Feature/c2019/w1/depression icd11

.gitignore

@@ -43,3 +43,4 @@ vignettes/*.pdf
 *.docx
 *.html
 *.dta
+*.pdf

doc/outcomes/cohorte_2019/ola_1/Description_depression_ICD11.Rmd

@@ -0,0 +1,377 @@
+---
+title: "Edad con Salud -- cohort 2019 -- wave 1 -- 'depression_ICD11'"
+output:
+  word_document:
+    reference_docx: !expr ecs.data::get_pkg_docx_template()
+  pdf_document: default
+csl: "`r ecs.data::get_proj_csl_file()`"
+bibliography: "`r ecs.data::get_proj_bib_file()`"
+editor_options:
+  markdown:
+    wrap: 80
+---
+
+```{r setup, include=FALSE}
+# Activar los paquetes que R necesita para ejecutar el código:
+
+library(Statamarkdown)
+
+# Ruta al ejecutable de Stata (Ejecuta `sysdir` en Stata para encontrar la ruta)
+
+# Opciones de configuración de las salidas de R y Stata:
+
+knitr::opts_chunk$set( # Para todos los 'chunks' de código:
+  echo        = FALSE, #   - No muestra la sintaxis en el documento
+  results     = 'hide',#   - Omite los resultados de ejecutar la sintaxis
+  cleanlog    = TRUE,  #   - Omite repetir sintaxis en resultados de Stata
+  collectcode = TRUE   #   - Reutiliza el código de Stata de 'chunks' anteriores
+)
+```
+
+# Variable information
+
++---------------------------+------------------+------------+-----------+
+| **Main variable name**    | **Label**        | **Format** | **Code**  |
++:==========================+:=================+============+===========+
+| depression_lifetime       | Lifetime         | Binary     | -   0=No; |
+|                           | (c2019_w1)       |            | -   1=Yes |
++---------------------------+------------------+------------+-----------+
+| depression_lifetime_proxy | Lifetime         | Binary     | -   0=No; |
+|                           | depression for   |            | -   1=Yes |
+|                           | proxy (c2019_w1) |            |           |
++---------------------------+------------------+------------+-----------+
+
+# Variable description
+
+Depression has become a major public health issue as it is one of the main
+causes of disability worldwide, with an even greater impact on developed
+countries. According to The ICD-10 Classification of Mental and Behavioural
+Disorders, Diagnostic criteria for research
+[@world_health_organization_icd-10_1992], the main characteristics of depression
+are the presence of a sustained depressed mood, the loss of interest or pleasure
+in activities normally pleasurable and/or the decreased energy or increased
+fatigability. In addition to these main criteria, the ICD-10 Diagnostic criteria
+for research proposes several contributing factors that can be present or
+absent: loss of confidence and self-esteem, feelings of self-reproach or guilt,
+recurrent thoughts of death or suicide, diminished ability to think or
+concentrate, change in psychomotor activity, sleep disturbance, and changes in
+appetite with the corresponding weight change. Moreover, the classification
+proposes a three-level gradient of severity depending on the amount of criteria
+present in each case, from mild to severe. The ICD-11
+[@worldhealthorganization2019] refers to the same symptoms but strengthens the
+criteria, making the diagnosis of depression more demanding than its
+predecessor. In order to address these criteria and be able to assess the
+lifetime presence or absence of a depressive episode, as well as its severity,
+we used an adapted version of the Composite International Diagnostic Interview
+(CIDI 3.0), a comprehensive, fully-structured interview designed to be used by
+trained lay interviewers for the assessment of mental disorders according to the
+definitions and criteria of ICD-11 (criteria can been seen at [ICD-11 for
+Mortality and Morbidity Statistics
+(who.int](https://icd.who.int/browse11/l-m/en#/http%3a%2f%2fid.who.int%2ficd%2fentity%2f578635574)[)](https://icd.who.int/browse11/l-m/en#/http%3a%2f%2fid.who.int%2ficd%2fentity%2f1563440232)
+It is intended for use in epidemiological and cross-cultural studies, as well as
+for clinical and research purposes.
+
+# Explanation of how the variables were created
+
+Information from the CIDI depression module was used for the creation of the
+depression variables. Algorithms based on the ICD-11 were used for the
+endorsement of depressive episode at some point in their lives (lifetime
+prevalence; variable `depression_lifetime`). More precisely, the following
+criteria must be fulfilled:
+
+i)  Symptoms should last at least two weeks;
+
+ii) The clinical presentation does not fulfill the diagnostic requirements for a
+    Mixed Episode;
+
+iii) The episode is not attributable to psychoactive substance use or to any
+     organic mental disorder
+
+iv) The concurrent presence of at least five of the following symptoms:
+
+    -   **Affective cluster:** (1) Depressed mood, (2) Markedly diminished
+        interest or pleasure;
+    -   **Cognitive-behavioural cluster:** (3) Reduced ability to concentrate
+        and sustain attention, (4) Beliefs of low self-worth or excessive and
+        inappropriate guilt, (5) Hopelessness about the future, (6) Reccurent
+        thoughts of death;
+    -   **Neurovegetative cluster:** (7) Significantly disrupted sleep, (8)
+        Significant change in appetite or weight, (9) Psychomotor agitation or
+        retardation, (10) Reduce energy, or fatigue;
+
+v)  At least one symptom from the affective cluster (depressed mood, loss of
+    interest).
+
+For reasons of precision and availability of information, certain criteria could
+not be taken into account ("The symptoms result in significant distress or
+significant impairment in personal, family, social, educational, occupational or
+other important areas of functioning." and "Symptoms are not best explained by
+bereavement").
+
+The coding of this algorithm is very complex and requires many different
+criteria to be taken into account. We have tried to make use of uniform coding
+criteria for implementing the computation of the different symptoms and
+diagnostic criteria, and also separating clearly the computation of the
+*positive*/*negative*/*missing* cases, to make the code the clearest possible.
+The following general principles have been followed when possible:
+
+-   All the non-valid responses are considered to be *negative* responses; that
+    is, if an item has been answered with "*Don't know*" (`888`) or "Refused"
+    (`999`), it is assumed that the criterion is "not met" (=`0`).
+
+-   Only the variables that are kept in the final dataset are labelled.
+
+-   First, all the cases are set to `.` ("Missing" value).
+
+-   Then, the negative cases are recoded to `0` (diagnostic "No").
+
+-   Finally, the positive cases are recoded to `1` (diagnostic "Yes").
+
+-   Unless stated otherwise, the cases are explicitly recoded to their final
+    value exclusively and exhaustively, such that the number of cases recoded to
+    `0`/`1` in each step must be exactly the same as the number of `0`/`1` cases
+    finally in the variable. This allows for an additional check of recoding
+    errors.
+
+-   When the values need to be compared for unequality (operator `!=`) against a
+    non-missing value, it must be taken into account that a "missing" value
+    gives a `1` result instead of a missing in Stata. Therefore, in order to
+    avoid recoding "missing" values into non-missing ones, the "missing" values
+    must be excluded from the comparison. This principle is used generally
+    throughout the algorithm; when used differently, it is explained in the
+    syntax.
+
+-   When these principles are not strictly followed, an annotation is added
+    right below, explaining how it changes from them and why.
+
+# Syntax used to create the variable (Stata 15)
+
+```{stata load-data}
+* Cohorte 2019, ola 1:
+use "~\UAM\Marta Miret Garcia - Bases de datos maestras Edad con Salud\Ola_3\Cohorte_2019\rawdata_c2019w1.dta"
+```
+
+```{stata generate-outcomes, echo=TRUE}
+*# "Value labels (defined for all the outcome variables in the dataset)":
+label define yesno    0 "No" 1 "Yes"
+
+
+***#"VARIABLE `depression_lifetime`: Depressive episode (6A70)"
+
+*#Criterion 1: "The depressive episode should last for at least 2 weeks"
+gen     d_crit1 = .
+replace d_crit1 = 0 if (q4211!=1 & q4211!=.) | (q4213!=1 & q4213!=.)
+replace d_crit1 = 1 if  q4211==1             |  q4213==1
+
+*#Criterion 2: "The clinical presentation does not fulfil the diagnostic
+*#             requirements for a Mixed Episode"
+gen d_crit2 =0
+replace d_crit2 = 1 if q4233!=1 & q4225_causemed2!=1
+replace d_crit2 = . if q4233==. & q4225_causemed2==.
+
+*#Criterion 3: "The episode is not attributable to psychoactive substance use or
+*#             to any organic mental disorder"
+gen     d_crit3 = .
+replace d_crit3 = 0 if                            q4224b==1              | (q4224==1 & (q4225_causemed12==1 | q4225_causemed23==1 | q4225_causemed24==1 | q4225_causemed25==1 | q4225_causemed30==1 | q4225_causemed31==1))
+replace d_crit3 = 1 if (q4224a!=1 & q4224a!=.) | (q4224b!=1 & q4224b!=.) | (q4224==1 & (q4225_causemed12!=1 & q4225_causemed23!=1 & q4225_causemed24!=1 & q4225_causemed25!=1 & q4225_causemed30!=1 & q4225_causemed31!=1))
+*#"NOTE: When `q4224b==1` it is necessarily the case that `q4224a==1`,
+*#       so only `q4224b` out of these two needs to be checked for considering
+*#       the criterion negative."
+
+*#Filling of the three first criteria above (Criterion 1, 2 and 3):
+gen     d_crit_123 = .
+replace d_crit_123 = 0 if d_crit1==0 | d_crit2==0 | d_crit3==0
+replace d_crit_123 = 1 if d_crit1==1 & d_crit2==1 & d_crit3==1
+*#"NOTE: The criterion named "d_crit123" includes all the three exclusion criteria
+*#       of the ICD11. Those three criteria are coded in different points because
+*#       they do not take into account a minimum threshold of symptoms as the two
+*#       other bellow (Criterion 4 and Criterion 5)."
+
+*#Criterion 4: "A total of at least five symptoms from the following list should
+*#             be present."
+
+*# AFFECTIVE CLUSTER:
+
+*#S1: "Depressed mood to a degree that is definitely abnormal for the
+*#    individual, present for most of the day and almost every day, largely
+*#    uninfluenced by circumstances, and sustained for at least 2 weeks"
+gen     d_s1 = .
+replace d_s1 = 0 if (q4220a!=1 & q4220a!=.) & q4220b!=1 & q4220c!=1
+replace d_s1 = 1 if  q4220a==1              | q4220b==1 | q4220c==1
+*#"NOTE: When `q4220b` or `q4220d` are "missing" it may be due to the interview
+*#       skip logic in `q4220a` or `q4220c`, respectively. But if there is a
+*#       response in`q4220a` there must be one also in `q4220c`. Therefore, only
+*#       `q4220a` needs to be checked for missingness".
+
+*#S2: "Loss of interest or pleasure in activities that are normally pleasurable
+*#    (including sexual desire)"
+gen     d_s2 = .
+replace d_s2 = 0 if (q4220e!=1 & q4220e!=.) & q4220f!=1
+replace d_s2 = 1 if  q4220e==1              | q4220f==1
+
+*# COGNITIVE-BEHAVIOURAL CLUSTER:
+
+*#S3: "Complaints or evidence of diminished ability to think or concentrate,
+*#    such as indecisiveness or vacillation"
+gen     d_s3 = .
+replace d_s3 = 0 if q4222h!=1 & q4222h!=. & q4222i!=1 & q4222j!=1
+replace d_s3 = 1 if q4222h==1             | q4222i==1 | q4222j==1
+*#"NOTE: When `q4222i` and `q4222j` are 'missing' it may be due to the
+*#       interview skip logic in `q4222h`. Therefore, only `q4222h` needs
+*#       to be checked for missingness".
+
+*#S4: "Beliefs of low self-worth or excessive and inappropriate guilt that may
+*#    be manifestly delusional"
+gen     d_s4 = .
+replace d_s4 = 0 if ((q4222k!=1 & q4222k!=.) & (q4222l!=1 & q4222l!=.) & q4222m!=1) | (q4222n!=1 & q4222n!=.)
+replace d_s4 = 1 if q4222k==1                | q4222l==1               | q4222m==1  |  q4222n==1
+*#"NOTE: When `q4222m` is "missing" it may be due to the interview
+*#       skip logic in `q4222l`. Therefore, only `q4222k` and `q4222l`
+*#       need to be checked for missingness".
+
+*#S5: "Hopelessness about the future."
+gen     d_s5 = .
+replace d_s5 = 0 if q4220d!=1 & q4220d!=.
+replace d_s5 = 1 if q4220d==1
+*#"NOTE: Symptom presents in the ICD10 as, (d) bleak and pessimistic views of
+*#       the future;"
+
+*#S6: "Recurrent thoughts of death or suicide, or any suicidal behaviour"
+gen     d_s6 = .
+replace d_s6 = 0 if q4222r!=1 & q4222r!=. & q4222s!=1 & q4222t!=1 & q4222u!=1 & q4222v!=1
+replace d_s6 = 1 if q4222r==1             | q4222s==1 | q4222t==1 | q4222u==1 | q4222v==1
+*#"NOTE: When any of the two last items are 'missing' it may be due to
+*#       the interview skip logic in `q4222t`. But if there is a
+*#       response in `q4222r` there must be one also in `q4222s` and
+*#       `q4222t`.Therefore, only `q4222r` needs to be checked for
+*#       missingness".
+
+*# NEUROVEGETATIVE CLUSTER:
+
+*#S7: "Sleep disturbance of any type"
+gen     d_s7 = .
+replace d_s7 = 0 if (q4222c!=1 & q4222c!=.) & q4222d!=1
+replace d_s7 = 1 if q4222c==1               | q4222d==1
+*#"NOTE: When `q4222d` is 'missing' it may be due to the interview skip
+*#       logic in `q4222c`. Therefore, only `q4222c` is checked for
+*#       missingness".
+
+*#S8: "Change in appetite (decrease or increase) with corresponding weight
+*#    change"
+gen     d_s8 = .
+replace d_s8 = 0 if (q4222a!=1 & q4222a!=.) | (q4222b!=1 & q4222b!=.)
+replace d_s8 = 1 if  q4222a==1              &  q4222b==1
+
+*#S9: "Change in psychomotor activity, with agitation or retardation (either
+*#    subjective or objective)"
+gen     d_s9 = .
+replace d_s9 = 0 if (q4222f!=1 & q4222f!=.  & q4222fa!=1) | (q4222g!=1 & q4222ga!=1 & q4222g!=.)
+replace d_s9 = 1 if  q4222f==1 |              q4222fa==1  |  q4222g==1 | q4222ga==1
+*#"NOTE: When the three last items are 'missing' it may be due to the
+*#       interview skip logic in `q4222f`. Therefore, only `q4222f` needs
+*#       to be checked for missingness".
+
+*#S10: "Decreased energy or increased fatigability"
+gen     d_s10 = .
+replace d_s10 = 0 if q4222e!=1 & q4222e!=.
+replace d_s10 = 1 if q4222e==1
+
+*#"Sum of depressive symptoms"
+egen d_symptot = rowtotal (d_s1 d_s2 d_s3 d_s4 d_s5 d_s6 d_s7 d_s8 d_s9 d_s10), missing
+
+*#"To fulfill Criterion 4, at least five symptoms should be present".
+gen     d_crit4 = .
+replace d_crit4 = 0 if d_symptot<5 
+replace d_crit4 = 1 if d_symptot>=5 & d_symptot!=.
+
+
+*#Criterion 5: "At least one symptom from the affective cluster must be present"
+
+*#"Sum of depressive symptoms of affective cluster"
+egen d_afftotal = rowtotal (d_s1 d_s2), missing
+
+*#"To fulfil criterion 5 at least one symptoms of the affective cluster should
+*# be present".
+gen     d_crit5 = .
+replace d_crit5 = 0 if d_afftotal <1 
+replace d_crit5 = 1 if d_afftotal==1 | d_afftotal==2
+
+
+***#"Has the person skipped the lifetime depression module?"
+
+*#"Depression symptoms recoded into 0/1 to compute the tally":
+recode q4220a-q4222v (1=1) (2=0) (888 999=.)
+
+*#"Filter variables":
+gen  f4217     = q4214==1 & q4215==4 & q4216==4 if q4214!=.
+egen f4221_sum = rowtotal (q4220a-q4220f), missing
+egen f4223_sum = rowtotal (q4220a-q4222v), missing
+
+*#"Variable "skipped" computation":
+gen     d_skipped = .
+replace d_skipped = q4202!=1                   if q4202!=.
+replace d_skipped = q4211!=1    | d_skipped==1 if q4211!=.    
+replace d_skipped = q4213!=1    | d_skipped==1 if q4213!=.    
+replace d_skipped = q4218!=1    | d_skipped==1 if q4218!=.    
+replace d_skipped = f4217==1    | d_skipped==1 if f4217!=.    
+replace d_skipped = f4221_sum<1 | d_skipped==1 if f4221_sum!=.
+replace d_skipped = f4223_sum<2 | d_skipped==1 if f4223_sum!=.
+*#"NOTE: For clarity, this recoding adds the criteria incrementally. This
+*#       implies that the new "truth values" (0/1 resulting from each
+*#       comparison) are "logically added" (therefore the "OR" operation)
+*#       to the current values".
+
+
+***#"Lifetime depression diagnostic variable":
+gen     depression_lifetime = .
+replace depression_lifetime = 0 if d_skipped==1 | d_crit_123==0 | d_crit4==0 | d_crit5==0
+replace depression_lifetime = 1 if d_skipped==0 & d_crit_123==1 & d_crit4==1 & d_crit5==1
+label values   depression_lifetime yesno
+label variable depression_lifetime "Lifetime depression (c2019_w1)"
+
+
+***#"VARIABLE `depression_lifetime_proxy`: Depressive episode for proxy participants"
+recode P4040 (1=1) (2=0) (888=0) (999=0), gen (depression_lifetime_proxy)
+label values   depression_lifetime_proxy yesno
+label variable depression_lifetime_proxy "Lifetime depression for proxy (c2019_w1)"
+
+```
+
+<br>
+
+```{stata descriptives, collectcode=FALSE, results='markup'}
+codebook depression_lifetime depression_lifetime_proxy
+```
+
+```{stata save-data}
+keep q0007a_result ID_ECS proxy subsample_pre interview_pre depression_lifetime depression_lifetime_proxy 
+
+* Cohorte 2019, ola 1:
+
+saveold "~\UAM\Marta Miret Garcia - Documentacion Edad con Salud\Edad con salud - Ola 3\Outcomes\Cohorte 2019\Outcome datasets\Outcome_depression_ICD11.dta", replace version(13)
+```
+
+# Contact person:
+
+-   Name: Lea Francia (UAM)
+-   e-mail: [lea.francia\@inv.uam.es](mailto:lea.francia@inv.uam.es){.email}
+
+Original version:
+
+-   Name: Daniel Morillo (UAM)
+-   e-mail:
+    [daniel.morillo\@inv.uam.es](mailto:daniel.morillo@inv.uam.es){.email}
+-   Phone number: (+34) 914975816
+
+# References
+
+::: {#refs}
+:::
+
+\newpage
+
+# Session info
+
+```{r, results='markup'}
+devtools::session_info()
+```

www/Edad_con_salud_outcome_vars.bib

@@ -270,3 +270,12 @@ @techreport{world_health_organization_icd-10_1992
 	note = {ISBN: 9787117019576
 number-of-pages: 362},
 }
+
+@book{worldhealthorganization2019,
+	title = {International Statistical Classification of Diseases and Related Health Problems (11th ed.)},
+	author = {World Health Organization, },
+	year = {2019},
+	date = {2019},
+	edition = {11},
+	url = {https://icd.who.int/}
+}