.Rhistory

facet_wrap (~ Behavior) +
geom_text(aes(label= P.Value, x= Species, y= P.Value), vjust= -0.6) +
theme(text = element_text(size = 15)) +
theme(axis.text.x = element_text(size = 6.5)) +
labs(caption= "Figure 1: Is Hand Preference Independent of Individual?") +
scale_fill_manual(values = c("#C84E00", "#E89923", "#1D6363"))
ggplot(by_focal, aes(x= Species, y= P.Value, fill = Species)) +
geom_bar(stat= 'identity', color = "black") +
theme_classic()+
xlab("Species of Lemur") +
ylab("P-Value (less than 0.05 is significant)") +
facet_wrap (~ Behavior) +
geom_text(aes(label= P.Value, x= Species, y= P.Value), vjust= -0.6) +
theme(text = element_text(size = 15)) +
theme(axis.text.x = element_text(size = 7)) +
labs(caption= "Figure 1: Is Hand Preference Independent of Individual?") +
scale_fill_manual(values = c("#C84E00", "#E89923", "#1D6363"))
ggplot(by_species, aes(x= Behavior, y= P.Value)) +
geom_bar(stat= 'identity', color = "black", fill = "#988675") +
theme_classic()+
xlab("Behavior") +
ylab("P-Value (less than 0.05 is significant)") +
geom_text(aes(label= P.Value, x= Behavior, y= P.Value), vjust= -0.5) +
theme(text = element_text(size = 20)) +
theme(axis.text.x = element_text(size = 10)) +
labs(caption= "Figure 3: Is Hand Preference Independent of Species?")
ggplot(by_species, aes(x= Behavior, y= P.Value)) +
geom_bar(stat= 'identity', color = "black", fill = "#DAD0C6") +
theme_classic()+
xlab("Behavior") +
ylab("P-Value (less than 0.05 is significant)") +
geom_text(aes(label= P.Value, x= Behavior, y= P.Value), vjust= -0.5) +
theme(text = element_text(size = 20)) +
theme(axis.text.x = element_text(size = 10)) +
labs(caption= "Figure 3: Is Hand Preference Independent of Species?")
ggplot(by_species, aes(x= Behavior, y= P.Value)) +
geom_bar(stat= 'identity', color = "black", fill = "#DAD0C6") +
theme_classic()+
xlab("Behavior") +
ylab("P-Value (less than 0.05 is significant)") +
geom_text(aes(label= P.Value, x= Behavior, y= P.Value), vjust= -0.5) +
theme(text = element_text(size = 15)) +
theme(axis.text.x = element_text(size = 10)) +
labs(caption= "Figure 3: Is Hand Preference Independent of Species?")
table(left_fg$Species)
left_fg <-
l_foodGrasps %>%
filter(Side == "L")
table(left_fg$Species)
right_fg <-
l_foodGrasps %>%
filter(Side == "R")
table(right_fg$Species)
table(left_fg$Species)
left_fg <-
l_foodGrasps %>%
filter(Side == "L")
table(left_fg$Species)
right_fg <-
l_foodGrasps %>%
filter(Side == "R")
table(right_fg$Species)
table(right_fg$Species)
table(left_fg$Individual)
table(left_fg$Individual)
table(right_fg$Individual)
table(left_rg$Species)
table(right_rg$Species)
library(tidyverse)
library(readr)
library(dplyr)
library(ggplot2)
L_PreClean <- read.csv("~/Documents/GitHub/Lefty_Lemurs/LeftyLemurs_Original.csv")
summary(L_PreClean)
L_PreClean <- rename(L_PreClean, Troop = Troop.............A..B..C..D...., Time = Time..H.M.S., Note = Focal.sample.note......................................................................................................................................................please.include.as.much.detail.as.possible...If.a.note.is.about.a.grooming.bout..for.example..include.stop.time.in.the.same.cell.)
L_PreClean$Category <- str_replace(L_PreClean$Category, ",", "")
L_PreClean$Category = toupper(L_PreClean$Category)
L_HFdata <-
L_PreClean %>%
filter(str_detect(Category, "RH|RF|LH|LF"))
# do not run
# lefty_justEthogram <-
# L %>%  select(Category) %>%
# filter(str_detect(Category, "BP|QP|L|AG|SG|F|E|CL|HC|R|G|"))
# do not run: L_HFdata$Limb <- L_PreClean$Category
# do not run: L_PreClean2 <- L_PreClean %>% relocate (Limb, .before = Note)
# do not run: lefty_split <- L_PreClean2$Category <- str_replace(L_PreClean$Limb, "BP|QP|L|AG|SG|F|E|CL|HC|R|G|", "")
# do not run: lefty_fullsplit <- L_PreClean2$Limb <- str_replace(L_PreClean$Category, "LF|LH|RF|RH|", "")
# write_csv(L_PreClean,"Lefty_Lemurs.csv")
L <- read.csv("~/Documents/GitHub/Lefty_Lemurs/LeftyLemurs_Clean.csv")
head(L)
table(L$Limb)
ggplot (L, aes(x= reorder (Limb, Limb, table ))) +
geom_bar(color = "black", fill = "#012169") +
theme_classic() +
xlab("Limb") +
ylab("Total Times Using Each Limb") +
ggtitle("Total Limb Use Across Lemurs") +
coord_flip()
ggplot (L, aes(x= reorder (Limb, Limb, table ))) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Limb") +
ylab("Total Times Using Each Limb") +
ggtitle("Total Limb Use Across Lemur Species") +
coord_flip() +
facet_wrap (~ Species, scales = "free")
ggplot (L, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Limb Use Between Lemur Species") +
facet_wrap (~ Species, scales = "free")
ggplot (L, aes(x= reorder (Side, Side, table ))) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right") +
ylab("Total Times Using Each Limb") +
ggtitle("Limb Use Between Lemur Species") +
coord_flip() +
facet_wrap (~ Species, scales = "free")
ggplot (L, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Limb Use Between Lemur Species") +
facet_wrap (~ Species,)
ggplot (L, aes(x = reorder (Limb, Limb, table ))) +
geom_bar(color = "black", fill = "#1D6363") +
theme_classic() +
xlab("Limb") +
ylab("Total Times Using Each Limb") +
ggtitle("Total Limb Use Between Sexes: Lemurs Are Not Lefties") +
coord_flip() +
facet_wrap (~ Sex, scales = "free")
ggplot (L, aes(x= reorder (Side, Side, table ))) +
geom_bar(color = "black", fill = "#1D6363") +
theme_classic() +
xlab("Left or Right") +
ylab("Total Times Using Each Limb") +
ggtitle("Total Limb Use Between Sexes: Lemurs Are Not Lefties") +
coord_flip() +
facet_wrap (~ Sex, scales = "free")
ggplot (L, aes(x= reorder (Category, Category, table ))) +
geom_bar(color = "black", fill = "#0577B1") +
theme_classic() +
xlab("Type of Behavior") +
ylab("Total Times Using Each Limb") +
ggtitle("Behavior Across Sexes") +
coord_flip() +
facet_wrap (~ Sex,scales = "free")
summary(L)
library(psych)
describeBy(L[c(4,1:12)], group = "Category")
# take out feet use data
l_hands <-
L %>%
select(H.F) %>%
filter(str_detect(H.F, "H"))
# add the other stuff back
l_hands <- inner_join(l_hands, L, by = "H.F")
l_hands <- unique(l_hands)
# actually I also don't want to look at all the categories bc some were added just for fun and are probably not important
l_handstuff <-
l_hands %>%
select(Category) %>%
filter(str_detect(Category, "E|L|R|SG"))
# WHY WON'T IT TAKE OUT LA
# add the other stuff back why did it even go away
l_handstuff <- inner_join(l_handstuff, l_hands, by = "Category")
# I can remove the H.F row because all of it is hand
l_handstuff <- l_handstuff %>% select(-H.F)
# removing Limb row bc side says the same thing
l_handstuff <- l_handstuff %>% select(-Limb)
# removing mystery duplicates
l_handstuff <- unique(l_handstuff)
l_noLA <-
l_handstuff %>%
filter(Category == "E"  |  Category == "L" |  Category == "R" |  Category == "SG" | Category != "LA" )
#wow I forgot you can do that
ggplot (l_noLA, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use Between Lemur Species") +
facet_wrap (~ Species, scales = "free")
ggplot (l_noLA, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("Type of Behavior") +
ggtitle("Hand Use Between Behaviors") +
facet_wrap (~ Category, scales = "free")
l_grasps <-
l_noLA %>%
filter(Category == "E"  |  Category == "L" |  Category == "R")
ggplot (l_grasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use for Grasping Between Lemur Species") +
facet_wrap (~ Species, scales = "free")
ggplot (l_grasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use for Grasping Between Sexes") +
facet_wrap (~ Sex, scales = "free")
l_foodGrasps <-
l_grasps %>%
filter(Category == "E")
ggplot (l_foodGrasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use for Food Grasping Between Lemur Species") +
facet_wrap (~ Species, scales = "free")
ggplot (l_foodGrasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use for Food Grasping Between Individuals") +
facet_wrap (~ Focal, scales = "free")
ggplot (l_foodGrasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use for Food Grasping Between Individuals") +
facet_wrap (~ Focal)
ggplot (l_noLA, aes(x= Category)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Activity") +
ylab("Occurrences") +
ggtitle("Hand Use for Activities by Species") +
facet_wrap (~ Species)
ggplot (l_foodGrasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Activity") +
ylab("Occurrences") +
ggtitle("Hand Used for Food Grasping Between Species") +
facet_wrap (~ Species)
ggplot (l_foodGrasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use for Grasping Between Individuals") +
facet_wrap (~ Focal, scales = "free" )
ggplot (l_foodGrasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Side") +
ylab("Occurrences") +
ggtitle("Hand Used for Food Grasping Between Species") +
facet_wrap (~ Species)
ggplot (L, aes(x= Focal)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Focal") +
ylab("Occurrences") +
ggtitle("# of Times Using Each Limb") +
facet_wrap (~ Side)
ggplot (l_foodGrasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Side") +
ylab("Occurrences") +
ggtitle("Hand Used for Food Grasping Between Sex") +
facet_wrap (~ Sex, scales = "free")
L %>%
group_by(Side) %>%
summarise (n = n()) %>%
mutate(proportion = n / sum(n))
l_handstuff %>%
group_by(Side) %>%
summarise (n = n()) %>%
mutate(proportion = n / sum(n))
binom.test(218, 305, p = .75, alternative = "two.sided")
# tbl_handGrasps <- as.data.frame(l_noLA) %>%
# group_by(Side, Sex) %>%
# summarize(qty = sum(Freq)) %>%
# ungroup() %>%
#  spread(key = Sex, value = qty)
# mat_handGrasps <- as.matrix(tbl_handGrasps[-1])
# rownames(mat_handGrasps) <- levels(tbl_handGrasps$Side)
# chisq.test(mat_handGrasps)
ggplot (l_grasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use for Grasping Between Sexes") +
facet_wrap (~ Sex, scales = "free")
#I echo: false
ggplot (L, aes(x= Limb)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Limb") +
ylab("# of Times Using Each Limb") +
ggtitle("Limb Use Between Individuals") +
facet_wrap (~ Focal)
l_feet <-
L %>%
filter(Category == "BP")
ggplot (l_feet, aes(x= Limb)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Limb") +
ylab("# of Times Using Each Limb") +
ggtitle("Foot Use Between Individuals") +
facet_wrap (~ Focal)
ggplot(L, aes(x = Category, y = Age, color = Side)) +
geom_jitter()  +
theme_classic() +
xlab("Type of Behavior") +
ylab("Age of Lemur") +
ggtitle("Does Age Affect Limb Use?") +
scale_color_manual(values = c("#1D6363", "#E89923"))
ggplot (l_noLA, aes(x= Category, fill = Side)) +
geom_bar(color = "black") +
theme_classic() +
xlab("Type of Behavior") +
ylab("# of Times Using Each Limb") +
ggtitle("Limb Use Between Lemur Species") +
facet_wrap (~ Species, scales = "free") +
scale_fill_manual(values = c("#1D6363", "#E89923"))
ggplot (l_noLA, aes(x= Side, fill = interaction(Category, Side))) +
geom_bar(color = "black") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Limb Use Between Lemur Species") +
facet_wrap (~ Species, scales = "free")
write_csv (l_grasps, "HandGrasps.csv")
table(l_grasps$Side, l_grasps$Species)
chisq.test(table(l_grasps$Side, l_grasps$Species))
table(l_grasps$Side, l_grasps$Sex)
chisq.test(table(l_grasps$Side, l_grasps$Sex))
table(l_grasps$Side, l_grasps$Focal)
chisq.test(table(l_grasps$Side, l_grasps$Focal))
table(l_grasps$Side, l_grasps$Category)
chisq.test(table(l_grasps$Side, l_grasps$Category))
table(l_grasps$Side, l_grasps$Age)
chisq.test(table(l_grasps$Side, l_grasps$Age))
ggplot (l_grasps, aes(x= Side)) +
geom_bar(color = "black", fill = "#C84E00") +
theme_classic() +
xlab("Left or Right Side") +
ylab("# of Times Using Each Limb") +
ggtitle("Hand Use for Grasping Between Individuals") +
facet_wrap (~ Focal, scales = "free")
l_foodGrasps <-
l_grasps %>%
filter(Category == "E")
l_locGrasps <-
l_grasps %>%
filter(Category == "L")
l_RestGrasps <-
l_grasps %>%
filter(Category == "R")
left_fg <-
l_foodGrasps %>%
filter(Side == "L")
table(left_fg$Focal)
right_fg <-
l_foodGrasps %>%
filter(Side == "R")
table(right_fg$Focal)
left_fg <-
l_foodGrasps %>%
filter(Side == "L")
table(left_fg$Species)
right_fg <-
l_foodGrasps %>%
filter(Side == "R")
table(right_fg$Species)
table(left_fg$Sex)
table(right_fg$Sex)
library(RVAideMemoire)
FG_Sifaka <- matrix(c(3, 6, 2, 7, 32, 21, 16, 16), nrow = 4, ncol = 2, byrow = T)
rownames(FG_Sifaka) <- c('Furia', 'Gisela', 'Thrax', 'Rupert')
colnames(FG_Sifaka) <- c('Freq_L', 'Freq_R')
G.test(FG_Sifaka)
FG_Mongoz <- matrix(c(28, 6, 9, 19, 4, 14, 1, 9), nrow = 4, ncol = 2, byrow = T)
rownames(FG_Mongoz) <- c('Rico', 'Carolina', 'Duggan', 'Maddie')
colnames(FG_Mongoz) <- c('Freq_L', 'Freq_R')
G.test(FG_Mongoz)
FG_lcat <- matrix(c(9, 1, 10, 23, 0, 47, 16, 19 ), nrow = 4, ncol = 2, byrow = T)
rownames(FG_lcat) <- c('Sophia', 'Sierra Mist', 'Randy', 'Licinius')
colnames(FG_lcat) <- c('Freq_L', 'Freq_M')
G.test(FG_lcat)
left_rg <-
l_RestGrasps %>%
filter(Side == "L")
table(left_rg$Focal)
right_rg <-
l_RestGrasps %>%
filter(Side == "R")
table(right_rg$Focal)
RG_Sifaka <- matrix(c(7, 4, 16, 16, 8, 11, 16, 22), nrow = 4, ncol = 2, byrow = T)
rownames(RG_Sifaka) <- c('Furia', 'Gisela', 'Thrax', 'Rupert')
colnames(RG_Sifaka) <- c('Freq_L', 'Freq_M')
G.test(RG_Sifaka)
RG_Mongoz <- matrix(c(2, 4, 1, 3, 0, 0, 1, 5), nrow = 4, ncol = 2, byrow = T)
rownames(RG_Mongoz) <- c('Rico', 'Carolina', 'Duggan', 'Maddie')
colnames(RG_Mongoz) <- c('Freq_L', 'Freq_M')
G.test(RG_Mongoz)
FG_lcat <- matrix(c(0, 0, 0, 2, 0, 0, 1, 7), nrow = 4, ncol = 2, byrow = T)
rownames(FG_lcat) <- c('Sophia', 'Sierra Mist', 'Randy', 'Licinius')
colnames(FG_lcat) <- c('Freq_L', 'Freq_M')
G.test(FG_lcat)
left_grasps <-
l_grasps %>%
filter(Side == "L")
table(left_grasps$Focal)
right_grasps <-
l_grasps %>%
filter(Side == "R")
table(right_grasps$Focal)
g_sifaka <- matrix(c(67, 71, 35, 37), nrow = 2, ncol = 2, byrow = T)
rownames(g_sifaka) <- c('Males', 'Females')
colnames(g_sifaka) <- c('Freq_L', 'Freq_R')
fisher.test(g_sifaka)
g_mongoz <- matrix(c(21, 35, 10, 31), nrow = 2, ncol = 2, byrow = T)
rownames(g_mongoz) <- c('Males', 'Females')
colnames(g_mongoz) <- c('Freq_L', 'Freq_R')
fisher.test(g_mongoz)
g_lcat <- matrix(c(42, 79, 24, 49), nrow = 2, ncol = 2, byrow = T)
rownames(g_lcat) <- c('Males', 'Females')
colnames(g_lcat) <- c('Freq_L', 'Freq_R')
fisher.test(g_lcat)
table(left_fg$Focal)
table(right_fg$Focal)
fg_all <- matrix(c(16, 25, 19, 24, 32, 61, 10, 28, 40, 37, 5, 23), nrow = 6, ncol = 2, byrow = T)
rownames(fg_all) <- c('LcatM', 'LcatF', 'EmonM', 'EmonF', 'PcoqM', 'PcoqF')
colnames(fg_all) <- c('FreqL', 'FreqR')
G.test(fg_all)
l_locGrasps <-
l_grasps %>%
filter(Category == "L")
left_lg <-
l_locGrasps %>%
filter(Side == "L")
table(left_lg$Focal)
right_lg <-
l_locGrasps %>%
filter(Side == "R")
table(right_lg$Focal)
lg_all <- matrix(c(4, 3, 1, 5, 8, 14, 12, 13, 3, 1, 7, 4), nrow = 6, ncol = 2, byrow = T)
rownames(lg_all) <- c('LcatM', 'LcatF', 'EmonM', 'EmonF', 'PcoqM', 'PcoqF')
colnames(lg_all) <- c('FreqL', 'FreqR')
G.test(lg_all)
l_FoodGrasps <-
l_grasps %>%
filter(Category == "R")
left_fg <-
l_FoodGrasps %>%
filter(Side == "L")
table(left_fg$Focal)
right_fg <-
l_FoodGrasps %>%
filter(Side == "R")
table(right_fg$Focal)
fg_all <- matrix(c(1, 7, 0, 2, 2, 4, 2, 8, 24, 33, 23, 20), nrow = 6, ncol = 2, byrow = T)
rownames(fg_all) <- c('LcatM', 'LcatF', 'EmonM', 'EmonF', 'PcoqM', 'PcoqF')
colnames(fg_all) <- c('FreqL', 'FreqR')
G.test(fg_all)
by_focal <- read.csv("~/Documents/GitHub/Lefty_Lemurs/ByFocal.csv")
ggplot(by_focal, aes(x= Species, y= P.Value, fill = Species)) +
geom_bar(stat= 'identity', color = "black") +
theme_classic()+
xlab("Species of Lemur") +
ylab("P-Value (less than 0.05 is significant)") +
facet_wrap (~ Behavior) +
geom_text(aes(label= P.Value, x= Species, y= P.Value), vjust= -0.6) +
theme(text = element_text(size = 15)) +
theme(axis.text.x = element_text(size = 7)) +
labs(caption= "Figure 1: Is Hand Preference Independent of Individual?") +
scale_fill_manual(values = c("#C84E00", "#E89923", "#1D6363"))
by_sex <- read.csv("~/Documents/GitHub/Lefty_Lemurs/BySex.csv")
ggplot(by_sex, aes(x= Species, y= P.Value, fill = Species)) +
geom_bar(stat= 'identity', color = "black") +
theme_classic()+
xlab("Species of Lemur") +
ylab("P-Value (less than 0.05 is significant)") +
geom_text(aes(label= P.Value, x= Species, y= P.Value), vjust= -0.6) +
theme(text = element_text(size = 15)) +
theme(axis.text.x = element_text(size = 10)) +
labs(caption= "Figure 2: Is Hand Preference Independent of Sex?") +
scale_fill_manual(values = c("#C84E00", "#E89923", "#1D6363"))
by_species <- read.csv("~/Documents/GitHub/Lefty_Lemurs/BySpecies.csv")
ggplot(by_species, aes(x= Behavior, y= P.Value)) +
geom_bar(stat= 'identity', color = "black", fill = "#DAD0C6") +
theme_classic()+
xlab("Behavior") +
ylab("P-Value (less than 0.05 is significant)") +
geom_text(aes(label= P.Value, x= Behavior, y= P.Value), vjust= -0.5) +
theme(text = element_text(size = 15)) +
theme(axis.text.x = element_text(size = 10)) +
labs(caption= "Figure 3: Is Hand Preference Independent of Species?")
table(left_rg$Species)
table(right_rg$Species)