| -rw-r--r-- | analysis/year.R | 20 | ||||
| -rw-r--r-- | src/Makefile.am | 39 | ||||
| -rw-r--r-- | src/aggregator.c | 6 | ||||
| -rw-r--r-- | src/assign/assign_protein_type.c (renamed from src/assign_protein_type.c) | 87 | ||||
| -rw-r--r-- | src/assign/assign_protein_type.h (renamed from src/assign_protein_type.h) | 0 | ||||
| -rw-r--r-- | src/error/check_error.c (renamed from src/check_error.c) | 0 | ||||
| -rw-r--r-- | src/error/check_error.h (renamed from src/check_error.h) | 0 | ||||
| -rw-r--r-- | src/error/check_h5_error.c (renamed from src/check_h5_error.c) | 0 | ||||
| -rw-r--r-- | src/error/check_h5_error.h (renamed from src/check_h5_error.h) | 0 | ||||
| -rw-r--r-- | src/error/check_ncbi_error.c (renamed from src/check_ncbi_error.c) | 0 | ||||
| -rw-r--r-- | src/error/check_ncbi_error.h (renamed from src/check_ncbi_error.h) | 0 | ||||
| -rw-r--r-- | src/load/load_influenza_aa_dat.c (renamed from src/load_influenza_aa_dat.c) | 4 | ||||
| -rw-r--r-- | src/load/load_influenza_aa_dat.h (renamed from src/load_influenza_aa_dat.h) | 0 | ||||
| -rw-r--r-- | src/load/load_influenza_faa.c (renamed from src/load_influenza_faa.c) | 10 | ||||
| -rw-r--r-- | src/load/load_influenza_faa.h (renamed from src/load_influenza_faa.h) | 0 | ||||
| -rw-r--r-- | src/model/gi_type_data.h | 21 | ||||
| -rw-r--r-- | src/model/gi_type_data_init.c | 36 | ||||
| -rw-r--r-- | src/model/gi_type_data_init.h | 14 | ||||
| -rw-r--r-- | src/model/sequence_data.h (renamed from src/sequence_data.h) | 5 | ||||
| -rw-r--r-- | src/model/sequence_data_init.c (renamed from src/sequence_data_init.c) | 6 | ||||
| -rw-r--r-- | src/model/sequence_data_init.h (renamed from src/sequence_data_init.h) | 0 | ||||
| -rw-r--r-- | src/updator.c | 4 |
22 files changed, 181 insertions, 71 deletions
diff --git a/analysis/year.R b/analysis/year.R index b7da3c8..6d68925 100644 --- a/analysis/year.R +++ b/analysis/year.R @@ -5,21 +5,23 @@ require(hdf5); hdf5load("/home/don/exp007/src/influenza.h5", tidy = TRUE); A <- influenza.aa.dat; - B <- influenza.faa; +# Join the two tables by GB value. +C <- merge (A, B, by.x = "GenBank accession number", by.y = "GB"); + # All records for 1918. Based on code from # http://wiki.r-project.org/rwiki/doku.php?id=tips:data-frames:select_observations -C <- A[A$Year == 1918, ] +D <- C[C$Year == 1918, ] -# Countries represented in the 1918 dataset. -C$Country; +summary (D); -# All record with a year value. -D <- A[A$Year != 0, ]; +# Countries represented in the 1918 dataset. +D$Country; -hist(D$Year); +D[D$"Protein Type" == "HA", ] -B[B$GI == 305182, ] +# All record with a year value. +E <- A[A$Year != 0, ]; -B[B$"Protein Type" == "HA", ] +hist(E$Year); |
