test_data.Rmd

---
title: "Testing data"
csl: the-american-naturalist.csl
output:
  html_document:
    theme: cerulean
    toc: yes
  pdf_document:
    toc: yes
<!-- bibliography: references.bib -->
editor_options: 
  chunk_output_type: console
---

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<style type="text/css">
.main-container {
  max-width: 1370px;
  margin-left: auto;
  margin-right: auto;
}
</style>

```{r general_options, include = FALSE}
knitr::knit_hooks$set(
  margin = function(before, options, envir) {
    if (before) par(mgp = c(1.5, .5, 0), bty = "n", plt = c(.105, .97, .13, .97))
    else NULL
  },
  prompt = function(before, options, envir) {
    options(prompt = if (options$engine %in% c("sh", "bash")) "$ " else "> ")
  })

knitr::opts_chunk$set(margin = TRUE, prompt = TRUE, comment = "",
                      collapse = TRUE, cache = FALSE, autodep = TRUE,
                      dev.args = list(pointsize = 11), fig.height = 3.5,
                      fig.width = 4.24725, fig.retina = 2, fig.align = "center")

options(width = 137)
```

```{r}
if (! "readr" %in% rownames(installed.packages())) install.packages("readr")
pacs <- readr::read_csv("https://raw.githubusercontent.com/ecomore2/pacs/master/data/pacs.csv",
                        col_types = paste(c("icfnD", rep("c", 5), rep("D", 4), rep("f", 3)), collapse = ""))
```

```{r}
library(dplyr)
```

## Errors on the dates

Let's explore the time differences between the 4 dates:

```{r}
pacs %>% 
  filter(abs(onset - hospitalization) > 15 |
         abs(onset - consultation) > 15 |
         abs(onset - sample_collection) > 15 |
         abs(hospitalization - consultation) > 15 |
         abs(hospitalization - sample_collection) > 15 |
         abs(consultation    - sample_collection) > 15) %>% 
  select(id, onset, hospitalization, consultation, sample_collection)
```

```{r include = FALSE, eval = FALSE}
write.csv("dates_to_check.csv", quote = FALSE, row.names = FALSE)
```

*   1: error on the year
*   4: day and month were switched for onset and consultation
*   6: day and month were switcheid for hospitalization and consultation
*   7: day and month were switched for onset
*  28: day and month were switched for onset
*  33: day and month were switched for onset
*  71: year for consultation and sample_collection are not compatible
*  85: I suspect it should be be December 2012, but should be verified
* 159: probably no error
* 167: day and month were switched for consultation and sample_collection

## Positive cases without any date

```{r}
pacs %>% 
  filter(is.na(onset), is.na(hospitalization), is.na(consultation), is.na(sample_collection)) %>% 
  filter(pcr == "positive" | ns1 == "positive") %>% 
  select(id) %>% 
  unlist() %>%
  unname()
```