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}); Cargamos los datos
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 535756 28.7 1208875 64.6 643711 34.4
Vcells 907377 7.0 8388608 64.0 1649632 12.6[1] "2023-05-06 08:53:17 -04"Show code
load("data2_lca2_imp_2023_05_06.RData")
Cargamos los paquetes
Show code
knitr::opts_chunk$set(echo = TRUE)
if(!require(poLCA)){install.packages("poLCA")}
if(!require(poLCAParallel)){devtools::install_github("QMUL/poLCAParallel@package")}
if(!require(compareGroups)){install.packages("compareGroups")}
if(!require(parallel)){install.packages("parallel")}
if(!require(Hmisc)){install.packages("Hmisc")}
if(!require(tidyverse)){install.packages("tidyverse")}
try(if(!require(sjPlot)){install.packages("sjPlot")})
if(!require(emmeans)){install.packages("emmeans")}
if(!require(nnet)){install.packages("nnet")}
if(!require(here)){install.packages("here")}
if(!require(doParallel)){install.packages("doParallel")}
if(!require(progress)){install.packages("progress")}
if(!require(caret)){install.packages("caret")}
if(!require(rpart)){install.packages("rpart")}
if(!require(rpart.plot)){install.packages("rpart.plot")}
if(!require(partykit)){install.packages("partykit")}
if(!require(randomForest)){install.packages("randomForest")}
if(!require(ggcorrplot)){install.packages("ggcorrplot")}
if(!require(polycor)){install.packages("polycor")}
if(!require(tableone)){install.packages("tableone")}
if(!require(broom)){install.packages("broom")}
if(!require(plotly)){install.packages("plotly")}
if(!require(rsvg)){install.packages("rsvg")}
if(!require(DiagrammeRsvg)){install.packages("DiagrammeRsvg")}
#if(!require(poLCA)){githubinstall::gh_install_packages("poLCA", ref = github_pull("14"))}
#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:
#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:#:
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Definimos ciertas constantes
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clus_iter= 500 #500
n_thread <- parallel::detectCores()
nrep <- clus_iter # number of different initial values (could be n_thread too)
n_class_max <- 10 # maximum number of classes to investigate
n_bootstrap <- 100 #30 # 50 number of bootstrap samples
print(n_thread)
[1] 8Análisis de clases latentes
Modelo alternativo
Análisis ACL alt
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#Biemer, P. P., & Wiesen, C. (2002). Measurement error evaluation of self-reported drug use: a latent class analysis of the US National Household Survey on Drug Abuse. Journal of the Royal Statistical Society: Series A (Statistics in Society), 165(1), 97–119. doi:10.1111/1467-985x.00612
#lca_entropia(x="ppio", seed= 2125, k= 8, f= f_preds, dat= mydata_preds, nbr_repet= 30, na_rm= T)
#3
#<div style="border: 1px solid #ddd; padding: 5px; overflow-y: scroll; height:400px; overflow-x: scroll; width:100%">
# f is the selected variables
# dat is the data
# nb_var is the number of selected variables
# k is the number of latent class generated
# nbr_repet is the number of repetition to
# reach the convergence of EM algorithm
# x es el código para las variables de los modelos
#seed es el numero random para las semillas. ej: 4345.
#Modo de calcular el mejor modelo.
#z_ #
#2023-01-20
#https://github.com/QMUL/poLCAParallel/blob/master/exec/3_blrt.R
#0h s
f_adj<-cbind(CAUSAL, EDAD_MUJER_REC, PUEBLO_ORIGINARIO_REC, PAIS_ORIGEN_REC, HITO1_EDAD_GEST_SEM_REC, MACROZONA, PREV_TRAMO_REC)~ outcome
seed<-2125
old <- Sys.time()
require(progress)
set.seed(seed)
model_array_adj <- list() # Initialize an empty list to store the results
pb <- progress_bar$new(total = n_class_max, message_class = "Running poLCA")
#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_
for (k in 1:n_class_max) {
nrep_int <- nrep # Initialize nrep to a reasonable value
while (nrep_int >= 1) { # Try running poLCA with decreasing nrep until nrep reaches 1
tryCatch({
set.seed(seed)
mod <- poLCAParallel::poLCA(
f_adj,
mydata_preds3 %>% dplyr::mutate(outcome=ifelse(outcome==1,1,0)), # %>% janitor::tabyl(outcome)
nclass = k,
nrep = nrep_int,
maxiter = 1e4,
n.thread = 12,
verbose = FALSE
)
model_array_adj[[k]] <- mod # Store the result if no error occurs
break # Exit the loop if poLCA succeeds
}, error = function(e) {
message(paste("Error in poLCA for k =", k, ", nrep =", nrep_int, ":", conditionMessage(e)))
nrep_int <- nrep_int / 2 # Reduce nrep by half if poLCA fails
})
}
#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_
pb$tick() # Increment the progress bar
cat(sprintf("\r%d%% completed", round(k/n_class_max*100))) # Print progress percentage
Sys.sleep(.05)
}
ALERT: covariates not allowed when nclass=1;
will be ignored.
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pb$terminate() # Close the progress bar
cat(': Done') # Print "Done" message
: DoneShow code
model_array_adj_ppio<-model_array_adj
#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_
#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#BOOTSTRAP#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_
#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_
new_med<-(Sys.time())
paste0("The model took ",round(new_med-old,2)," until every LCA was computed")
[1] "The model took 6.18 until every LCA was computed"Luego calculamos la razón de verosimilitud mediante remuestreo bootstrap (BLRT) entre los distintos modelos con el que asume una clase menos.
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# store p values for each nclass, 1 to n_class_max
# store 0 for 1 number of class, ie this says you cannot have zero number of
# classes
p_value_array_adj <- c(0)
# for all number of classes investigated:
# - store the log likelihood ratio
# - store all bootstrap samples log likelihoods ratios
fitted_log_ratio_array_adj <- rep(NaN, n_class_max)
bootstrap_log_ratio_array_adj <- list()
#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_#_
# do the bootstrap likelihood ratio test for each number of classes
for (nclass in 2:n_class_max) {
# get the null and alt models
# these are models with one number of class differences
null_model_adj <- model_array_adj_ppio[[nclass - 1]]
alt_model_adj <- model_array_adj_ppio[[nclass]]
# for each bootstrap sample, store the log likelihood ratio here
bootstrap_results_adj <- poLCAParallel::blrt(
null_model_adj, alt_model_adj,
n_bootstrap, n_thread, nrep
)
# log likelihood ratio to compare the two models
fitted_log_ratio_array_adj[nclass] <- bootstrap_results_adj[["fitted_log_ratio"]]
# store the log likelihoods ratios for all bootstrap samples
bootstrap_log_ratio_array_adj[[nclass]] <-
bootstrap_results_adj[["bootstrap_log_ratio"]]
# store the p value for this nclass
p_value_array_adj <- c(p_value_array_adj, bootstrap_results_adj[["p_value"]])
#progress bar
cat(paste0(round(nclass / n_class_max * 100), '% completed'))
Sys.sleep(.05)
if (nclass == n_class_max) cat(': Done')
else cat('\014')
}
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[1] "The model took 14.29 minutes"Show code
model_array_ppio2 <- model_array_adj
fitted_log_ratio_array_adj_ppio <- fitted_log_ratio_array_adj
bootstrap_log_ratio_array_adj_ppio <- bootstrap_log_ratio_array_adj
bootstrap_results_adj_ppio <- bootstrap_results_adj
p_value_array_adj_ppio <- p_value_array_adj
# Get the BIC values for all models in model_array_ppio2
bic_values_adj <- sapply(model_array_ppio2, function(model) model$bic)
# Identify the index of the model with the lowest BIC
best_model_index_adj <- which.min(bic_values_adj)
# Select the best model
LCA_best_model_adj_ppio <- model_array_ppio2[[best_model_index_adj]]
#####################################################################################################################################################################
#Within poLCA, parameter estimates are obtained by a procedure that repeatedly improves estimates.
#This is stopped when no further improvements are obtained, or until a maximum number of iterations is reached. The starting values are the values at which such repetitions were started. Increasing the number 4 R. ACHTERHOF ET AL.of iterations (cycles within each estimation) and setting more different starting values for each repetition results in a greater likelihood that the global (rather than local) maximum of the log-likelihood function (and thus, the best possible solution) is reached. The maximum number of iterations was chosen as 10.000, and 500 different sets of starting values were used (thus going beyond the recommendations by Linzer & Lewis, 2011; Oberski, 2016). As such, the influence of chance was minimized while the reproducibility of the results was maximized#
Resultados ACL alt
Hicimos un gráfico de los resultados
Show code
# Initialize an empty data frame
tab_ppio2 <- data.frame()##
# Loop through each model
for (i in 2:n_class_max) {
skip_to_next <- FALSE
# Get the model and the previous model
mod2 <- model_array_ppio2[[i]]
mod2_min1 <- model_array_ppio2[[(i-1)]]
# Check if the model has valid predictions
if (is.null(mod2$predclass)) {
skip_to_next <- TRUE
}
# If the model has valid predictions, calculate the measures and add them to the data frame
if (!skip_to_next) {
# Number of latent classes
mod2$C <- max(t(matrix(apply(mod2$y, 2, max))))
# Number of manifest variables
mod2$J <- ncol(mod2$y)
# Total number of items
mod2$I <- mod2$J * mod2$C
# Degrees of freedom
mod2$df <- mod2$C^mod2$I - mod2$npar - 1
# Chi-square test
mod2$Chisq.pvalue <- (1 - pchisq(mod2$Chisq, mod2$df))
# AIC
mod2$aic <- round(mod2$aic, 2)
# BIC
mod2$bic <- round(mod2$bic, 2)
# Adjusted BIC n*=(n+2)/24 (https://github.com/dlinzer/poLCA/issues/10)
mod2$aBIC <- round((-2 * mod2$llik) + (log((mod2$N+2)/24) * mod2$npar), 2)
# Conditional AIC
mod2$cAIC <- round((-2 * mod2$llik) + (2 * mod2$Nobs * log(mod2$N/mod2$Nobs)), 2)
# approximate weight of evidence criterion #https://jbds.isdsa.org/public/journals/1/html/v2n2/qiu/
mod2$awe <- round((-2 * mod2$llik) + (2 * mod2$npar * log(mod2$Nobs)+1.5), 2)
# Gsq: deviance
mod2$Gsq
# Likelihood ratio test
mod2$Gsq.pvalue <- (1 - pchisq(mod2$Gsq, mod2$df))
# Relative entropy
mod2$RelEnt <- round(relative.entropy(mod2), 2)
# Entropy R-squared
mod2$EntR2 <- round(entropy.R2(mod2), 2)
# Deviance change
mod2$DevChange <- round(mod2_min1$Gsq - mod2$Gsq, 2)
# Degrees of freedom change
mod2$dfChange <- mod2_min1$resid.df - mod2$resid.df
# P-value for deviance change
mod2$pvalDevChange <- round(pchisq(mod2$DevChange, mod2$dfChange, lower.tail = FALSE), 4)
mod2$BLRT <- round(fitted_log_ratio_array_adj_ppio[[i]],2)
mod2$BLRT.pvalue <- p_value_array_adj_ppio[[i]]
# Add the model index to the data frame
mod2$ModelIndex <- i
tab_ppio2 <- rbind.data.frame(tab_ppio2, t(data.matrix(mod2[c("llik", "Chisq", "Chisq.pvalue", "resid.df", "aic", "bic", "aBIC", "cAIC", "awe", "Gsq", "Gsq.pvalue", "RelEnt", "EntR2", "DevChange", "dfChange", "pvalDevChange", "ModelIndex","BLRT", "BLRT.pvalue")])))
# } else {}
}
}
# identify the list-like columns
list_cols2 <- sapply(tab_ppio2, is.list)
# unlist the list-like columns
unlisted_cols2 <- lapply(tab_ppio2[list_cols2], unlist)
# bind the unlisted columns as a data frame
tab_ppio2 <- cbind(tab_ppio2[!list_cols2], do.call(cbind, unlisted_cols2))
#Erase rownames
rownames(tab_ppio2) <- NULL
manualcolors2 <- c('indianred1', 'cornflowerblue', 'gray50', 'darkolivegreen4', 'slateblue2',
'firebrick4', 'goldenrod4')
levels2 <- c("llik", "Chisq", "Chisq.pvalue", "resid.df", "aic", "bic", "aBIC", "cAIC", "awe",
"Gsq", "Gsq.pvalue", "RelEnt", "EntR2", "DevChange", "dfChange",
"pvalDevChange", "BLRT", "BLRT.pvalue")
labels2 <- c('Log-Verosimilitud', 'Chi2', 'valor p Chi2', 'Grados de libertad',
'Criterio de Información\nde Akaike(AIC)'','Criterio de Información\nBayesiano (BIC)')''BIC Ajustado (SABIC)')'"AIC Corregido"o'Peso de evidencia aproximado(awe)')'G-squared/Deviance'e''Valor p G-squared'd''Entropía Relativa'va'Entropía R2' R'Cambio en Deviance\n(con modelo previo)'io'Grados de libertad del cambio'bi'valor p cambio deviance'nc'BLRT'LR'valor p BLRT')RT')
fig_lca_fit2<- tab_ppio2 %>%
dplyr::mutate_if(is.character, as.numeric) %>% # convert character columns to numeric
tidyr::pivot_longer(cols = -ModelIndex, #"evryone but index"
names_to = "indices", values_to = "value", values_drop_na = F) %>%
dplyr::mutate(indices = factor(indices, levels = levels2, labels = labels2)) %>%
dplyr::filter(grepl("(AIC|BIC|awe)",indices, ignore.case=T))%>%
dplyr::mutate(ModelIndex= factor(ModelIndex, levels=2:n_class_max)) %>%
ggplot(aes(x = ModelIndex, y = value, group = indices, color = indices, linetype = indices)) +
geom_line(size = 1.5) +
scale_color_manual(values = manualcolors) +
#scale_linetype_manual(values = c("solid", "dashed", "dotted")) +
labs(x = "Número de clases"", y=="Valor"", color=="Medida"", linetype=="Medida"))++
#facet_wrap(.~indices, scales = "free_y", nrow = 4, ncol = 1) +
theme_bw()
fig_lca_fit2
Show code
ggsave("_fig2_comparison_adj_imp.png",fig_lca_fit2, dpi=600)
Luego en una tabla
Show code
| ModelIndex | llik | Chisq | Chisq.pvalue | resid.df | aic | bic | aBIC | cAIC | awe | Gsq | Gsq.pvalue | RelEnt | EntR2 | DevChange | dfChange | pvalDevChange | BLRT | BLRT.pvalue |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | -27132.08 | 11595.052 | 1 | 3735 | 54372.15 | 54709.11 | 54537.52 | 54264.15 | 55155.56 | 4753.085 | 1 | 0.94 | 0.93 | 2837.46 | 28 | 0 | 2884.37 | 0 |
| 3 | -26844.96 | 9256.635 | 1 | 3707 | 53853.92 | 54365.59 | 54105.03 | 53689.92 | 55042.76 | 4246.279 | 1 | 0.80 | 0.77 | 506.81 | 28 | 0 | 574.23 | 0 |
| 4 | -26674.22 | 9473.370 | 1 | 3679 | 53568.44 | 54254.83 | 53905.30 | 53348.44 | 55162.71 | 3946.200 | 1 | 0.75 | 0.73 | 300.08 | 28 | 0 | 341.48 | 0 |
| 5 | -26532.59 | 8561.743 | 1 | 3651 | 53341.19 | 54202.29 | 53763.79 | 53065.19 | 55340.89 | 3646.079 | 1 | 0.78 | 0.76 | 300.12 | 28 | 0 | 283.25 | 0 |
| 6 | -26431.42 | 8457.283 | 1 | 3623 | 53194.84 | 54230.65 | 53703.18 | 52862.84 | 55599.97 | 3559.346 | 1 | 0.75 | 0.73 | 86.73 | 28 | 0 | 202.35 | 0 |
| 7 | -26354.63 | 9186.551 | 1 | 3595 | 53097.26 | 54307.80 | 53691.36 | 52709.26 | 55907.83 | 3398.872 | 1 | 0.83 | 0.80 | 160.47 | 28 | 0 | 153.57 | 0 |
| 8 | -26559.78 | 8141.894 | 1 | 3567 | 53563.56 | 54948.81 | 54243.40 | 53119.56 | 56779.56 | 3672.379 | 1 | 0.89 | 0.88 | -273.51 | 28 | 1 | -410.30 | 1 |
| 9 | -26783.30 | 8942.604 | 1 | 3539 | 54066.60 | 55626.56 | 54832.18 | 53566.60 | 57688.02 | 4073.041 | 1 | 0.91 | 0.86 | -400.66 | 28 | 1 | -447.03 | 1 |
| 10 | -26679.26 | 8587.431 | 1 | 3511 | 53914.52 | 55649.20 | 54765.84 | 53358.52 | 57941.38 | 3927.284 | 1 | 0.88 | 0.78 | 145.76 | 28 | 0 | 208.08 | 0 |
Presentamos el modelo con mejor ajuste
Show code
print(LCA_best_model_adj_ppio) #
Conditional item response (column) probabilities,
by outcome variable, for each class (row)
$CAUSAL
Pr(1) Pr(2) Pr(3) Pr(4)
class 1: 0 0.2744 0.7256 0.0000
class 2: 0 0.0084 0.0000 0.9916
class 3: 0 0.0803 0.9197 0.0000
class 4: 0 0.4250 0.5750 0.0000
class 5: 0 0.9798 0.0202 0.0000
$EDAD_MUJER_REC
Pr(1) Pr(2) Pr(3) Pr(4) Pr(5) Pr(6)
class 1: 0 0.0447 0.3088 0.3244 0.2613 0.0607
class 2: 0 0.3289 0.3128 0.2186 0.1180 0.0218
class 3: 0 0.0000 0.1087 0.3114 0.5061 0.0739
class 4: 0 0.0167 0.3010 0.3270 0.3012 0.0541
class 5: 0 0.0084 0.2213 0.4345 0.3010 0.0349
$PUEBLO_ORIGINARIO_REC
Pr(1) Pr(2) Pr(3)
class 1: 0.2179 0.7232 0.0589
class 2: 0.1480 0.8092 0.0428
class 3: 0.1340 0.8660 0.0000
class 4: 0.1547 0.8099 0.0354
class 5: 0.1094 0.8444 0.0462
$PAIS_ORIGEN_REC
Pr(1) Pr(2) Pr(3)
class 1: 0 0.9729 0.0271
class 2: 0 0.7796 0.2204
class 3: 0 0.9213 0.0787
class 4: 0 0.0215 0.9785
class 5: 0 0.8871 0.1129
$HITO1_EDAD_GEST_SEM_REC
Pr(1) Pr(2) Pr(3) Pr(4) Pr(5) Pr(6)
class 1: 0 0.0000 0.2774 0.3734 0.2268 0.1224
class 2: 0 0.7875 0.2098 0.0000 0.0000 0.0027
class 3: 0 0.0113 0.6007 0.2615 0.1121 0.0144
class 4: 0 0.0202 0.3157 0.3964 0.2029 0.0648
class 5: 0 0.2755 0.2299 0.4904 0.0000 0.0043
$MACROZONA
Pr(1) Pr(2) Pr(3) Pr(4) Pr(5) Pr(6)
class 1: 0 0.2692 0.2011 0.2253 0.0895 0.2148
class 2: 0 0.4224 0.1552 0.1172 0.1351 0.1700
class 3: 0 0.6725 0.1154 0.0615 0.0781 0.0726
class 4: 0 0.6093 0.0989 0.0253 0.2396 0.0268
class 5: 0 0.4086 0.1608 0.1635 0.1206 0.1464
$PREV_TRAMO_REC
Pr(1) Pr(2) Pr(3) Pr(4) Pr(5)
class 1: 0 0.0165 0.6578 0.3210 0.0047
class 2: 0 0.0615 0.6811 0.1927 0.0647
class 3: 0 0.5466 0.1775 0.2695 0.0064
class 4: 0 0.0151 0.6038 0.2733 0.1078
class 5: 0 0.1055 0.5341 0.3604 0.0000
Estimated class population shares
0.3811 0.1946 0.1759 0.0987 0.1498
Predicted class memberships (by modal posterior prob.)
0.3782 0.1937 0.1494 0.1135 0.1652
=========================================================
Fit for 5 latent classes:
=========================================================
2 / 1
Coefficient Std. error t value Pr(>|t|)
(Intercept) -1.86652 0.15552 -12.002 0
outcome 1.41025 0.16503 8.545 0
=========================================================
3 / 1
Coefficient Std. error t value Pr(>|t|)
(Intercept) -2.30304 0.29346 -7.848 0
outcome 1.76958 0.27174 6.512 0
=========================================================
4 / 1
Coefficient Std. error t value Pr(>|t|)
(Intercept) -1.98117 0.23503 -8.429 0
outcome 0.78006 0.20284 3.846 0
=========================================================
5 / 1
Coefficient Std. error t value Pr(>|t|)
(Intercept) -1.42421 0.19326 -7.369 0.000
outcome 0.61667 0.18216 3.385 0.001
=========================================================
number of observations: 3789
number of estimated parameters: 138
residual degrees of freedom: 3651
maximum log-likelihood: -26532.59
AIC(5): 53341.19
BIC(5): 54202.29
X^2(5): 8561.743 (Chi-square goodness of fit)
ALERT: estimation algorithm automatically restarted with new initial values
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save.image("data2_lca2_adj_imp.RData")
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require(tidyverse)
sesion_info <- devtools::session_info()
print(Sys.time())
[1] "2023-05-06 23:10:54 -04"Show code
dplyr::select(
tibble::as_tibble(sesion_info$packages),
c(package, loadedversion, source)
) %>%
DT::datatable(filter = 'top', colnames = c('Row number' =1,'Variable' = 2, 'Percentage'= 3),
caption = htmltools::tags$caption(
style = 'caption-side: top; text-align: left;',
'', htmltools::em('Packages')),
options=list(
initComplete = htmlwidgets::JS(
"function(settings, json) {",
"$(this.api().tables().body()).css({
'font-family': 'Helvetica Neue',
'font-size': '50%',
'code-inline-font-size': '15%',
'white-space': 'nowrap',
'line-height': '0.75em',
'min-height': '0.5em'
});",#;
"}")))