index.Rmd

---
title: "Medstar APS"
output: html_document
  # flexdashboard::flex_dashboard:
  #   vertical_layout: scroll
  #   orientation: columns
---

```{r setup, message=FALSE, warning=FALSE, results='hide', include=FALSE}
library(flexdashboard)
library(viridis)
library(ggplot2)
library(dplyr)
library(naniar)
library(freqtables)
library(purrr)
library(haven)
```

```{r sourcecode, message=FALSE, warning=FALSE, results='hide', include=FALSE}
source_rmd = function(file, ...) {
  tmp_file = tempfile(fileext=".R")
  on.exit(unlink(tmp_file), add = TRUE)
  knitr::purl(file, output=tmp_file)
  source(file = tmp_file, ...)
}
```

```{r sourcecode_dashboards, message=FALSE, results='hide', include=FALSE}
# source_rmd("dashboard_01_import.Rmd")
# source_rmd("dashboard_02_merge.Rmd")
```

```{r freq_tables_function, message=FALSE, warning=FALSE, results='hide', include=FALSE }
freq_tables <- function(.data, .col) {
  .data %>% 
    freq_table({{.col}}) %>% 
    arrange(desc(n)) %>% 
    freq_format("n (percent %)", digits = 1) %>% 
    select(var, cat, formatted_stats) 
}
```

Dashboard for Data Quality Checks
===========================================

Sections {.tabset}
-------------------------------------------


### Consent

```{r consentindex, echo=FALSE}
consent_stats <- map(
  .x = set_names(c("consent_created_by", "consent_timestamp", "consent_status",
                   "consent_record_month", "consent_record_year",
                   "consent_interview_month", "consent_interview_year")),
  .f = ~ freq_tables(merged_consented, !!sym(.x)))

consent_stats
```


### Sociodemographics

```{r socioindex, echo=FALSE}
socio_socio_stats <- map(
  .x = set_names(c("sociodemographic_created_by", "sociodemographic_status",
                   "sode_people", "sode_hispanic","sode_military",
                   "sode_unwanted", "sode_sexual", "hsi_contact",
                   "x_record_month", "x_record_year", "sogi_identity", 
                   "sode_marital", "sode_race", "sode_school", "sode_employed", 
                   "sode_income", "sogi_orientation")),
  .f = ~ freq_tables(merged_consented, !!sym(.x)))

socio_socio_stats
```


```{r sociographindex, echo=FALSE}
# age <- merged_consented$sode_age_years
hist(merged_consented$sode_age_years,
     main = "Distribution of Age",
     xlab = "Age",
     col = "chocolate")
```


### APS Investigations

```{r apsindex, echo=FALSE}
aps_stats <- map_df(
  .x = set_names(c("aps_investigation_created_by",
                   "aps_investigation_status", "aps_report", "aps_times",
                   "aps_recent", "x_record_month", "x_record_year",
                   "xc_lead_panel_summary_count", "aps_first")),
  .f = ~ freq_tables(merged_consented, !!sym(.x)))

aps_stats
```


### Clutter scale

```{r homeinspectionindex, echo=FALSE}
clutter_stats <- map_df(
  .x = set_names(c("clutter_scale_created_by", "clutter_living", "look_kitchen",
                   "clutter_kitchen", "look_bedroom", "clutter_bedroom",
                   "look_living", "clutter_living_photo",
                   "clutter_kitchen_photo", "clutter_bedroom_photo",
                   "clutter_scale_status")),
  .f = ~ freq_tables(merged_consented, !!sym(.x)))

clutter_stats
```


### General Health

```{r generalhealthindex, echo=FALSE}
genhealth_pen_stats <- map_df(
    .x = set_names(c("general_health_created_by", "health_bp_systolic",
                     "health_heart", "health_oxygen","health_temp",
                     "health_pain", "health_bp_diastolic", 
                     "outcomes_health_general", "outcomes_health_vigorous",  
                     "outcomes_health_moderate", "outcomes_health_uphill",
                     "outcomes_health_bend", "outcomes_health_block", 
                     "outcomes_health_bathe", "outcomes4_weeks_pain", 
                     "outcomes_month_social", "outcomes_month_nervous", 
                     "outcomes_month_calm", "outcomes_month_blue", 
                     "outcomes_month_happy", "outcomes_month_dumps", "outcomes_tf_ill",
                     "outcomes_tf_anybody", "outcomes_tf_bad", "outcomes_tf_health",
                     "depres_satisfied", "depres_hopeless", "depres_better",
                     "depres_activities", "depres_empty", "depres_bored",
                     "depres_spirits", "depres_afraid", "depres_happy",
                     "depres_helpless", "depres_home", "depres_memory",
                     "depres_alive", "depres_worthless", "depres_energy",
                     "nesarc_drink", "nesarc_months","peg_pain", "peg_enjoyment",
                     "peg_activity")),
    .f = ~ freq_tables(merged_consented, !!sym(.x)))

genhealth_pen_stats
```

### Gift Card

```{r giftcardindex, echo=FALSE}


gift_card_stats <- map_df(
    .x = set_names(c("gift_card_created_by", "gift_card_status",
                     "x_interviewer_name", "gift_card_i_d",
                     "x_qualtrics", "x_record_month", "x_record_year",
                     "xc_peg", "xc_mo_feelings", "xc_mo_outcomes_tf",
                     "xc_depres_scale","xc_finance_person",
                     "xc_physical_person", "xc_sexual_person",
                     "xc_aps_reported", "xc_interview_month", "xc_interview_year",
                     "xc_interview_month_year_abbr", "xc_mo_health", "xc_auditc",
                     "xc_neglect_person", "xc_aps_report", "xc_neglect_person")),
    .f = ~ freq_tables(merged_consented, !!sym(.x)))

# not working:
# xc_eai_general_assessment, xc_eai_abuse_indicators,
# xc_eai_neglect_indicators, xc_eai_exploitation_indicators,
# xc_eai_abandonment_indicators, xc_eai_environmental, xc_emotional_incident_person

# not included: x_randomizer, xc_u_r_l, xc_case_i_d, xc_detect, xcsummary

gift_card_stats
```

### Observational Measures

```{r observationalindex, echo=FALSE}
observational_stats <- map_df(
    .x = set_names(c("observational_measures_created_by", "clothes", "hygiene",
                     "poor_hygiene", "nutrition", "malnutrition", "skin_integrity",
                     "hair", "nails", "bruising", "fractures", "stages_healing", "abuse_statement",
                     "contracture", "decubitus", "dehydration", "diarrhea", "depression",
                     "impaction", "urine_burn", "obvious_disease", "inappropriate_medication",
                     "repetitive_hosp_admission", "neglect_statement", "money_misuse",
                     "evidence", "goods_for_services", "inability_account_money",
                     "exploitation_statement", "caretaker_withdrawn_care", "left_alone_unsafe",
                     "abandonment_statement", "yard_sidewalk", "roof", "windows",
                     "walls", "odor", "kitchen_cleanliness", "bathroom_cleanliness",
                     "bedroom_cleanliness", "living_room_cleanliness", "structural_problems",
                     "pets", "utilities", "unusual_odor", "disarray_hoarding", "health_safety_concern",
                     "caregiver_lack_knowledge", "caregiver_unengaged", "caregiver_frustrated",
                     "caregiver_anxious", "isolated_home", "depressed", "poor_personal_hygiene",
                     "inadequately_clothed", "difficulty_medications", "unmet_needs",
                     "report_elder_abuse", "hoarding_medications",
                     "observational_measures_status", "interior_condition",
                     "clutter", "neglect_comments", "exploitation_comments",
                     "abandonment_comments", "exterior_condition",
                     "summary_evidence_abuse", "summary_evidence_neglect",
                     "summary_evidence_exploitation",
                     "summary_evidence_abandonment", "general_assessment_comments",
                     "lacerations", "sexual_abuse", "abuse_indicators_comments",
                     "x_record_month", "x_record_year",
                     "aps_reported", "aps_reported_confirmation_number",
                     "aps_reported_method", "xc_case_i_d", "at_physical",
                     "at_phys_why", "at_sexual", "at_sex_why", "at_emotional",
                     "at_emot_why", "at_neglect", "at_neg_why", "at_abandon",
                     "at_aban_why", "at_financial", "at_fina_why", "at_self",
                     "at_self_why", "xc_lead_panel_summary_count",
                     "xc_lead_panel_summary_comment_count",
                     "xc_lead_panel_summary", "c_detect_status")),
    .f = ~ freq_tables(merged_consented, !!sym(.x)))

observational_stats
```


### Self-Report

```{r selfreportindex, echo=FALSE}
self_report_neglect_stats <- map_df(
    .x = set_names(c("self_report_created_by", "self_report_status",
                     "neglect_go", "neglect_go_reliable", "neglect_food",
                     "neglect_food_help", "neglect_food_reliable", "neglect_house",
                     "neglect_house_help", "neglect_house_reliable", "neglect_clean",
                     "neglect_ready", "finance_person_permission",
                     "finance_person_decisions", "finance_copies", "finance_person_forged",
                     "finance_person_tricked", "finance_person_stolen",
                     "finance_stranger_permission", "finance_stranger_forged",
                     "finance_stranger_tricked", "emotional_yelled",
                     "emotional_embarrassed", "emotional_harassed",
                     "emotional_harassed_age", "emotional_refused",
                     "emotional_incident_reported", "emotional_person_live",
                     "emotional_person_alcohol", "emotional_person_counseling",
                     "emotional_person_police", "emotional_person_job",
                     "emotional_person_help", "emotional_person_no_live",
                     "physical_hit", "physical_hit_age", "physical_restrain",
                     "physical_hurt", "physical_incident60", "physical_incident_reported",
                     "physical_incident_person", "physical_person", "physical_person_live",
                     "physical_person_alcohol", "physical_person_counseling",
                     "physical_person_police",  "physical_person_job",
                     "physical_person_help", "physical_person_no_live",
                     "sexual_harm", "sexual_touched", "sexual_touched_age",
                     "sexual_forced", "sexual_forced_age", "sexual_picture",
                     "sexual_picture_times", "sexual_picture_age",
                     "sexual_incident60", "sexual_incident_reported",
                     "sexual_incident_person", "sexual_person", "sexual_person_live",
                     "sexual_person_alcohol", "sexual_person_police",
                     "sexual_person_job", "sexual_person_help",
                     "sexual_person_no_live", "emotional_yelled_times_times",
                     "emotional_yelled_age_years", "emotional_embarrassed_times_times",
                     "emotional_embarrassed_age_years", "emotional_harassed_times_times",
                     "emotional_harassed_age_years", "emotional_refused_times_times",
                     "emotional_refused_age_years", "emotional_incident60",
                     "physical_hit_times_times", "physical_hit_age_years",
                     "physical_restrain_times_times", "physical_restrain_age_years",
                     "physical_hurt_times_times", "physical_hurt_age_years",
                     "sexual_harm_times_times", "sexual_harm_age_years",
                     "sexual_touched_times_times", "sexual_touched_age_years",
                     "sexual_forced_times_times", "sexual_forced_age_years",
                     "sexual_picture_times_times", "sexual_picture_age_years",
                     "finance_stranger_permission_times_times",
                     "finance_stranger_permission_age",
                     "finance_stranger_permission_age_years",
                     "finance_stranger_forged_times", "finance_stranger_forged_times_times",
                     "finance_stranger_forged_age", "finance_stranger_forged_age_years",
                     "finance_stranger_tricked_times", "finance_stranger_tricked_times_times",
                     "finance_stranger_tricked_age", "finance_stranger_tricked_age_years",
                     "xc_emotional_list", "xc_physical_list", "xc_sexual_list",
                     "finance_person_permission65","finance_person_permission_last_time",
                     "finance_person_forged65", "finance_person_forged_last_time",
                     "finance_person_tricked65", "finance_person_tricked_last_time",
                     "finance_person_stolen65", "finance_person_stolen_last_time",
                     "finance_stranger_permission65", "finance_stranger_permission_last_time",
                     "finance_stranger_forged65", "finance_stranger_forged_last_time",
                     "finance_stranger_tricked65", "finance_stranger_tricked_last_time",
                     "emotional_yelled65", "emotional_yelled_last_time",
                     "emotional_embarrassed65", "emotional_embarrassed_last_time",
                     "emotional_harassed65", "emotional_harassed_last_time",
                     "emotional_refused65", "emotional_refused_last_time",
                     "emotional_incident_reported_v2", "emotional_person_live_then",
                     "emotional_person_live_now", "physical_hit65",
                     "physical_hit_last_time", "physical_restrain65",
                     "physical_restrain_last_time", "physical_hurt65",
                     "physical_hurt_last_time", "physical_incident_reported_v2",
                     "physical_incident_person_v2", "physical_person_live_then",
                     "physical_person_live_now", "sexual_harm65",
                     "sexual_harm_last_time", "sexual_touched65",
                     "sexual_touched_last_time", "sexual_forced65",
                     "sexual_forced_last_time", "sexual_picture65",
                     "sexual_picture_last_time", "sexual_incident_reported_v2",
                     "sexual_incident_person_v2","sexual_person_live_then",
                     "sexual_person_live_now", "report_influence",
                     "xc_lead_panel_summary_count", "neglect_go_help",
                     "neglect_clean_help", "neglect_clean_reliable",
                     "neglect_ready", "neglect_ready_help", "neglect_ready_reliable",
                     "neglect_bills", "neglect_bills_help", "neglect_bills_reliable",
                     "neglect_person", "neglect_statement", "neglect_comments",
                     "finance_help", "finance_person", "emotional_yelled_times",
                     "emotional_yelled_age", "emotional_embarrassed_age",
                     "emotional_embarrassed_times", "emotional_harassed_times",
                     "emotional_refused_times", "emotional_refused_age",
                     "emotional_incident_person", "emotional_person_friends",
                     "physical_hit_times", "physical_restrain_times",
                     "physical_restrain_age", "physical_hurt_times",
                     "physical_hurt_age", "physical_person_friends",
                     "sexual_harm_times", "sexual_harm_age", "sexual_touched_times",
                     "sexual_forced_times", "sexual_person_counseling",
                     "sexual_person_friends", "finance_stranger_permission_times",
                     "fear_future", "fear_afraid", "fear_grateful", "fear_forward",
                     "fear_important", "emotional_incident_person_v2",
                     "report_private", "neglect_comments", "fear_afraid_response",
                     "fear_future_response", "fear_grateful_response",
                     "fear_forward_response", "fear_important_response" )),
    .f = ~ freq_tables(merged_consented, !!sym(.x)))

self_report_neglect_stats
```