Test the installation of fgeo

maurolepore commented 5 years ago

I'm looking for volunteers to test the installation process of the fgeo package. Your feedback will make fgeo easier to use and benefit the ForestGEO commumity.

Could you install fgeo? Which installation option (1 or 2) did you use?
What problems did you experience?
What was unclear/confusing?

Please let me know any issue, comment, or idea for improvement. Write below or at maurolepore@gmail.com.

cc': @RutujaCT, @crscalpone, @kccushman, @ervanSTRI, @jess-shue, @DanielZuleta, @ngokangmin, @gonzalezeb, @dkenfack, @ekraichak, @forestgeoguest, @mopicon, @ValentineHerr

ValentineHerr commented 5 years ago

Hi @maurolepore, here is what I experienced/noticed:

I was able to install fgeo. I used option 2.

In ?fgeo.abundance::abundance
- [ ] "count woods" sounds weird. Maybe say "count individuals"?
- [ ] I think vft2[2,3] should be 1.2, isn't it ?
- [ ] would be good to show how to count abundance of stems and not only individual trees (e.i. a multi-stem tree with 2 stems counts for 2)
fgeo.base::check_crutial_name does not show up when running fgeo_help(), like suggested in installation page. ?fgeo.base::check_crutial_name returns No documentation for ‘check_crutial_name’ in specified packages and libraries: you could try ‘??check_crutial_name’. ??check_crutial_name returns "No results found"
- fgeo_help("datasets") shows a different set of documentation than in your installation page:

fgeo_help("datasets")

In your installation page you write: stem6 <- download_data("luquillo_stem6_random") but it seems that there no need to do that, stem6 already exsits (along with other datasets), see ?fgeo.x::datasets.

I hope this helps a little!

maurolepore commented 5 years ago

Thanks @ValentineHerr! This helps a lot.

I can test the installation process in a fresh R environment but it is only via feedback that I can learn how it behaves in real-people's environments.

Your comments beyond installation are great. They highlight stuff I became blind to.

gonzalezeb commented 5 years ago

Hi @maurolepore, I also used option 2, no problem, I did had to run update.packages(), very useful.

I got curious about fgeo.tool::pick_main_stem(). I think it is very clear what pick_main_stem() does, but not for pick_main_stemid(). You wrote: It only picks the main stemid(s) of each tree in each census and keeps all stems per treeid. If it keeps all stems, which one is the main?

One cannot test these functions with stem6 because all stems are "main" as shown in column codes, so there are not multistems (sorry, I din't explore other datasets, I will later)..

I hope this is useful..

ekraichak commented 5 years ago

@maurolepore: Not sure what went wrong in my installation. The fgeo package appears to be installed okay, but I cannot use the download_data function. Not sure which package it comes from. I did upload.packages() and fgeo.install::install_github2() already.

My help files also are also different from @ValentineHerr. I only have four things showing up.

Looks like some associated packages are missing from my installation.

maurolepore commented 5 years ago

Thank you @gonzalezeb! The documentation and the function itself now remind users of the expected R environment. I'm glad you noticed update.packages().

RE: *main_stem() vs. *main_stemid():

You make me realize that I should document this better. pick_main_stemid() is rarely needed and may confuse more often than help. Here is a simplified example that I'm hoping to include in the help file. Do you think this would be clear for most people? Please don't be 'polite', I need to communicate this clearly.

# One `treeID` with multiple stems. 
# `stemID == 1.1` has two measurements (due to buttresses). We want to pick the main one.
# `stemID == 1.2` has a single measurement. It should be preserved.
census <- tribble(
    ~sp, ~treeID, ~stemID,  ~hom, ~dbh, ~CensusID,
  "sp1",     "1",   "1.1",   140,   40,         1,  # main stemID: `hom` > than next row
  "sp1",     "1",   "1.1",   130,   60,         1,
  "sp1",     "1",   "1.2",   130,   55,         1,  # main stemID: The only one

)

# Picks the main stemid of each stem
pick_main_stemid(census)#> # A tibble: 3 x 6
#>   sp    treeID stemID   hom   dbh CensusID
#>   <chr> <chr>  <chr>  <dbl> <dbl>    <dbl>
#> 1 sp1   1      1.1      140    40        1
#> 2 sp1   1      1.2      130    55        1

maurolepore commented 5 years ago

@ekraichak, thanks for this comment!

Installation

You are right, you have an older version of fgeo that has some packages more and some packages less than the latest version. I'm surprised that fgeo.install::install_github2() did not trigger the installation of the missing packages -- fgeo.install::install_github2() is lazy and does not re-install something that you already have, but it should install what you don't have.

My homework:

Add a test for this scenario.
Document (maybe throw a message) how to update via remove.packages("fgeo") + rerun fgeo.install::intall_github2(). Example below.

Docs

My help files also are also different ... I only have four things showing up.

That makes sense. The help files that show up depend on the version of each package you have installed. Now you are a bit behing. For example, here is my output of fgeo::fgeo_help("abundance"):

ekraichak commented 5 years ago

Thanks, @maurolepore. It works now! It didn't occur to me that I should remove the old package first (duh!). Also for someone like me who doesn't update the packages often, the update_packages() can take an interesting long time. The documentation is now the same as your example.

maurolepore commented 5 years ago

It didn't occur to me that I should remove the old package first (duh!).

It's always not yours but the designer's fault (i.e. me :)

maurolepore commented 5 years ago

fgeo.install::install_github2()
#> Expected R environment:
#> * R version is recent
#> * All packages are updated (run `update.packages()`)
#> * No other R session is running
#> * Current R session is clean (click Session > Restart R)
#> All CRAN dependencies are installed.
#> All fgeo packages are installed.
#> Next you may run `?follow_up`

?follow_up

maurolepore commented 5 years ago

Thanks all! I've used your feedback to improve the installation process of fgeo.

If anyone else installs fgeo I'm still very interested in knowing your experience about the installation process itself (https://forestgeo.github.io/fgeo/#installation).

hoganhaben commented 5 years ago

installation worked for me.
below R console printout (copied & pasted):

Console output

```R R version 3.5.1 (2018-07-02) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Workspace loaded from C:/Users/hogie/Dropbox (Personal)/Enquist Dendrometers (1)/.RData] Loading required package: arm Loading required package: MASS Attaching package: ‘MASS’ The following object is masked _by_ ‘.GlobalEnv’: survey Loading required package: Matrix Loading required package: lme4 Attaching package: ‘lme4’ The following object is masked _by_ ‘.GlobalEnv’: allFit arm (Version 1.10-1, built: 2018-4-12) Working directory is C:/Users/hogie/Dropbox (Personal)/Enquist Dendrometers (1) > install.packages("devtools") Installing package into ‘C:/Users/hogie/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/devtools_2.0.1.zip' Content type 'application/zip' length 385030 bytes (376 KB) downloaded 376 KB package ‘devtools’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpUVTsfK\downloaded_packages > devtools::install_github("forestgeo/fgeo", upgrade = "never") Downloading GitHub repo forestgeo/fgeo@master Downloading GitHub repo forestgeo/fgeo.analyze@master Downloading GitHub repo forestgeo/fgeo.tool@master √ checking for file 'C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpUVTsfK\remotes31443f5c64a2\forestgeo-fgeo.tool-b497631/DESCRIPTION' (515ms) - preparing 'fgeo.tool': (539ms) √ checking DESCRIPTION meta-information - checking for LF line-endings in source and make files and shell scripts - checking for empty or unneeded directories - building 'fgeo.tool_0.0.0.9005.tar.gz' Installing package into ‘C:/Users/hogie/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) * installing *source* package 'fgeo.tool' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'fgeo.tool' finding HTML links ... done add_id html add_status_tree html add_subquad html add_var html allquadratslopes html as_censuses html calcslope html check_crucial_names html dir_list html drop_if_na html drop_twice_dead html extract_from_habitat html extract_insensitive html fgeo.tool-package html fgeo_elevation html fgeo_topography html fill_na html filter_status html find_data_of_class html findborderquads html flag_if html flag_if_group html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/flag_if_group.Rd:19: file link 'inform' in package 'rlang' does not exist and so has been treated as a topic from_var_to_var html guess_plotdim html is_multiple html list_csv html list_df html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/list_df.Rd:25: file link 'full_join' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/list_df.Rd:19: file link 'full_join' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/list_df.Rd:47: file link 'full_join' in package 'dplyr' does not exist and so has been treated as a topic lookup html name_dfs html nms html nms_extract_anycase html nms_lowercase html nms_restore_newvar html nms_tidy html nms_try_rename html pick html pick_drop html pick_main_stem html pick_plotname html pick_recensus html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/pick_recensus.Rd:37: file link 'anti_join' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/pick_recensus.Rd:28: file link 'anti_join' in package 'dplyr' does not exist and so has been treated as a topic pick_top html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/pick_top.Rd:33: file link 'tail' in package 'utils' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/pick_top.Rd:52: file link 'tail' in package 'utils' does not exist and so has been treated as a topic pipe html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/pipe.Rd:10: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic quadslope html rdata_df html read_censuses html read_fgeo html read_with html recode_subquad html reexports html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:35: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:35: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:35: file link 'count' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:35: file link 'add_count' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:37: file link '%||%' in package 'rlang' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:41: file link 'starts_with' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:41: file link 'ends_with' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:41: file link 'contains' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:41: file link 'matches' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:41: file link 'num_range' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:41: file link 'one_of' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:41: file link 'everything' in package 'tidyselect' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/reexports.Rd:41: file link 'last_col' in package 'tidyselect' does not exist and so has been treated as a topic rename_matches html sanitize html finding level-2 HTML links ... done suffix_match html suffix_tags_beyond_edge html tidyeval html to_df html to_df.demography_impl html to_df.krig_lst html to_df.tt_lst html to_tidy_names html tool_example html type_ensure html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/type_ensure.Rd:35: file link 'modify_at' in package 'purrr' does not exist and so has been treated as a topic type_fgeo html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/type_fgeo.Rd:19: file link 'read.csv' in package 'utils' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/type_fgeo.Rd:20: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/type_fgeo.Rd:22: file link 'read_csv' in package 'readr' does not exist and so has been treated as a topic Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpMXHuFa/R.INSTALL3b1854dc6d23/fgeo.tool/man/type_fgeo.Rd:61: file link 'read_csv' in package 'readr' does not exist and so has been treated as a topic ** building package indices ** testing if installed package can be loaded * DONE (fgeo.tool) In R CMD INSTALL √ checking for file 'C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpUVTsfK\remotes314455d43ace\forestgeo-fgeo.analyze-b3272cf/DESCRIPTION' (373ms) - preparing 'fgeo.analyze': √ checking DESCRIPTION meta-information - checking for LF line-endings in source and make files and shell scripts - checking for empty or unneeded directories Removed empty directory 'fgeo.analyze/vignettes' - looking to see if a 'data/datalist' file should be added - building 'fgeo.analyze_0.0.0.9003.tar.gz' Installing package into ‘C:/Users/hogie/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) * installing *source* package 'fgeo.analyze' ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'fgeo.analyze' finding HTML links ... done abundance html abundance_byyr html abundanceperquad2 html check_crucial_names html demography_impl html example_byyr html fgeo.analyze-package html luquillo_top3_sp html pipe html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpCaN4Gd/R.INSTALL2a18532b3266/fgeo.analyze/man/pipe.Rd:10: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic reexports html summary.tt_lst html tt_test html *** copying figures ** building package indices ** testing if installed package can be loaded * DONE (fgeo.analyze) In R CMD INSTALL Downloading GitHub repo forestgeo/fgeo.map@master √ checking for file 'C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpUVTsfK\remotes314419a23203\forestgeo-fgeo.map-761b4c3/DESCRIPTION' (359ms) - preparing 'fgeo.map': (363ms) √ checking DESCRIPTION meta-information ... - checking for LF line-endings in source and make files and shell scripts (355ms) - checking for empty or unneeded directories - building 'fgeo.map_0.0.0.9402.tar.gz' Installing package into ‘C:/Users/hogie/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) * installing *source* package 'fgeo.map' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'fgeo.map' finding HTML links ... done autoplot.fgeo_habitat html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/Rtmpg9kyUp/R.INSTALL5df440e2328a/fgeo.map/man/autoplot.fgeo_habitat.Rd:10: missing file link 'fgeo_habitat' autoplot.sp_elev html autoplot_by_species html autoplot_by_species.sp_elev html elev html fgeo.map-package html header_dbh_bubbles html header_tag_status html headers html paginate html pipe html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/Rtmpg9kyUp/R.INSTALL5df440e2328a/fgeo.map/man/pipe.Rd:10: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic plot_dbh_bubbles_by_quadrat html plot_tag_status_by_subquadrat html reexports html sp html sp_elev html theme_dbh_bubbles html finding level-2 HTML links ... done theme_default html theme_tag_status html themes html vft_1quad html *** copying figures ** building package indices ** testing if installed package can be loaded * DONE (fgeo.map) In R CMD INSTALL Skipping install of 'fgeo.tool' from a github remote, the SHA1 (b497631f) has not changed since last install. Use `force = TRUE` to force installation √ checking for file 'C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpUVTsfK\remotes31444b5f1c8d\forestgeo-fgeo-03afa62/DESCRIPTION' (588ms) - preparing 'fgeo': √ checking DESCRIPTION meta-information - checking for LF line-endings in source and make files and shell scripts - checking for empty or unneeded directories - building 'fgeo_0.0.0.9002.tar.gz' Installing package into ‘C:/Users/hogie/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) * installing *source* package 'fgeo' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'fgeo' finding HTML links ... done fgeo-package html fgeo_dependencies html fgeo_docs html fgeo_help html fgeo_link html fgeo_pkgs html pipe html Rd warning: C:/Users/Public/Documents/Wondershare/CreatorTemp/RtmpGAa2Se/R.INSTALL7bc16641cb9/fgeo/man/pipe.Rd:10: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic ** building package indices ** testing if installed package can be loaded ... ```

...
* DONE (fgeo)
In R CMD INSTALL
> library(fgeo)
-- Attaching packages --------------------------------------- fgeo 0.0.0.9002 --
v fgeo.x       0.0.0.9000     v fgeo.analyze 0.0.0.9003
v fgeo.tool    0.0.0.9005     v fgeo.map     0.0.0.9402

maurolepore commented 5 years ago

@hoganhaben, thank you very much for your feedback!

maurolepore commented 5 years ago

I've been working hard in making the installation of fgeo simpler and faster. Can you please try these instructions?

Please let me know if it worked smoothly or you had any issue. Also, please let me know what OS (e.g. mac, windows, linux) and R version you are using.

Thanks to your help we are close to announcing fgeo more widely.

ekraichak commented 5 years ago

thanks for your hard work on the package. The installation and the instructions worked great for me. I'm working R 3.5.1 and MacOS Mojave (10.14.2). A few thoughts on the process here:

1- update.packages() can be slow and tedious for a lazy R user like me, because I have to type a lot of "yes" to get them to update everything I have neglected. So many I should have thought about update.packages(ask = F).

2- Explore fgeo I'm not sure I understand the interactive part quite clearly. When I ran the code, I pop the documentation page back in my browser (not the viewer in RStudio). Was that the expected outcome?

3- The importing and exporting part with purrr is brilliant, but it can be confusing for beginners. Not sure how much it is necessary for the downstream tutorials, but compared to the rest of the instruction, this section sounds a bit too advanced and could be intimidating for someone who just start using package.

thanks again for working so hard on this. I personally enjoy the verb-based function and the pipe. Hope the others find them useful as well :)

maurolepore commented 5 years ago

@ekraichak, thanks a lot for your awesome feedback! I edited the installation instructions and examples to reflect your advice (see commits linked above).

Thanks for noticing that the section about importing/exporting data was not crucial to understanding the rest of the examples. I also think that code is intimidating so I wrote this little package: https://maurolepore.github.io/tor/ -- I would love to hear you comments and suggestions. Here is an example:

(rdata_files <- fgeo.x::example_path("rdata"))
#> [1] "C:/Users/LeporeM/Documents/R/win-library/3.5/fgeo.x/extdata/rdata"
dir(rdata_files)
#> [1] "tree5.RData" "tree6.RData"

tor::list_rdata(rdata_files)
#> $tree5
#> # A tibble: 3 x 19
#>   treeID stemID tag   StemTag sp    quadrat    gx    gy MeasureID CensusID
#>    <int>  <int> <chr> <chr>   <chr> <chr>   <dbl> <dbl>     <int>    <int>
#> 1    104    143 10009 10009   DACE~ 113      10.3  245.    439947        5
#> 2    119    158 1001~ 100104  MYRS~ 1021    183.   410.    466597        5
#> 3    180    225 1001~ 100174  CASA~ 921     165.   410.    466623        5
#> # ... with 9 more variables: dbh <dbl>, pom <chr>, hom <dbl>,
#> #   ExactDate <date>, DFstatus <chr>, codes <chr>, nostems <dbl>,
#> #   status <chr>, date <dbl>
#> 
#> $tree6
#> # A tibble: 3 x 19
#>   treeID stemID tag   StemTag sp    quadrat    gx    gy MeasureID CensusID
#>    <int>  <int> <chr> <chr>   <chr> <chr>   <dbl> <dbl>     <int>    <int>
#> 1    104    143 10009 10009   DACE~ 113      10.3  245.    582850        6
#> 2    119    158 1001~ 100104  MYRS~ 1021    183.   410.    578696        6
#> 3    180    225 1001~ 100174  CASA~ 921     165.   410.    617049        6
#> # ... with 9 more variables: dbh <dbl>, pom <chr>, hom <dbl>,
#> #   ExactDate <date>, DFstatus <chr>, codes <chr>, nostems <dbl>,
#> #   status <chr>, date <dbl>

Created on 2019-02-02 by the reprex package (v0.2.1)

maurolepore commented 5 years ago

@ValentineHerr, @gonzalezeb, @ekraichak, and @hoganhaben,

Thanks a lot for reviewing fgeo. To acknowledge your contribution you are now listed as reviewers.

Although I would love to keep you engaged in the development of fgeo, I expect nothing else than what you have already done.

If you want to be excluded from the reviewers list, let me konw.
If you want to stay in the reviewers list, please check that your name, email, and website are ok. You can see the commits above or find yourself in the Developers section of fgeo's website. If all is OK, fine. If not, feel free to edit the files DESCRIPTION and _pkgdown.yml and submit a pull request -- or let me know and I can do it for you.

hoganhaben commented 5 years ago

@maurolepore looks good. Let me know what else I can help you with.

one quick thing, I could not find the function fgeo_browse_reference() in my version of the install. I could by my version of the fgeo code, not sure. but FYI. thoughts?

R console output below.

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Workspace loaded from C:/Users/hogie/Dropbox/R WD/.RData]

> library("fgeo")
-- Attaching packages --------------------------------------- fgeo 0.0.0.9002 --
v fgeo.x       0.0.0.9000     v fgeo.analyze 0.0.0.9003
v fgeo.tool    0.0.0.9005     v fgeo.map     0.0.0.9402

> if (interactive()) {
+     # To search on the viewer; accepts keywords
+     fgeo_help()
+     # To search on a web browser
+     fgeo_browse_reference() 
+ }
Error in fgeo_browse_reference() : 
  could not find function "fgeo_browse_reference"
> fgeo_help()
> options(
+     repos = c(
+         CRAN = "https://cran.rstudio.com/",
+         forestgeo = "https://forestgeo.github.io/drat"
+     )
+ )
> 
> update.packages("fgeo")
> library("fgeo")
> if (interactive()) {
+     # To search on the viewer; accepts keywords
+     fgeo_help()
+     # To search on a web browser
+     fgeo_browse_reference() 
+ }
Error in fgeo_browse_reference() : 
  could not find function "fgeo_browse_reference"

maurolepore commented 5 years ago

Thanks @hoganhaben!

You are right, your version of fgeo lacks fgeo_reference() (opens your browser here).

Please try this and let me know how it goes.

# Setup: Include ForestGEO's CRAN-like repository when searching for packages
install.packages("drat")
drat::addRepo("forestgeo")

# Update all packages (best but see below)
update.packages(ask = FALSE)

# Or remove fgeo and re-install it (if you don't want to update other packages)
remove.packages(fgeo:::fgeo_packages())
install.packages("fgeo")

maurolepore commented 5 years ago

@hoganhaben, your update failed because the the call to update.packages() is incorrect.

# Good
update.packages()

# Bad
update.packages("fgeo")

That is a common mistake and I should show that clearly.

maurolepore commented 5 years ago

@ValentineHerr, @gonzalezeb, @ekraichak, and @hoganhaben,

I invited you all to join the forestgeo slack workspace. You should get an email with instructions to join. Slack is super cool and you may want to try it with me to test if this free tool could add value to your own organizations. Lots of people use slack not only to develop software but also to teach courses, organize conferences, everything.

Feel free to not join, seriously. I understand we are all flooded with notifications.

maurolepore commented 5 years ago

@crscalpone, I forgot to mention you in two comments that are relevant to you too:

forestgeo / forum

Test the installation of fgeo #19

Installation

Docs