Publications by Frank
ENEC 562 - Final Project
Introduction This document is to analyze the vegetation-mammal community dataset. library(ggplot2) library(dplyr) library(vegan) library(rstatix) mam <- read.csv("master.csv") mam <- mam %>% filter(rowSums(select(., 7:14) != 0) > 0) %>% select(-rara) #some sites got 0, must excludec Select and check data Select only count data: mam1...
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Stat Coursework
set.seed(231) ### Plotting the log-likelihood of the mean parameter y = round(rexp(40, rate=1/5), 2) y ## [1] 4.41 5.45 22.45 1.26 8.73 4.70 1.04 1.88 4.83 0.01 0.86 3.69 ## [13] 9.53 8.97 4.72 0.41 5.84 4.09 7.59 0.92 4.97 3.43 1.85 4.45 ## [25] 9.01 5.40 5.91 0.37 8.22 7.68 3.93 8.72 1.54 3.48 6.53 4.65 #...
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Logit Tennis
library(devtools) ## Warning: package 'devtools' was built under R version 4.3.1 ## Loading required package: usethis ## Warning: package 'usethis' was built under R version 4.3.1 library(deuce) ## Loading required package: jsonlite ## Warning: package 'jsonlite' was built under R version 4.3.1 ## Loading required package: dplyr ## Warning: package...
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Metrics and IBI scores for All sites - Chap2
Introduction These are codes I used to run NMDS on IBI and metric data calculated using the MBSStools package. Load the package Package vegan is the package in R that you can use to run multivariate analyses (Oksanen et al., 2022). library(vegan) Load data Data can be found here. library(readxl) metric_ibi_allsites <- read_excel("F:/GitHub Pro...
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PCA of Water Chemistry
Introduction These are the codes I used to run PCA of my averaged water chemistry data. Instead of using the princomp() function, I am going to try out the rda() function from the vegan package (Oksanen et al. 2012). Any comment is welcome. Load data My dataset can be found here. library(readxl) wc <- read_excel("F:/Thesis stuff/Data Analys...
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Discharge analysis - Climate change vs. Hydrology
Introduction To investigate the impacts of climate change on stream hydrology, it is important to examine the long-term trends. However, in urban watersheds, the question is then how to disentangle the effects of urbanization and climate change on hydrology. Villa Nova Flow duration curve I first want to know how flow duration curves differ d...
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PCA of Metric Data
Introduction These are the codes I used to run PCA for my metric data calculated using the MBSStools package (Leppo, 2021). Again, I welcome any feedback if there is any to further improve my codes. Load data library(readxl) metric_data <- read_excel("~/thesis-codes/Part b (09-19)/Main Matrices No Zero.xlsx", sheet = "MetricIBI") Make a ...
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NMDS Combined Density
Introduction These are the codes I used to run an NMDS for the density of benthic macroinvertebrate collected at ten sites in Red Run watershed in four seasons/months in 1987-1988 and 2009. Credit goes to Dr. Jackie Zorz. Check out her work here. Load the package Package vegan is the package in R that you can use to run multivariate analyses (O...
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IBI score report - 2012
Introduction This is sample report for IBI score calculations of sites collected in 2012. Import dataset Set up arguments for later calculation library(MBSStools) # Metrics, Index, Benthic Macroinvertebrates, genus # (generate values then scores) myIndex <- "MBSS.2005.Bugs" # Thresholds thresh <- metrics_scoring # get metric names for myI...
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Part a: 1987-2009 - Lost Gained - Weighted Tolerance Values
Introduction This is sample report for a randomization test on the weighted mean tolerance values of lost taxa in Red Run. Taxa include all families, orders, and genera. However, Chironomidae and Oligochaeta were excluded due to taxonomic bias and high abundance. library(readxl) b1wtv <- read_excel("C:/Users/tiena/OneDrive - Towson University/Th...
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