Merge branch 'rodents-533' of https://github.com/weecology/PortalData …

…into rodents-533
weecology · Nov 7, 2024 · 36641ed · 36641ed
2 parents c886f04 + 870385d
commit 36641ed
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -36,9 +36,11 @@ jobs:
       - name: Setup R (Ubuntu)
         uses: eddelbuettel/github-actions/r2u-setup@master
 
-      - name: Install system dependencies
+
+      - name: Install Python and packages
         run: |
-          pipx install --include-deps pandas numpy landsatxplore
+          python -m pip install --upgrade pip
+          python -m pip install pandas numpy landsatxplore
 
       - name: Install packages
         run: Rscript install-packages.R

diff --git a/DataCleaningScripts/clean_pit_tags.R b/DataCleaningScripts/clean_pit_tags.R
@@ -1,6 +1,3 @@
-
-
-
 #
 # determines if a tag is a PIT tag by its structure
 #  requires species input for comparison, returns a logical vector

diff --git a/DataCleaningScripts/get_regional_weather.R b/DataCleaningScripts/get_regional_weather.R
@@ -1,7 +1,7 @@
-library(httr)
-library(jsonlite)
-library(dplyr)
-library(lubridate)
+library(httr, warn.conflicts=FALSE, quietly = TRUE)
+library(jsonlite, warn.conflicts=FALSE, quietly = TRUE)
+library(dplyr, warn.conflicts=FALSE, quietly = TRUE)
+library(lubridate, warn.conflicts=FALSE, quietly = TRUE)
 
 # Explicitly assign magrittr pipe operator
 `%>%` <- magrittr::`%>%`

diff --git a/DataCleaningScripts/new_rodent_data.r b/DataCleaningScripts/new_rodent_data.r
@@ -1,10 +1,10 @@
 # This script is for cleaning new rodent data.  Data must first be entered in two separate sheets in
 # an excel file, by two different people to reduce entry error.
 
-library(openxlsx)
-library(sqldf)
-library(RCurl)
-library(dplyr)
+library(openxlsx, warn.conflicts=FALSE, quietly = TRUE)
+library(sqldf, warn.conflicts=FALSE, quietly = TRUE)
+library(RCurl, warn.conflicts=FALSE, quietly = TRUE)
+library(dplyr, warn.conflicts=FALSE, quietly = TRUE)
 
 source('DataCleaningScripts/general_data_cleaning_functions.R')
 source('DataCleaningScripts/rodent_data_cleaning_functions.R')

diff --git a/DataCleaningScripts/old_weather_overlap.R b/DataCleaningScripts/old_weather_overlap.R
@@ -12,7 +12,7 @@ source("DataCleaningScripts/new_weather_data.r")
 # Open raw .dat file of new data
 filepath = "~/Dropbox (UFL)/Portal/PORTAL_primary_data/Weather/Raw_data/2002_Station/"
 
-metfile <- "Met526"
+metfile <- "Met534"
 
 rawdata <- read.csv(paste(filepath,metfile,'.dat',sep=''),head=F,sep=',',
                    col.names=c('code','year','jday','hour','precipitation','airtemp','RH'))

diff --git a/DataCleaningScripts/rodent_data_cleaning_functions.R b/DataCleaningScripts/rodent_data_cleaning_functions.R
@@ -1,4 +1,4 @@
-library(dplyr)
+library(dplyr, warn.conflicts=FALSE, quietly = TRUE)
 
 currentdir = getwd()
 

diff --git a/DataCleaningScripts/update_ndvi.R b/DataCleaningScripts/update_ndvi.R
@@ -3,7 +3,7 @@
 # https://www.usgs.gov/landsat-missions/landsat-collection-2-level-2-science-products
 
 `%>%` <- magrittr::`%>%`
-library(terra)
+library(terra, warn.conflicts=FALSE, quietly = TRUE)
 
 #' @title create_portal_area
 #'
@@ -84,7 +84,7 @@ summarize_ndvi_snapshot <- function(records, targetpath = tempdir()) {
   print(records["display_id"])
   source <- "USGS"
   sensor <- paste0("Landsat", records["satellite"])
-  date <- as.Date(records["acquisition_date"])
+  date <- lubridate::ymd_hms(format(records["acquisition_date"], format = "%Y-%m-%d %T %Z"))
 
   r <- extract_and_mask_raster(records, targetpath)
 
@@ -96,7 +96,7 @@ summarize_ndvi_snapshot <- function(records, targetpath = tempdir()) {
   md <- median(values(r),na.rm=T)
   mi <- min(values(r),na.rm=T)
   ma <- max(values(r),na.rm=T)
-  va <- var(values(r),na.rm=T)
+  va <- var(values(r),na.rm=T)[1,1]
   pix <- length(values(r))
 
   d <- data.frame(date = as.Date(date), sensor = sensor, source = source,

diff --git a/DataCleaningScripts/update_portal_plant_censuses.R b/DataCleaningScripts/update_portal_plant_censuses.R
@@ -5,7 +5,7 @@
 # you must manually change it's value to zero
 # If a season gets skipped entirely, it should also be manually added
 
-library(dplyr)
+library(dplyr, warn.conflicts=FALSE, quietly = TRUE)
 
 #' Appends new census dates to Portal_plant_censuses
 #'

diff --git a/DataCleaningScripts/update_portal_plots.R b/DataCleaningScripts/update_portal_plots.R
@@ -1,5 +1,5 @@
-library(zoo)
-library(dplyr)
+library(zoo, warn.conflicts=FALSE, quietly = TRUE)
+library(dplyr, warn.conflicts=FALSE, quietly = TRUE)
 
 #' Appends new dates to Portal_plots
 #'

diff --git a/DataCleaningScripts/update_portal_rodent_trapping.r b/DataCleaningScripts/update_portal_rodent_trapping.r
@@ -1,8 +1,8 @@
 # This creates the Portal_rodent_trapping.csv file in the Rodents folder
 # Record of which plots were or were not trapped in each census and exact dates
 
-library(dplyr)
-library(zoo)
+library(dplyr, warn.conflicts=FALSE, quietly = TRUE)
+library(zoo, warn.conflicts=FALSE, quietly = TRUE)
 
 #' Appends new trapping dates to Portal_rodent_trapping
 #'

diff --git a/NDVI/ndvi.csv b/NDVI/ndvi.csv
@@ -3484,3 +3484,12 @@
 2024-09-14,"Landsat9","USGS",4422,0.173520664484033,0,0.000632123801695432,0.118960499898486,0.398667167522295
 2024-09-15,"Landsat8","USGS",4422,0.17025756402245,0,0.00055928485460436,0.120118623266412,0.379759732720423
 2024-09-23,"Landsat9","USGS",4422,0.167676355093998,0,0.00063424708970505,0.115105957893011,0.364816615862614
+2024-09-30,"Landsat9","USGS",4422,0.172568612806747,0,0.000494937339088828,0.123923577888206,0.335097179865221
+2024-10-01,"Landsat8","USGS",4422,0.166459781440317,0,0.000543715142538043,0.114510263525275,0.328321623322148
+2024-10-08,"Landsat8","USGS",4422,0.165106511068842,0,0.000506610375668904,0.115104776957244,0.329573601645699
+2024-10-09,"Landsat9","USGS",4422,0.163941535906633,0,0.000485204046313852,0.116881268485778,0.317717607625432
+2024-10-16,"Landsat9","USGS",4422,0.149134311322764,0,0.00039804975228395,0.10748957570742,0.281760004394518
+2024-10-17,"Landsat8","USGS",4422,0.1604018867701,1.74129353233831,0.000873001576652171,0.0678971456100207,0.318145747109597
+2024-10-24,"Landsat8","USGS",4422,0.160642248438728,0,0.000481665685045098,0.113067961979703,0.319706957638722
+2024-10-25,"Landsat9","USGS",4422,0.157566866599098,0,0.000452752872489841,0.110638886780744,0.301651741293532
+2024-11-01,"Landsat9","USGS",4422,0.160292985228627,66.0334690185436,0.00028536222862143,0.117894326596515,0.245805390358092
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # PortalData
 
 <!-- badges: start -->
-[![Build Status](https://github.com/weecology/PortalData/workflows/CI/badge.svg)](https://github.com/weecology/PortalData/actions)
+[![Build Status](https://github.com/weecology/PortalData/actions/workflows/main.yml/badge.svg)](https://github.com/weecology/PortalData/actions/workflows/main.yml)
 [![License](http://i.creativecommons.org/p/zero/1.0/88x31.png)](https://raw.githubusercontent.com/weecology/PortalData/main/LICENSE)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1215988.svg)](https://doi.org/10.5281/zenodo.1215988)
 [![NSF-1929730](https://img.shields.io/badge/NSF-1929730-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1929730)

diff --git a/Rodents/moon_dates.csv b/Rodents/moon_dates.csv
@@ -584,3 +584,4 @@
 583,2024-08-04,532,2024-08-10
 584,2024-09-02,NA,NA
 585,2024-10-02,NA,NA
+586,2024-10-31,NA,NA
diff --git a/Weather/Portal_storms.csv b/Weather/Portal_storms.csv
@@ -37571,3 +37571,7 @@
 "2024-10-18 23:30:00",1383,12.72,0
 "2024-10-18 23:35:00",1384,12.73,0
 "2024-10-18 23:40:00",1385,12.72,0
+"2024-11-03 17:15:00",1386,12.89,0.254
+"2024-11-03 17:20:00",1387,12.88,0
+"2024-11-03 17:25:00",1388,12.86,0
+"2024-11-03 17:30:00",1389,12.86,0