#THIS FILE CONTAINS CODE FOR MODELING FREQUENCY OF OCCURRENCE DATA IN A GENERAL MIXED EFFECTS LINEAR REGRESSION MODEL
# STEP 0: LOAD PACKAGES
library(tidyverse)## Warning: package 'tidyverse' was built under R version 4.3.3## Warning: package 'ggplot2' was built under R version 4.3.3## Warning: package 'tibble' was built under R version 4.3.3## Warning: package 'tidyr' was built under R version 4.3.3## Warning: package 'readr' was built under R version 4.3.3## Warning: package 'purrr' was built under R version 4.3.3## Warning: package 'dplyr' was built under R version 4.3.3## Warning: package 'stringr' was built under R version 4.3.3## Warning: package 'forcats' was built under R version 4.3.3## Warning: package 'lubridate' was built under R version 4.3.3## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(dplyr)
library(readxl)## Warning: package 'readxl' was built under R version 4.3.3library(lme4)## Warning: package 'lme4' was built under R version 4.3.3## Loading required package: Matrix## Warning: package 'Matrix' was built under R version 4.3.3##
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## expand, pack, unpacklibrary(lmerTest)## Warning: package 'lmerTest' was built under R version 4.3.3##
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## lmer
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## steplibrary(performance)## Warning: package 'performance' was built under R version 4.3.3library(emmeans)## Warning: package 'emmeans' was built under R version 4.2.3library(multcomp)## Warning: package 'multcomp' was built under R version 4.2.3## Loading required package: mvtnorm## Warning: package 'mvtnorm' was built under R version 4.3.3## Loading required package: survival
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## select
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## amllibrary(broom.mixed)## Warning: package 'broom.mixed' was built under R version 4.2.3COMMON ABBREVIATIONS THROUGHOUT WORKFLOW: FoC_Pcri = Frequency of Occurrence of Curly Leaf Pondweed (aka Pcri / CLP) FoC_Mspi = Frequency of Occurrence of Eurasian Watermilfoil (aka Mspi / EWM) FoC_Nat = Frequency of Occurrence of Native Macrophytes (aka Nat) FoC_tot = Frequency of Occurrence of All Aquatic Macrophytes (aka tot) SECCHI = SECCHI DEPTH IN METERS TP = TOTAL EPILIMNETIC PHOSPHORUS Sig Letters = Significant Letters ALUM = ALUMINUM SULFATE TREATMENT PERIOD = GROUPING OF DATA BASED ON WHEN ALUM TREATMENT OCCURRED PRE = PRE-ALUM TREATMENT, BEFORE ANY ALUM HAS BEEN APPLIED DURING = DURING-ALUM TREATMENT, BETWEEN THE FIRST AND LAST ALUM TREATMENT APPLICATION POST = POST-ALUM TREATMENT, AFTER ALUM HAS BEEN APPLIED SEASON = TIME OF YEAR SAMPLING TOOK PLACE EARLY = SAMPLING PERFORMED BETWEEN APRIL AND JUNE LATE = SAMPLING PERFORMED BETWEEN JULY AND SEPTEMBER D_S = DEPTH CLASSIFICATION OF LAKE BASED ON MAX DEPTH DEEP (D)= MAX DEPTH GREATER THAN 15 FEET SHALLOW (S) = MAX DEPTH LESS THAN 15 FEET
DISCLAIMER: IF JUST CLP, EWM, OR NAT IS IN THE COMMENTS I’M REFERRING TO THE FREQUENCY OF OCCURRENCE
# STEP 1: LOAD IN PVALUES FOR EACH MODEL
models <- read.csv("C:/Users/k_hem/OneDrive/Desktop/UMN AV Data/PvaluesModelsUSGS.csv")# STEP 2: RUN P ADJUSTMENT CODE
models$fdr <- p.adjust(models$p_value, method = "fdr") # USE P ADJUST TO ACCOUNT FOR FALSE POSITIVES AND STORE RESULTS IN NEW COLUMN 'FDR', SPECIFY MODEL TO TEST AND COLUMN TO CALCULATE WITH
# STEP 2.1: DISPLAY RESULTS
print(models)## comparison p_value model fdr
## 1 intercept 1.260000e-28 tp 2.126250e-27
## 2 periodduring 1.964692e-02 tp 3.274487e-02
## 3 periodpost 1.300000e-05 tp 3.510000e-05
## 4 d_sS 6.790079e-02 tp 9.963703e-02
## 5 seasonlate 3.480000e-23 tp 2.936250e-22
## 6 periodduring:d_sS 9.583838e-01 tp 9.583838e-01
## 7 periodpost:d_sS 1.031078e-01 tp 1.420363e-01
## 8 periodduring:seasonlate 1.439092e-02 tp 2.428468e-02
## 9 periodpost:seasonlate 4.574405e-01 tp 5.233429e-01
## 10 d_sS:seasonlate 1.965300e-03 tp 4.019932e-03
## 11 Intercept 1.050000e-27 secchi 1.575000e-26
## 12 periodduring 5.531339e-02 secchi 8.438258e-02
## 13 periodpost 5.812920e-04 secchi 1.256027e-03
## 14 d_sS 3.390000e-09 secchi 1.204342e-08
## 15 seasonlate 1.120000e-103 secchi 5.040000e-102
## 16 periodduring:d_sS 8.281993e-01 secchi 8.600531e-01
## 17 periodpost:d_sS 1.423744e-02 secchi 2.428468e-02
## 18 d_sS:seasonlate 3.992158e-01 secchi 4.646046e-01
## 19 periodduring:seasonlate 1.570000e-18 secchi 9.634091e-18
## 20 periodpost:seasonlate 2.950000e-12 secchi 1.284677e-11
## 21 Intercept 5.673769e-01 clp 6.382990e-01
## 22 period2post 5.861460e-04 clp 1.256027e-03
## 23 d_sS 1.680585e-01 clp 2.181529e-01
## 24 seasonlate 4.200000e-125 clp 2.835000e-123
## 25 period2post:d_sS 1.690000e-08 clp 5.432143e-08
## 26 period2post:seasonlate 2.040000e-24 clp 2.520000e-23
## 27 d_sS:seasonlate 1.920000e-23 clp 1.993846e-22
## 28 period2post:d_sS:seasonlate 3.250000e-05 clp 8.602941e-05
## 29 Intercept 8.675081e-01 clp2 8.931477e-01
## 30 period2post 9.300000e-10 clp2 3.692647e-09
## 31 d_sS 9.065482e-02 clp2 1.276759e-01
## 32 seasonlate 1.860000e-143 clp2 2.511000e-141
## 33 period2post:d_sS 2.250000e-15 clp2 1.052069e-14
## 34 period2post:seasonlate 6.380000e-32 clp2 1.435500e-30
## 35 d_sS:seasonlate 3.340000e-30 clp2 6.441429e-29
## 36 period2post:d_sS:seasonlate 6.270000e-08 clp2 1.923750e-07
## 37 (Intercept) 2.500197e-03 ewm 4.821809e-03
## 38 periodpost 1.280000e-21 ewm 8.640000e-21
## 39 periodpre 2.070000e-16 ewm 1.164375e-15
## 40 seasonlate 5.200000e-22 ewm 3.900000e-21
## 41 periodpost:seasonlate 1.210000e-09 ewm 4.414865e-09
## 42 periodpre:seasonlate 2.720000e-07 ewm 7.982609e-07
## 43 (Intercept) 2.500197e-03 ewm2 4.821809e-03
## 44 periodpost 1.280000e-21 ewm2 8.640000e-21
## 45 periodpre 2.070000e-16 ewm2 1.164375e-15
## 46 seasonlate 5.200000e-22 ewm2 3.900000e-21
## 47 periodpost:seasonlate 1.210000e-09 ewm2 4.414865e-09
## 48 periodpre:seasonlate 2.720000e-07 ewm2 7.982609e-07
## 49 (Intercept) 1.922824e-01 natives 2.472202e-01
## 50 periodduring 1.510000e-19 natives 9.707143e-19
## 51 periodpost 2.260000e-15 natives 1.052069e-14
## 52 d_sS 8.917269e-01 natives 9.051363e-01
## 53 seasonlate 1.276040e-04 natives 3.132098e-04
## 54 periodduring:d_sS 7.264868e-03 natives 1.290470e-02
## 55 periodpost:d_sS 1.570947e-03 natives 3.262736e-03
## 56 periodduring:seasonlate 3.501612e-02 natives 5.627591e-02
## 57 periodpost:seasonlate 5.707285e-02 natives 8.560927e-02
## 58 d_sS:seasonlate 2.618150e-03 natives 4.978173e-03
## 59 periodduring:d_sS:seasonlate 8.734585e-03 natives 1.531388e-02
## 60 periodpost:d_sS:seasonlate 7.331437e-01 natives 7.855111e-01
## 61 (Intercept) 2.215493e-01 natives2 2.769366e-01
## 62 periodduring 1.070000e-15 natives2 5.555769e-15
## 63 periodpost 1.410000e-15 natives2 7.050000e-15
## 64 d_sS 9.526043e-01 natives2 9.583838e-01
## 65 seasonlate 5.675950e-04 natives2 1.256027e-03
## 66 periodduring:d_sS 4.189914e-03 natives2 7.748471e-03
## 67 periodpost:d_sS 4.411520e-04 natives2 9.925920e-04
## 68 periodduring:seasonlate 5.420592e-02 natives2 8.411263e-02
## 69 periodpost:seasonlate 3.621070e-01 natives2 4.288109e-01
## 70 d_sS:seasonlate 5.162593e-03 natives2 9.292667e-03
## 71 periodduring:d_sS:seasonlate 1.533660e-04 natives2 3.569726e-04
## 72 periodpost:d_sS:seasonlate 3.881070e-01 natives2 4.556039e-01
## 73 (Intercept) 2.154421e-01 all 2.718195e-01
## 74 periodduring 8.032806e-02 all 1.153648e-01
## 75 periodpost 1.442950e-04 all 3.417513e-04
## 76 seasonlate 1.880000e-68 all 5.076000e-67
## 77 d_sS 7.778106e-01 all 8.139878e-01
## 78 periodduring:seasonlate 3.220000e-23 all 2.898000e-22
## 79 periodpost:seasonlate 2.240000e-24 all 2.520000e-23
## 80 periodduring:d_sS 4.810000e-06 all 1.352812e-05
## 81 periodpost:d_sS 9.173747e-02 all 1.276759e-01
## 82 seasonlate:d_sS 9.260000e-09 all 3.049024e-08
## 83 periodduring:seasonlate:d_sS 6.862000e-01 all 7.410960e-01
## 84 periodpost:seasonlate:d_sS 2.148012e-03 all 4.264436e-03
## 85 (Intercept) 2.154421e-01 all2 2.718195e-01
## 86 periodduring 8.032806e-02 all2 1.153648e-01
## 87 periodpost 1.442950e-04 all2 3.417513e-04
## 88 seasonlate 1.880000e-68 all2 5.076000e-67
## 89 d_sS 7.778106e-01 all2 8.139878e-01
## 90 periodduring:seasonlate 3.220000e-23 all2 2.898000e-22
## 91 periodpost:seasonlate 2.240000e-24 all2 2.520000e-23
## 92 periodduring:d_sS 4.810000e-06 all2 1.352812e-05
## 93 periodpost:d_sS 9.173747e-02 all2 1.276759e-01
## 94 seasonlate:d_sS 9.260000e-09 all2 3.049024e-08
## 95 periodduring:seasonlate:d_sS 6.862000e-01 all2 7.410960e-01
## 96 periodpost:seasonlate:d_sS 2.148012e-03 all2 4.264436e-03
## 97 tot 1.640000e-01 tbass 2.149515e-01
## 98 tot 1.607000e-01 thalfmoon 2.126912e-01
## 99 tot 8.733000e-01 thyland 8.931477e-01
## 100 tot 2.431000e-01 tkeller 3.010872e-01
## 101 tot 4.714000e-02 tlong 7.399884e-02
## 102 tot 7.570000e-05 triley 1.892500e-04
## 103 tot 7.670000e-01 twass 8.139878e-01
## 104 nat 3.596000e-02 tbass 5.711294e-02
## 105 nat 1.270000e-03 thalfmoon 2.678906e-03
## 106 nat 4.205000e-01 thyland 4.851923e-01
## 107 nat 5.210000e-05 tkeller 1.352596e-04
## 108 nat 5.563000e-02 tlong 8.438258e-02
## 109 nat 1.850000e-08 triley 5.808140e-08
## 110 nat 5.604000e-01 twass 6.357479e-01
## 111 pcri 5.850000e-01 tbass 6.473361e-01
## 112 pcri 1.272000e-01 thalfmoon 1.717200e-01
## 113 pcri 3.620000e-01 thyland 4.288109e-01
## 114 pcri 5.939000e-02 tkeller 8.810604e-02
## 115 pcri 3.140000e-02 tlong 5.107229e-02
## 116 pcri 6.093000e-01 triley 6.687439e-01
## 117 pcri 2.790000e-01 twass 3.424091e-01
## 118 mspi 3.293000e-01 thyland 3.969241e-01
## 119 mspi 1.260000e-01 tkeller 1.717200e-01
## 120 mspi 1.138000e-02 triley 1.969615e-02
## 121 mspi 1.350000e-01 twass 1.804455e-01
## 122 tep 7.280000e-05 tbass 1.854340e-04
## 123 tep 1.200000e-05 tbass 3.306122e-05
## 124 tep 5.800000e-01 thalfmoon 6.471074e-01
## 125 tep 3.180000e-01 thalfmoon 3.867568e-01
## 126 tep 9.530000e-14 thyland 4.288500e-13
## 127 tep 4.500000e-03 thyland 8.209459e-03
## 128 tep 2.200000e-16 tkeller 1.188000e-15
## 129 sec 1.200000e-09 tkeller 4.414865e-09
## 130 sec 1.820000e-04 tlong 4.164407e-04
## 131 sec 3.670000e-03 tlong 6.881250e-03
## 132 sec 5.000000e-11 triley 2.109375e-10
## 133 sec 3.910000e-09 triley 1.353462e-08
## 134 sec 5.760000e-10 twass 2.356364e-09
## 135 sec 2.790000e-02 twass 4.593293e-02sessionInfo()## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 22621)
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## Matrix products: default
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## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] broom.mixed_0.2.9.5 boot_1.3-30 multcomp_1.4-25
## [4] TH.data_1.1-2 MASS_7.3-58.1 survival_3.4-0
## [7] mvtnorm_1.2-4 emmeans_1.10.0 performance_0.10.9
## [10] lmerTest_3.1-3 lme4_1.1-35.1 Matrix_1.6-5
## [13] readxl_1.4.3 lubridate_1.9.3 forcats_1.0.0
## [16] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
## [19] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
## [22] ggplot2_3.5.0 tidyverse_2.0.0
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## loaded via a namespace (and not attached):
## [1] sass_0.4.9 jsonlite_1.8.8 splines_4.2.2
## [4] bslib_0.6.1 cellranger_1.1.0 yaml_2.3.8
## [7] globals_0.16.3 numDeriv_2016.8-1.1 pillar_1.9.0
## [10] backports_1.4.1 lattice_0.20-45 glue_1.7.0
## [13] digest_0.6.35 minqa_1.2.6 colorspace_2.1-0
## [16] sandwich_3.1-0 htmltools_0.5.7 pkgconfig_2.0.3
## [19] broom_1.0.5 listenv_0.9.1 xtable_1.8-4
## [22] scales_1.3.0 tzdb_0.4.0 timechange_0.3.0
## [25] generics_0.1.3 cachem_1.0.8 withr_3.0.0
## [28] furrr_0.3.1 cli_3.6.2 magrittr_2.0.3
## [31] estimability_1.5 evaluate_0.23 parallelly_1.37.1
## [34] fansi_1.0.6 future_1.33.1 nlme_3.1-160
## [37] tools_4.2.2 hms_1.1.3 lifecycle_1.0.4
## [40] munsell_0.5.0 compiler_4.2.2 jquerylib_0.1.4
## [43] rlang_1.1.3 grid_4.2.2 nloptr_2.0.3
## [46] rstudioapi_0.15.0 rmarkdown_2.26 gtable_0.3.4
## [49] codetools_0.2-18 R6_2.5.1 zoo_1.8-12
## [52] knitr_1.45 fastmap_1.1.1 utf8_1.2.4
## [55] insight_0.19.9 stringi_1.8.3 parallel_4.2.2
## [58] Rcpp_1.0.12 vctrs_0.6.5 tidyselect_1.2.1
## [61] xfun_0.42 coda_0.19-4.1