missing graphFun() thru install.packages("mosaic")

dtkaplan commented 4 years ago

There was a graphFun() in an earlier version of {mosaicCalc}. It was introduced with an eye toward making a ggplot2-compatible system of plotting for functions. But we decided to move in a different direction and have written a new suite of ggplot2-compatible graphics for {mosaicCalc}. These will be deployed in the next CRAN release. We we're delayed from finalizing them due to the ... well ... you know.

@Danioy I've put the current version of the new suite in the DEVELOPMENT version of mosaicCalc. You can install it with

remotes::install_github("ProjectMOSAIC/mosaicCalc", ref="beta")

The functions to look at are contour_plot() and slice_plot().

nicholasjhorton commented 2 years ago

Have you also installed the mosaicCalc package?

piiskop commented 2 years ago

> remotes::install_github("ProjectMOSAIC/mosaicCalc", ref="beta")

Downloading GitHub repo ProjectMOSAIC/mosaicCalc@beta ✓ checking for file ‘/tmp/Rtmp8QaT6B/remotes17c4963245010/ProjectMOSAIC-mosaicCalc-142f94d/DESCRIPTION’ ... ─ preparing ‘mosaicCalc’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘mosaicCalc_0.5.6.tar.gz’

Installing package into ‘/home/kalmer/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified)

installing source package ‘mosaicCalc’ ... using staged installation R inst byte-compile and prepare package for lazy loading ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path
DONE (mosaicCalc)

library(mosaicCalc)

slice_plot(epi$S(t) ~ t, domain(t = 0:20)) %>% slice_plot(epi$I(t) ~ t, color = "red")

Error in slice_plot(., epi$I(t) ~ t, color = "red") : could not find function "slice_plot"

dtkaplan commented 2 years ago

I'm interested to find out what's going wrong here. Is it possible that the version of {mosaicCalc} being loaded is not the one you (correctly) installed from the beta branch of the github repo? Sometimes there's both a personal library and a system library. If you're using RStudio, try removing {mosaicCalc} on the packages tab, then reinstalling (from "beta", as you did).

nicholasjhorton commented 2 years ago

I get the following when I try to reproduce the penultimate example (I don't have access to the epi object so can't try that one):

library(mosaicCalc)
#> Loading required package: mosaicCore
#> Registered S3 method overwritten by 'mosaic':
#>   method                           from   
#>   fortify.SpatialPolygonsDataFrame ggplot2
#> 
#> Attaching package: 'mosaicCalc'
#> The following object is masked from 'package:stats':
#> 
#>     D
slice_plot(A * x^2 ~ x, domain(x <- range(-2, 3)))
#> Warning in validate_domain(domain, free_args): Using -5 to 5 in domain for
#> missing domain names.
#> Warning in validate_domain(domain, free_args): Missing domain names: x, A

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.1.0 (2021-05-18)
#>  os       macOS Big Sur 10.16
#>  system   x86_64, darwin17.0
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2022-02-08
#>  pandoc   2.11.4 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.1.0)
#>  backports     1.4.1   2021-12-13 [1] CRAN (R 4.1.0)
#>  broom         0.7.12  2022-01-28 [1] CRAN (R 4.1.0)
#>  checkmate     2.0.0   2020-02-06 [1] CRAN (R 4.1.0)
#>  cli           3.1.1   2022-01-20 [1] CRAN (R 4.1.2)
#>  colorspace    2.0-2   2021-06-24 [1] CRAN (R 4.1.0)
#>  crayon        1.4.2   2021-10-29 [1] CRAN (R 4.1.0)
#>  crosstalk     1.2.0   2021-11-04 [1] CRAN (R 4.1.0)
#>  data.table    1.14.2  2021-09-27 [1] CRAN (R 4.1.0)
#>  DBI           1.1.2   2021-12-20 [1] CRAN (R 4.1.0)
#>  digest        0.6.29  2021-12-01 [1] CRAN (R 4.1.0)
#>  dplyr       * 1.0.7   2021-06-18 [1] CRAN (R 4.1.0)
#>  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.0)
#>  evaluate      0.14    2019-05-28 [1] CRAN (R 4.1.0)
#>  fansi         1.0.2   2022-01-14 [1] CRAN (R 4.1.2)
#>  farver        2.1.0   2021-02-28 [1] CRAN (R 4.1.0)
#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.0)
#>  forcats       0.5.1   2021-01-27 [1] CRAN (R 4.1.0)
#>  fs            1.5.2   2021-12-08 [1] CRAN (R 4.1.0)
#>  generics      0.1.2   2022-01-31 [1] CRAN (R 4.1.2)
#>  ggdendro      0.1.22  2020-09-13 [1] CRAN (R 4.1.0)
#>  ggforce       0.3.3   2021-03-05 [1] CRAN (R 4.1.0)
#>  ggformula   * 0.10.1  2021-01-13 [1] CRAN (R 4.1.0)
#>  ggplot2     * 3.3.5   2021-06-25 [1] CRAN (R 4.1.0)
#>  ggrepel       0.9.1   2021-01-15 [1] CRAN (R 4.1.0)
#>  ggridges    * 0.5.3   2021-01-08 [1] CRAN (R 4.1.0)
#>  ggstance    * 0.3.5   2020-12-17 [1] CRAN (R 4.1.0)
#>  glue          1.6.1   2022-01-22 [1] CRAN (R 4.1.2)
#>  gridExtra     2.3     2017-09-09 [1] CRAN (R 4.1.0)
#>  gtable        0.3.0   2019-03-25 [1] CRAN (R 4.1.0)
#>  haven         2.4.3   2021-08-04 [1] CRAN (R 4.1.0)
#>  highr         0.9     2021-04-16 [1] CRAN (R 4.1.0)
#>  hms           1.1.1   2021-09-26 [1] CRAN (R 4.1.0)
#>  htmltools     0.5.2   2021-08-25 [1] CRAN (R 4.1.0)
#>  htmlwidgets   1.5.4   2021-09-08 [1] CRAN (R 4.1.0)
#>  httr          1.4.2   2020-07-20 [1] CRAN (R 4.1.0)
#>  jsonlite      1.7.3   2022-01-17 [1] CRAN (R 4.1.2)
#>  knitr         1.37    2021-12-16 [1] CRAN (R 4.1.0)
#>  labeling      0.4.2   2020-10-20 [1] CRAN (R 4.1.0)
#>  labelled      2.9.0   2021-10-29 [1] CRAN (R 4.1.0)
#>  lattice     * 0.20-45 2021-09-22 [1] CRAN (R 4.1.0)
#>  lazyeval      0.2.2   2019-03-15 [1] CRAN (R 4.1.0)
#>  leaflet       2.0.4.1 2021-01-07 [1] CRAN (R 4.1.0)
#>  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.1.0)
#>  lubridate     1.8.0   2021-10-07 [1] CRAN (R 4.1.0)
#>  magrittr      2.0.2   2022-01-26 [1] CRAN (R 4.1.2)
#>  MASS          7.3-55  2022-01-13 [1] CRAN (R 4.1.2)
#>  Matrix      * 1.4-0   2021-12-08 [1] CRAN (R 4.1.0)
#>  metR          0.11.0  2021-09-20 [1] CRAN (R 4.1.0)
#>  mosaic        1.8.3   2021-01-18 [1] CRAN (R 4.1.0)
#>  mosaicCalc  * 0.5.6   2022-02-08 [1] Github (ProjectMOSAIC/mosaicCalc@142f94d)
#>  mosaicCore  * 0.9.0   2021-01-16 [1] CRAN (R 4.1.0)
#>  mosaicData  * 0.20.2  2021-01-16 [1] CRAN (R 4.1.0)
#>  munsell       0.5.0   2018-06-12 [1] CRAN (R 4.1.0)
#>  pillar        1.7.0   2022-02-01 [1] CRAN (R 4.1.2)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.1.0)
#>  plotly        4.10.0  2021-10-09 [1] CRAN (R 4.1.0)
#>  plyr          1.8.6   2020-03-03 [1] CRAN (R 4.1.0)
#>  polyclip      1.10-0  2019-03-14 [1] CRAN (R 4.1.0)
#>  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.1.0)
#>  R.cache       0.15.0  2021-04-30 [1] CRAN (R 4.1.0)
#>  R.methodsS3   1.8.1   2020-08-26 [1] CRAN (R 4.1.0)
#>  R.oo          1.24.0  2020-08-26 [1] CRAN (R 4.1.0)
#>  R.utils       2.11.0  2021-09-26 [1] CRAN (R 4.1.0)
#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.1.0)
#>  Rcpp          1.0.8   2022-01-13 [1] CRAN (R 4.1.2)
#>  readr         2.1.2   2022-01-30 [1] CRAN (R 4.1.2)
#>  reprex        2.0.1   2021-08-05 [1] CRAN (R 4.1.0)
#>  rlang         1.0.1   2022-02-03 [1] CRAN (R 4.1.2)
#>  rmarkdown     2.11    2021-09-14 [1] CRAN (R 4.1.0)
#>  rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.1.0)
#>  scales        1.1.1   2020-05-11 [1] CRAN (R 4.1.0)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.1.0)
#>  stringi       1.7.6   2021-11-29 [1] CRAN (R 4.1.0)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.1.0)
#>  styler        1.6.2   2021-09-23 [1] CRAN (R 4.1.0)
#>  tibble        3.1.6   2021-11-07 [1] CRAN (R 4.1.0)
#>  tidyr         1.2.0   2022-02-01 [1] CRAN (R 4.1.2)
#>  tidyselect    1.1.1   2021-04-30 [1] CRAN (R 4.1.0)
#>  tweenr        1.0.2   2021-03-23 [1] CRAN (R 4.1.0)
#>  tzdb          0.2.0   2021-10-27 [1] CRAN (R 4.1.0)
#>  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.1.0)
#>  vctrs         0.3.8   2021-04-29 [1] CRAN (R 4.1.0)
#>  viridisLite   0.4.0   2021-04-13 [1] CRAN (R 4.1.0)
#>  withr         2.4.3   2021-11-30 [1] CRAN (R 4.1.0)
#>  xfun          0.29    2021-12-14 [1] CRAN (R 4.1.0)
#>  yaml          2.2.2   2022-01-25 [1] CRAN (R 4.1.2)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

^{Created on 2022-02-08 by the reprex package (v2.0.1)}

rpruim commented 2 years ago

It is unclear what this example is supposed to do with the A variable. A quick scan of the documentation didn't make it clear to me what the intended behavior is. If you set the domain for A to a single value, you get a nice plot of the the function with A held constant.

@dtkaplan, is slice_plot() supposed to be choosing several values of A and plotting them separately? Are you missing a group somewhere so that ggplot knows which dots should be connected?

rpruim commented 2 years ago

@piiskop , After installing {mosaicCalc} from github, did you restart R? If not, you may have an unstable cache of R packages. See if restarting R resolves the issue.

dtkaplan commented 2 years ago

Here's Nick's example: slice_plot(A * x^2 ~ x, domain(x <- range(-2, 3)))

The problem is that <- is being used rather than x=. With x<- there's no name for the argument. slice_plot() checks that the domain corresponds to the name given in the RHS of the tilde expression.

As for the A matter. makeFun() and the related functions---slice_plot() builds a function from the tilde expression using makeFun(). Symbolic parameters such as A (which isn't listed on the RHS of the tilde) are made formal arguments for the created function. To graph the function, you need to provide a numerical value for such parameters. For instance:

f <- makeFun(A * x^2 ~ x)
slice_plot(f(x, A=2) ~ x, domain(x=-2:2))

The case for plotting the function for several values of A in the same frame is to pipe into additional slice_plot() commands.

piiskop commented 2 years ago

@piiskop , After installing {mosaicCalc} from github, did you restart R? If not, you may have an unstable cache of R packages. See if restarting R resolves the issue.

I can't remember what I did, probably tried several things until I can use _sliceplot again.

ProjectMOSAIC / mosaicCalc

missing graphFun() thru install.packages("mosaic") #4