fill_NA | R Documentation |
fill_NA
function for the imputations purpose.Regular imputations to fill the missing data. Non missing independent variables are used to approximate a missing observations for a dependent variable. Quantitative models were built under Rcpp packages and the C++ library Armadillo.
fill_NA(x, model, posit_y, posit_x, w = NULL, logreg = FALSE, ridge = 1e-06) ## S3 method for class 'data.frame' fill_NA(x, model, posit_y, posit_x, w = NULL, logreg = FALSE, ridge = 1e-06) ## S3 method for class 'data.table' fill_NA(x, model, posit_y, posit_x, w = NULL, logreg = FALSE, ridge = 1e-06) ## S3 method for class 'matrix' fill_NA(x, model, posit_y, posit_x, w = NULL, logreg = FALSE, ridge = 1e-06)
x |
a numeric matrix or data.frame/data.table (factor/character/numeric/logical) - variables |
model |
a character - posibble options ("lda","lm_pred","lm_bayes","lm_noise") |
posit_y |
an integer/character - a position/name of dependent variable |
posit_x |
an integer/character vector - positions/names of independent variables |
w |
a numeric vector - a weighting variable - only positive values, Default:NULL |
logreg |
a boolean - if dependent variable has log-normal distribution (numeric). If TRUE log-regression is evaluated and then returned exponential of results., Default: FALSE |
ridge |
a numeric - a value added to diagonal elements of the x'x matrix, Default:1e-5 |
load imputations in a numeric/logical/character/factor (similar to the input type) vector format
fill_NA(data.frame)
: S3 method for data.frame
fill_NA(data.table)
: s3 method for data.table
fill_NA(matrix)
: S3 method for matrix
There is assumed that users add the intercept by their own. The miceFast module provides the most efficient environment, the second recommended option is to use data.table and the numeric matrix data type. The lda model is assessed only if there are more than 15 complete observations and for the lms models if number of independent variables is smaller than number of observations.
fill_NA_N
VIF
library(miceFast) library(dplyr) library(data.table) ### Data # airquality dataset with additional variables data(air_miss) ### Intro: dplyr # IMPUTATIONS air_miss <- air_miss %>% # Imputations with a grouping option (models are separately assessed for each group) # taking into account provided weights group_by(groups) %>% do(mutate(., Solar_R_imp = fill_NA( x = ., model = "lm_pred", posit_y = "Solar.R", posit_x = c("Wind", "Temp", "Intercept"), w = .[["weights"]] ))) %>% ungroup() %>% # Imputations - discrete variable mutate(x_character_imp = fill_NA( x = ., model = "lda", posit_y = "x_character", posit_x = c("Wind", "Temp") )) %>% # logreg was used because almost log-normal distribution of Ozone # imputations around mean mutate(Ozone_imp1 = fill_NA( x = ., model = "lm_bayes", posit_y = "Ozone", posit_x = c("Intercept"), logreg = TRUE )) %>% # imputations using positions - Intercept, Temp mutate(Ozone_imp2 = fill_NA( x = ., model = "lm_bayes", posit_y = 1, posit_x = c(4, 6), logreg = TRUE )) %>% # multiple imputations (average of x30 imputations) # with a factor independent variable, weights and logreg options mutate(Ozone_imp3 = fill_NA_N( x = ., model = "lm_noise", posit_y = "Ozone", posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), w = .[["weights"]], logreg = TRUE, k = 30 )) %>% mutate(Ozone_imp4 = fill_NA_N( x = ., model = "lm_bayes", posit_y = "Ozone", posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), w = .[["weights"]], logreg = TRUE, k = 30 )) %>% group_by(groups) %>% do(mutate(., Ozone_imp5 = fill_NA( x = ., model = "lm_pred", posit_y = "Ozone", posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), w = .[["weights"]], logreg = TRUE ))) %>% do(mutate(., Ozone_imp6 = fill_NA_N( x = ., model = "pmm", posit_y = "Ozone", posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), w = .[["weights"]], logreg = TRUE, k = 20 ))) %>% ungroup() %>% # Average of a few methods mutate(Ozone_imp_mix = rowMeans(select(., starts_with("Ozone_imp")))) %>% # Protecting against collinearity or low number of observations - across small groups # Be carful when using a grouping option # because of lack of protection against collinearity or low number of observations. # There could be used a tryCatch(fill_NA(...),error=function(e) return(...)) group_by(groups) %>% do(mutate(., Ozone_chac_imp = tryCatch( fill_NA( x = ., model = "lda", posit_y = "Ozone_chac", posit_x = c( "Intercept", "Month", "Day", "Temp", "x_character_imp" ), w = .[["weights"]] ), error = function(e) .[["Ozone_chac"]] ))) %>% ungroup() # Sample of results air_miss[which(is.na(air_miss[, 1]))[1:5], ] ### Intro: data.table # IMPUTATIONS # Imputations with a grouping option (models are separately assessed for each group) # taking into account provided weights data(air_miss) setDT(air_miss) air_miss[, Solar_R_imp := fill_NA_N( x = .SD, model = "lm_bayes", posit_y = "Solar.R", posit_x = c("Wind", "Temp", "Intercept"), w = .SD[["weights"]], k = 100 ), by = .(groups)] %>% # Imputations - discrete variable .[, x_character_imp := fill_NA( x = .SD, model = "lda", posit_y = "x_character", posit_x = c("Wind", "Temp", "groups") )] %>% # logreg was used because almost log-normal distribution of Ozone # imputations around mean .[, Ozone_imp1 := fill_NA( x = .SD, model = "lm_bayes", posit_y = "Ozone", posit_x = c("Intercept"), logreg = TRUE )] %>% # imputations using positions - Intercept, Temp .[, Ozone_imp2 := fill_NA( x = .SD, model = "lm_bayes", posit_y = 1, posit_x = c(4, 6), logreg = TRUE )] %>% # model with a factor independent variable # multiple imputations (average of x30 imputations) # with a factor independent variable, weights and logreg options .[, Ozone_imp3 := fill_NA_N( x = .SD, model = "lm_noise", posit_y = "Ozone", posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), w = .SD[["weights"]], logreg = TRUE, k = 30 )] %>% .[, Ozone_imp4 := fill_NA_N( x = .SD, model = "lm_bayes", posit_y = "Ozone", posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), w = .SD[["weights"]], logreg = TRUE, k = 30 )] %>% .[, Ozone_imp5 := fill_NA( x = .SD, model = "lm_pred", posit_y = "Ozone", posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), w = .SD[["weights"]], logreg = TRUE ), .(groups)] %>% .[, Ozone_imp6 := fill_NA_N( x = .SD, model = "pmm", posit_y = "Ozone", posit_x = c("Intercept", "x_character_imp", "Wind", "Temp"), w = .SD[["weights"]], logreg = TRUE, k = 10 ), .(groups)] %>% # Average of a few methods .[, Ozone_imp_mix := apply(.SD, 1, mean), .SDcols = Ozone_imp1:Ozone_imp6] %>% # Protecting against collinearity or low number of observations - across small groups # Be carful when using a data.table grouping option # because of lack of protection against collinearity or low number of observations. # There could be used a tryCatch(fill_NA(...),error=function(e) return(...)) .[, Ozone_chac_imp := tryCatch( fill_NA( x = .SD, model = "lda", posit_y = "Ozone_chac", posit_x = c( "Intercept", "Month", "Day", "Temp", "x_character_imp" ), w = .SD[["weights"]] ), error = function(e) .SD[["Ozone_chac"]] ), .(groups)] # Sample of results air_miss[which(is.na(air_miss[, 1]))[1:5], ]
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