tiptop_ml_hhs_quality_report_mad_toliary.Rmd

```{r parameters, include=FALSE}
source("tiptop_hhs_quality.R")
source("lang.R")
source("tokens.R")

# Report language
kReportLang <- "EN"
language <- kLang[[kReportLang]]


# Data retrieval: {api, file}
data_retrieval_mode = "file"
# API
api_url   = redcap_api_url
api_token = hhs_endline_mada # TIPTOP HHS Endline DRC
non_retrieved_records = c("cluster", "facility")
# File
file_prefix = "TIPTOPHHSEndlineMadagascarMALGACHE"
file_content = "_DATA_WITH_NO_DUPS_"
file_date   ="2021-09-22"
file_time   ="11:23"

# Study area description
study_area_id           = 2
country_name            = "MADAGASCAR"
study_area_label        = "Toliary II"
study_area_column       = "toliary_2"
sample_size             = 568
partner.name            = "MANISA"
# sample_size * 5 (5 households to find one eligible woman)
household_to_be_visited = 2840

data_timestamp = dataTimestamp(data_retrieval_mode, file_date, file_time)
```

```{r title, include=FALSE}
#Languages
report.title <- paste(language$head.survey, '-', language$head.report, ':', country_name, '-', study_area_label)
```

---
title: "`r report.title`"
author: "Máximo Ramírez Robles"
date: `r data_timestamp`
output:
  html_document: default
  pdf_document: default
---

<style>
.main-container{
  max-width: 1200px;
  margin-left: auto;
  margin-right: auto;
}
.col-container{
  overflow: auto;
  position: relative;
}
.col-left{
  float: left;
  width: 50%;
}
.col-left-40{
  float: left;
  width: 40%;
}
.col-right{
  float: right;
  width: 50%;
}
.col-bottom{
  position: absolute;
  bottom: 0px;
}
.big-number{
  font-size: 95px;
}
.medium-number{
  font-size: 40px;
}
.text-center{
  text-align: center;
}
.text-right{
  text-align: right;
}
.text-left{
  text-align: left;
}
.vertical-small-padding{
  padding: 0 15px 0 15px;
}
.minnor-header{
  font-size: 18px;
}
.text-color-medium-value{
  color: #585859;
}
.text-color-big-value{
  color: #31708f;
}
</style>

```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(echo = TRUE, fig.width = 18, fig.height = 7.5)

hhs_data = readData(data_retrieval_mode, file_prefix, file_content, file_date, file_time, api_url, 
                    api_token, non_retrieved_records)
hhs_data = hhs_data[hhs_data$district == study_area_id, ]
hhs_data = hhs_data[!is.na(hhs_data$record_id), ]

# Global variables
last_record_date = lastRecordDate(hhs_data)
number_of_records = numberOfRecords(hhs_data)
```

```{r out.width="30px", echo=FALSE}
knitr::include_graphics("github_icon.png")
```
[`r language$head.github`](https://github.com/maxramirez84/r_tiptop_baseline_hhs_data_quality_report)

## `r language$progress.title`

`r sprintf(language$progress.records, number_of_records)` 
(`r sprintf(language$progress.last, last_record_date)`).

`r language$progress.partner` [`r partner.name`](http://www.manisa.mg).

```{r recruited_women_area, echo=FALSE}
# Midline dataset adjustments
# ended_pregnancy variable was removed
#changed date format due to error in formatting after exporting in csv.
hhs_data$interview_date <- as.POSIXct(hhs_data$interview_date, format = "%Y-%m-%d %H:%M:%S")
hhs_data$end_last_pregnancy <- as.POSIXct(hhs_data$end_last_pregnancy, format = "%Y-%m-%d")

hhs_data$diff_in_days = difftime(hhs_data$interview_date, hhs_data$end_last_pregnancy, units = "days")
hhs_data$diff_in_months = floor((hhs_data$diff_in_days / 365) * 12)
hhs_data$ended_pregnancy[hhs_data$diff_in_months > 6] = 0
hhs_data$ended_pregnancy[hhs_data$diff_in_months <= 6] = 1


consented   = numberOfparticipantsWhoConsented(hhs_data)
recruitment = recruitmentRate(hhs_data, sample_size)
```

```{r remove_lat_lon, echo=FALSE}
#CHECK LAT LON AS NA
hhs_data$latitude <- NA
hhs_data$longitude <- NA
```

### `r language$progress.subtitle1`

<div class="col-left text-center">
  `r language$progress.women` @ `r study_area_label`

  <span class="big-number">`r recruitment`%</span>

  `r consented` / `r sample_size`
</div>

<div class="col-right text-center">
</div>


```{r visited_households_area, echo=FALSE}
# visitedHouseholdsArea(hhs_data, household_to_be_visited, sample_size, study_area_label)
```

<p style="page-break-before: always">

```{r progress_area_1, echo=FALSE}
progressOfArea(hhs_data, study_area_column, study_area_label, interval = 10, required_visits_mean = 60, lang = language)
```

<p style="page-break-before: always">

## `r paste(language$profile.title)`

### `r sprintf(language$profile.subtitle1, study_area_label)`

```{r trial_profile_area_1, echo=FALSE, results="asis"}
trialProfileOfArea(hhs_data, study_area_column)
```

<p style="page-break-before: always">

## `r language$dups.title`

### `r sprintf(language$dups.subtitle1, study_area_label)`

```{r duplicates_summary_area_1, echo=FALSE, results="asis"}
duplicatesSummary(hhs_data, study_area_column)
```

### `r language$dups.subtitle2`
`r language$dups.desc1`

```{r duplicated_households, echo=FALSE}
printDuplicatedHouseholds(hhs_data, study_area_column, study_area_label)
```

### `r language$dups.subtitle3`
`r language$dups.desc2`

```{r duplicated_records, echo=FALSE}
printDuplicatedRecords(hhs_data, study_area_column, study_area_label)
```

<p style="page-break-before: always">

## `r language$indicators.title`

<span style="color: red"><b>`r language$indicators.impt`:</b></span>
`r language$indicators.desc`

### `r language$indicators.subtitle1`

<div class="col-container">
```{r sp_indicators, echo=FALSE}
ciptp_knowledge      = cIPTpKnowledgeRate(hhs_data)
ciptp_administration = cIPTpAdministrationRate(hhs_data)

SPIndicators(hhs_data, study_area_label)
```

<div class="col-left text-center">
  <div class="col-container">
  <span class="minnor-header">`r sprintf(language$indicators.subtitle2, study_area_label,language$indicators.subtitle3)`
  
  <div class="col-left col-bottom text-right vertical-small-padding text-color-medium-value">
  <span class="medium-number">`r ciptp_knowledge`%</span><br/>
  `r language$indicators.header1`
  </div>
  <div class="col-right text-left vertical-small-padding text-color-big-value">
  <span class="big-number">`r ciptp_administration`%</span><br/>
  `r language$indicators.header2`
  </div>
  </div>
  <br/>
  <div class="col-container">
  </div>
</div>
</div>

### `r language$indicators.subtitle4`

```{r anc_indicators, echo=FALSE}
ANCIndicators(hhs_data, study_area_label)
```