library("dplyr")
library("lme4") 
library("car")
library("emmeans")
library("multcompView")

#Get Session Info 
sessionInfo()

#set working directory
setwd("~/Desktop/Ant-Aphid Interaction/aai_data_sheets")

# load dataset
aai <- read.table("ant_aphid_data_analysis_stem_leaf_comparisons_samples_15_to_30_by_host_plant_year_fv.txt", sep = "\t", header = TRUE)

# test if tending duration is different from zero when aphids feed on stems
x <- aai %>%
  filter(aphid_placement_on_plant == "stem" & ant_treatment == "ants") %>% 
  pull("tending_time_minutes")

t.test(x, mu = 0)

# test if tending duration is different from zero when aphids feed on leaf
y <- aai %>% 
  filter(aphid_placement_on_plant == "leaf" & ant_treatment == "ants") %>% 
  pull("tending_time_minutes")

t.test(y, mu = 0)


# test the influence of host and aphid position on tending duration with year as a fixed effect
aai2 <- aai %>% 
  filter(ant_treatment == "ants")

lm2 <- lmer(tending_time_minutes ~ host * aphid_placement_on_plant * (1 | year), 
            data = aai2, REML = FALSE)
Anova(lm2)
lm2.pw <- emmeans(lm2, "aphid_placement_on_plant")
pairs(lm2.pw)


# test the influence of host plant, aphid position and TCA presence aphid biomass with year as a fixed effect
lm3 <- lmer(aphid_position_biomass ~ host * aphid_placement_on_plant * ant_treatment * (1 | year), 
            data = aai, REML = FALSE)
Anova(lm3)
lm3.pw <- emmeans(lm3, "aphid_placement_on_plant", by = c("host","ant_treatment"))
pairs(lm3.pw)



#sessinInfo()

#R version 4.1.0 (2021-05-18)
#Platform: x86_64-apple-darwin17.0 (64-bit)
#Running under: macOS Big Sur 11.6.4

#Matrix products: default
#LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

#locale:
#  [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

#attached base packages:
#  [1] stats     graphics  grDevices utils     datasets  methods   base     

#other attached packages:
#  [1] multcompView_0.1-8 emmeans_1.7.1-1    car_3.0-12         carData_3.0-4     
# [5] lme4_1.1-27.1      Matrix_1.4-0       dplyr_1.0.7       

#loaded via a namespace (and not attached):
#  [1] Rcpp_1.0.7       pillar_1.6.4     compiler_4.1.0   nloptr_1.2.2.3   tools_4.1.0     
# [6] boot_1.3-28      lifecycle_1.0.1  tibble_3.1.6     nlme_3.1-153     lattice_0.20-45 
# [11] pkgconfig_2.0.3  rlang_0.4.12     DBI_1.1.2        parallel_4.1.0   mvtnorm_1.1-3   
# [16] coda_0.19-4      generics_0.1.1   vctrs_0.3.8      grid_4.1.0       tidyselect_1.1.1
# [21] glue_1.6.0       R6_2.5.1         fansi_0.5.0      survival_3.2-13  multcomp_1.4-17 
# [26] TH.data_1.1-0    minqa_1.2.4      tidyr_1.1.4      purrr_0.3.4      magrittr_2.0.1  
# [31] backports_1.4.1  codetools_0.2-18 ellipsis_0.3.2   MASS_7.3-54      splines_4.1.0   
# [36] pbkrtest_0.5.1   assertthat_0.2.1 abind_1.4-5      xtable_1.8-4     sandwich_3.0-1  
# [41] utf8_1.2.2       estimability_1.3 broom_0.7.10     crayon_1.4.2     zoo_1.8-9