This package provides functions to assist with summarizing, analyzing, visualizing, and reporting freshwater fish population monitoring data.
Add flffishltm repository to package repository list.
options(repos = c(
flfishltm = "https://jasono6359.r-universe.dev",
CRAN = "https://cloud.r-project.org"))
To add a persistent reference to the repository you can add the above code to your .Rprofile file. To quickly open and edit .Rprofile use:
usethis::edit_r_profile(scope = "user")
Once the repository has been referenced, flfishltm can be installed
using
install.packages("flfishltm")
Load package
library(flfishltm)
## basic example code
Create data summary tables
data(newnans)
newn_sum <- ltm.data.summary("Newnans", newnans)
Access summary tables
names(newn_sum)
#> [1] "SpeciesList" "SpeciesHistory" "CPUE_Tab_number" "CPUE_number"
#> [5] "CPUE_number_SE" "CPUE_Tab_weight" "CPUE_weight" "CPUE_weight_SE"
#> [9] "Comp_num" "Comp_wt" "Year_Sites" "Comp_Sum"
#> [13] "TotalCount" "RawData" "annual_summary"
head(newn_sum$CPUE_number)
#> Year yr Threadfin Shad Golden Shiner Bowfin Swamp Darter
#> 1 2006 - 2007 2006 0.6666667 0.9066667 0.2266667 0.006666667
#> 2 2007 - 2008 2007 0.1000000 0.9066667 0.2400000 0.020000000
#> 3 2008 - 2009 2008 0.9000000 0.5120000 0.1880000 0.044000000
#> 4 2009 - 2010 2009 1.0160000 0.4240000 0.2520000 0.000000000
#> 5 2010 - 2011 2010 1.5400000 0.2440000 0.1320000 0.008000000
#> 15 2011 - 2012 2011 NA NA NA NA
#> Brown Bullhead Bluegill Redear Sunfish Black Crappie Warmouth
#> 1 0.9933333 17.82667 0.3466667 0.7133333 0.640
#> 2 0.3266667 10.75333 1.0866667 0.2800000 0.520
#> 3 0.4120000 7.38800 0.3520000 0.4240000 0.236
#> 4 0.4000000 4.58000 0.1880000 0.3840000 0.392
#> 5 0.0760000 1.13200 0.0680000 0.2760000 0.240
#> 15 NA NA NA NA NA
#> Brook Silverside Florida Gar Gizzard Shad Eastern Mosquitofish
#> 1 0.333333333 0.7133333 0.4733333 1.106667
#> 2 0.006666667 0.5266667 0.7266667 10.986667
#> 3 0.344000000 0.7720000 0.3560000 3.408000
#> 4 0.540000000 0.8320000 0.2920000 2.732000
#> 5 0.148000000 0.8240000 0.5000000 0.732000
#> 15 NA NA NA NA
#> Lake Chubsucker Largemouth Bass Least Killifish Yellow Bullhead
#> 1 0.01333333 0.006666667 0.000 0.00000000
#> 2 0.03333333 0.073333333 0.120 0.01333333
#> 3 0.06000000 0.064000000 0.000 0.00000000
#> 4 0.02400000 0.084000000 0.020 0.00000000
#> 5 0.00800000 0.040000000 0.008 0.00400000
#> 15 NA NA NA NA
#> Golden Topminnow Sailfin Molly Bluefin Killifish Brown Hoplo Flier
#> 1 0.00000000 0.000 0.000 0.000 0.000
#> 2 0.01333333 0.000 0.000 0.000 0.000
#> 3 0.00000000 0.012 0.000 0.000 0.000
#> 4 0.06800000 0.004 0.020 0.008 0.000
#> 5 0.00800000 0.000 0.004 0.000 0.004
#> 15 NA NA NA NA NA
#> Inland Silverside Taillight Shiner Chain Pickerel Flagfish White Catfish
#> 1 0.000 0.000 0.000 0 0
#> 2 0.000 0.000 0.000 0 0
#> 3 0.000 0.000 0.000 0 0
#> 4 0.000 0.000 0.000 0 0
#> 5 0.216 0.004 0.004 0 0
#> 15 NA NA NA NA NA
#> sunfish species bluegill-redear hybrid All
#> 1 0 0 24.97333
#> 2 0 0 26.73333
#> 3 0 0 15.47200
#> 4 0 0 12.26000
#> 5 0 0 6.22000
#> 15 NA NA NA
newn_sum$Year_Sites
#> # A tibble: 14 × 2
#> Sample `dplyr::n_distinct(Site)`
#> <chr> <int>
#> 1 2006 - 2007 15
#> 2 2007 - 2008 15
#> 3 2008 - 2009 25
#> 4 2009 - 2010 25
#> 5 2010 - 2011 25
#> 6 2012 - 2013 25
#> 7 2013 - 2014 25
#> 8 2014 - 2015 25
#> 9 2015 - 2016 25
#> 10 2016 - 2017 25
#> 11 2017 - 2018 25
#> 12 2018 - 2019 25
#> 13 2019 - 2020 25
#> 14 2020 - 2021 25
create cpue plot and subset by species and size class
cpue.plot(newn_sum, speciesList = c("BLUE", "RESU"))
#> # A tibble: 28 × 15
#> # Groups: WaterBody, Year, Season, SpeciesCode, SpeciesCommon [28]
#> WaterBody Year Season SpeciesCode SpeciesCommon SpeciesScientific mean_CPUE
#> <fct> <dbl> <chr> <chr> <chr> <fct> <dbl>
#> 1 Newnans L… 2006 Fall BLUE Bluegill Lepomis macrochi… 17.8
#> 2 Newnans L… 2006 Fall RESU Redear Sunfi… Lepomis microlop… 0.347
#> 3 Newnans L… 2007 Fall BLUE Bluegill Lepomis macrochi… 10.8
#> 4 Newnans L… 2007 Fall RESU Redear Sunfi… Lepomis microlop… 1.09
#> 5 Newnans L… 2008 Fall BLUE Bluegill Lepomis macrochi… 7.39
#> 6 Newnans L… 2008 Fall RESU Redear Sunfi… Lepomis microlop… 0.352
#> 7 Newnans L… 2009 Fall BLUE Bluegill Lepomis macrochi… 4.58
#> 8 Newnans L… 2009 Fall RESU Redear Sunfi… Lepomis microlop… 0.188
#> 9 Newnans L… 2010 Fall BLUE Bluegill Lepomis macrochi… 1.13
#> 10 Newnans L… 2010 Fall RESU Redear Sunfi… Lepomis microlop… 0.068
#> # ℹ 18 more rows
#> # ℹ 8 more variables: sd_CPUE <dbl>, se_CPUE <dbl>, max_CPUE <dbl>,
#> # min_CPUE <dbl>, cv_CPUE <dbl>, sizeStrata <chr>, lower <dbl>, upper <dbl>
For help see function help documentation.
?cpue.plot
# or
help(cpue.plot)
Check out the intro vignette for more examples
RShowDoc("flfishltm_intro", type = "html", package = "flfishltm")
Source code available on github