(-20, 50), # deg C
"^DBH($|_)" = c(0, 500), # cm
"^LEAF_WET($|_)" = c(0, 100), # %
"^SAP_DT($|_)" = c(-10, 10), # deg C
"^T_BOLE($|_)" = c(-50, 70), # deg C
"^T_CANOPY($|_)" = c(-50, 70), # deg C
"^CH4($|_)" = c(0, 15000), # nmolCH4 mol^-1
"^CH4_MIXING_RATIO($|_)" = c(0, 15000), # nmolCH4 mol^-1
"^CO($|_)" = c(0, NA_real_), # nmolCO mol^-1
"^CO2($|_)" = c(150, 1200), # umolCO2 mol^-1
# "^CO2_MIXING_RATIO($|_)" = c(150, 1200), # umolCO2 mol^-1
"^CO2_SIGMA($|_)" = c(0, 150), # umolCO2 mol^-1
"^CO2C13($|_)" = c(NA_real_, -6), # permil
"^FC($|_)" = c(-100, 100), # umolCO2 m^-2 s^-1
"^FCH4($|_)" = c(-500, 4000), # nmolCH4 m^-2 s^-1
"^H2O($|_)" = c(0, 100), # mmolH2O mol^-1
"^H2O_MIXING_RATIO($|_)" = c(0, 100), # mmolH2O mol^-1
"^H2O_SIGMA($|_)" = c(0, 15), # mmolH2O mol^-1
"^N2O($|_)" = c(0, NA_real_), # nmolN2O mol^-1
"^N2O_MIXING_RATIO($|_)" = c(0, NA_real_), # nmolN2O mol^-1
"^NO($|_)" = c(0, NA_real_), # nmolNO mol^-1
"^NO2($|_)" = c(0, NA_real_), # nmolNO2 mol^-1
"^O3($|_)" = c(0, NA_real_), # nmolO3 mol^-1
"^SC($|_)" = c(-100, 100), # umolCO2 m^-2 s^-1
"^SO2($|_)" = c(0, NA_real_), # nmolSO2 mol^-1
"^FH2O($|_)" = c(-10, 20), # mmolH2O m^-2 s^-1
"^G($|_)" = c(-250, 400), # W m^-2
"^H($|_)" = c(-450, 900), # W m^-2
"^LE($|_)" = c(-450, 900), # W m^-2
"^SG($|_)" = c(-100, 250), # W m^-2
"^SH($|_)" = c(-150, 150), # W m^-2
"^SLE($|_)" = c(-150, 150), # W m^-2
"^PA($|_)" = c(60, 105), # kPa
"^PBLH($|_)" = c(0, 3000), # m
"^RH($|_)" = c(0, 100), # %
"^T_SONIC($|_)" = c(-50, 50), # deg C
"^T_SONIC_SIGMA($|_)" = c(0, 5), # deg C
"^TA($|_)" = c(-50, 50), # deg C
"^VPD($|_)" = c(0, 80), # hPa
"^D_SNOW($|_)" = c(0, 500), # cm
"^P($|_)" = c(0, 50), # mm
"^P_RAIN($|_)" = c(0, 50), # mm
"^P_SNOW($|_)" = c(0, 50), # mm
"^RUNOFF($|_)" = c(0, 200), # mm
"^STEMFLOW($|_)" = c(0, 200), # mm
"^THROUGHFALL($|_)" = c(0, 20), # mm
"^ALB($|_)" = c(0, 100), # %
"^APAR($|_)" = c(0, 2300), # umolPhoton m^-2 s^-1
"^EVI($|_)" = c(-1, 1), # nondimensional
"^FAPAR($|_)"= c(0, 100), # %
"^FIPAR($|_)"= c(0, 100), # %
"^LW_BC_IN($|_)" = c(50, 600), # W m^-2
"^LW_BC_OUT($|_)" = c(100, 750), # W m^-2
"^LW_IN($|_)" = c(50, 600), # W m^-2
"^LW_OUT($|_)" = c(100, 750), # W m^-2
"^MCRI($|_)" = c(0, 10), # nondimensional
"^MTCI($|_)" = c(0, 10), # nondimensional
"^NDVI($|_)" = c(-1, 1), # nondimensional
"^NETRAD($|_)"= c(-200, 1100), # W m^-2
"^NIRV($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^PPFD_BC_IN($|_)" = c(0, 2400), # umolPhoton m^-2 s^-1
"^PPFD_BC_OUT($|_)" = c(0, 2000), # umolPhoton m^-2 s^-1
"^PPFD_DIF($|_)" = c(0, 1400), # umolPhoton m^-2 s^-1
"^PPFD_DIR($|_)" = c(0, 2400), # umolPhoton m^-2 s^-1
"^PPFD_IN($|_)" = c(0, 2400), # umolPhoton m^-2 s^-1
"^PPFD_OUT($|_)" = c(0, 2000), # umolPhoton m^-2 s^-1
"^PRI($|_)" = c(-1, 1), # nondimensional
"^R_UVA($|_)" = c(0, 85), # W m^-2
"^R_UVB($|_)" = c(0, 20), # W m^-2
"^REDCI($|_)" = c(0, 10), # nondimensional
"^REP($|_)" = c(400, 800), # nm
"^SPEC_NIR_IN($|_)" = c(0, 2), # W m^-2 nm^-1
"^SPEC_NIR_OUT($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^SPEC_NIR_REFL($|_)" = c(0, 1), # nondimensional
"^SPEC_PRI_REF_IN($|_)" = c(0, 2), # W m^-2 nm^-1
"^SPEC_PRI_REF_OUT($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^SPEC_PRI_REF_REFL($|_)" = c(0, 1), # nondimensional
"^SPEC_PRI_TGT_IN($|_)" = c(0, 2), # W m^-2 nm^-1
"^SPEC_PRI_TGT_OUT($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^SPEC_PRI_TGT_REFL($|_)" = c(0, 1), # nondimensional
"^SPEC_RED_IN($|_)" = c(0, 2), # W m^-2 nm^-1
"^SPEC_RED_OUT($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^SPEC_RED_REFL($|_)" = c(0, 1), # nondimensional
"^SR($|_)" = c(0, 10), # nondimensional
"^SW_BC_IN($|_)" = c(0, 1300), # W m^-2
"^SW_BC_OUT($|_)"= c(0, 800), # W m^-2
"^SW_DIF($|_)" = c(0, 750), # W m^-2
"^SW_DIR($|_)" = c(0, 1300), # W m^-2
"^SW_IN($|_)" = c(0, 1300), # W m^-2
"^SW_OUT($|_)" = c(0, 800), # W m^-2
"^TCARI($|_)" = c(0, 10), # nondimensional
"^SWC($|_)" = c(0, 100), # %
"^SWP($|_)" = c(-750, 0), # kPa
"^TS($|_)" = c(-40, 65), # deg C
"^TSN($|_)" = c(-40, 4), # deg C
"^WTD($|_)" = c(-10, 10), # m
"^TAU($|_)" = c(-10, 2), # kg m^-1 s^-2
"^U_SIGMA($|_)" = c(0, 12), # m s^-1
"^USTAR($|_)" = c(0, 8), # m s^-1
"^V_SIGMA($|_)" = c(0, 10), # m s^-1
"^W_SIGMA($|_)" = c(0, 5), # m s^-1
"^WD($|_)" = c(0, 360), # degree
"^WD_SIGMA($|_)" = c(0, 180), # degree
"^WS($|_)" = c(0, 40), # m s^-1
"^WS_MAX($|_)" = c(0, 50), # m s^-1
"^GPP($|_)" = c(-30, 100), # umolCO2 m^-2 s^-1
"^NEE($|_)" = c(-100, 100), # umolCO2 m^-2 s^-1
"^RECO($|_)" = c(-20, 50) # umolCO2 m^-2 s^-1
)
}
# --- INTERNAL: PRM units (ASCII) ---------------------------------------------
.prm_units <- function() {
c(
"^COND_WATER($|_)" = "uS cm^-1",
"^DO($|_)" = "umol L^-1",
"^PCH4($|_)" = "nmolCH4 mol^-1",
"^PCO2($|_)" = "umolCO2 mol^-1",
"^PN2O($|_)" = "nmolN2O mol^-1",
"^PPFD_UW_IN($|_)" = "umolPhotons m^-2 s^-1",
"^TW($|_)" = "deg C",
"^DBH($|_)" = "cm",
"^LEAF_WET($|_)" = "%",
"^SAP_DT($|_)" = "deg C",
"^SAP_FLOW($|_)" = "mmolH2O m^-2 s^-1",
"^T_BOLE($|_)" = "deg C",
"^T_CANOPY($|_)" = "deg C",
"^CH4($|_)" = "nmolCH4 mol^-1",
"^CH4_MIXING_RATIO($|_)" = "nmolCH4 mol^-1",
"^CO($|_)" = "nmolCO mol^-1",
"^CO2($|_)" = "umolCO2 mol^-1",
"^CO2_MIXING_RATIO($|_)" = "umolCO2 mol^-1",
"^CO2_SIGMA($|_)" = "umolCO2 mol^-1",
"^CO2C13($|_)" = "permil",
"^FC($|_)" = "umolCO2 m^-2 s^-1",
"^FCH4($|_)" = "nmolCH4 m^-2 s^-1",
"^FN2O($|_)" = "nmolN2O m^-2 s^-1",
"^FNO($|_)" = "nmolNO m^-2 s^-1",
"^FNO2($|_)" = "nmolNO2 m^-2 s^-1",
"^FO3($|_)" = "nmolO3 m^-2 s^-1",
"^H2O($|_)" = "mmolH2O mol^-1",
"^H2O_MIXING_RATIO($|_)" = "mmolH2O mol^-1",
"^H2O_SIGMA($|_)" = "mmolH2O mol^-1",
"^N2O($|_)" = "nmolN2O mol^-1",
"^N2O_MIXING_RATIO($|_)" = "nmolN2O mol^-1",
"^NO($|_)" = "nmolNO mol^-1",
"^NO2($|_)" = "nmolNO2 mol^-1",
"^O3($|_)" = "nmolO3 mol^-1",
"^SC($|_)" = "umolCO2 m^-2 s^-1",
"^SCH4($|_)" = "nmolCH4 m^-2 s^-1",
"^SN2O($|_)" = "nmolN2O m^-2 s^-1",
"^SNO($|_)" = "nmolNO m^-2 s^-1",
"^SNO2($|_)" = "nmolNO2 m^-2 s^-1",
"^SO2($|_)" = "nmolSO2 mol^-1",
"^SO3($|_)" = "nmolO3 m^-2 s^-1",
"^FH2O($|_)" = "mmolH2O m^-2 s^-1",
"^G($|_)" = "W m^-2",
"^H($|_)" = "W m^-2",
"^LE($|_)" = "W m^-2",
"^SB($|_)" = "W m^-2",
"^SG($|_)" = "W m^-2",
"^SH($|_)" = "W m^-2",
"^SLE($|_)" = "W m^-2",
"^PA($|_)" = "kPa",
"^PBLH($|_)" = "m",
"^RH($|_)" = "%",
"^T_SONIC($|_)" = "deg C",
"^T_SONIC_SIGMA($|_)" = "deg C",
"^TA($|_)" = "deg C",
"^VPD($|_)" = "hPa",
"^D_SNOW($|_)" = "cm",
"^P($|_)" = "mm",
"^P_RAIN($|_)" = "mm",
"^P_SNOW($|_)" = "mm",
"^RUNOFF($|_)" = "mm",
"^STEMFLOW($|_)" = "mm",
"^THROUGHFALL($|_)" = "mm",
"^ALB($|_)" = "%",
"^APAR($|_)" = "umolPhoton m^-2 s^-1",
"^EVI($|_)" = "nondimensional",
"^FAPAR($|_)"= "%",
"^FIPAR($|_)"= "%",
"^LW_BC_IN($|_)" = "W m^-2",
"^LW_BC_OUT($|_)" = "W m^-2",
"^LW_IN($|_)" = "W m^-2",
"^LW_OUT($|_)" = "W m^-2",
"^MCRI($|_)" = "nondimensional",
"^MTCI($|_)" = "nondimensional",
"^NDVI($|_)" = "nondimensional",
"^NETRAD($|_)"= "W m^-2",
"^NIRV($|_)" = "W m^-2 sr^-1 nm^-1",
"^PPFD_BC_IN($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_BC_OUT($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_DIF($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_DIR($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_IN($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_OUT($|_)" = "umolPhoton m^-2 s^-1",
"^PRI($|_)" = "nondimensional",
"^R_UVA($|_)" = "W m^-2",
"^R_UVB($|_)" = "W m^-2",
"^REDCI($|_)" = "nondimensional",
"^REP($|_)" = "nm",
"^SPEC_NIR_IN($|_)" = "W m^-2 nm^-1",
"^SPEC_NIR_OUT($|_)" = "W m^-2 sr^-1 nm^-1",
"^SPEC_NIR_REFL($|_)" = "nondimensional",
"^SPEC_PRI_REF_IN($|_)" = "W m^-2 nm^-1",
"^SPEC_PRI_REF_OUT($|_)" = "W m^-2 sr^-1 nm^-1",
"^SPEC_PRI_REF_REFL($|_)" = "nondimensional",
"^SPEC_PRI_TGT_IN($|_)" = "W m^-2 nm^-1",
"^SPEC_PRI_TGT_OUT($|_)" = "W m^-2 sr^-1 nm^-1",
"^SPEC_PRI_TGT_REFL($|_)" = "nondimensional",
"^SPEC_RED_IN($|_)" = "W m^-2 nm^-1",
"^SPEC_RED_OUT($|_)" = "W m^-2 sr^-1 nm^-1",
"^SPEC_RED_REFL($|_)" = "nondimensional",
"^SR($|_)" = "nondimensional",
"^SW_BC_IN($|_)" = "W m^-2",
"^SW_BC_OUT($|_)"= "W m^-2",
"^SW_DIF($|_)" = "W m^-2",
"^SW_DIR($|_)" = "W m^-2",
"^SW_IN($|_)" = "W m^-2",
"^SW_OUT($|_)" = "W m^-2",
"^TCARI($|_)" = "nondimensional",
"^SWC($|_)" = "%",
"^SWP($|_)" = "kPa",
"^TS($|_)" = "deg C",
"^TSN($|_)" = "deg C",
"^WTD($|_)" = "m",
"^TAU($|_)" = "kg m^-1 s^-2",
"^U_SIGMA($|_)" = "m s^-1",
"^USTAR($|_)" = "m s^-1",
"^V_SIGMA($|_)" = "m s^-1",
"^W_SIGMA($|_)" = "m s^-1",
"^WD($|_)" = "degree",
"^WD_SIGMA($|_)" = "degree",
"^WS($|_)" = "m s^-1",
"^WS_MAX($|_)" = "m s^-1",
"^GPP($|_)" = "umolCO2 m^-2 s^-1",
"^NEE($|_)" = "umolCO2 m^-2 s^-1",
"^RECO($|_)" = "umolCO2 m^-2 s^-1"
)
}
# --- INTERNAL: PRM descriptions (from AmeriFlux Tech Note, Table A1) ----------
.prm_desc <- function() {
c(
"^COND_WATER($|_)" = "Conductivity of water",
"^DO($|_)" = "Dissolved oxygen in water",
"^PCH4($|_)" = "Dissolved methane (CH4) in water",
"^PCO2($|_)" = "Dissolved carbon dioxide (CO2) in water",
"^PN2O($|_)" = "Dissolved nitrous oxide (N2O) in water",
"^PPFD_UW_IN($|_)" = "Photosynthetic photon flux density, underwater, incoming",
"^TW($|_)" = "Water temperature",
"^DBH($|_)" = "Tree diameter at breast height",
"^LEAF_WET($|_)" = "Leaf wetness (0-100)",
"^SAP_DT($|_)" = "Sapflow probe temperature difference",
"^T_BOLE($|_)" = "Bole temperature",
"^T_CANOPY($|_)" = "Canopy/surface temperature",
"^CH4($|_)" = "Methane (CH4) mole fraction (wet air)",
"^CH4_MIXING_RATIO($|_)" = "Methane (CH4) mole fraction (dry air)",
"^CO($|_)" = "Carbon monoxide (CO) mole fraction (wet air)",
"^CO2($|_)" = "Carbon dioxide (CO2) mole fraction (wet air)",
"^CO2_MIXING_RATIO($|_)" = "Carbon dioxide (CO2) mole fraction (dry air)",
"^CO2_SIGMA($|_)" = "Std. dev. of CO2 mole fraction (wet air)",
"^CO2C13($|_)" = "Stable isotope delta13C of CO2 (permil)",
"^FC($|_)" = "CO2 turbulent flux (no storage correction)",
"^FCH4($|_)" = "CH4 turbulent flux (no storage correction)",
"^H2O($|_)" = "Water vapor in mole fraction (wet air)",
"^H2O_MIXING_RATIO($|_)" = "Water vapor in mole fraction (dry air)",
"^H2O_SIGMA($|_)" = "Std. dev. of water vapor mole fraction",
"^N2O($|_)" = "N2O mole fraction (wet air)",
"^N2O_MIXING_RATIO($|_)" = "N2O mole fraction (dry air)",
"^NO($|_)" = "NO mole fraction (wet air)",
"^NO2($|_)" = "NO2 mole fraction (wet air)",
"^O3($|_)" = "O3 mole fraction (wet air)",
"^SC($|_)" = "CO2 storage flux",
"^SO2($|_)" = "SO2 mole fraction (wet air)",
"^FH2O($|_)" = "Water vapor (H2O) turbulent flux (no storage correction)",
"^G($|_)" = "Soil heat flux",
"^H($|_)" = "Sensible heat flux (no storage correction)",
"^LE($|_)" = "Latent heat flux (no storage correction)",
"^SG($|_)" = "Soil heat storage flux above plates",
"^SH($|_)" = "Sensible heat storage flux",
"^SLE($|_)" = "Latent heat storage flux",
"^PA($|_)" = "Atmospheric pressure",
"^PBLH($|_)" = "Planetary boundary layer height",
"^RH($|_)" = "Relative humidity (0-100)",
"^T_SONIC($|_)" = "Sonic temperature",
"^T_SONIC_SIGMA($|_)" = "Std. dev. of sonic temperature",
"^TA($|_)" = "Air temperature",
"^VPD($|_)" = "Vapor pressure deficit",
"^D_SNOW($|_)" = "Snow depth",
"^P($|_)" = "Precipitation",
"^P_RAIN($|_)" = "Rainfall",
"^P_SNOW($|_)" = "Snowfall",
"^RUNOFF($|_)" = "Runoff",
"^STEMFLOW($|_)" = "Stemflow",
"^THROUGHFALL($|_)" = "Throughfall",
"^ALB($|_)" = "Albedo (0-100)",
"^APAR($|_)" = "Absorbed PAR",
"^EVI($|_)" = "Enhanced Vegetation Index",
"^FAPAR($|_)"= "Fraction of absorbed PAR (0-100)",
"^FIPAR($|_)"= "Fraction of intercepted PAR (0-100)",
"^LW_BC_IN($|_)" = "Longwave radiation, below canopy incoming",
"^LW_BC_OUT($|_)" = "Longwave radiation, below canopy outgoing",
"^LW_IN($|_)" = "Longwave radiation, incoming",
"^LW_OUT($|_)" = "Longwave radiation, outgoing",
"^MCRI($|_)" = "Carotenoid Reflectance Index",
"^MTCI($|_)" = "MERIS Terrestrial Chlorophyll Index",
"^NDVI($|_)" = "Normalized Difference Vegetation Index",
"^NETRAD($|_)"= "Net radiation",
"^NIRV($|_)" = "Near Infrared Vegetation Index",
"^PPFD_BC_IN($|_)" = "PPFD, below canopy incoming",
"^PPFD_BC_OUT($|_)" = "PPFD, below canopy outgoing",
"^PPFD_DIF($|_)" = "PPFD, diffuse incoming",
"^PPFD_DIR($|_)" = "PPFD, direct incoming",
"^PPFD_IN($|_)" = "PPFD, incoming",
"^PPFD_OUT($|_)" = "PPFD, outgoing",
"^PRI($|_)" = "Photochemical Reflectance Index",
"^R_UVA($|_)" = "UVA radiation, incoming",
"^R_UVB($|_)" = "UVB radiation, incoming",
"^REDCI($|_)" = "Red-Edge Chlorophyll Index",
"^REP($|_)" = "Red-Edge Position",
"^SPEC_NIR_IN($|_)" = "NIR band radiation, incoming (hemispherical)",
"^SPEC_NIR_OUT($|_)" = "NIR band radiation, outgoing",
"^SPEC_NIR_REFL($|_)" = "NIR band reflectance",
"^SPEC_PRI_REF_IN($|_)" = "PRI reference band radiation, incoming",
"^SPEC_PRI_REF_OUT($|_)" = "PRI reference band radiation, outgoing",
"^SPEC_PRI_REF_REFL($|_)" = "PRI reference band reflectance",
"^SPEC_PRI_TGT_IN($|_)" = "PRI target band radiation, incoming",
"^SPEC_PRI_TGT_OUT($|_)" = "PRI target band radiation, outgoing",
"^SPEC_PRI_TGT_REFL($|_)" = "PRI target band reflectance",
"^SPEC_RED_IN($|_)" = "Red band radiation, incoming (hemispherical)",
"^SPEC_RED_OUT($|_)" = "Red band radiation, outgoing",
"^SPEC_RED_REFL($|_)" = "Red band reflectance",
"^SR($|_)" = "Simple Ratio",
"^SW_BC_IN($|_)" = "Shortwave radiation, below canopy incoming",
"^SW_BC_OUT($|_)"= "Shortwave radiation, below canopy outgoing",
"^SW_DIF($|_)" = "Shortwave radiation, diffuse incoming",
"^SW_DIR($|_)" = "Shortwave radiation, direct incoming",
"^SW_IN($|_)" = "Shortwave radiation, incoming",
"^SW_OUT($|_)" = "Shortwave radiation, outgoing",
"^TCARI($|_)" = "Transformed Chlorophyll Absorption in Reflectance Index",
"^SWC($|_)" = "Soil water content (volumetric, 0-100)",
"^SWP($|_)" = "Soil water potential",
"^TS($|_)" = "Soil temperature",
"^TSN($|_)" = "Snow temperature",
"^WTD($|_)" = "Water table depth",
"^TAU($|_)" = "Momentum flux",
"^U_SIGMA($|_)" = "Std. dev. of along-wind velocity",
"^USTAR($|_)" = "Friction velocity",
"^V_SIGMA($|_)" = "Std. dev. of cross-wind velocity",
"^W_SIGMA($|_)" = "Std. dev. of vertical velocity",
"^WD($|_)" = "Wind direction",
"^WD_SIGMA($|_)" = "Std. dev. of wind direction",
"^WS($|_)" = "Wind speed",
"^WS_MAX($|_)" = "Max wind speed in averaging period",
"^GPP($|_)" = "Gross primary productivity",
"^NEE($|_)" = "Net ecosystem exchange",
"^RECO($|_)" = "Ecosystem respiration"
)
}
# --- EXPORTED: rules tibble for vignettes/docs --------------------------------
#' Get the PRM rules as a tibble (for vignettes & checks)
#' @return A tibble with columns: family (regex), variable (base), min, max, units, description
#' @export
get_prm_rules <- function() {
rl <- .prm_rules()
un <- .prm_units()
de <- .prm_desc()
fam <- names(rl) # regex, e.g. ^SWC($|_)
base <- sub("^\\^(.+)\\(\\$\\|_\\)$", "\\1", fam) # SWC
tibble::tibble(
family = fam, # keep for compatibility
variable = base,
min = unname(vapply(rl, function(x) as.numeric(x[1]), numeric(1))),
max = unname(vapply(rl, function(x) as.numeric(x[2]), numeric(1))),
description = unname(de[fam]),
units = unname(un[fam])
)
}
# --- EXPORTED: main function ---------------------------------------------------
#' Apply Physical Range Module (PRM) bounds to AmeriFlux-style data
#'
#' Clamps values to PRM ranges by variable *family* (e.g., `^SWC($|_)`, `^P($|_)`).
#' Columns with "QC" in their names are skipped by default. Out-of-range values
#' are set to `NA`. No columns are removed.
#'
#' @param .data A data.frame or tibble.
#' @param include Optional character vector of base family names to apply (e.g., "SWC", "P").
#' If `NULL`, all families are applied.
#' @param skip_qc Logical; when TRUE, skip columns that look like flags:
#' names ending/containing `_QC` or `_SSITC_TEST` (case-insensitive).
#' Default: TRUE.
#' @param note Logical; print a per-column summary with expected units, PRM range, and counts.
#' @param summarize Logical; if `TRUE`, return a list with `data` and `summary`; otherwise return only the clamped data frame.
#'
#' @return If `summarize = TRUE`, a list with `data` and `summary`; else a data.frame.
#' @export
apply_prm <- function(.data,
include = NULL,
skip_qc = TRUE,
note = TRUE,
summarize = TRUE) {
stopifnot(is.data.frame(.data))
summarize <- isTRUE(summarize) # normalize flag
rules <- .prm_rules()
# --- Always start with an empty tibble
empty_tbl <- tibble::tibble(
column = character(), family = character(),
min = numeric(), max = numeric(),
n_non_na_before = integer(), n_replaced = integer(), pct_replaced = numeric()
)
summ <- empty_tbl
if (!is.null(include)) {
stopifnot(is.character(include))
base <- sub("^\\^(.+)\\(\\$\\|_\\)$", "\\1", names(rules))
keep <- base %in% unique(include)
rules <- rules[keep]
}
before <- .data
applied <- list()
for (pat in names(rules)) {
lim <- rules[[pat]]
min_v <- lim[1]; max_v <- lim[2]
cols <- grep(pat, names(.data), value = TRUE)
if (skip_qc) {
cols <- cols[!grepl("(^|_)QC($|_)", cols, ignore.case = TRUE)]
cols <- cols[!grepl("SSITC_TEST($|_)", cols, ignore.case = TRUE)]
}
if (!length(cols)) next
family_name <- sub("^\\^(.+)\\(\\$\\|_\\)$", "\\1", pat)
for (col in cols) {
x <- suppressWarnings(as.numeric(.data[[col]]))
keep <- !is.na(x)
if (!is.na(min_v)) keep <- keep & x >= min_v
if (!is.na(max_v)) keep <- keep & x <= max_v
x[!keep] <- NA_real_
.data[[col]] <- x
b <- suppressWarnings(as.numeric(before[[col]]))
applied[[length(applied) + 1L]] <- data.frame(
column = col,
family = family_name,
min = min_v,
max = max_v,
n_non_na_before = sum(!is.na(b)),
n_replaced = sum(is.na(x) & !is.na(b)),
stringsAsFactors = FALSE
)
}
}
if (length(applied)) {
# Avoid dplyr::bind_rows() NULL behavior; guard rbind
summ_df <- do.call(rbind, applied)
summ <- tibble::as_tibble(summ_df)
summ <- summ |>
dplyr::mutate(
pct_replaced = ifelse(n_non_na_before > 0, 100 * n_replaced / n_non_na_before, 0)
) |>
dplyr::arrange(dplyr::desc(n_replaced))
if (all(summ$n_replaced == 0L)) {
if (note) message("PRM: no replacements made.")
# keep `summ` as the canonical EMPTY tibble
summ <- empty_tbl
} else if (note) {
u_vec <- .prm_units()
names(u_vec) <- sub("^\\^(.+)\\(\\$\\|_\\)$", "\\1", names(u_vec))
fmt <- function(z) ifelse(is.na(z), "NA", as.character(z))
lines <- mapply(function(col, fam, lo, hi, nrep, pct) {
paste0(
"* ", col, "\n",
" expected units: ", u_vec[[fam]], ", PRM range: ", fmt(lo), " to ", fmt(hi), "\n",
" ", nrep, " values set to NA (", sprintf("%.1f", pct), "% of data)"
)
}, summ$column, summ$family, summ$min, summ$max, summ$n_replaced, summ$pct_replaced,
SIMPLIFY = TRUE)
message(paste0("PRM summary:\n", paste(lines, collapse = "\n")))
}
} else {
# No matching columns at all
if (note) message("PRM: no replacements made.")
summ <- empty_tbl
}
# --- normalize summary type & return shape (ALWAYS a tibble)
if (is.null(summ)) {
summ <- data.frame(
column = character(), family = character(),
min = numeric(), max = numeric(),
n_non_na_before = integer(), n_replaced = integer(), pct_replaced = numeric(),
stringsAsFactors = FALSE
)
}
if (!inherits(summ, "data.frame")) {
summ <- as.data.frame(summ, stringsAsFactors = FALSE)
}
if (requireNamespace("tibble", quietly = TRUE)) {
summ <- tibble::as_tibble(summ)
} else {
class(summ) <- c("tbl_df","tbl",class(summ))
}
if (!inherits(summ, "data.frame")) summ <- as.data.frame(summ, stringsAsFactors = FALSE)
if (requireNamespace("tibble", quietly = TRUE)) summ <- tibble::as_tibble(summ)
if (!summarize) return(.data)
list(data = .data, summary = summ)
}
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Defines functions apply_prm get_prm_rules .prm_desc .prm_units .prm_rules
Documented in apply_prm get_prm_rules
if (getRversion() >= "2.15.1") {
utils::globalVariables(c("n_non_na_before", "n_replaced"))
}
# --- INTERNAL: PRM rules (single source of truth) -----------------------------
.prm_rules <- function() {
list(
"^COND_WATER($|_)" = c(0, 10000), # uS cm^-1
"^DO($|_)" = c(0, NA_real_), # umol L^-1
"^PCH4($|_)" = c(0, NA_real_), # nmolCH4 mol^-1
"^PCO2($|_)" = c(0, 10000), # umolCO2 mol^-1
"^PN2O($|_)" = c(0, NA_real_), # nmolN2O mol^-1
"^PPFD_UW_IN($|_)" = c(0, 2400), # umolPhotons m^-2 s^-1
"^TW($|_)" = c(-20, 50), # deg C
"^DBH($|_)" = c(0, 500), # cm
"^LEAF_WET($|_)" = c(0, 100), # %
"^SAP_DT($|_)" = c(-10, 10), # deg C
"^T_BOLE($|_)" = c(-50, 70), # deg C
"^T_CANOPY($|_)" = c(-50, 70), # deg C
"^CH4($|_)" = c(0, 15000), # nmolCH4 mol^-1
"^CH4_MIXING_RATIO($|_)" = c(0, 15000), # nmolCH4 mol^-1
"^CO($|_)" = c(0, NA_real_), # nmolCO mol^-1
"^CO2($|_)" = c(150, 1200), # umolCO2 mol^-1
# "^CO2_MIXING_RATIO($|_)" = c(150, 1200), # umolCO2 mol^-1
"^CO2_SIGMA($|_)" = c(0, 150), # umolCO2 mol^-1
"^CO2C13($|_)" = c(NA_real_, -6), # permil
"^FC($|_)" = c(-100, 100), # umolCO2 m^-2 s^-1
"^FCH4($|_)" = c(-500, 4000), # nmolCH4 m^-2 s^-1
"^H2O($|_)" = c(0, 100), # mmolH2O mol^-1
"^H2O_MIXING_RATIO($|_)" = c(0, 100), # mmolH2O mol^-1
"^H2O_SIGMA($|_)" = c(0, 15), # mmolH2O mol^-1
"^N2O($|_)" = c(0, NA_real_), # nmolN2O mol^-1
"^N2O_MIXING_RATIO($|_)" = c(0, NA_real_), # nmolN2O mol^-1
"^NO($|_)" = c(0, NA_real_), # nmolNO mol^-1
"^NO2($|_)" = c(0, NA_real_), # nmolNO2 mol^-1
"^O3($|_)" = c(0, NA_real_), # nmolO3 mol^-1
"^SC($|_)" = c(-100, 100), # umolCO2 m^-2 s^-1
"^SO2($|_)" = c(0, NA_real_), # nmolSO2 mol^-1
"^FH2O($|_)" = c(-10, 20), # mmolH2O m^-2 s^-1
"^G($|_)" = c(-250, 400), # W m^-2
"^H($|_)" = c(-450, 900), # W m^-2
"^LE($|_)" = c(-450, 900), # W m^-2
"^SG($|_)" = c(-100, 250), # W m^-2
"^SH($|_)" = c(-150, 150), # W m^-2
"^SLE($|_)" = c(-150, 150), # W m^-2
"^PA($|_)" = c(60, 105), # kPa
"^PBLH($|_)" = c(0, 3000), # m
"^RH($|_)" = c(0, 100), # %
"^T_SONIC($|_)" = c(-50, 50), # deg C
"^T_SONIC_SIGMA($|_)" = c(0, 5), # deg C
"^TA($|_)" = c(-50, 50), # deg C
"^VPD($|_)" = c(0, 80), # hPa
"^D_SNOW($|_)" = c(0, 500), # cm
"^P($|_)" = c(0, 50), # mm
"^P_RAIN($|_)" = c(0, 50), # mm
"^P_SNOW($|_)" = c(0, 50), # mm
"^RUNOFF($|_)" = c(0, 200), # mm
"^STEMFLOW($|_)" = c(0, 200), # mm
"^THROUGHFALL($|_)" = c(0, 20), # mm
"^ALB($|_)" = c(0, 100), # %
"^APAR($|_)" = c(0, 2300), # umolPhoton m^-2 s^-1
"^EVI($|_)" = c(-1, 1), # nondimensional
"^FAPAR($|_)"= c(0, 100), # %
"^FIPAR($|_)"= c(0, 100), # %
"^LW_BC_IN($|_)" = c(50, 600), # W m^-2
"^LW_BC_OUT($|_)" = c(100, 750), # W m^-2
"^LW_IN($|_)" = c(50, 600), # W m^-2
"^LW_OUT($|_)" = c(100, 750), # W m^-2
"^MCRI($|_)" = c(0, 10), # nondimensional
"^MTCI($|_)" = c(0, 10), # nondimensional
"^NDVI($|_)" = c(-1, 1), # nondimensional
"^NETRAD($|_)"= c(-200, 1100), # W m^-2
"^NIRV($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^PPFD_BC_IN($|_)" = c(0, 2400), # umolPhoton m^-2 s^-1
"^PPFD_BC_OUT($|_)" = c(0, 2000), # umolPhoton m^-2 s^-1
"^PPFD_DIF($|_)" = c(0, 1400), # umolPhoton m^-2 s^-1
"^PPFD_DIR($|_)" = c(0, 2400), # umolPhoton m^-2 s^-1
"^PPFD_IN($|_)" = c(0, 2400), # umolPhoton m^-2 s^-1
"^PPFD_OUT($|_)" = c(0, 2000), # umolPhoton m^-2 s^-1
"^PRI($|_)" = c(-1, 1), # nondimensional
"^R_UVA($|_)" = c(0, 85), # W m^-2
"^R_UVB($|_)" = c(0, 20), # W m^-2
"^REDCI($|_)" = c(0, 10), # nondimensional
"^REP($|_)" = c(400, 800), # nm
"^SPEC_NIR_IN($|_)" = c(0, 2), # W m^-2 nm^-1
"^SPEC_NIR_OUT($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^SPEC_NIR_REFL($|_)" = c(0, 1), # nondimensional
"^SPEC_PRI_REF_IN($|_)" = c(0, 2), # W m^-2 nm^-1
"^SPEC_PRI_REF_OUT($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^SPEC_PRI_REF_REFL($|_)" = c(0, 1), # nondimensional
"^SPEC_PRI_TGT_IN($|_)" = c(0, 2), # W m^-2 nm^-1
"^SPEC_PRI_TGT_OUT($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^SPEC_PRI_TGT_REFL($|_)" = c(0, 1), # nondimensional
"^SPEC_RED_IN($|_)" = c(0, 2), # W m^-2 nm^-1
"^SPEC_RED_OUT($|_)" = c(0, 2), # W m^-2 sr^-1 nm^-1
"^SPEC_RED_REFL($|_)" = c(0, 1), # nondimensional
"^SR($|_)" = c(0, 10), # nondimensional
"^SW_BC_IN($|_)" = c(0, 1300), # W m^-2
"^SW_BC_OUT($|_)"= c(0, 800), # W m^-2
"^SW_DIF($|_)" = c(0, 750), # W m^-2
"^SW_DIR($|_)" = c(0, 1300), # W m^-2
"^SW_IN($|_)" = c(0, 1300), # W m^-2
"^SW_OUT($|_)" = c(0, 800), # W m^-2
"^TCARI($|_)" = c(0, 10), # nondimensional
"^SWC($|_)" = c(0, 100), # %
"^SWP($|_)" = c(-750, 0), # kPa
"^TS($|_)" = c(-40, 65), # deg C
"^TSN($|_)" = c(-40, 4), # deg C
"^WTD($|_)" = c(-10, 10), # m
"^TAU($|_)" = c(-10, 2), # kg m^-1 s^-2
"^U_SIGMA($|_)" = c(0, 12), # m s^-1
"^USTAR($|_)" = c(0, 8), # m s^-1
"^V_SIGMA($|_)" = c(0, 10), # m s^-1
"^W_SIGMA($|_)" = c(0, 5), # m s^-1
"^WD($|_)" = c(0, 360), # degree
"^WD_SIGMA($|_)" = c(0, 180), # degree
"^WS($|_)" = c(0, 40), # m s^-1
"^WS_MAX($|_)" = c(0, 50), # m s^-1
"^GPP($|_)" = c(-30, 100), # umolCO2 m^-2 s^-1
"^NEE($|_)" = c(-100, 100), # umolCO2 m^-2 s^-1
"^RECO($|_)" = c(-20, 50) # umolCO2 m^-2 s^-1
)
}
# --- INTERNAL: PRM units (ASCII) ---------------------------------------------
.prm_units <- function() {
c(
"^COND_WATER($|_)" = "uS cm^-1",
"^DO($|_)" = "umol L^-1",
"^PCH4($|_)" = "nmolCH4 mol^-1",
"^PCO2($|_)" = "umolCO2 mol^-1",
"^PN2O($|_)" = "nmolN2O mol^-1",
"^PPFD_UW_IN($|_)" = "umolPhotons m^-2 s^-1",
"^TW($|_)" = "deg C",
"^DBH($|_)" = "cm",
"^LEAF_WET($|_)" = "%",
"^SAP_DT($|_)" = "deg C",
"^SAP_FLOW($|_)" = "mmolH2O m^-2 s^-1",
"^T_BOLE($|_)" = "deg C",
"^T_CANOPY($|_)" = "deg C",
"^CH4($|_)" = "nmolCH4 mol^-1",
"^CH4_MIXING_RATIO($|_)" = "nmolCH4 mol^-1",
"^CO($|_)" = "nmolCO mol^-1",
"^CO2($|_)" = "umolCO2 mol^-1",
"^CO2_MIXING_RATIO($|_)" = "umolCO2 mol^-1",
"^CO2_SIGMA($|_)" = "umolCO2 mol^-1",
"^CO2C13($|_)" = "permil",
"^FC($|_)" = "umolCO2 m^-2 s^-1",
"^FCH4($|_)" = "nmolCH4 m^-2 s^-1",
"^FN2O($|_)" = "nmolN2O m^-2 s^-1",
"^FNO($|_)" = "nmolNO m^-2 s^-1",
"^FNO2($|_)" = "nmolNO2 m^-2 s^-1",
"^FO3($|_)" = "nmolO3 m^-2 s^-1",
"^H2O($|_)" = "mmolH2O mol^-1",
"^H2O_MIXING_RATIO($|_)" = "mmolH2O mol^-1",
"^H2O_SIGMA($|_)" = "mmolH2O mol^-1",
"^N2O($|_)" = "nmolN2O mol^-1",
"^N2O_MIXING_RATIO($|_)" = "nmolN2O mol^-1",
"^NO($|_)" = "nmolNO mol^-1",
"^NO2($|_)" = "nmolNO2 mol^-1",
"^O3($|_)" = "nmolO3 mol^-1",
"^SC($|_)" = "umolCO2 m^-2 s^-1",
"^SCH4($|_)" = "nmolCH4 m^-2 s^-1",
"^SN2O($|_)" = "nmolN2O m^-2 s^-1",
"^SNO($|_)" = "nmolNO m^-2 s^-1",
"^SNO2($|_)" = "nmolNO2 m^-2 s^-1",
"^SO2($|_)" = "nmolSO2 mol^-1",
"^SO3($|_)" = "nmolO3 m^-2 s^-1",
"^FH2O($|_)" = "mmolH2O m^-2 s^-1",
"^G($|_)" = "W m^-2",
"^H($|_)" = "W m^-2",
"^LE($|_)" = "W m^-2",
"^SB($|_)" = "W m^-2",
"^SG($|_)" = "W m^-2",
"^SH($|_)" = "W m^-2",
"^SLE($|_)" = "W m^-2",
"^PA($|_)" = "kPa",
"^PBLH($|_)" = "m",
"^RH($|_)" = "%",
"^T_SONIC($|_)" = "deg C",
"^T_SONIC_SIGMA($|_)" = "deg C",
"^TA($|_)" = "deg C",
"^VPD($|_)" = "hPa",
"^D_SNOW($|_)" = "cm",
"^P($|_)" = "mm",
"^P_RAIN($|_)" = "mm",
"^P_SNOW($|_)" = "mm",
"^RUNOFF($|_)" = "mm",
"^STEMFLOW($|_)" = "mm",
"^THROUGHFALL($|_)" = "mm",
"^ALB($|_)" = "%",
"^APAR($|_)" = "umolPhoton m^-2 s^-1",
"^EVI($|_)" = "nondimensional",
"^FAPAR($|_)"= "%",
"^FIPAR($|_)"= "%",
"^LW_BC_IN($|_)" = "W m^-2",
"^LW_BC_OUT($|_)" = "W m^-2",
"^LW_IN($|_)" = "W m^-2",
"^LW_OUT($|_)" = "W m^-2",
"^MCRI($|_)" = "nondimensional",
"^MTCI($|_)" = "nondimensional",
"^NDVI($|_)" = "nondimensional",
"^NETRAD($|_)"= "W m^-2",
"^NIRV($|_)" = "W m^-2 sr^-1 nm^-1",
"^PPFD_BC_IN($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_BC_OUT($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_DIF($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_DIR($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_IN($|_)" = "umolPhoton m^-2 s^-1",
"^PPFD_OUT($|_)" = "umolPhoton m^-2 s^-1",
"^PRI($|_)" = "nondimensional",
"^R_UVA($|_)" = "W m^-2",
"^R_UVB($|_)" = "W m^-2",
"^REDCI($|_)" = "nondimensional",
"^REP($|_)" = "nm",
"^SPEC_NIR_IN($|_)" = "W m^-2 nm^-1",
"^SPEC_NIR_OUT($|_)" = "W m^-2 sr^-1 nm^-1",
"^SPEC_NIR_REFL($|_)" = "nondimensional",
"^SPEC_PRI_REF_IN($|_)" = "W m^-2 nm^-1",
"^SPEC_PRI_REF_OUT($|_)" = "W m^-2 sr^-1 nm^-1",
"^SPEC_PRI_REF_REFL($|_)" = "nondimensional",
"^SPEC_PRI_TGT_IN($|_)" = "W m^-2 nm^-1",
"^SPEC_PRI_TGT_OUT($|_)" = "W m^-2 sr^-1 nm^-1",
"^SPEC_PRI_TGT_REFL($|_)" = "nondimensional",
"^SPEC_RED_IN($|_)" = "W m^-2 nm^-1",
"^SPEC_RED_OUT($|_)" = "W m^-2 sr^-1 nm^-1",
"^SPEC_RED_REFL($|_)" = "nondimensional",
"^SR($|_)" = "nondimensional",
"^SW_BC_IN($|_)" = "W m^-2",
"^SW_BC_OUT($|_)"= "W m^-2",
"^SW_DIF($|_)" = "W m^-2",
"^SW_DIR($|_)" = "W m^-2",
"^SW_IN($|_)" = "W m^-2",
"^SW_OUT($|_)" = "W m^-2",
"^TCARI($|_)" = "nondimensional",
"^SWC($|_)" = "%",
"^SWP($|_)" = "kPa",
"^TS($|_)" = "deg C",
"^TSN($|_)" = "deg C",
"^WTD($|_)" = "m",
"^TAU($|_)" = "kg m^-1 s^-2",
"^U_SIGMA($|_)" = "m s^-1",
"^USTAR($|_)" = "m s^-1",
"^V_SIGMA($|_)" = "m s^-1",
"^W_SIGMA($|_)" = "m s^-1",
"^WD($|_)" = "degree",
"^WD_SIGMA($|_)" = "degree",
"^WS($|_)" = "m s^-1",
"^WS_MAX($|_)" = "m s^-1",
"^GPP($|_)" = "umolCO2 m^-2 s^-1",
"^NEE($|_)" = "umolCO2 m^-2 s^-1",
"^RECO($|_)" = "umolCO2 m^-2 s^-1"
)
}
# --- INTERNAL: PRM descriptions (from AmeriFlux Tech Note, Table A1) ----------
.prm_desc <- function() {
c(
"^COND_WATER($|_)" = "Conductivity of water",
"^DO($|_)" = "Dissolved oxygen in water",
"^PCH4($|_)" = "Dissolved methane (CH4) in water",
"^PCO2($|_)" = "Dissolved carbon dioxide (CO2) in water",
"^PN2O($|_)" = "Dissolved nitrous oxide (N2O) in water",
"^PPFD_UW_IN($|_)" = "Photosynthetic photon flux density, underwater, incoming",
"^TW($|_)" = "Water temperature",
"^DBH($|_)" = "Tree diameter at breast height",
"^LEAF_WET($|_)" = "Leaf wetness (0-100)",
"^SAP_DT($|_)" = "Sapflow probe temperature difference",
"^T_BOLE($|_)" = "Bole temperature",
"^T_CANOPY($|_)" = "Canopy/surface temperature",
"^CH4($|_)" = "Methane (CH4) mole fraction (wet air)",
"^CH4_MIXING_RATIO($|_)" = "Methane (CH4) mole fraction (dry air)",
"^CO($|_)" = "Carbon monoxide (CO) mole fraction (wet air)",
"^CO2($|_)" = "Carbon dioxide (CO2) mole fraction (wet air)",
"^CO2_MIXING_RATIO($|_)" = "Carbon dioxide (CO2) mole fraction (dry air)",
"^CO2_SIGMA($|_)" = "Std. dev. of CO2 mole fraction (wet air)",
"^CO2C13($|_)" = "Stable isotope delta13C of CO2 (permil)",
"^FC($|_)" = "CO2 turbulent flux (no storage correction)",
"^FCH4($|_)" = "CH4 turbulent flux (no storage correction)",
"^H2O($|_)" = "Water vapor in mole fraction (wet air)",
"^H2O_MIXING_RATIO($|_)" = "Water vapor in mole fraction (dry air)",
"^H2O_SIGMA($|_)" = "Std. dev. of water vapor mole fraction",
"^N2O($|_)" = "N2O mole fraction (wet air)",
"^N2O_MIXING_RATIO($|_)" = "N2O mole fraction (dry air)",
"^NO($|_)" = "NO mole fraction (wet air)",
"^NO2($|_)" = "NO2 mole fraction (wet air)",
"^O3($|_)" = "O3 mole fraction (wet air)",
"^SC($|_)" = "CO2 storage flux",
"^SO2($|_)" = "SO2 mole fraction (wet air)",
"^FH2O($|_)" = "Water vapor (H2O) turbulent flux (no storage correction)",
"^G($|_)" = "Soil heat flux",
"^H($|_)" = "Sensible heat flux (no storage correction)",
"^LE($|_)" = "Latent heat flux (no storage correction)",
"^SG($|_)" = "Soil heat storage flux above plates",
"^SH($|_)" = "Sensible heat storage flux",
"^SLE($|_)" = "Latent heat storage flux",
"^PA($|_)" = "Atmospheric pressure",
"^PBLH($|_)" = "Planetary boundary layer height",
"^RH($|_)" = "Relative humidity (0-100)",
"^T_SONIC($|_)" = "Sonic temperature",
"^T_SONIC_SIGMA($|_)" = "Std. dev. of sonic temperature",
"^TA($|_)" = "Air temperature",
"^VPD($|_)" = "Vapor pressure deficit",
"^D_SNOW($|_)" = "Snow depth",
"^P($|_)" = "Precipitation",
"^P_RAIN($|_)" = "Rainfall",
"^P_SNOW($|_)" = "Snowfall",
"^RUNOFF($|_)" = "Runoff",
"^STEMFLOW($|_)" = "Stemflow",
"^THROUGHFALL($|_)" = "Throughfall",
"^ALB($|_)" = "Albedo (0-100)",
"^APAR($|_)" = "Absorbed PAR",
"^EVI($|_)" = "Enhanced Vegetation Index",
"^FAPAR($|_)"= "Fraction of absorbed PAR (0-100)",
"^FIPAR($|_)"= "Fraction of intercepted PAR (0-100)",
"^LW_BC_IN($|_)" = "Longwave radiation, below canopy incoming",
"^LW_BC_OUT($|_)" = "Longwave radiation, below canopy outgoing",
"^LW_IN($|_)" = "Longwave radiation, incoming",
"^LW_OUT($|_)" = "Longwave radiation, outgoing",
"^MCRI($|_)" = "Carotenoid Reflectance Index",
"^MTCI($|_)" = "MERIS Terrestrial Chlorophyll Index",
"^NDVI($|_)" = "Normalized Difference Vegetation Index",
"^NETRAD($|_)"= "Net radiation",
"^NIRV($|_)" = "Near Infrared Vegetation Index",
"^PPFD_BC_IN($|_)" = "PPFD, below canopy incoming",
"^PPFD_BC_OUT($|_)" = "PPFD, below canopy outgoing",
"^PPFD_DIF($|_)" = "PPFD, diffuse incoming",
"^PPFD_DIR($|_)" = "PPFD, direct incoming",
"^PPFD_IN($|_)" = "PPFD, incoming",
"^PPFD_OUT($|_)" = "PPFD, outgoing",
"^PRI($|_)" = "Photochemical Reflectance Index",
"^R_UVA($|_)" = "UVA radiation, incoming",
"^R_UVB($|_)" = "UVB radiation, incoming",
"^REDCI($|_)" = "Red-Edge Chlorophyll Index",
"^REP($|_)" = "Red-Edge Position",
"^SPEC_NIR_IN($|_)" = "NIR band radiation, incoming (hemispherical)",
"^SPEC_NIR_OUT($|_)" = "NIR band radiation, outgoing",
"^SPEC_NIR_REFL($|_)" = "NIR band reflectance",
"^SPEC_PRI_REF_IN($|_)" = "PRI reference band radiation, incoming",
"^SPEC_PRI_REF_OUT($|_)" = "PRI reference band radiation, outgoing",
"^SPEC_PRI_REF_REFL($|_)" = "PRI reference band reflectance",
"^SPEC_PRI_TGT_IN($|_)" = "PRI target band radiation, incoming",
"^SPEC_PRI_TGT_OUT($|_)" = "PRI target band radiation, outgoing",
"^SPEC_PRI_TGT_REFL($|_)" = "PRI target band reflectance",
"^SPEC_RED_IN($|_)" = "Red band radiation, incoming (hemispherical)",
"^SPEC_RED_OUT($|_)" = "Red band radiation, outgoing",
"^SPEC_RED_REFL($|_)" = "Red band reflectance",
"^SR($|_)" = "Simple Ratio",
"^SW_BC_IN($|_)" = "Shortwave radiation, below canopy incoming",
"^SW_BC_OUT($|_)"= "Shortwave radiation, below canopy outgoing",
"^SW_DIF($|_)" = "Shortwave radiation, diffuse incoming",
"^SW_DIR($|_)" = "Shortwave radiation, direct incoming",
"^SW_IN($|_)" = "Shortwave radiation, incoming",
"^SW_OUT($|_)" = "Shortwave radiation, outgoing",
"^TCARI($|_)" = "Transformed Chlorophyll Absorption in Reflectance Index",
"^SWC($|_)" = "Soil water content (volumetric, 0-100)",
"^SWP($|_)" = "Soil water potential",
"^TS($|_)" = "Soil temperature",
"^TSN($|_)" = "Snow temperature",
"^WTD($|_)" = "Water table depth",
"^TAU($|_)" = "Momentum flux",
"^U_SIGMA($|_)" = "Std. dev. of along-wind velocity",
"^USTAR($|_)" = "Friction velocity",
"^V_SIGMA($|_)" = "Std. dev. of cross-wind velocity",
"^W_SIGMA($|_)" = "Std. dev. of vertical velocity",
"^WD($|_)" = "Wind direction",
"^WD_SIGMA($|_)" = "Std. dev. of wind direction",
"^WS($|_)" = "Wind speed",
"^WS_MAX($|_)" = "Max wind speed in averaging period",
"^GPP($|_)" = "Gross primary productivity",
"^NEE($|_)" = "Net ecosystem exchange",
"^RECO($|_)" = "Ecosystem respiration"
)
}
# --- EXPORTED: rules tibble for vignettes/docs --------------------------------
#' Get the PRM rules as a tibble (for vignettes & checks)
#' @return A tibble with columns: family (regex), variable (base), min, max, units, description
#' @export
get_prm_rules <- function() {
rl <- .prm_rules()
un <- .prm_units()
de <- .prm_desc()
fam <- names(rl) # regex, e.g. ^SWC($|_)
base <- sub("^\\^(.+)\\(\\$\\|_\\)$", "\\1", fam) # SWC
tibble::tibble(
family = fam, # keep for compatibility
variable = base,
min = unname(vapply(rl, function(x) as.numeric(x[1]), numeric(1))),
max = unname(vapply(rl, function(x) as.numeric(x[2]), numeric(1))),
description = unname(de[fam]),
units = unname(un[fam])
)
}
# --- EXPORTED: main function ---------------------------------------------------
#' Apply Physical Range Module (PRM) bounds to AmeriFlux-style data
#'
#' Clamps values to PRM ranges by variable *family* (e.g., `^SWC($|_)`, `^P($|_)`).
#' Columns with "QC" in their names are skipped by default. Out-of-range values
#' are set to `NA`. No columns are removed.
#'
#' @param .data A data.frame or tibble.
#' @param include Optional character vector of base family names to apply (e.g., "SWC", "P").
#' If `NULL`, all families are applied.
#' @param skip_qc Logical; when TRUE, skip columns that look like flags:
#' names ending/containing `_QC` or `_SSITC_TEST` (case-insensitive).
#' Default: TRUE.
#' @param note Logical; print a per-column summary with expected units, PRM range, and counts.
#' @param summarize Logical; if `TRUE`, return a list with `data` and `summary`; otherwise return only the clamped data frame.
#'
#' @return If `summarize = TRUE`, a list with `data` and `summary`; else a data.frame.
#' @export
apply_prm <- function(.data,
include = NULL,
skip_qc = TRUE,
note = TRUE,
summarize = TRUE) {
stopifnot(is.data.frame(.data))
summarize <- isTRUE(summarize) # normalize flag
rules <- .prm_rules()
# --- Always start with an empty tibble
empty_tbl <- tibble::tibble(
column = character(), family = character(),
min = numeric(), max = numeric(),
n_non_na_before = integer(), n_replaced = integer(), pct_replaced = numeric()
)
summ <- empty_tbl
if (!is.null(include)) {
stopifnot(is.character(include))
base <- sub("^\\^(.+)\\(\\$\\|_\\)$", "\\1", names(rules))
keep <- base %in% unique(include)
rules <- rules[keep]
}
before <- .data
applied <- list()
for (pat in names(rules)) {
lim <- rules[[pat]]
min_v <- lim[1]; max_v <- lim[2]
cols <- grep(pat, names(.data), value = TRUE)
if (skip_qc) {
cols <- cols[!grepl("(^|_)QC($|_)", cols, ignore.case = TRUE)]
cols <- cols[!grepl("SSITC_TEST($|_)", cols, ignore.case = TRUE)]
}
if (!length(cols)) next
family_name <- sub("^\\^(.+)\\(\\$\\|_\\)$", "\\1", pat)
for (col in cols) {
x <- suppressWarnings(as.numeric(.data[[col]]))
keep <- !is.na(x)
if (!is.na(min_v)) keep <- keep & x >= min_v
if (!is.na(max_v)) keep <- keep & x <= max_v
x[!keep] <- NA_real_
.data[[col]] <- x
b <- suppressWarnings(as.numeric(before[[col]]))
applied[[length(applied) + 1L]] <- data.frame(
column = col,
family = family_name,
min = min_v,
max = max_v,
n_non_na_before = sum(!is.na(b)),
n_replaced = sum(is.na(x) & !is.na(b)),
stringsAsFactors = FALSE
)
}
}
if (length(applied)) {
# Avoid dplyr::bind_rows() NULL behavior; guard rbind
summ_df <- do.call(rbind, applied)
summ <- tibble::as_tibble(summ_df)
summ <- summ |>
dplyr::mutate(
pct_replaced = ifelse(n_non_na_before > 0, 100 * n_replaced / n_non_na_before, 0)
) |>
dplyr::arrange(dplyr::desc(n_replaced))
if (all(summ$n_replaced == 0L)) {
if (note) message("PRM: no replacements made.")
# keep `summ` as the canonical EMPTY tibble
summ <- empty_tbl
} else if (note) {
u_vec <- .prm_units()
names(u_vec) <- sub("^\\^(.+)\\(\\$\\|_\\)$", "\\1", names(u_vec))
fmt <- function(z) ifelse(is.na(z), "NA", as.character(z))
lines <- mapply(function(col, fam, lo, hi, nrep, pct) {
paste0(
"* ", col, "\n",
" expected units: ", u_vec[[fam]], ", PRM range: ", fmt(lo), " to ", fmt(hi), "\n",
" ", nrep, " values set to NA (", sprintf("%.1f", pct), "% of data)"
)
}, summ$column, summ$family, summ$min, summ$max, summ$n_replaced, summ$pct_replaced,
SIMPLIFY = TRUE)
message(paste0("PRM summary:\n", paste(lines, collapse = "\n")))
}
} else {
# No matching columns at all
if (note) message("PRM: no replacements made.")
summ <- empty_tbl
}
# --- normalize summary type & return shape (ALWAYS a tibble)
if (is.null(summ)) {
summ <- data.frame(
column = character(), family = character(),
min = numeric(), max = numeric(),
n_non_na_before = integer(), n_replaced = integer(), pct_replaced = numeric(),
stringsAsFactors = FALSE
)
}
if (!inherits(summ, "data.frame")) {
summ <- as.data.frame(summ, stringsAsFactors = FALSE)
}
if (requireNamespace("tibble", quietly = TRUE)) {
summ <- tibble::as_tibble(summ)
} else {
class(summ) <- c("tbl_df","tbl",class(summ))
}
if (!inherits(summ, "data.frame")) summ <- as.data.frame(summ, stringsAsFactors = FALSE)
if (requireNamespace("tibble", quietly = TRUE)) summ <- tibble::as_tibble(summ)
if (!summarize) return(.data)
list(data = .data, summary = summ)
}
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