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Feb 26, 2024
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additional text to vignette 1 #20

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additional text to vignette 1
edward-burn Feb 26, 2024
1beca05
add ggplot to suggests
edward-burn Feb 26, 2024
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -21,6 +21,7 @@ Imports:
Depends:
R (>= 2.10)
Suggests:
ggplot2,
knitr,
rmarkdown,
testthat (>= 3.0.0)
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7 changes: 7 additions & 0 deletions man/omock-package.Rd
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40 changes: 37 additions & 3 deletions vignettes/a01_Creating_synthetic_clinical_tables.Rmd
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@@ -1,5 +1,5 @@
---
title: "a01_Creating_synthetic_clinical_tables"
title: "Creating synthetic clinical tables"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{a01_Creating_synthetic_clinical_tables}
Expand All @@ -14,8 +14,42 @@ knitr::opts_chunk$set(
)
```

```{r setup}
The omock package provides functionality to quickly create a cdm reference containing synthetic data based on population settings specified by the user.

First, let's load packages required for this vignette.
```{r, message=FALSE, warning=FALSE}
library(omock)
library(dplyr)
library(ggplot2)
```

Here we explain making a mock cdm table using mockPerson, mockObservationPeriod, etc
Now, in three lines of code, we can create a cdm reference with a person and observation period table for 1000 people.
```{r}
cdm <- emptyCdmReference(cdmName = "synthetic cdm") %>%
mockPerson(nPerson = 1000) %>%
mockObservationPeriod()

cdm

cdm$person %>% glimpse()

cdm$observation_period %>% glimpse()
```

We can add further requirements around the population we create. For example we can require that they were born between 1960 and 1980 like so.
```{r}
cdm <- emptyCdmReference(cdmName = "synthetic cdm") %>%
mockPerson(nPerson = 1000,
birthRange = c("1960-01-01", "1980-12-31")) %>%
mockObservationPeriod()
```

```{r}
cdm$person %>%
collect() %>%
ggplot() +
geom_histogram(aes(as.integer(year_of_birth)),
binwidth = 1, colour = "grey") +
theme_minimal() +
xlab("Year of birth")
```
2 changes: 1 addition & 1 deletion vignettes/a02_Creating_synthetic_cohorts.Rmd
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@@ -1,5 +1,5 @@
---
title: "a02_Creating_synthetic_cohorts"
title: "Creating synthetic cohorts"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{a02_Creating_synthetic_cohorts}
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