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###    Calculando Missing landmarks 
###  
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# Clear plots
if(!is.null(dev.list())) dev.off()
# Clear console
cat("\014") 
# Clean workspace
rm(list=ls())
#Checking and clean memory use
gc()
#################################

getwd()

setwd("G:/Meu Drive/Artigo O. destructor/TPSs/Finais (landmarks calculados)/Mandíbulas/NMNH")

# (1) Loading packages

install.packages("geomorph")

sessionInfo() #check which packages are load

library(geomorph)


# (2) Read TPS file
Example_landmarks<-readland.tps("NMNH_Mlateral_Landmarks_test_hueco_inventado.TPS", specID = "imageID", negNA = TRUE)
dim(Example_landmarks) #check the dimension (n landmarks, 2/3d, sample size)
Example_landmarks[,,1] # see the first specimen coordinates

# If your TPS file has missing data you should estime or delete the individuals
Example_landmarks_noNA<-estimate.missing(Example_landmarks, method = "Reg") #estimate missing data. Check the help of this function for more info.
#?estimate.missing
str(Example_landmarks_noNA)

# (3) Create a table file to input the variables (sex, species, population, lat, long, etc...)
#write.csv(pepe,file = "Variables_Callicebus_Lateral.csv") #create a table from the original tps data to make the same order 
writeland.tps(Example_landmarks_noNA, file = "NMNH_Mlateral_Landmarks_Test_calculados.TPS", scale = NULL, specID = TRUE)