Open bbest opened 4 years ago
Handled some of this in noaa-onms/cinms#5
After making sure "spp_targets.csv" was made available offline (and the other xquartz-related trouble shooting) I'm getting the following error:
Quitting from lines 30-31 (barnacles.Rmd)
Error: Problem with filter()
input ..1
.
x object 'sp_target' not found
ℹ Input ..1
is sp_target %in% spp_targets
.
Backtrace:
█
Specifically, lines 30-31 in barnacles.Rmd:
plot_intertidal_nms(d_csv, "CINMS", "CHTBAL", "Acorn Barnacles [target = balanus | chthamalus_balanus]", c("balanus", "chthamalus_balanus"))
I'm not sure why the issue is with "spp_targets.csv", this is a small .csv that serves as a reference for the names of species in the actual data files
In rocky.R there are various filter for "spp_targets" (a column in spp_targets.csv) e.g. line 180: filter(sp_target %in% spp_targets)
Hey @mspector13,
You should've gotten an email about above git commit message since I mentioned you @mspector13.
Please try knitting barnacles.Rmd
again as the data files in github_info-intertidal_data - NMS - Google Drive have been updated to include the expected columns, like sp_target
in sanctuary_species_percentcover.csv
.
Right on @bbest , thanks!
Unfortunately, Im currently still not able to knit barnacles.Rmd.
However, I can run each code chunk line by line to get the desired outputs, which is a huge improvement!
Below is the error message I get when I knit this file.
List of 10 $ name : chr "PopupTable" $ version : chr "0.0.1" $ src :List of 1 ..$ file: chr "" $ meta : NULL $ script : NULL $ stylesheet: chr "popup.css" $ head : NULL $ attachment: NULL $ package : NULL $ all_files : logi TRUE
Ok @mspector13,
Since it works for me using latest R 4.0.2 and RStudio, go ahead and try installing the latest R and RStudio, then knit again:
> devtools::session_info()
─ Session info ──
setting value
version R version 4.0.2 (2020-06-22)
os macOS Catalina 10.15.6
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2020-09-01
Captions and external sources have been added to the figures for this .Rmd
file. However, I'm getting the same error message as I did when I tried to knit Algal-groups.Rmd
:
Quitting from lines 16-17 (barnacles.Rmd)
Error in get_nms_ply(nms) : could not find function "get_nms_ply"
Calls:
Everything for this modal window should be ready to go once this error is fixed
All code moved to nms4r, so hopefully problems above are no more.
Also, I'm questioning appropriateness of request 1. order the sites in the legend from north to south not alphabetical given East to West orientation of Channel Island sites:
Melissa had the following suggested improvements for the interactive plots 1) order the sites in the legend from north to south not alphabetical 2) keep color consistent for a given site between indicators (e.g., if Sokol Pt is blue for mussel plot then it should be blue for barnacle plot) 3) the lines for sites are hard to see (thin and faint) unless you hover on one. Can they be thicker/brighter while still allowing the one on hover to be even more prominent?