init repo

.Rbuildignore

@@ -0,0 +1,4 @@
+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$

.Rprofile

@@ -0,0 +1,3 @@
+source("renv/activate.R")
+
+devtools::load_all()

.drake/.gitignore

@@ -0,0 +1,2 @@
+*
+!/.gitignore

.gitignore

@@ -0,0 +1,21 @@
+# R auxiliary files
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+
+# Other files types
+
+# htlm output
+Todo.html
+Documents/*.html
+*.docx
+
+# Project folders
+
+# data_raw
+*.rda
+*.rds
+
+# Mac auxiliary files
+.DS_Store

Analysis/Analysis_Drake.R

@@ -0,0 +1,84 @@
+########################
+####    Analysis    ####
+########################
+
+#----    load env    ----
+env <- devtools::load_all()$env
+
+#----    Plan   -----
+
+# load plan
+plan <- get_analysis_plan()
+
+# Configure the analysis plan
+config <- drake::drake_config(plan,
+                              prework = "devtools::load_all()",
+                              envir = env)
+
+# Plot the analysis plan
+drake::vis_drake_graph(config, font_size = 16, targets_only = FALSE)
+
+#----    Make    ----
+
+# Delate the analysis results
+# drake::clean(destroy = TRUE)
+
+# Run the analysis
+drake::make(prework = "devtools::load_all()",
+            envir = env,
+            plan = plan)
+
+# Plot the analysis plan
+drake::vis_drake_graph(config, font_size = 16, targets_only = FALSE)
+
+#----    load    ----
+
+# data
+drake::loadd(data_munged)
+
+#---- cluster ----
+
+# cluster tat
+drake::loadd(cluster_mother_tat)
+drake::loadd(cluster_father_tat)
+
+plot(cluster_mother_tat, main = "Dendrogramma")
+rect.hclust(cluster_mother_tat, k=4, border="red")
+plot(cluster_father_tat, main = "Dendrogramma")
+rect.hclust(cluster_father_tat, k=4, border="red")
+
+drake::loadd(data_cluster_tat)
+table(data_cluster_tat$cluster_mother_tat)
+table(data_cluster_tat$cluster_father_tat)
+
+plot_scores_mother(data = data_cluster_tat)
+plot_scores_father(data = data_cluster_tat)
+
+# mclust
+drake::loadd(mclust_mother)
+drake::loadd(mclust_father)
+
+plot(mclust_mother)
+summary(mclust_mother)
+
+plot(mclust_father)
+summary(mclust_father)
+
+#---- brms models ----
+
+drake::loadd(fit_int)
+
+summary(fit_int)
+plot(brms::conditional_effects(fit_int), ask = FALSE)
+
+plot(fit_int)
+
+drake::loadd(stan_data)
+
+str(fit_int$fit)
+#-----
+
+
+
+
+#----

Analysis/draft.R

@@ -0,0 +1,115 @@
+load("Data/ddef_datiECR.rda")
+ddef=ddef_datiECR[ddef_datiECR$age_year<12.30,]
+ddef<- subset(ddef, ddef$fas !="NA")
+nrow(ddef) #847
+
+#---- cluster madre ----
+
+dcM <- dist(ddef[,c(60:71)], method = "euclidean") # distance matrix
+fit <- hclust(dcM, method="ward.D")
+plot(fit, main = "Dendrogramma")
+# dal dendrogramma sembrano emergere 4 cluster
+rect.hclust(fit, k=4, border="red")
+ddef$gruppiattM <- as.factor(cutree(fit, k=4))
+table(ddef$gruppiattM)
+
+
+# profilo
+fattore=rep(c("Ansia","Evitamento"),rep(dim(ddef)[1],2))
+y=c(scale(ddef$Anxm),scale(ddef$Avm))
+y1=c(ddef$Anxm,ddef$Avm)
+gruppo=rep(ddef$gruppiattM,2)
+dprof=data.frame(y,y1,fattore,gruppo)
+
+
+dprof$nomi.gruppi=factor(dprof$gruppo,labels=c("Gruppo1: Sicuri (n = 231)","Gruppo 2: Ansiosi (n = 286)","Gruppo 3: Ansiosi-Evitanti (n = 100)","Gruppo 4: Evitanti (n = 230)"))
+par(mar=c(6, 5, 4, 2) + 0.1)
+
+sciplot::bargraph.CI(fattore, y, group = nomi.gruppi, data=dprof,legend=T,ylim=c(-2.4,1.6),x.leg=1.2, y.leg=-1.2,ylab="Punteggi standardizzati",xlab="",cex.lab=.8,cex.leg=.8, col=c("yellow","green","blue","red"))
+
+
+#---- cluster padre ----
+
+dcP <- dist(ddef[,c(99:110)], method = "euclidean") # distance matrix
+fit <- hclust(dcP, method="ward.D")
+plot(fit, main = "Dendrogramma")
+# dal dendrogramma sembrano emergere 4 cluster
+rect.hclust(fit, k=4, border="red")
+ddef$gruppiattP <- as.factor(cutree(fit, k=4))
+
+# Profilo
+fattore=rep(c("Ansia","Evitamento"),rep(dim(ddef)[1],2))
+y=c(scale(ddef$Anxp),scale(ddef$Avp))
+y1=c(ddef$Anxp,ddef$Avp)
+gruppo=rep(ddef$gruppiattP,2)
+dprof=data.frame(y,y1,fattore,gruppo)
+
+dprof$nomi.gruppi=factor(dprof$gruppo,labels=c("Gruppo1: Sicuri (n = 206)","Gruppo 2: Ansiosi (n = 230)","Gruppo 3: Evitanti (n = 311 )","Gruppo 4: Ansiosi-Evitanti (n = 100)"))
+
+par(mar=c(6, 5, 4, 2) + 0.1)
+
+sciplot::bargraph.CI(fattore, y, group = nomi.gruppi, data=dprof,legend=T,ylim=c(-2.4,1.6),x.leg=1.2, y.leg=-1.2,ylab="Punteggi standardizzati",xlab="",cex.lab=.8,cex.leg=.8, col=c("yellow","green","blue","red"))
+
+prop.table(table(ddef$gruppiattP, ddef$gruppiattM), margin = 1)
+str(ddef$gruppiattP)
+
+cor(as.numeric(ddef$gruppiattP), as.numeric(ddef$gruppiattM))
+
+#---- fit ext ----
+
+hist(ddef$externalizing_sum)
+
+fit_ext <- glm(round(externalizing_sum,0) ~ genere * gruppiattP * gruppiattM, ddef,
+               family = "poisson")
+summary(fit_ext)
+car::Anova(fit_ext)
+plot(fit_ext)
+
+performance::check_zeroinflation(fit_ext)
+
+plot(effects::allEffects(fit_ext))
+
+# log transform
+hist(log(ddef$externalizing_sum))
+
+#---- fit ext no 0 ----
+
+sum(ddef$externalizing_sum > 0)
+ddef_ext0 <- ddef[ddef$externalizing_sum > 0, ]
+hist(ddef_ext0$externalizing_sum)
+
+fit_ext0 <- glm(round(externalizing_sum,0) ~ genere * gruppiattP * gruppiattM, ddef_ext0, family = "poisson")
+summary(fit_ext0)
+car::Anova(fit_ext0)
+plot(fit_ext0)
+
+plot(effects::allEffects(fit_ext0))
+
+
+summary(fit_ext0$residuals)
+hist(fit_ext0$residuals)
+
+
+#---- fit int ----
+
+hist(ddef$internalizing_sum)
+sum(ddef$internalizing_sum > 0)
+
+fit_int <- glm(round(internalizing_sum,0) ~ genere * gruppiattP * gruppiattM, ddef, family = "poisson")
+summary(fit_int)
+car::Anova(fit_int)
+
+
+fit_int_ext <- lm(cbind(internalizing_sum, externalizing_sum) ~ genere * gruppiattP * gruppiattM, ddef)
+
+
+
+performance::check_zeroinflation(fit_int)
+
+plot(effects::allEffects(fit_int))
+
+
+#----
+
+
+

Attachement.Rproj

@@ -0,0 +1,21 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

DESCRIPTION

@@ -0,0 +1,37 @@
+Package: Attachment
+Type: Package
+Title: What the Package Does (Title Case)
+Version: 0.1.0
+Author@R:
+  c(person(given = "Claudio",
+           family = "Zandonella Callegher",
+           role = c("aut", "cre"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-7721-6318")),
+    person(given = "Tatiana",
+           family = "Marci",
+           role = "aut",
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0002-2813-0312"))
+    person(given = "Gianmarco",
+           family = "Altoè",
+           role = "aut",
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0003-1154-9528"))
+           )
+Maintainer: Claudio Zandonella Callegher <[email protected]>
+Description: Analysis of atttachemnet theory
+License: 
+Encoding: UTF-8
+Depends:
+    tidyverse,
+    devtools
+Imports:
+    rmarkdown
+Suggests: 
+    knitr,
+    testthat (>= 3.0.0)
+LazyData: true
+Config/testthat/edition: 3
+RoxygenNote: 7.1.1
+VignetteBuilder: knitr