Set-up temperature-R0 code and vignette #3
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Nice work @EmilieFinch! I've left a few inline comments in the files. Overall, it's looking good and is a solid foundation to develop from.
Let me know if you're unable to fix any of the failing checks and I'm happy to help out.
| #' CxpiWNVxl; CxtaWEEV; CxtaWNVx; CxunWNVx | ||
| #'@return numeric vector of relative R0 values corresponding to input temperature values | ||
| #'@export | ||
| temperature_r0 <- function(data, vector_pathogen){ |
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Will need an example (using @examples) at some point as it's an exported function, but this can be added later.
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Fab, have added example here.
R/temperature_r0.R
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| #' @description This function takes an input series of mean temperature values in °C | ||
| #' and returns estimated relative R0 values according to temperature-R0 curves in | ||
| #' from Mordecai et al 2019 https://doi.org/10.1111/ele.13335 |
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There is also the @references tag from Roxygen to add full references to function documentation.
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Have moved reference to the @references tag, thanks!
R/temperature_r0.R
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| if(!vector_pathogen %in% vector_reference$vector_pathogen){ | ||
| message("Vector-pathogen code is not recognised. This should be one of: | ||
| AeaeDENV; AeaeZIKV; AealDENV; AetaRVFV; | ||
| AetaSINV; AetrEEEV; AngaPfal; CxanMVEx; | ||
| CxanRRVx; CxpiSINV; CxpiWNVxl; CxtaWEEV; | ||
| CxtaWNVx; CxunWNVx.") |
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This can probably be replaced by match.arg() (which is a function from base R).
It comes with a couple of features that you may not want or differ from the current code.
- It defaults to the first element in the options vector.
- It errors if the user gives an string not in the options vector, whereas currently it's a message.
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I've switched this to match.arg() but added a nicer error message with a tryCatch()
R/temperature_r0.R
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| r0_posteriors <- eval(parse(text = paste0(vector_pathogen, "_R0"))) | ||
| constant_temps <- eval(parse(text = paste0(vector_pathogen, "_T"))) |
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I think it would be good to rewrite this without the use of eval(parse()) as this can be a code vulnerability, especially if what is being evaluated is a user-defined input. We can discuss what these lines do and what the best alternative is.
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Yes makes sense - I've moved the data from data to inst/extdata which has solved this issue as it's now called with system.file()
R/temperature_r0.R
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| # Wrangle posteriors | ||
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| tr0 <- r0_posteriors |> |
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It may be better to rewrite this without the pipe (|>) as chained operations with the pipe can make functions harder to debug and by using |> you impose a minimum version of R on the package users of 4.1.0. As you're using {dplyr} then you can switch to %>% without taking on any other dependencies.
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Have amended, thanks!
| @@ -0,0 +1,14 @@ | |||
| #' Fiji 2014. | |||
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The other data sets will also need to be documented to remove the warnings from R CMD check.
| @@ -7,6 +7,3 @@ | |||
| # * https://testthat.r-lib.org/articles/special-files.html | |||
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| library(testthat) | |||
| library(packagetemplate) | |||
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| test_check("packagetemplate", stop_on_warning = FALSE) | |||
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I assume you removed this to stop the tests failing? I think it would be better to not remove it and replace packagetemplate with climateR0 so that any unit tests you write in the future will be automatically run.
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Yes makes sense, have updated accordingly.
vignettes/temperature_R0.Rmd
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| ) | ||
| ``` | ||
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| Temperature is an important driver of vector-borne disease transmission, affecting vector reproduction, development, and survival, as well as the probability of pathogen transmission. Previous work by [Mordecai and colleagues](https://onlinelibrary.wiley.com/doi/10.1111/ele.13335) empirically estimated the effect of temperature on different vector traits, and used these to develop models of temperature dependent R~0~. |
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The reference can be added using a bibliography file and automatically render the reference list (similar to LaTeX). You don't need to do this in this PR, but could be a nice enhancement in the future.
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I'll leave this for now but would be nice to add in the future.
This PR adds preliminary package functionality including:
temperature_r0function which takes a time-series of temperature data and a specified vector-pathogen combination as inputs and returns median posterior estimates of relative R0