Week 13 Homework
Kelsey Deweese
2024-11-11
Du_Alemseged <- read.csv("C:/Users/kelse/OneDrive/Documents/Research Design Analysis/Files to Import/DuAlemseged_2018.csv", row.names = 1)
Du_Alemseged_transposed <- t(Du_Alemseged)
head(Du_Alemseged_transposed)## Acinonyx sp Aepyceros melampus Aepyceros shungurae
## Lonyumun 0 0 0
## Moiti 0 0 3
## Lokochot 0 0 16
## TuluBor 0 0 6
## upperBurgi 1 32 0
## KBS 2 69 0
## aff.Hippopotamus aethiopicus aff.Hippopotamus karumensis
## Lonyumun 0 0
## Moiti 0 0
## Lokochot 0 0
## TuluBor 0 0
## upperBurgi 4 37
## KBS 34 49
## aff.Hippopotamus protamphibius Agriotherium sp. Antidorcas recki
## Lonyumun 4 0 0
## Moiti 1 0 0
## Lokochot 8 0 0
## TuluBor 16 1 3
## upperBurgi 0 0 15
## KBS 1 0 51
## Aonyx sp. Australopithecus afarensis Australopithecus anamensis
## Lonyumun 0 0 23
## Moiti 0 0 1
## Lokochot 0 0 0
## TuluBor 0 1 0
## upperBurgi 0 0 0
## KBS 1 0 0
## Beatragus antiquus Beatragus hunteri Camelus grattardi
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 0 0
## TuluBor 0 0 4
## upperBurgi 2 0 0
## KBS 7 0 0
## Caracal/Leptailurus sp. Cephalophus sp.
## Lonyumun 0 0
## Moiti 0 0
## Lokochot 0 0
## TuluBor 4 0
## upperBurgi 0 0
## KBS 0 1
## Ceratotherium mauritanicum/simum Cercocebus sp.
## Lonyumun 0 0
## Moiti 0 0
## Lokochot 0 0
## TuluBor 0 0
## upperBurgi 8 0
## KBS 21 4
## Cercopithecoides kimeui Cercopithecoides williamsi Cercopithecus sp.
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 1 0 0
## TuluBor 1 1 1
## upperBurgi 7 8 0
## KBS 6 0 3
## Chasmaporthetes sp. Civettictis sp. Colobus freedmani
## Lonyumun 1 0 0
## Moiti 0 0 0
## Lokochot 0 0 0
## TuluBor 0 0 0
## upperBurgi 0 4 1
## KBS 0 0 2
## Connochaetes gentryi Crocuta dietrichi Crocuta eturono Crocuta ultra
## Lonyumun 0 0 0 0
## Moiti 0 0 0 0
## Lokochot 7 1 0 1
## TuluBor 0 0 1 0
## upperBurgi 13 6 0 4
## KBS 16 1 1 10
## Damaliscus eppsi Damaliscus niro Damaliscus sp nov
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 0 0
## TuluBor 1 0 0
## upperBurgi 3 0 0
## KBS 66 3 0
## Deinotherium bozasi Diceros bicornis Dinofelis aronoki
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 2 0 0
## TuluBor 7 0 0
## upperBurgi 12 1 10
## KBS 13 8 1
## Dinofelis petteri Dinofelis piveteaui Elephas recki
## Lonyumun 0 0 0
## Moiti 1 0 0
## Lokochot 0 0 0
## TuluBor 1 0 13
## upperBurgi 0 0 39
## KBS 0 0 38
## Enhydriodon afman Equus quagga Equus grevyi Equus koobiforensis
## Lonyumun 1 0 0 0
## Moiti 0 0 0 0
## Lokochot 1 0 0 0
## TuluBor 2 0 0 0
## upperBurgi 1 0 0 40
## KBS 0 0 0 25
## Equus tabeti Eurygnathohippus cornelianus
## Lonyumun 0 0
## Moiti 0 0
## Lokochot 0 0
## TuluBor 0 0
## upperBurgi 0 1
## KBS 2 2
## Eurygnathohippus ethiopicum Eurygnathohippus hasumense
## Lonyumun 0 0
## Moiti 0 0
## Lokochot 0 2
## TuluBor 1 12
## upperBurgi 21 1
## KBS 24 0
## Gazella granti Gazella janenschi Gazella praethomsoni
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 0 4
## TuluBor 0 0 4
## upperBurgi 0 4 21
## KBS 1 5 11
## Genetta genetta/maculata Genetta nyakitongwer Giraffa jumae
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 0 1
## TuluBor 0 0 2
## upperBurgi 2 0 2
## KBS 0 1 8
## Giraffa pygmaea Giraffa stillei-gracilis Hippopotamus gorgops
## Lonyumun 1 0 0
## Moiti 0 0 0
## Lokochot 4 3 0
## TuluBor 1 1 0
## upperBurgi 8 10 6
## KBS 21 18 17
## Hippotragus gigas Homo erectus Homo habilis Homo rudolfensis
## Lonyumun 0 0 0 0
## Moiti 0 0 0 0
## Lokochot 0 0 0 0
## TuluBor 0 0 0 0
## upperBurgi 3 3 4 1
## KBS 3 6 2 0
## Homotherium sp. Hyaena hyaena Hydrictis gudho Ictonyx sp.
## Lonyumun 10 0 0 0
## Moiti 0 0 0 0
## Lokochot 0 0 0 0
## TuluBor 1 0 0 0
## upperBurgi 18 2 1 1
## KBS 8 3 0 0
## Kobus ancystrocera Kobus ellipsiprymnus Kobus kob Kobus leche
## Lonyumun 0 0 0 0
## Moiti 0 0 0 0
## Lokochot 0 0 1 0
## TuluBor 9 0 5 0
## upperBurgi 8 9 14 3
## KBS 43 4 32 15
## Kobus oricornus Kobus sigmoidalis Kolpochoerus limnetes
## Lonyumun 0 0 0
## Moiti 1 2 0
## Lokochot 6 2 2
## TuluBor 31 13 7
## upperBurgi 0 128 236
## KBS 0 81 159
## Lophocebus sp. Loxodonta adaurora Loxodonta exoptata Lupulella sp.
## Lonyumun 0 0 0 0
## Moiti 0 0 0 0
## Lokochot 0 0 0 1
## TuluBor 0 0 4 0
## upperBurgi 1 6 0 5
## KBS 2 0 0 2
## Lutrinae gen nov sp nov Madoqua sp. Megalotragus isaaci
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 0 0
## TuluBor 0 0 0
## upperBurgi 1 0 35
## KBS 0 1 34
## Megantereon sp. Megantereon whitei Mellivora sp. Menelikia leakeyi
## Lonyumun 0 0 0 0
## Moiti 0 0 0 13
## Lokochot 0 0 0 0
## TuluBor 0 0 0 13
## upperBurgi 1 0 1 0
## KBS 2 0 0 0
## Menelikia lyrocera Metridiochoerus andrewsi
## Lonyumun 0 0
## Moiti 0 0
## Lokochot 0 1
## TuluBor 0 0
## upperBurgi 31 93
## KBS 81 230
## Metridiochoerus compactus Metridiochoerus hopwoodi
## Lonyumun 0 0
## Moiti 0 0
## Lokochot 0 0
## TuluBor 0 0
## upperBurgi 0 3
## KBS 14 29
## Metridiochoerus modestus Neotragus sp. Notochoerus euilus/scotti
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 0 4
## TuluBor 0 0 41
## upperBurgi 5 0 124
## KBS 7 0 6
## Nyanzachoerus kanamensis Orycteropus sp. Oryx sp. Panthera leo
## Lonyumun 1 0 0 0
## Moiti 0 0 0 0
## Lokochot 1 0 0 0
## TuluBor 3 0 0 0
## upperBurgi 0 0 2 4
## KBS 0 0 11 0
## Panthera pardus Papio sp. Paracolobus mutiwa Parahyaena sp.
## Lonyumun 0 0 0 0
## Moiti 0 0 0 0
## Lokochot 0 0 0 0
## TuluBor 0 0 0 0
## upperBurgi 4 1 2 0
## KBS 1 1 0 0
## Paranthropus boisei Parapapio ado Parmularius altidens
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 1 0
## TuluBor 0 1 0
## upperBurgi 6 0 0
## KBS 38 0 1
## Parmularius angusticornis Pelorovis oldowayensis
## Lonyumun 0 0
## Moiti 0 0
## Lokochot 1 0
## TuluBor 1 0
## upperBurgi 0 3
## KBS 2 12
## Pelorovis turkanensis Phacochoerus sp. Plesiogulo sp.
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 0 0
## TuluBor 0 0 1
## upperBurgi 6 0 0
## KBS 53 1 0
## Pseudocivetta ingens Raphicerus sp. Redunca sp.
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 0 0 0
## TuluBor 0 0 0
## upperBurgi 2 0 1
## KBS 3 4 0
## Rhinocolobus turkanaensis Simatherium kohllarseni
## Lonyumun 1 0
## Moiti 0 0
## Lokochot 0 4
## TuluBor 2 24
## upperBurgi 10 0
## KBS 1 0
## Sivatherium maurusium Theropithecus brumpti Theropithecus oswaldi
## Lonyumun 0 0 0
## Moiti 0 0 0
## Lokochot 2 10 2
## TuluBor 3 39 2
## upperBurgi 8 1 261
## KBS 35 0 105
## Torolutra ougandensis Tragelaphus kyaloae Tragelaphus nakuae
## Lonyumun 0 14 0
## Moiti 0 1 0
## Lokochot 0 1 0
## TuluBor 0 0 27
## upperBurgi 1 0 16
## KBS 1 0 6
## Tragelaphus rastafari Tragelaphus strepsiceros
## Lonyumun 0 0
## Moiti 1 0
## Lokochot 17 0
## TuluBor 0 0
## upperBurgi 0 37
## KBS 0 76Question 1
a.
Du_Alspecies <- ncol(Du_Alemseged_transposed)
Du_Almembers <- nrow(Du_Alemseged_transposed)
Du_Alspecies## [1] 116Du_Almembers## [1] 8b.
sum_individuals_per_member <- rowSums(Du_Alemseged_transposed)
sum_individuals_per_member## Lonyumun Moiti Lokochot TuluBor upperBurgi KBS Okote
## 56 24 107 311 1426 1658 648
## Chari
## 12c.
sum_species_abundance <- apply(Du_Alemseged_transposed, 2, sum)
sum_species_abundance## Acinonyx sp Aepyceros melampus
## 4 105
## Aepyceros shungurae aff.Hippopotamus aethiopicus
## 25 60
## aff.Hippopotamus karumensis aff.Hippopotamus protamphibius
## 99 30
## Agriotherium sp. Antidorcas recki
## 1 73
## Aonyx sp. Australopithecus afarensis
## 1 1
## Australopithecus anamensis Beatragus antiquus
## 24 12
## Beatragus hunteri Camelus grattardi
## 1 4
## Caracal/Leptailurus sp. Cephalophus sp.
## 4 1
## Ceratotherium mauritanicum/simum Cercocebus sp.
## 31 49
## Cercopithecoides kimeui Cercopithecoides williamsi
## 15 9
## Cercopithecus sp. Chasmaporthetes sp.
## 4 1
## Civettictis sp. Colobus freedmani
## 5 11
## Connochaetes gentryi Crocuta dietrichi
## 42 8
## Crocuta eturono Crocuta ultra
## 2 27
## Damaliscus eppsi Damaliscus niro
## 78 3
## Damaliscus sp nov Deinotherium bozasi
## 1 34
## Diceros bicornis Dinofelis aronoki
## 9 11
## Dinofelis petteri Dinofelis piveteaui
## 2 9
## Elephas recki Enhydriodon afman
## 100 5
## Equus quagga Equus grevyi
## 1 9
## Equus koobiforensis Equus tabeti
## 66 6
## Eurygnathohippus cornelianus Eurygnathohippus ethiopicum
## 3 50
## Eurygnathohippus hasumense Gazella granti
## 16 2
## Gazella janenschi Gazella praethomsoni
## 9 43
## Genetta genetta/maculata Genetta nyakitongwer
## 4 1
## Giraffa jumae Giraffa pygmaea
## 15 38
## Giraffa stillei-gracilis Hippopotamus gorgops
## 33 30
## Hippotragus gigas Homo erectus
## 6 21
## Homo habilis Homo rudolfensis
## 6 1
## Homotherium sp. Hyaena hyaena
## 38 5
## Hydrictis gudho Ictonyx sp.
## 1 1
## Kobus ancystrocera Kobus ellipsiprymnus
## 60 13
## Kobus kob Kobus leche
## 101 19
## Kobus oricornus Kobus sigmoidalis
## 38 229
## Kolpochoerus limnetes Lophocebus sp.
## 472 3
## Loxodonta adaurora Loxodonta exoptata
## 6 4
## Lupulella sp. Lutrinae gen nov sp nov
## 8 1
## Madoqua sp. Megalotragus isaaci
## 4 77
## Megantereon sp. Megantereon whitei
## 4 2
## Mellivora sp. Menelikia leakeyi
## 2 26
## Menelikia lyrocera Metridiochoerus andrewsi
## 114 344
## Metridiochoerus compactus Metridiochoerus hopwoodi
## 91 47
## Metridiochoerus modestus Neotragus sp.
## 14 1
## Notochoerus euilus/scotti Nyanzachoerus kanamensis
## 175 5
## Orycteropus sp. Oryx sp.
## 2 13
## Panthera leo Panthera pardus
## 16 5
## Papio sp. Paracolobus mutiwa
## 5 2
## Parahyaena sp. Paranthropus boisei
## 1 60
## Parapapio ado Parmularius altidens
## 2 1
## Parmularius angusticornis Pelorovis oldowayensis
## 4 24
## Pelorovis turkanensis Phacochoerus sp.
## 69 1
## Plesiogulo sp. Pseudocivetta ingens
## 1 5
## Raphicerus sp. Redunca sp.
## 4 1
## Rhinocolobus turkanaensis Simatherium kohllarseni
## 14 28
## Sivatherium maurusium Theropithecus brumpti
## 49 50
## Theropithecus oswaldi Torolutra ougandensis
## 500 2
## Tragelaphus kyaloae Tragelaphus nakuae
## 16 51
## Tragelaphus rastafari Tragelaphus strepsiceros
## 18 132hist(sum_species_abundance,
main = "Species' Abundances Summed Across All Geological Members",
xlab = "Species Abundance",
col = "green",
border = "black",
breaks = 10) 
Question 2
a.
rownames(Du_Alemseged_transposed)## [1] "Lonyumun" "Moiti" "Lokochot" "TuluBor" "upperBurgi"
## [6] "KBS" "Okote" "Chari"Du_Alemseged_transposed_clean <- Du_Alemseged_transposed[!(rownames(Du_Alemseged_transposed) == "Moiti" | rownames(Du_Alemseged_transposed) == "Chari"), ]
rownames(Du_Alemseged_transposed_clean)## [1] "Lonyumun" "Lokochot" "TuluBor" "upperBurgi" "KBS"
## [6] "Okote"b.
library(vegan)## Warning: package 'vegan' was built under R version 4.4.2## Loading required package: permute## Warning: package 'permute' was built under R version 4.4.2## Loading required package: lattice## This is vegan 2.6-8Du_Alemseged_transformed <- decostand(Du_Alemseged_transposed_clean, method = "total", na.rm = TRUE)c.
Du_Alemseged_transformed_max <- decostand(Du_Alemseged_transposed_clean, method = "max", na.rm = TRUE)Question 3
a.
library(analogue)## Warning: package 'analogue' was built under R version 4.4.2## analogue version 0.17-7bray_curtis_distance <- distance(Du_Alemseged_transformed_max, method = "bray", dist = TRUE)
bray_curtis_distance## Lonyumun Lokochot TuluBor upperBurgi KBS
## Lokochot 0.8072691
## TuluBor 0.9044055 0.6748145
## upperBurgi 0.9535535 0.9045310 0.8814380
## KBS 0.9794999 0.9231547 0.8883805 0.5131858
## Okote 0.9939168 0.9477496 0.9554672 0.7413686 0.7117554b.
# UpperBurgi and KBS Question 4
a.
library(MASS)
nmds_result <- isoMDS(bray_curtis_distance, k = 2) ## initial value 6.025396
## iter 5 value 0.575968
## iter 10 value 0.047258
## iter 10 value 0.000000
## iter 10 value 0.000000
## final value 0.000000
## convergedb.
plot(nmds_result$points,
xlab = "NMDS Dimension 1",
ylab = "NMDS Dimension 2",
main = "NMDS Plot of Geological Members",
pch = 19,
col = "white")
text(nmds_result$points,
labels = rownames(nmds_result$points),
cex = 0.8,
pos = 3,
col = "darkgreen",
xpd = TRUE)
# well xpd = true makes the text pop up above the plot and that is way more fun than fixing the axis limits to me right now. c.
nmds_result$stress## [1] 2.848668e-14d.
# Yes the ordination mresults match my answer from 3B. KBS and upperBurgi are the closest together. e.
# Lokochot and TuluBor are the most dissimilar to Okote because they are the futhest away. Question 5
a.
hclust_result <- hclust(bray_curtis_distance, method = "average")b.
plot(hclust_result, hang = -1,
main = "UPGMA Cluster Analysis of Geological Members",
xlab = "Geological Members",
ylab = "Distance")
c.
# Yes, my cluster analysis matches my 3B and 4E answers. d.
# Okote, upperBurgi, and KBS are the most similar, as they cluster closely together. Lokochot and TuluBor are also more similar to each other, while Lonyumun is somewhat related to them but not as closely as the first group. The further apart the members are, the more dissimilar they are, with Okote and TuluBor being the most dissimilar from one another.