R/cleaning.R
In mahagadorn/MISTAKE_FIX: Not A Trait DataBase
clean.natdb <- function(x){
# Argument handling
if(!inherits(x, "natdb"))
stop("'", deparse(substitute(x)), "' must be of type 'natdb'")
if(!is.null(x$numeric)){
x$numeric <- x$numeric[x$numeric$variable != "",]
x$numeric$variable <- tolower(x$numeric$variable)
x$numeric$variable <- gsub(".", "_", x$numeric$variable, fixed=TRUE)
x$numeric$variable <- gsub("^leaf[0-9]$", "leaf", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^puncture_[0-3]$", "puncture", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^area_cm2$", "area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^area_m2$", "area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^av_female_length$", "female_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^av_male_width$", "male_width", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^ash_g_dry_weight_1$", "ash_g_dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^ash_g_dry_weight_2$", "ash_g_dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^ash_g_dry_weight_3$", "ash_g_dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_ash$", "ash", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_female_adult_weight$", "female_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_dry_weight$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_indiv__leaf_area$", "leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_ldmc$", "leaf_dry_matter_content", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_puncture$", "leaf_puncturability", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_sla$", "specific_leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bamax__cm2_$", "bamax", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bill_length1$", "bill_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^area_cm2$", "area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^area$", "m2", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^birth_or_hatching_svl_cm$", "birth_snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^birth_or_hatching_weight_g$", "birth_weight", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_wt$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bodymass_speclevel$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bodymass_value$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bodytemp_c$", "body_temperature", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^dbh$", "diameter_at_breast_height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^dbh__cm_$", "diameter_at_breast_height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^diam$", "diameter", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^dry_weight$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^egg_mass_g$", "egg_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^dry_wgt$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_area$", "foliar_area_mm2", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_area_mm2_1$", "", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^growth_svl$", "growth_snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^head_height_mm$", "head_height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^head_l$", "head_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^height__m_$", "height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^height_apex$", "height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^ldmc$", "leaf_dry_matter_content", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_6_sla$", "specific_leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_density_g_cm3$", "leaf_density", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_life_span$", "leaf_lifespan", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_nitrogen_content$", "leaf_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_toughness__mn_m_2_$", "leaf_toughness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf1_area$", "leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_dry_weight$", "leaf_dry_weight", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_ldmc$", "leaf_dry_matter_content", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_sla$", "species_leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_dry_weight$", "leaf_dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_c$", "leaf_carbon", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_n$", "leaf_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaflength$", "leaf_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafcn$", "leaf_carbon_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafthck_avd$", "leaf_thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafthck_avi$", "leaf_thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafthickness$", "leaf_thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafwidth$", "leaf_width", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^length__um_$", "length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^lma__g_m_2_$", "leaf_mass_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^lma_g_m2$", "leaf_mass_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mass_g$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^male_svl_cm$", "male_snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^maximum_longevity_y$", "maximum_longevity", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mean_clutch_size$", "clutch_size", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mean_female_svl_adults$", "female_snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mean_head_length$", "head_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mean_glossa_length__mm_$", "glossa_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^perch_diam_cm$", "perch_diam", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^perch_height$", "", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^perch_temp_c$", "perch_temp", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^photosynthetic_capacitity_per_unit_leaf_mass$", "photosynthetic_capacitity", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^phototsynthetic_capacity_per_area$", "phototsynthetic_capacity", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^phototsynthetic_capacity_per_mass$", "phototsynthetic_capacity", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^plant_height__m_$", "height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^plant_width__m_$", "width", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^respiration_rt_ind$", "respiration_rate", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^respiration_rt_mg$", "respiration_rate", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rjuv__cm2_$", "rjuv", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rmax__cm2_$", "rmax", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rootbiomasst8$", "root_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rootlengtht0$", "root_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rootlengtht8$", "root_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rootrgr$", "root_relative_growth_rate", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^seedlength$", "seed_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^seedmaxwidth$", "max_seed_width", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^seedthick$", "seed_thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^shootbiomasst8$", "shoot_biomass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^shootdens12$", "shoot_density", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^shootdens13$", "shoot_density", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^shootheightt0$", "shoot_height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^soil_n$", "soil_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^soil_c$", "soil_carbon", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^soil_p$$", "soil_phosphorous", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^soil_ph$", "soil_pH", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^solitary_vessels____$", "solitary_vessels", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^sproutd_mm$", "sproutd", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^sqrt_spider_prey_consumed$", "spider_prey_consumed", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^sqrt_sundew_prey_consumed$", "sundew_prey_consumed", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^sqrt_toad_prey_consumed$", "toad_prey_consumed", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^stumpd_mm$", "stumpd", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^svl$", "snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^svl_mm$", "snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^thick_m$", "thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^thick_mm$", "thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_dry_mass$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_fresh_weight__g_$", "fresh_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_mass$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_mass_dry$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_mass_value$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^phenolics$", "phenolics", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_sundews$", "sundews", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^totalspermnumber_in_millions$", "sperm", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^tree_height$", "height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^volume_m3$", "volume", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^volume_male$", "male_volume", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^volume_female$", "female_volume", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^weaning_body_mass$", "weaning_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^weight_g$", "weight", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^wet_wgt$", "wet_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^wood_density__g_cm_3_$", "wood_density", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_mass$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_mass_female$", "female_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_mass_male$", "female_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_size$", "size", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_m2_mm2$", "foliar", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_m2_mm2_1$", "", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_nitrogen_content____$", "foliar_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^head_lengthength$", "head_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_carbonc$", "leaf_carbon", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_carboncn$", "leaf_carbon_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_carbonc$", "", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$species <- tolower(gsub(" ", "_", x$numeric$species))
}
if(!is.null(x$categorical)){
x$categorical$variable <- tolower(x$categorical$variable)
x$categorical$variable <- gsub(" |\\.", "_", x$categorical$variable)
x$categorical$species <- tolower(gsub(" ", "_", sanitize_text(x$categorical$species), perl=TRUE, useBytes=TRUE))
}
return(x)
}
clean.natdb.names <- function(x, thresh, ...){
# Argument handling
if(!inherits(x, "natdb"))
stop("'", deparse(substitute(x)), "' must be of type 'natdb'")
spp <- unique(c(unique(x$numeric$species), unique(x$categorical$species)))
dwn.spp <- gnr_resolve(spp)
dwn.spp <- dwn.spp[!duplicated(dwn.spp$user_supplied_name),]
dwn.spp$matched_name <- tolower(sapply(strsplit(dwn.spp$matched_name, " "), function(x) paste(x[1:2],collapse="_")))
if(!missing(thresh))
dwn.spp <- dwn.spp[dwn.spp$score >= thresh,]
lookup <- with(dwn.spp, setNames(matched_name, user_supplied_name))
x$numeric$species <- lookup[x$numeric$species]
x$categorical$species <- lookup[x$categorical$species]
return(x)
}
clean.natdb.units <- function(x, choices, ...){
# Argument handling
if(!inherits(x, "natdb"))
stop("'", deparse(substitute(x)), "' must be of type 'natdb'")
if(missing(choices)){
choices <- tapply(x$numeric$units, x$numeric$variable, function(y) names(sort(table(y),decreasing=TRUE)[1]))
choices <- Filter(Negate(is.null), choices)
}
for(i in seq_along(choices)){
old.unit <- unique(x$numeric$units[x$numeric$variable==names(choices)[i]])
for(j in seq_along(old.unit)){
with(x$numeric,
converted <- tryCatch(
convert(value[variable==names(choices)[i] & units==old.unit[j]], old.unit, choices[i]),
error=function(y) NA
))
if(any(Negate(is.na)(converted))){
x$numeric$units[x$numeric$variable==names(choices)[i] & x$numeric$units==old.unit[j]] <- choices[i]
x$numeric$value[x$numeric$variable==names(choices)[i] & x$numeric$units==old.unit[j]] <- converted
}
}
}
return(x)
}
mahagadorn/MISTAKE_FIX documentation built on May 31, 2019, 5:21 p.m.
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clean.natdb <- function(x){
# Argument handling
if(!inherits(x, "natdb"))
stop("'", deparse(substitute(x)), "' must be of type 'natdb'")
if(!is.null(x$numeric)){
x$numeric <- x$numeric[x$numeric$variable != "",]
x$numeric$variable <- tolower(x$numeric$variable)
x$numeric$variable <- gsub(".", "_", x$numeric$variable, fixed=TRUE)
x$numeric$variable <- gsub("^leaf[0-9]$", "leaf", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^puncture_[0-3]$", "puncture", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^area_cm2$", "area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^area_m2$", "area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^av_female_length$", "female_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^av_male_width$", "male_width", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^ash_g_dry_weight_1$", "ash_g_dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^ash_g_dry_weight_2$", "ash_g_dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^ash_g_dry_weight_3$", "ash_g_dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_ash$", "ash", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_female_adult_weight$", "female_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_dry_weight$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_indiv__leaf_area$", "leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_ldmc$", "leaf_dry_matter_content", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_puncture$", "leaf_puncturability", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^average_sla$", "specific_leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bamax__cm2_$", "bamax", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bill_length1$", "bill_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^area_cm2$", "area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^area$", "m2", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^birth_or_hatching_svl_cm$", "birth_snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^birth_or_hatching_weight_g$", "birth_weight", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_wt$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bodymass_speclevel$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bodymass_value$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^bodytemp_c$", "body_temperature", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^dbh$", "diameter_at_breast_height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^dbh__cm_$", "diameter_at_breast_height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^diam$", "diameter", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^dry_weight$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^egg_mass_g$", "egg_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^dry_wgt$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_area$", "foliar_area_mm2", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_area_mm2_1$", "", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^growth_svl$", "growth_snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^head_height_mm$", "head_height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^head_l$", "head_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^height__m_$", "height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^height_apex$", "height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^ldmc$", "leaf_dry_matter_content", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_6_sla$", "specific_leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_density_g_cm3$", "leaf_density", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_life_span$", "leaf_lifespan", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_nitrogen_content$", "leaf_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_toughness__mn_m_2_$", "leaf_toughness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf1_area$", "leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_dry_weight$", "leaf_dry_weight", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_ldmc$", "leaf_dry_matter_content", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_sla$", "species_leaf_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_dry_weight$", "leaf_dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_c$", "leaf_carbon", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_n$", "leaf_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaflength$", "leaf_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafcn$", "leaf_carbon_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafthck_avd$", "leaf_thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafthck_avi$", "leaf_thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafthickness$", "leaf_thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leafwidth$", "leaf_width", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^length__um_$", "length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^lma__g_m_2_$", "leaf_mass_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^lma_g_m2$", "leaf_mass_area", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mass_g$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^male_svl_cm$", "male_snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^maximum_longevity_y$", "maximum_longevity", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mean_clutch_size$", "clutch_size", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mean_female_svl_adults$", "female_snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mean_head_length$", "head_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^mean_glossa_length__mm_$", "glossa_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^perch_diam_cm$", "perch_diam", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^perch_height$", "", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^perch_temp_c$", "perch_temp", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^photosynthetic_capacitity_per_unit_leaf_mass$", "photosynthetic_capacitity", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^phototsynthetic_capacity_per_area$", "phototsynthetic_capacity", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^phototsynthetic_capacity_per_mass$", "phototsynthetic_capacity", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^plant_height__m_$", "height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^plant_width__m_$", "width", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^respiration_rt_ind$", "respiration_rate", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^respiration_rt_mg$", "respiration_rate", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rjuv__cm2_$", "rjuv", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rmax__cm2_$", "rmax", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rootbiomasst8$", "root_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rootlengtht0$", "root_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rootlengtht8$", "root_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^rootrgr$", "root_relative_growth_rate", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^seedlength$", "seed_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^seedmaxwidth$", "max_seed_width", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^seedthick$", "seed_thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^shootbiomasst8$", "shoot_biomass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^shootdens12$", "shoot_density", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^shootdens13$", "shoot_density", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^shootheightt0$", "shoot_height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^soil_n$", "soil_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^soil_c$", "soil_carbon", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^soil_p$$", "soil_phosphorous", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^soil_ph$", "soil_pH", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^solitary_vessels____$", "solitary_vessels", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^sproutd_mm$", "sproutd", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^sqrt_spider_prey_consumed$", "spider_prey_consumed", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^sqrt_sundew_prey_consumed$", "sundew_prey_consumed", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^sqrt_toad_prey_consumed$", "toad_prey_consumed", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^stumpd_mm$", "stumpd", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^svl$", "snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^svl_mm$", "snout_vent_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^thick_m$", "thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^thick_mm$", "thickness", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_dry_mass$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_fresh_weight__g_$", "fresh_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_mass$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_mass_dry$", "dry_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_mass_value$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^phenolics$", "phenolics", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^total_sundews$", "sundews", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^totalspermnumber_in_millions$", "sperm", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^tree_height$", "height", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^volume_m3$", "volume", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^volume_male$", "male_volume", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^volume_female$", "female_volume", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^weaning_body_mass$", "weaning_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^weight_g$", "weight", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^wet_wgt$", "wet_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^wood_density__g_cm_3_$", "wood_density", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_mass$", "mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_mass_female$", "female_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_mass_male$", "female_mass", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^body_size$", "size", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_m2_mm2$", "foliar", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_m2_mm2_1$", "", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^foliar_nitrogen_content____$", "foliar_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^head_lengthength$", "head_length", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_carbonc$", "leaf_carbon", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_carboncn$", "leaf_carbon_nitrogen", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$variable <- gsub("^leaf_carbonc$", "", x$numeric$variable, perl=TRUE, useBytes=TRUE)
x$numeric$species <- tolower(gsub(" ", "_", x$numeric$species))
}
if(!is.null(x$categorical)){
x$categorical$variable <- tolower(x$categorical$variable)
x$categorical$variable <- gsub(" |\\.", "_", x$categorical$variable)
x$categorical$species <- tolower(gsub(" ", "_", sanitize_text(x$categorical$species), perl=TRUE, useBytes=TRUE))
}
return(x)
}
clean.natdb.names <- function(x, thresh, ...){
# Argument handling
if(!inherits(x, "natdb"))
stop("'", deparse(substitute(x)), "' must be of type 'natdb'")
spp <- unique(c(unique(x$numeric$species), unique(x$categorical$species)))
dwn.spp <- gnr_resolve(spp)
dwn.spp <- dwn.spp[!duplicated(dwn.spp$user_supplied_name),]
dwn.spp$matched_name <- tolower(sapply(strsplit(dwn.spp$matched_name, " "), function(x) paste(x[1:2],collapse="_")))
if(!missing(thresh))
dwn.spp <- dwn.spp[dwn.spp$score >= thresh,]
lookup <- with(dwn.spp, setNames(matched_name, user_supplied_name))
x$numeric$species <- lookup[x$numeric$species]
x$categorical$species <- lookup[x$categorical$species]
return(x)
}
clean.natdb.units <- function(x, choices, ...){
# Argument handling
if(!inherits(x, "natdb"))
stop("'", deparse(substitute(x)), "' must be of type 'natdb'")
if(missing(choices)){
choices <- tapply(x$numeric$units, x$numeric$variable, function(y) names(sort(table(y),decreasing=TRUE)[1]))
choices <- Filter(Negate(is.null), choices)
}
for(i in seq_along(choices)){
old.unit <- unique(x$numeric$units[x$numeric$variable==names(choices)[i]])
for(j in seq_along(old.unit)){
with(x$numeric,
converted <- tryCatch(
convert(value[variable==names(choices)[i] & units==old.unit[j]], old.unit, choices[i]),
error=function(y) NA
))
if(any(Negate(is.na)(converted))){
x$numeric$units[x$numeric$variable==names(choices)[i] & x$numeric$units==old.unit[j]] <- choices[i]
x$numeric$value[x$numeric$variable==names(choices)[i] & x$numeric$units==old.unit[j]] <- converted
}
}
}
return(x)
}
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