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New version #61
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reformatting code
remove 1:T and sapply (use seq_len and apply instead)
…trol and adding examples to these functions
…les in estimate_R to use make_config
…to new-version
…et travis checks passed
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This all looks good to me, other than the fact that tests have been removed.
Why do they need to be re-done? Has the output of EpiEstim changed so much that they don't work? If so, why has the output changed so much?
Surely it's worth re-implementing the tests before this gets merged, else it will never get done.
…he mean for big datasets
These were the following changes I made: 1. estimate_r changed to estimate_R 2. plot = FALSE was no longer a parameter 3. The new output was a class "estimate_R", but the saved results weren't Example 2, however fails as I mentioned earlier and it appears to be due to the sampling bug that was fixed in R 3.6. Since this is a trivial sampling, I'm going to hard-code the values to avoid having to set or reset the default sampler.
Co-Authored-By: Jake Stockwin <[email protected]>
re-add tests and ensure they work
Add more travis tests and update coarseDataTools remote
Agree this is ready to go. I'll do a final review and then we can get this merged! |
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Just a couple of very minor comments, otherwise this looks good. Will be very good to get this merged finally!
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🚢 🎉 🎈
I've run a dependencies check and found the following are actually used in version 2: library('itdepends')
#> Registered S3 methods overwritten by 'ggplot2':
#> method from
#> [.quosures rlang
#> c.quosures rlang
#> print.quosures rlang
library('dplyr')
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
dep_usage_pkg("EpiEstim") %>%
filter(!pkg %in% c("base", "EpiEstim")) %>%
count(pkg, fun) %>%
print(n = 50)
#> # A tibble: 38 x 3
#> pkg fun n
#> <chr> <chr> <int>
#> 1 coarseDataTools dic.fit.mcmc 2
#> 2 coda as.mcmc 2
#> 3 coda as.mcmc.list 1
#> 4 coda gelman.diag 1
#> 5 fitdistrplus fitdist 2
#> 6 ggplot2 aes 12
#> 7 ggplot2 aes_string 6
#> 8 ggplot2 geom_hline 2
#> 9 ggplot2 geom_line 8
#> 10 ggplot2 geom_ribbon 6
#> 11 ggplot2 ggplot 6
#> 12 ggplot2 ggtitle 8
#> 13 ggplot2 lims 6
#> 14 ggplot2 scale_colour_manual 4
#> 15 ggplot2 scale_fill_manual 4
#> 16 ggplot2 theme 6
#> 17 ggplot2 xlab 6
#> 18 ggplot2 xlim 4
#> 19 ggplot2 ylab 6
#> 20 ggplot2 ylim 4
#> 21 graphics plot 2
#> 22 grDevices palette 4
#> 23 gridExtra arrangeGrob 1
#> 24 gridExtra grid.arrange 1
#> 25 incidence as.incidence 2
#> 26 reshape2 melt 3
#> 27 scales alpha 4
#> 28 stats pgamma 5
#> 29 stats plnorm 4
#> 30 stats pweibull 4
#> 31 stats qgamma 9
#> 32 stats qlnorm 2
#> 33 stats qweibull 2
#> 34 stats rgamma 1
#> 35 stats rmultinom 1
#> 36 stats rnorm 2
#> 37 stats sd 1
#> 38 utils modifyList 1 Created on 2019-06-03 by the reprex package (v0.3.0) So, I'm wondering about the following imports in the DESCRIPTION:
We could probably get rid of reshape2 by using base R's stack and reshape at some point. |
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