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annecori
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@annecori annecori commented Jun 6, 2018

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thibautjombart and others added 30 commits May 15, 2018 10:59
remove 1:T and sapply (use seq_len and apply instead)
@annecori annecori requested a review from jstockwin June 6, 2018 13:53
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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.

zkamvar and others added 6 commits May 28, 2019 15:40
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
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zkamvar commented May 29, 2019

The tests have been re-implemented in #67 and #69, so this should be ready to merge

@jstockwin jstockwin self-requested a review May 29, 2019 15:40
@jstockwin jstockwin self-assigned this May 29, 2019
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Agree this is ready to go. I'll do a final review and then we can get this merged!

@zkamvar zkamvar mentioned this pull request May 29, 2019
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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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🚢 🎉 🎈

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zkamvar commented Jun 3, 2019

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:

  1. plyr it's listed in imports, but is not present in namespace
  2. plotly It's imported in the plot.R file, but never used
  3. grid is not used at all

We could probably get rid of reshape2 by using base R's stack and reshape at some point.

@jstockwin jstockwin merged commit 1537bff into master Jun 4, 2019
@jstockwin jstockwin deleted the new-version branch June 4, 2019 12:57
@zkamvar zkamvar mentioned this pull request Jul 3, 2019
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4 participants