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Home Page: https://sepmein.github.io/snt/
License: Other
Analysis code for malaria
Home Page: https://sepmein.github.io/snt/
License: Other
When doing data management, we often need to review the data columns to get insight of the raw data structure. It would be really nice if we could have a document automatically generated reports could reflect on the data structures.
There are a large chunk of code lack of management in main.r, I need to reconstruct them into separate files.
Data process could be separated into several steps.
When importing data, some of the data columns often needed to be check duplicates. Data in the columns often not exactly matches.
A fuzzy match function need to be developed for faster duplication detection.
A very promising function was described here in the blog: https://blog.devgenius.io/approximate-string-matching-in-r-using-jaro-winkler-similarity-a93436ecf38f
When creating a new projects, it could be quite normal to copy paste codes from other projects.
These codes include comments to refine R code structure, codes to extract rainfall, population or other raster data.
Code templates could let us get started much faster.
Add a snt::config
function that will be allowed to store the default location.
When generating maps for SNT analysis, maps are often needed to be presented. We often need to present a combination of interventions through colors.
In R
, there are a few packages and function allow us to generate colors.
ADM1 boundary currently do not show in the map. Need to load from shapefile. If no shapefile provided by country, need to calculate from ADM2 districts.
@sepmein
Create a universal line graph that could be used to display various information such as rainfall, prevalence, mortality.
Raster resource loaded multiple times
When comparing the set of data frame, a correlation test was needed to check the correlations between two datasets.
There are a few algorithm built in R or available from other packages. I need to
After the extraction of rainfall raster file, I need to manually extract year and month from the filename as follows.
resource_rainfall_adm2$data |>
mutate(
year = stringr::str_extract(file, "\\d{4}"),
month = stringr::str_extract(file, "\\d{2}(?=.tif)")
)
So I need to manually do it every time I need to extract file.
The better way is to incorporate this codes inside the Rainfall
resource class.
In the main.R
RasterResource
load_single_folder
function, I'm now using normal for
function for the loop, it is slow and not using cpu. To speed up execution, should introduce parallel execution.
When calculating pop in a district, snt
should be able to sum all the numbers in the area.
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