531347b8b018314cde4559b10a3c4577 *DESCRIPTION
3e68759db3d5875e1d9179f1835093fc *NAMESPACE
c21061907f04c79045787fefef8c4b1d *NEWS.md
ab4744ab930fd592f1f770c35aa38c2b *R/DataSimulation.R
8abf008dbdbd1e309c6821c1e0889c07 *R/EnvironmentalFit.R
a1ce111287b6eced41003d65f48d8f41 *R/EvaluationCriteria.R
c88ebe4ece5e4418e9a3622048739213 *R/IBDModels.R
e8aa65cdeadf1991154c2a07ca1086c6 *R/IrregularSamplingTimes.R
78c986993286bc903e7594361ee70ccb *R/NullModel.R
1374e60a5e272a6f79fa719296ea146b *R/RatesToProbabilities.R
4af2ee454a65cee844a4e550fe4e7de6 *R/RegularSamplingTimes.R
5aa2b8ee8af77c5427fa0ff687a6fbe7 *R/alonso15.R
1a69a1819452370011f8462f2deab521 *R/da_MacKenzie_mle.R
f5f666b721d713eaddc850eba43ca91d *R/da_mle_cedp.R
8b4cd5a954e250df66d604d9280a4b21 *R/da_upgma_AIC_cedp.R
d0ef0fc033a95d623f559a7dd5f0872c *R/idaho.R
78d90929763c6fd4634662364fa378c5 *R/island.R
849bd86918912bb422c245d5169bcef8 *R/lakshadweep.R
ad34e7b0b751a6ccd0ac565bb488039f *R/lakshadweepPLUS.R
5d4c61108ed824e36299be1bef6545ce *R/simberloff.R
09d8a1ca3c6e04c557361c93a8a8dc63 *build/vignette.rds
8b729c72322c972f605903b8e6a93e63 *cleanup
6757059b87fa7992967066adec969097 *configure
58b9d4f4cfbe0c845e42cf81b9a9d864 *configure.ac
1cd1e6c50f8e6201c7bf0f92f6b3c334 *data/alonso15.RData
f8f8802df20456e3f7d619158d99d9a2 *data/idaho.RData
b472df58f5e21b457220e87ce079cd7d *data/lakshadweep.RData
b7536239b307cf03916bd6b43e343c92 *data/lakshadweepPLUS.RData
f27212073f7ffb6c558ad44c4c4a1edb *data/simberloff.RData
5fc1a2bcedccb46b625c8b86e9321161 *inst/CITATION
3c06f3e14077d2e28a97b2331067be4a *inst/doc/IBDmodels.R
0665cf0f32d97b516a9057ab0e811753 *inst/doc/IBDmodels.Rmd
16a0c5af1ef27f8082b750ce855a7963 *inst/doc/IBDmodels.html
541430a531ac5934ff67114b31b3ffa0 *inst/doc/detectability.R
51cb2d93aa491ef77bf88051eb7ec344 *inst/doc/detectability.Rmd
549d5e9a674ac45372e9b419369957f7 *inst/doc/detectability.html
5306d6e4cb60861c96b2a9fa029f1b3d *inst/doc/island.R
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cd1d250c247efbbd69b8336e91862d0e *man/akaikeic.Rd
6160f8bdea60e39bc90741f14d777ffa *man/all_environmental_fit.Rd
45dc6ee550f2a8b9e0310b4c06b0b193 *man/alonso15.Rd
e4779fa27374a070b0052ac4e25dca77 *man/cetotrans.Rd
19a1e1387e2ff57f99175f1a8499e6da *man/data_generation.Rd
d00a41c63e9858e9113c5ca8f5fde891 *man/ibd_models.Rd
b6f6ef020e43ee26377ae994af38cd46 *man/idaho.Rd
443737925dc7bd6b52ef4f71b06aa6a4 *man/irregular_multiple_datasets.Rd
720af05f20250eb416fa6fbb7adc0d66 *man/irregular_single_dataset.Rd
9e583ef00b9bb29adacc1be2ab4e1bf7 *man/island.Rd
e553ec991d6e2cc3d6948fcc3b008bcb *man/lakshadweep.Rd
0af627590cf676b6784d22183211572b *man/lakshadweepPLUS.Rd
ba79be0c5a4a40dc1a3b524d464cd978 *man/mss_cedp.Rd
af18f175698122176b031b31dd10ed3e *man/r_squared.Rd
6e6eb92337aaa0fe51701155bf18ae25 *man/rates_calculator.Rd
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0d5b5b1bda2635730cded7242bea1a9a *man/simberloff.Rd
df2507d7ff887ba05a482ea74aad8372 *man/sss_cedp.Rd
a0e151385f8ce2ebf040455e2a002041 *man/upgma_model_selection.Rd
d71e7bb2dfa69963aee9552d78a554c5 *man/weight_of_evidence.Rd
ea6dd72264f45e57ed7f62026de31c42 *src/Checking_for_Parameter_Correctness.c
f6b9704bcec0faca5bca3aaf8f78786e *src/Counting_Replicates_per_Time.c
691945af594340ff3ac34cc6eb1da27d *src/Counting_Type_of_Transitions.c
2e1fdb2f95551e583c2bcdba6dddb793 *src/Create_Binary_Combination.c
97a7e80aab77a396c89ef4d3648ceb72 *src/EUCLIDIAN_DISTANCE_MATRIX.c
e23135f26958ce12fd1456591cdf7388 *src/GSL_MacKenzie_NLL_Uneven_Function.c
4ad42962b1adaa92f2c3f1810927b50f *src/GSL_MacKenzie_NLLikelihood_Function.c
5130965f6176d75033e5840831d3ddf3 *src/GSL_Minimization_Simplex.c
61fa96651268c60bd8a3b51710b7f122 *src/GSL_NLL_Function_Uneven.c
a8af37d591cb7869b69d56a68d725b94 *src/GSL_NLLikelihood_Function.c
66addcf31f7c9c0696c9472830afe995 *src/HEADERS.h
43d1d46fa9fdfb38885578439738e655 *src/IO_AKAIKE_Model_Selection.c
508a3f92be5aac7ceb73f9952f4eb83d *src/IO_AKAIKE_Model_Selection.h
fa113ab2eb7e0e6d5ccc5492fd6053b1 *src/IO_Missing_Values.c
1a18ca886b011b7a439eb05a1ec05264 *src/IO_Missing_Values.h
60e93b19a91f467fc4ee8146df84b67b *src/MODEL.h
5fb47314d562e8c70bb97fe7f6b20311 *src/MODEL_Parameter_Fitting_STRUCT_DEF.h
5abe3e12558cea288e42f6f2441531a2 *src/MODEL_Parameter_Model_STRUCT_DEF.h
761e3b0d4e6701b3abe7ae2b0965adc2 *src/MODEL_Parameter_Space_STRUCT_DEF.h
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7e0a7eef56eb6704f143b147e529a099 *src/MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.c
80a6dfee9e71845ac334f8bcfb5eac28 *src/MODEL_SELECTION_UPGMA_R_FUNCTION.c
2b2988121974d26b5f04762f8ffd2357 *src/MODEL_SELECTION_UPGMA_R_SHLIB.c
70c12a6e5c4ff10b0c98e26ccb533fc2 *src/MODEL_SP_Matrix_Data_STRUCT_DEF.h
ca37a76dafc1bf0121568dd3a2833ddf *src/MODEL_Time_Control_STRUCT_DEF.h
7190c3e01197c97623ad4f36c74b1cf8 *src/MacKenzie_NLLikelihood_Function.c
e334cd68551f0a817a9d6776ab81d659 *src/Makevars.in
0211568d3b13e190d057717fa5b15982 *src/Makevars.win
9326b11e0ad6517281ea06deb957ddf9 *src/Parameter_Model.c
f1d77db0a8a879f876312a79c9e722c3 *src/Parameter_Space_R_SHLIB.c
a513f40149c0e5c8a95352d98a8de58b *src/Probability_Rates.c
ab5deebf8207ce1cff7ea03904ac2a0a *src/R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c
56c891b11c74066a218bb635dfca234c *src/R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.c
e4b6a82d6af4c5299579b74ab96caf8c *src/R_SHLIB___mle_NLL_Uneven_Minimization.c
4c400a03731cb5492f7499cf66ded05c *src/Rates_into_Probabilities.c
6012e4fb88ac0bc2f5ec5b8bc295d062 *src/SP_Matrix_Data.c
62b43af4097038d5ef50fd6e4aceb477 *src/Time_Control.c
277d5ce8fa12e217206c68cbbac8f59e *src/Transition_Matrix.c
5b18e2f8242a97ef8def2bd438a483d3 *src/UPGMA_CLUSTERING_PARTITION.c
f38c906eb7755b6e89be31e46a539072 *src/da_IBT_Functions.h
4285f34045d33a630a12998ff6c82964 *src/da_IBT_Optimization.h
bc98e2fefcd3d253f3604f131c52bd14 *src/include.Parameter_Model.global.h
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7ef6ebd8b20ff001c301636116139208 *src/include.Time_Control.global.h
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7570058a894f35cbaa29ae1d42fa8c7a *src/upgma_clustering.c
f76069d9ba15a3a065c1a83a78f99c22 *src/upgma_clustering.h
e34585fcb5896ccb6ae0cd537ae91f97 *tests/testthat.R
68c9c9e93850099e0adc278f58af19ab *tests/testthat/g1.rds
16c9be416966d154e779d03abe5f55cb *tests/testthat/g2.rds
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73fba360b695ba032772c91fa88457a2 *tests/testthat/g4.rds
50fb5908b9315bf6d0f56a37a4daa5dc *tests/testthat/i1.rds
ac138b4d2bb1d3d4565581481aeb329e *tests/testthat/i2.rds
817491da7e5694e66241b4842d27c299 *tests/testthat/test_detectability.R
1ad529eb615d2856568dd7d3ffaaffcf *tests/testthat/test_environmental.R
9a4ff13876f865c4478e223c6e55207b *tests/testthat/test_general.R
4eff06f1c595a8ae7c330852e8ccab87 *tests/testthat/test_ibd.R
c33c014b809bd7585038e9cf172a6267 *tests/testthat/test_irregular.R
20f9b8ff1e34f3d037f1e46c400dd9d2 *tests/testthat/test_regular.R
0665cf0f32d97b516a9057ab0e811753 *vignettes/IBDmodels.Rmd
51cb2d93aa491ef77bf88051eb7ec344 *vignettes/detectability.Rmd
b5ff98ba6c5cb1111c869fd4e869a96b *vignettes/island.Rmd
