Hobotemp
Hobotemp
This is for managing and understanding your HOBO temperature data. This will work on any HOBO data that has been downloaded in csv format (not hproj format).
Requirements
Installation
remotes::install_github("rfrancolini/hobotemp")Function: read_hobotemp()
This function will take in raw hobotemp data and output a csv. Options include whether you want to define a site name (if not, itll pull it from the file name), if you want to define the start/stop times, have it automatically remove the first and last day (default setting), or keep all of the data, and if you want to write a file with a specific output name.
Read Example Data
library(hobotemp)
x <- read_hobotemp()
x## # A tibble: 9,025 x 5
## Reading DateTime Temp Intensity Site
## <int> <dttm> <dbl> <dbl> <chr>
## 1 53 2021-05-15 00:04:32 8.18 0 LittleDrisko
## 2 54 2021-05-15 00:19:32 8.18 0 LittleDrisko
## 3 55 2021-05-15 00:34:32 8.08 0 LittleDrisko
## 4 56 2021-05-15 00:49:32 8.18 0 LittleDrisko
## 5 57 2021-05-15 01:04:32 8.08 0 LittleDrisko
## 6 58 2021-05-15 01:19:32 8.08 0 LittleDrisko
## 7 59 2021-05-15 01:34:32 7.98 0 LittleDrisko
## 8 60 2021-05-15 01:49:32 7.88 0 LittleDrisko
## 9 61 2021-05-15 02:04:32 7.88 0 LittleDrisko
## 10 62 2021-05-15 02:19:32 7.88 0 LittleDrisko
## # ... with 9,015 more rowsRead Example Data with User Defined Site
library(hobotemp)
x <- read_hobotemp(site = "Little Drisko Island")
x## # A tibble: 9,025 x 5
## Reading DateTime Temp Intensity Site
## <int> <dttm> <dbl> <dbl> <chr>
## 1 53 2021-05-15 00:04:32 8.18 0 Little Drisko Island
## 2 54 2021-05-15 00:19:32 8.18 0 Little Drisko Island
## 3 55 2021-05-15 00:34:32 8.08 0 Little Drisko Island
## 4 56 2021-05-15 00:49:32 8.18 0 Little Drisko Island
## 5 57 2021-05-15 01:04:32 8.08 0 Little Drisko Island
## 6 58 2021-05-15 01:19:32 8.08 0 Little Drisko Island
## 7 59 2021-05-15 01:34:32 7.98 0 Little Drisko Island
## 8 60 2021-05-15 01:49:32 7.88 0 Little Drisko Island
## 9 61 2021-05-15 02:04:32 7.88 0 Little Drisko Island
## 10 62 2021-05-15 02:19:32 7.88 0 Little Drisko Island
## # ... with 9,015 more rowsRead Example Data With User Defined Start/Stop Dates
ss <- as.POSIXct(c("2021-05-20", "2021-06-01"), tz = "UTC")
xud <- read_hobotemp(clipped = "user", startstop = ss)
xud## # A tibble: 1,152 x 5
## Reading DateTime Temp Intensity Site
## <int> <dttm> <dbl> <dbl> <chr>
## 1 533 2021-05-20 00:04:32 8.38 0 LittleDrisko
## 2 534 2021-05-20 00:19:32 8.48 0 LittleDrisko
## 3 535 2021-05-20 00:34:32 8.48 0 LittleDrisko
## 4 536 2021-05-20 00:49:32 8.48 0 LittleDrisko
## 5 537 2021-05-20 01:04:32 8.58 0 LittleDrisko
## 6 538 2021-05-20 01:19:32 8.58 0 LittleDrisko
## 7 539 2021-05-20 01:34:32 8.68 0 LittleDrisko
## 8 540 2021-05-20 01:49:32 8.68 0 LittleDrisko
## 9 541 2021-05-20 02:04:32 8.78 0 LittleDrisko
## 10 542 2021-05-20 02:19:32 8.78 0 LittleDrisko
## # ... with 1,142 more rowsFunction: summarize_hobotemp()
Create a dataframe summarizing the temperature data, will group by site.
Summarize data, csv with one site
sum1 <- summarize_hobotemp(x)
print.data.frame(sum1)## Site mean.temp first.day last.day
## 1 Little Drisko Island 11.30466 2021-05-15 00:04:32 2021-08-17 00:04:32
## max.temp max.temp.date min.temp min.temp.date
## 1 16.046 2021-08-08 22:34:32 7.682 2021-05-15 07:34:32Summarize data, csv with more than one site
sum2 <- summarize_hobotemp(example_ridge_data())## Rows: 26018 Columns: 5
## -- Column specification --------------------------------------------------------
## Delimiter: ","
## chr (1): Site
## dbl (3): Reading, Temp, Intensity
## dttm (1): DateTime
##
## i Use `spec()` to retrieve the full column specification for this data.
## i Specify the column types or set `show_col_types = FALSE` to quiet this message.print.data.frame(sum2)## Site mean.temp first.day last.day max.temp
## 1 Cape Liz 12.95992 2021-06-05 00:11:44 2021-07-20 23:56:44 17.379
## 2 Damariscove 12.58830 2021-06-05 00:04:55 2021-07-20 23:49:55 17.475
## 3 Halfway Rock 12.35469 2021-06-05 00:14:09 2021-07-20 23:59:09 17.760
## 4 Isle Au Haut 11.61809 2021-06-05 00:00:00 2021-07-21 00:00:00 13.846
## 5 Marshall 11.38961 2021-06-10 00:00:00 2021-07-21 00:00:00 13.269
## max.temp.date min.temp min.temp.date
## 1 2021-07-18 20:41:44 9.571 2021-06-21 09:56:44
## 2 2021-07-16 19:04:55 8.680 2021-06-09 12:49:55
## 3 2021-07-18 18:14:09 9.077 2021-06-18 09:59:09
## 4 2021-07-08 10:00:00 8.779 2021-06-08 07:00:00
## 5 2021-07-16 18:45:00 9.077 2021-06-10 05:15:00Function: draw_scatter_plot()
This function will read in a csv of your HOBO data and draw a scatter plot with an overlapping trendline.
Draw Example Scatter Plot
tempplot_x <- draw_scatter_plot(x)
tempplot_x
Draw Example Scatter Plot with User Defined Start/Stop Dates and Title
tempplot_xud <- draw_scatter_plot(xud, main = "Temperature at Depth, End of May")
tempplot_xud
Function: draw_ridgeline_plot()
This function will create a color-coded ridgeline plot, adapted from here. This will have a line representing the temperature, as well as the space underneath the line colored in using a temperature gradient color scheme. Sites will appear in order they are in dataframe, unless “ordered” option is used.
Draw example ridgeline plot
ridgelineplot <- draw_ridgeline_plot()
ridgelineplot
Draw example ridgeline plot with specified site order (south to north)
SiteOrder <- c("Cape Liz", "Halfway Rock", "Damariscove", "Isle Au Haut", "Marshall")
ridgelineplotO <- draw_ridgeline_plot(ordered = SiteOrder)
ridgelineplotO
Function: draw_line_plot()
This function will create a line plot, with a colorblind friendly color pallette, and can currently take up to 15 sites at once. Sites will appear in legend (or will be facetted upon) in order they are in dataframe, unless “ordered” option is used.
Draw example line plot
lineplot <- draw_line_plot()
lineplot
Draw example line plot facetted with specified site order (south to north)
SiteOrder <- c("Cape Liz", "Halfway Rock", "Damariscove", "Isle Au Haut", "Marshall")
lineplotO <- draw_line_plot(ordered = SiteOrder, facet = "Site")
lineplotO