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(v1.8.1.9011) update prevalence of some genera

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dr. M.S. (Matthijs) Berends
2022-06-03 12:43:25 +02:00
parent 70a07bad39
commit 1b84564d36
35 changed files with 278 additions and 429 deletions
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36
man/mo_source.Rd
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@ -37,23 +37,29 @@ Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The
\section{How to Setup}{
Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:\preformatted{ | A | B |
Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:
\if{html}{\out{<div class="sourceCode">}}\preformatted{ | A | B |
--|--------------------|-----------------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | Escherichia coli |
3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
4 | | |
}
}\if{html}{\out{</div>}}
We save it as \code{"home/me/ourcodes.xlsx"}. Now we have to set it as a source:\preformatted{set_mo_source("home/me/ourcodes.xlsx")
We save it as \code{"home/me/ourcodes.xlsx"}. Now we have to set it as a source:
\if{html}{\out{<div class="sourceCode">}}\preformatted{set_mo_source("home/me/ourcodes.xlsx")
#> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
#> "Organisation XYZ" and "mo"
}
}\if{html}{\out{</div>}}
It has now created a file \code{"~/mo_source.rds"} with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.
And now we can use it in our functions:\preformatted{as.mo("lab_mo_ecoli")
And now we can use it in our functions:
\if{html}{\out{<div class="sourceCode">}}\preformatted{as.mo("lab_mo_ecoli")
#> Class <mo>
#> [1] B_ESCHR_COLI
@ -66,18 +72,22 @@ as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
#> Use mo_uncertainties() to review it.
#> Class <mo>
#> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
}
}\if{html}{\out{</div>}}
If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{ | A | B |
If we edit the Excel file by, let's say, adding row 4 like this:
\if{html}{\out{<div class="sourceCode">}}\preformatted{ | A | B |
--|--------------------|-----------------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | Escherichia coli |
3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
4 | lab_Staph_aureus | Staphylococcus aureus |
5 | | |
}
}\if{html}{\out{</div>}}
...any new usage of an MO function in this package will update your data file:\preformatted{as.mo("lab_mo_ecoli")
...any new usage of an MO function in this package will update your data file:
\if{html}{\out{<div class="sourceCode">}}\preformatted{as.mo("lab_mo_ecoli")
#> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
#> "Organisation XYZ" and "mo"
@ -86,11 +96,13 @@ If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{
mo_genus("lab_Staph_aureus")
#> [1] "Staphylococcus"
}
}\if{html}{\out{</div>}}
To delete the reference data file, just use \code{""}, \code{NULL} or \code{FALSE} as input for \code{\link[=set_mo_source]{set_mo_source()}}:\preformatted{set_mo_source(NULL)
To delete the reference data file, just use \code{""}, \code{NULL} or \code{FALSE} as input for \code{\link[=set_mo_source]{set_mo_source()}}:
\if{html}{\out{<div class="sourceCode">}}\preformatted{set_mo_source(NULL)
#> Removed mo_source file '/Users/me/mo_source.rds'
}
}\if{html}{\out{</div>}}
If the original file (in the previous case an Excel file) is moved or deleted, the \code{mo_source.rds} file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}} or any \code{\link[=mo_property]{mo_*}} function.
}