Error / ThermStats installation

[washfaq]

Hello, I am facing an error while trying to install "Thermstats".

devtools::install_github("rasenior/ThermStats")

Downloading GitHub repo rasenior/ThermStats@master Skipping 1 packages not available: HatchedPolygons √ checking for file 'C:\Users\washfaq\AppData\Local\Temp\RtmpGCyJqS\remotes3e30177e23b6\rasenior-ThermStats-8ad346e/DESCRIPTION' (748ms)

• preparing 'ThermStats': (1.1s) √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts (391ms)
• checking for empty or unneeded directories
• looking to see if a 'data/datalist' file should be added
• building 'ThermStats_0.9.3.tar.gz' (1.8s)

Installing package into ‘C:/Users/washfaq/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) ERROR: dependency 'HatchedPolygons' is not available for package 'ThermStats'

• removing 'C:/Users/washfaq/Documents/R/win-library/3.6/ThermStats' Error in i.p(...) : (converted from warning) installation of package ‘C:/Users/washfaq/AppData/Local/Temp/RtmpGCyJqS/file3e3031b0143c/ThermStats_0.9.3.tar.gz’ had non-zero exit status In addition: Warning messages: 1: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers 2: In untar2(tarfile, files, list, exdir) : skipping pax global extended headers

library(ThermStats) Error in library(ThermStats) : there is no package called ‘ThermStats’

My session information is as below; sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] grid stats graphics grDevices utils datasets methods base

other attached packages: [1] fields_9.8-3 maps_3.3.0 spam_2.2-2 dotCall64_1.0-0 Thermimage_3.2.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.1 rstudioapi_0.10 magrittr_1.5 usethis_1.5.0 devtools_2.0.2
[6] pkgload_1.0.2 R6_2.4.0 rlang_0.3.4 tools_3.6.0 pkgbuild_1.0.3
[11] sessioninfo_1.1.1 png_0.1-7 cli_1.1.0 withr_2.1.2 remotes_2.0.4
[16] yaml_2.2.0 assertthat_0.2.1 digest_0.6.19 rprojroot_1.3-2 crayon_1.3.4
[21] processx_3.3.1 callr_3.2.0 fs_1.3.1 ps_1.3.0 curl_3.3
[26] testthat_2.1.1 glue_1.3.1 memoise_1.1.0 tiff_0.1-5 compiler_3.6.0
[31] desc_1.2.0 backports_1.1.4 prettyunits_1.0.2

Any idea what might be going wrong? Thanks Waseem

[rasenior]

Ooops, it's because HatchedPolygons is a missing dependency. I'll look into this, but in the meantime if you first run:

devtools::install_github("statnmap/HatchedPolygons")

And then try again with:

devtools::install_github("rasenior/ThermStats")

It should work. Let me know!

[washfaq]

Yes, it is installed and working now. Thank you.

Another question is can we calculate following through ThermStats;

1. lower and higher temperature of Thermal image (required to measure Plant canopy temperature)?
2. Air temperature (Ta) of Thermal Image
3. Atmospheric vapour pressure deficit If yes, can you please share the script. Will be much grateful for your help. Thanks

[washfaq]

Hello, while analyzing plant thermal images, I got below error ;

Getting patches ...calculating neighbourhood weights Error in spdep::knearneigh(cbind(df$x, df$y), k = 8) : knearneigh: fewer data points than k

Any idea to fix this error.

[rasenior]

Apologies for the delay. I'll respond below to each issue in turn.

1. lower and higher temperature of Thermal image (required to measure Plant canopy temperature)?

Yes - any statistic you like (e.g. min, max) can be passed to get_stats or stats_by_group

2. Air temperature (Ta) of Thermal Image

Air temperature is not measured by thermal cameras. This is a parameter required for accurate conversion of the received infrared radiation to a temperature in °C, but it is something that you either estimate or, ideally, measure yourself using a thermometer, datalogger or weather station. The default setting in thermal cameras is usually 25°C. If you want to retrieve what the default setting on your camera was, try:

Thermimage::flirsettings("path/to/your/image")$Info$AtmosphericTemperature

But note that you can easily change this within ThermStats::batch_convert, via the argument ATemp

3. Atmospheric vapour pressure deficit If yes, can you please share the script. Will be much grateful for your help. Thanks

Again, you can't measure atmospheric information with a thermal camera. Vapour Pressure Deficit requires measurements of air temperature and relative humidity, which you could get from a whirling hygrometer, hygrochron datalogger or weather station. Another package of mine called MoistureCalc (https://github.com/rasenior/MoistureCalc) can calculate VPD from these two values, via the function calc_VPD

while analyzing plant thermal images, I got below error ;

Getting patches ...calculating neighbourhood weights Error in spdep::knearneigh(cbind(df$x, df$y), k = 8) : knearneigh: fewer data points than k

Any idea to fix this error.

I couldn't really tell you without seeing the data, but it seems odd that in a thermal image you should have fewer than 8 data points (which is what the error message is suggesting). Would you be able to share an example image with me? You can email it to rebecca.a.senior@gmail.com and I'll take a look.

[rasenior]

By the way, the paper describing the ThermStats package was just last week accepted for publication, and I think it will help you a lot as you try it out on your own data. I can let you know when it becomes available to view online? It'll be open access